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RES Calls

Period 2024-3 (November 1st -February 28st)

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on future heat wave episodes and greenhouse gas fluxes at the urban scale.
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 750

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project Integrated System Analysis of Urban Vegetation and agriculture(URBAG, 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes, 2) how urban/peri-urban agriculture and vegetation affect urban carbon budget and 3) improve the execution time of atmospheric simulations.

Area: Astronomy, Space and Earth Sciences
Title: In-depth gravitational lensing studies with the LVK network at O4 sensitivity and beyond
Leader: David Keitel
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 800

Abstract:
With its fourth observing run, the LIGO-Virgo-KAGRA network further pushes the frontiers of gravitational-wave astronomy, providing unprecedented distance reach and event rates. One novel effect we hope to detect soon is the gravitational lensing of gravitational waves by massive objects in the universe, which can produce multiple images of the same source or complex waveform deformations. We use RES supercomputers to run the cutting-edge parameter estimation tools with the latest signal models with the goal to robustly detect lensed gravitational waves. Such detections will provide a new probe of the cosmos, in particular for measuring the cosmic expansion rate, testing the nature of gravity, and studying populations of exotic compact objects.

Area: Life and Health Sciences
Title: Large-scale genomic analyses applied to study the genetic mechanisms of antibiotic resistance in enterococci
Leader: Francesc Coll
Institution: Instituto de Biomedicina de Valencia

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 581

Abstract:
This Activity takes place within project entitled “Studying the genetic mechanisms of antibiotic resistance in enterococci” funded by a “Consolidación Investigadora 2023” grant (grant reference: CNS2023-144312) awarded by the Agencia Estatal de Investigación. The aim of this project is to establish a complete concordance between phenotypic and genotypic antibiotic resistance in enterococci, building on previous findings (DOI: 10.1016/S2666-5247(23)00297-5), with the goal of enabling accurate antibiotic resistance detection from enterococci genomes for diagnosis and surveillance purposes. Large supercomputing resources are required to analyse a collection of up to 7,000 enterococcal genomes, including large volumes of small jobs and large population-based analyses requiring thousands of CPU hours and large RAM requirements.

Area: Physics
Title: Quantifying the thermophoretic effect in 2D materials with Friction Force Microscopy: Bridging heat transport with friction
Leader: Guilherme de Vilhena
Institution: Consejo Superior de Investigaciones Científicas

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 650

Abstract:
The interaction between energy flow, particularly heat transfer, and technological advancement has prompted a revolutionary shift in various domains. This has impacted various technological areas where the use of new materials, such as 2D materials, has found strong application. Therefore, a better understanding of heat transport processes in these types of systems is indispensable. In this work, we aim to establish a methodology to quantify the effects of a thermal gradient on the friction properties of different 2D materials through Friction Force Microscopy (FFM) experiments. For this purpose, we conducted atomistic Molecular Dynamics simulations to recreate FFM experiments of different 2D materials when exposed to a thermal gradient. The study aims to identify the best conditions for experimental testing in the laboratory. Thus, this

Area: Physics
Title: A novel approach to compute excitons and optical responses in solids from first-principles
Leader: Juan José Palacios Burgos
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1800

Abstract:
In this activity we aim to refine our new implementation to solve the Bethe-Salpeter equation in materials employing atom-centred basis functions, and employ it to compute excitonic spectra and optical properties (absorption and non-linear responses) in systems beyond those described by the Rytova-Keldysh potential, i.e. single layers. Our methodology is based on the density fitting technique in conjunction with Ewald summations to solve the conditional convergence of the emergent Coulomb series in solids. This approach is suitable to any kind of non-metallic material, and it may hopefully provide accurate enough spectra to describe non-linear optical tensors, such as the second-harmonic or the bulk photovoltaic effect. It will be released as part of the open-source code XATU.

Area: Physics 
Title: Modelling attosecond reflectivity in monolayer MoS2
Leader: Antonio Picon
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 3500

Abstract:

Observing the exciton dynamics in 2D materials at the attosecond time scale is one of the main current challenges for attosecond experiments. Those experiments require of theoretical modelling for interpreting the measurements and correlate them with the light-driven dynamics. In this proposal we plan to fill this gap by performing calculations with our developed code that enables us to simulate the light-driven dynamics as well as to account for exciton interactions in a real-time framework. The results of the calculations are expected to have a high impact in the community and be a reference for future attosecond spectroscopy experiments.

Area: Heterogeneous Chemistry and Solids
Title: Understanding the catalytic behaviour of Ru-based materials in the low temperature CO2 methanation
Leader: Mercedes Boronat Zaragoza
Institution: Instituto de Tecnología Química, UPV-CSIC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 998

Abstract:

A highly active and selective catalyst for low temperature CO2 methanation consisting of a combination of metallic ruthenium (Ru0), ruthenium oxide (RuO2) and a ruthenium oxycarbonate phase (RuOxCy) formed by interstitial carbon doped into RuO2 has been recently described. To maintain its long-term catalytic performance it is key to understand the reaction mechanism and the competing processes leading to catalyst deactivation, such as reduction of RuO2 to form Ru0 nanoparticles. In this project we use periodic DFT calculations to investigate the mechanism of H2 dissociation and CO2 hydrogenation to methane on different models including Ru0 NPs, RuO2 and RuOxCy phase, in order to identify the role of each phase on the catalyst activity and stability.

Period 2024-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on future heat wave episodes and greenhouse gas fluxes at the urban scale.
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 880

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project Integrated System Analysis of Urban Vegetation and agriculture(URBAG, 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes, 2) how urban/peri-urban agriculture and vegetation affect urban carbon budget and 3) improve the execution time of atmospheric simulations.

Area: Astronomy, Space and Earth Sciences
Title: Testing state-of-the-art gravitational waveform models for the fourth LIGO-Virgo-KAGRA observational period
Leader: Marta Colleoni
Institution: University of the Balearic Islands

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 300

Abstract:
With the LIGO-Virgo network entering the second half of its fourth observing run on 10 April 2024, the number of gravitational-wave detections is destined to grow further. Gravitational waveform models are a key element for the analysis of these events and the extraction of their properties. In this project, we will thoroughly test two new waveform models describing the signals emitted by the collision of compact objects such as neutron stars and black holes. Our new models combine accuracy and efficiency to fully reap the potential of future observations.

Area: Astronomy, Space and Earth Sciences
Title: In-depth gravitational lensing studies with the LVK network at O4 sensitivity and beyond
Leader: David Keitel
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 960

Abstract:
With its fourth observing run, the LIGO-Virgo-KAGRA network further pushes the frontiers of gravitational-wave astronomy, providing unprecedented distance reach and event rates. One novel effect we hope to detect soon is the gravitational lensing of gravitational waves by massive objects in the universe, which can produce multiple images of the same source or complex waveform deformations. We use RES supercomputers to run the cutting-edge parameter estimation tools with the latest signal models with the goal to robustly detect lensed gravitational waves. Such detections will provide a new probe of the cosmos, in particular for measuring the cosmic expansion rate, testing the nature of gravity, and studying populations of exotic compact objects.

Area: Astronomy, Space and Earth Sciences
Title: Extremely large microlensing magnification patterns for extragalactic strong gravitational lenses studies
Leader: Rodrigo Gil-Merino
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 120

Abstract:
Gravitational lensing occurs when a mass distribution lenses a background source Typically, at cosmological distances and in a strong lensing regime, the background source is a distant galaxy or a quasar. The lens is a much closer galaxy that bends the light, producing multiple images of the source. Comparing the different images of a gravitationally lensed distant quasar, substructure can be detected in the form of microlesing, a tool for gaining insights into the nature sources, as well as into the mass distribution of the lensing galaxies. The study of gravitational microlensing uses magnification patterns, that is, the projection of the light that crosses the lens plane onto the source plane. This project tries to test the production of very high resolution magnification patterns to face the computational problems that might arise.

Area: Physics
Title: Selective Inactivating pathogen with hard X-ray
Leader: Sergi Ruiz-Barragán
Institution: Universitat Politecnica de Catalunya

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1400

Abstract:
Light can interact with matter in different ways, such as second order nonlineal interactions. One instance is resonantly enhanced difference-frequency generation (re-DFG), where two light sources resonate at their difference frequency. Nonlinear effects are usually seen at high intensities like lasers. These have been studied in infrared and visible regions but are now explored in X-ray thanks to X-ray free-electron lasers, which can excite core electrons and ionize molecules. Theoretically, re-DFG with X-ray sources has been demonstrated by the host of this group. However, post-ionization molecular evolution remains uncertain. This project aims to theoretically comprehend and control re-DFG decay using X-ray sources.

Area: Physics
Title: Excitonic effects in the non-linear optical response of 2D materials
Leader: Juan José Palacios Burgos
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 3000

Abstract:
The generation of a direct or continuous current in a solid under a uniform oscillating light fileld is a non-linear optical phenomenon known as bulk photovoltaic effect (BPVE). The possibility of realizing this inherently quantum effect in homogeneous, non-centrosymmetric materials has made the BPVE an increasingly important topic for next-generation applications in nonlinear optics and optoelectronics. In order to correctly reproduce experimental results in gapped materials, it is essential to include the interaction between electrons and holes, giving rise to the formation of excitons. However, not much work has been devoted yet to include this theoretical ingredient in the BPVE. This computationally demanding task, perfectly suited for the RES facilities, is the aim of our project.

Area: Physics
Title: Modelling attosecond reflectivity in monolayer MoS2
Leader: Antonio Picon
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 3500

Abstract:
Observing the exciton dynamics in 2D materials at the attosecond time scale is one of the main current challenges for attosecond experiments. Those experiments require of theoretical modelling for interpreting the measurements and correlate them with the light-driven dynamics. In this proposal we plan to fill this gap by performing calculations with our developed code that enables us to simulate the light-driven dynamics as well as to account for exciton interactions in a real-time framework. The results of the calculations are expected to have a high impact in the community and be a reference for future attosecond spectroscopy experiments.

Area: Physics
Title: Quantifying the thermophoretic effect in 2D materials with Friction Force Microscopy: Bridging heat transport with friction
Leader: Guilherme de Vilhena
Institution: Consejo Superior de Investigaciones Científicas

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 480

Abstract:
The interaction between energy flow, particularly heat transfer, and technological advancement has prompted a revolutionary shift in various domains. This has impacted various technological areas where the use of new materials, such as 2D materials, has found strong application. Therefore, a better understanding of heat transport processes in these types of systems is indispensable. In this work, we aim to establish a methodology to quantify the effects of a thermal gradient on the friction properties of different 2D materials through Friction Force Microscopy (FFM) experiments. For this purpose, we conducted atomistic Molecular Dynamics simulations to recreate FFM experiments of different 2D materials when exposed to a thermal gradient. The study aims to identify the best conditions for experimental testing in the laboratory. Thus, this

Area: Homogeneous Chemistry
Title: Atomistic picture of the molecular and solvent rearrangements during energy transfer processes in photocatalysis
Leader: Albert Solé Daura
Institution: Institut Català d’Investigació Química (ICIQ)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2013.87

Abstract:
Energy transfer (EnT) photocatalysis has recently emerged as a powerful strategy to enable the excited-state reactivity of non-chromophoric compound via indirect excitation of substrates by photocatalysts. While these processes hold great potential and are gaining increasing interest, still very little is known about the reaction mechanisms governing the central EnT events. Here, we will combine DFT-MD simulations with the metadynamics enhanced-sampling technique to delve into the intricacies of alkene sensitization by photoexcited thioxanthone as a representative example of EnT. We expect to gain unique knowledge about the rearrangements that reactants and solvent molecules surrounding them undergo during EnT step with atomic resolution, fostering further advancement in this field.

Area: Homogeneous Chemistry
Title: Understanding the dynamical properties of H+ and OH- in heavy vs light water from ab initio simulations
Leader: Jorge Kohanoff
Institution: Universidad Politécnica de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1533.3

Abstract:
In this project, we perform extremely efficient ab initio simulations in order to obtain a remarkably accurate description of the diffusion process of the proton and hydroxide ions in heavy and light water. This is crucial for understanding a huge number of scientific problems, and for developing and improving many technological and industrial applications, in particular for materials for energy generation and storage in many domains (from electrochemistry to nuclear technology).
In addition, the data generated will be used as extremely reliable reference data for the training of machine learning potentials, further extending the number and depth of the possible applications.

Area: Heterogeneous Chemistry and Solids
Title: High-Throughput Discovery of New Catalysts for the Hydrogen Economy by Combining Ab Initio Calculations and Machine Learning
Leader: Javier LLorca
Institution: Technical University of Madrid & IMDEA Materials Institute

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 572.54

Abstract:
The objective of this investigation is to design new catalysts (based on intermetallic compounds) that can replace Pt as catalyst for the hydrogen evolution reaction and/or the oxygen reduction reaction. This objective will be achieved by modifying the electronic structure of the catalysts through the application of large elastic strains. The design of the optimum catalysts will be achieved through a high-throughput strategy based on the combination of density functional theory calculations and machine learning methods to select the combination of materials and strain state that improves the kinetics of the catalytic reactions.

Area: Heterogeneous Chemistry and Solids
Title: Optimizing CeO2-ZrO2 solid solutions as catalysts for alkane oxidative deydrogenation
Leader: Mercedes Boronat
Institution: Instituto de Tecnologia Quimica UPV-CSIC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 502

Abstract:
An efficient catalyst for propane oxidative dehydrogenation (ODH) to produce propene and water must combine a high oxygen storage capacity with a fast and selective reactivity at the catalyst surface. In this project we use periodic DFT calculations to investigate the mechanism of ODH and competing processes on the (111), (110) and (100) crystallographic facets of CeO2 and CeO2-ZrO2 catalyst models with different Zr content and distribution, in order to find the optimum catalyst composition and surface termination for this industrially relevant process

Period 2024-1 (March 1st - June 30th)

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on future heat wave episodes and greenhouse gas fluxes at the urban scale.
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 127
Assigned khours without priority: 753

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project Integrated System Analysis of Urban Vegetation and agriculture(URBAG, 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes, 2) how urban/peri-urban agriculture and vegetation affect urban carbon budget and 3) improve the execution time of atmospheric simulations.

Area: Life and Health Sciences
Title: In silico mechanistic study of carnitine palmitoyltransferase activity
Leader: Victor GUALLAR
Institution: Barcelona Supercomputing Center

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1230

Abstract:
Carnitine palmitoyltransferase is a transmembrane enzyme involved in the first steps of the beta-oxidation of long-chain fatty acids in the mitochondria. Thus, this enzyme (and their different isoforms) is involved in fatty acid metabolism, key in the study of several metabolic disorders. Moreover, three isoforms of carnitine palmitoyltransferase I (CPT1) exist, being CPT1a, CPT1b, and CPT1c. CPT1a is an active isoform, while the CPT1c isoform does not have any catalytic activity. Still, they share the catalytic motif and a high sequence identity between isoforms. However, no crystal structure of this protein currently exists limiting the mechanistic study of these enzymes. Herein, we propose a set of molecular-mechanic-based simulations to test our hypotheses on why one isoform is active and the other is not.

Area: Life and Health Sciences
Title: Exloring the versatility of squalene-hopene cyclase
Leader: Silvia Osuna
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2000

Abstract:
Life could not be sustained without the presence of enzymes, which are responsible for accelerating the chemical reactions in a biologically compatible timescale. Enzymes present other advantageous features such as high specificity and selectivity, plus they operate under very mild biological conditions. Inspired by these extraordinary characteristics, many scientists wondered about the possibility of engineering new enzymes for industrially-relevant targets. In this project, free energy surfaces will be estimated using QM/MM metadynamics to provide a rationale for the experimentally observed selectivity of some engineered squalene-hopene cyclases towards the production of different industrially-relevant monoterpenes such as camphene, pinene, limonene or ambroxide.

Area: Physics
Title: Abnormal Heat Transport Between Two Separated Bodies in Ultra-High-Vacuum
Leader: Guilherme de Vilhena
Institution: Consejo Superior de Investigaciones Científicas

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 650

Abstract:
Understanding and controlling heat transport at the nanoscale is arguably one of the largest pending challenges of Nanoscience. The field has witnessed a renewed interest with recent spectacular experiments including heat transport through single-atom; the first molecular nano-refrigerator; … However, the theoretical support is lagging ultimately hindering a de novo design of nanoscale heat transport. Here we combined advanced all-atom non-equilibrium simulations to provide such atomically detail understanding. Moreover, we directly tackle a major pressing issue on the field, i.e.: unveiling if heat-transfer in the 1-7nm range encloses a new-physics or instead can be understood as a peculiar form of heat transport emerging in nano-confined water.

Area: Physics
Title: Effect of thermodynamic promoters and NaCl on nucleation of carbon dioxide and nitrogen hydrates from computer simulation
Leader: Felipe J. BLas
Institution: Universidad de Huelva

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 9998

Abstract:
Hydrates are nonstoichiometric inclusion solid compounds in which guest molecules, such as carbon dioxide (CO2), nitrogen (N2), and tetrahydrofuran (THF) are enclathrated in the voids left by a periodic network of water molecules or host. Hydrates are considered strategic materials from the theoretical but also from the energetic, environmental, and economic points of view. In this project, we determine the interfacial free energy of CO2 and N2 hydrates, as well as the effect of NaCl and THF on the dissociation line of the CO2, using advanced computer simulation techniques and realistic microscopic models for the molecules under study. All predictions obtained in this work will be compared with experimental data taken from the literature and with previous results obtained by the research group.

Area: Physics
Title: Excitonic effects in the non-linear optical response of 2D materials
Leader: Juan José Palacios Burgos
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1500

Abstract:
The generation of a direct or continuous current in a solid under a uniform oscillating light fileld is a non-linear optical phenomenon known as bulk photovoltaic effect (BPVE). The possibility of realizing this inherently quantum effect in homogeneous, non-centrosymmetric materials has made the BPVE an increasingly important topic for next-generation applications in nonlinear optics and optoelectronics. In order to correctly reproduce experimental results in gapped materials, it is essential to include the interaction between electrons and holes, giving rise to the formation of excitons. However, not much work has been devoted yet to include this theoretical ingredient in the BPVE. This computationally demanding task, perfectly suited for the RES facilities, is the aim of our project.

Area: Heterogeneous Chemistry and Solids
Title: Optimizing CeO2-ZrO2 solid solutions as catalysts for alkane oxidative deydrogenation
Leader: Mercedes Boronat
Institution: Instituto de Tecnologia Quimica UPV-CSIC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 497

Abstract:
An efficient catalyst for propane oxidative dehydrogenation (ODH) to produce propene and water must combine a high oxygen storage capacity with a fast and selective reactivity at the catalyst surface. In this project we use periodic DFT calculations to investigate the mechanism of ODH and competing processes on the (111), (110) and (100) crystallographic facets of CeO2 and CeO2-ZrO2 catalyst models with different Zr content and distribution, in order to find the optimum catalyst composition and surface termination for this industrially relevant process.

Period 2023-3 (November 1st - February 29th)

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale.
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 700

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and Agriculture 2019-2025). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality and climate change using WRF

Area: Astronomy, Space and Earth Sciences
Title: Robust parameter estimation and lensing studies with the LVK network at O4 sensitivity and beyond
Leader: David Keitel
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1400

Abstract:
With its fourth observing run, the LIGO-Virgo-KAGRA network further pushes the frontiers of gravitational-wave astronomy, with improved sensitivity and unprecedented event rates. Efficiently processing these and achieving optimal measurement precision requires cutting-edge signal models and analysis methods. We will use RES supercomputers to run improved parameter estimation tools together with the latest waveform models, studying black holes and neutron stars and testing the impacts on gravitational-wave cosmology. We also work on bringing together gravitational waves with another prediction of general relativity: gravitationally lensed gravitational waves as a new probe of the cosmos, for which we will work on verifying the robustness of methods for identifying lensed candidates given uncertainties in lens and waveform models.

Area: Life and Health Sciences
Title: Remapping and reanalysis of 4000 Whole Genome Sequencing datasets from patients with rare disease to identify causative variants and provide a diagnosis
Leader: Dr. Sergi Beltran
Institution: CNAG-CRG

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2750

Abstract:
We wish to reanalyse 4,000 whole genome sequencing datasets for rare disease, using the latest available resources. The datasets come from across Europe and have been shared as part of the Solve-RD project. They have undergone prior exome sequencing analysis but no causative variants were identified We will realign to the GRCh38 version of the genome, and perform novel variant calling using GATK4.0 and a variety of tools for larger variant discovery. The data will then be fully integrated into the the RD-Connect Genome-Phenome
Analysis Platform (GPAP), which is a resource freely accessible to any bona fide rare disease researcher. This will undoubtedly result in more rare disease families receiving a diagnosis.

Area: Life and Health Sciences
Title: Exloring the versatility of squalene-hopene cyclase
Leader: Silvia Osuna
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 5800

Abstract:
Life could not be sustained without the presence of enzymes, which are responsible for accelerating the chemical reactions in a biologically compatible timescale. Enzymes present other advantageous features such as high specificity and selectivity, plus they operate under very mild biological conditions. Inspired by these extraordinary characteristics, many scientists wondered about the possibility of engineering new enzymes for industrially-relevant targets. In this project, free energy surfaces will be estimated using QM/MM metadynamics to provide a rationale for the experimentally observed selectivity of some engineered squalene-hopene cyclases towards the production of different industrially-relevant monoterpenes such as camphene, pinene or limonene.

Area: Homogeneous Chemistry
Title: Computational determination of acidity constants of polyoxometalates
Leader: Albert Solé Daura
Institution: Institut Català d’Investigació Química (ICIQ)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 4000

Abstract:
The accurate determination of acidity constants of complex polyoxometalate (POM) clusters, as well as the unambiguous identification of the most likely protonation sites is still a challenge for computational chemistry due to the intrinsic difficulties of capturing the dynamic nature of protons in solution and the solvent reorganizations around POMs that take place during acid-base events. Here, we will apply DFT-based Molecular Dynamics simulations in combination with the path-metadynamics enhanced sampling technique to account for an explicit, dynamic and quantum mechanical description of the solvent, aiming to obtain an accurate estimation of the free-energy variations along the process and atomically-resolved details about the underlying reaction mechanisms.

Area: Heterogeneous Chemistry and Solids
Title: Computational modeling of interstellar olivine surfaces and their interaction and reactivity with HCN
Leader: Albert Rimola
Institution: UAB

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1352
Assigned khours without priority: 148

Abstract:
Hydrogen cyanide (HCN) has been observed in all the environments characterizing the formation of planetary systems. Through polymerization, it forms biomolecules such as adenine, one of the building blocks of the molecules of life. These species are observed on meteorites, comets, and satellites, which are primarily made of silicates. We aim to investigate the role that intrstellar olivinic surfaces, Mg and Fe- containing silicates, have on the adsorption and reactivity of HCN. We expect to find a complex chemistry due to the possibility of both molecular and dissociative adsorption of HCN, which will be characterized from a spectroscopical point of view. We will study the polymerization of HCN on the surfaces as the first steps characterizing the formation of the nuclebase of adenine.

Period 2023-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale.
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 898.56

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and Agriculture 2019-2025). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality and climate change using WRF

Area: Astronomy, Space and Earth Sciences
Title: Convection-permitting climate simulations over Europe with WRF
Leader: Jesus Fernandez
Institution: Instituto de Física de Cantabria (IFCA), CSIC-Universidad de Cantabria

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 4455

Abstract:
As climate simulations approach km-scale resolution, the computational cost of sampling all future climate uncertainties becomes unfeasible. Hybrid downscaling approaches, such as statistical model emulators based on AI algorithms, could replace standard dynamical models simulations. One of the tasks of EU project IMPETUS4CHANGE is to explore such emulators to bridge the gap between global predictions and local impacts. This novel approach requires long km-scale simulations for training and evaluation. In this project, we are conducting such km-scale simulation with the WRF model over 80 years. This simulation as a part of a multi-model ensemble will be at the forefront of high-resolution climate predictions over Europe, becoming a key line of evidence for the assessment and understanding of local climate change and its impacts.

Area: Astronomy, Space and Earth Sciences
Title: Gravitational-wave parameter estimation and identifying candidates for gravitational lensing
Leader: David Keitel
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1500

Abstract:
With the detection of gravitational waves, a key prediction of Einstein’s theory of general relativity has been realised. Now, the fourth LIGO-Virgo-KAGRA observing run will bring unprecedented event numbers. We will use RES supercomputers to improve tools for estimating the parameters of these events and apply these, together with the latest waveform models, to the new data. We will also focus on another key prediction of general relativity: gravitational lensing, the bending of astronomical signals by heavy masses. This is already a fruitful tool in electromagnetic astronom and now our chances are growing to detect lensing of gravitational waves themselves, bringing together the two predictions for deeper studies of our cosmos. We will work on identifying lensed events and verifying robustness given uncertainties in waveform modelling.

Area: Physics
Title: Excitonic bulk photovoltaic effects in 2D dichalcogenides materials
Leader: Antonio Picon
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1500

Abstract:
The bulk photovoltaic effect (BPVE) is a phenomenon that consists in the generation of a DC current in a material after the absorption of IR/visible light. The second-order current that contributes to the BPVE is known as the shift current. First-principles Density Functional Theory (DFT) calculations of this quantity have been carried out during the last decade, seeking efficient materials that can be used for solar energy conversion. Here, we propose real-time calculations to model the material and calculate the BPVE. Our time-dynamics approach allows to include electron-hole effects in the calculation of shift currents, a theoretical challenge with almost no general understanding yet. We apply our methodology to molybdenum disulfide, a system that shows a high nonlinear response enhanced by excitons. These calculations provide then a r

Area: Physics
Title: Optical properties of organic acceptor molecules on Graphene/metal substrates
Leader: Cristina Díaz Blanco
Institution: Universidad Complutense de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 3538

Abstract:
The self-assembly of ordered arrangement of donor and acceptor molecules on graphene/metal substrates opens up a promising way to manufacture novel nanoscale materials with specific technologically desirable characteristics. In this project, we combine density functional theory (DFT) and many-body perturbation theory (MBPT) to study the optical properties of F4TCNQ and F6TCNN adsorbed on Graphene/Ru(0001) and Graphene/Ni(111), and the role of the moiré pattern on the modulation of these properties.

Area: Engineering and Mathematics
Title: Influence of free-stream turbulence on the aerodynamics of flapping wings
Leader: Stefano Olivieri
Institution: Universidad Carlos III de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 720

Abstract:
Bio-inspired micro-aerial vehicles (MAVs) are an attractive concept in low-to-moderate Reynolds number aerodynamics with applications, e.g., in remote environmental monitoring. The current knowledge of flapping flight is largely limited to configurations where the incoming flow is laminar and unperturbed, even though MAVs typically operate within the atmospheric boundary layer at low flight velocities, thus experiencing turbulent fluctuations with characteristic lengthscales and velocities comparables to those of the MAV itself. The goal of this activity is to generate novel insight into the impact of such turbulent perturbations on the aerodynamic performance of flapping wings by means of direct numerical simulations combining a physically-based (i.e., grid-induced turbulence) and a synthetic turbulence generation approach.

Area: Engineering and Mathematics
Title: Reduced Order Modeling of Rotating Detonation Engines using HPC simulations
Leader: Elena Beatriz Martín Ortega
Institution: Unievrsidad de VIGO

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1566

Abstract:
The project aims at generating an accurate and fast numerical tool to model different Rotating Detonation Engine (RDE) designs within a given range of parameters. This tool will be generated by combining simplified 2D numerical simulations (on an annular chamber domain) run in an HPC environment, similarity analysis, and reduced order modelling and will serve as a preliminary design tool of RDE. The CFD database will be built using 2D unsteady numerical simulations of reactive compressible Euler equations that include a chemical kinetics model for hydrogen in air and hydrogen in pure oxygen. Six input parameters will be considered in the RDE thermodynamic cycle for each type of fuel and a total of 288 cases will be solved. Evolution of flow fields along the computational domain, as well as thrust performance of the engine will be computed

Area: Heterogeneous Chemistry and Solids
Title: Electronic structure of intercalated bundle metamaterials
Leader: Juan José Vilatela
Institution: IMDEA Materiales

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1824

Abstract:
The aim of this activity is to compute the electronic dispersion relation of the intercalated CNT bundle by means of density functional theory (DFT) calculations. This electronic metamaterial contains a triangular honeycomb arrangement of the CNTs, in between which bromine molecules are arranged to form a hexagonal sublattice. The CNTs, thus will serve as a host matrix, and the first specific assessment is to learn whether this metamaterial contains a linear Dirac dispersion based on the hexagonal bromine sublattice.

Period 2023-1 (March 1st - June 31st)

Area: Astronomy, Space and Earth Sciences
Title: Mesoscale air-ocean interactions and their role in precipitation extremes over the western Mediterranean
Leader: Daniel Argüeso
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1000

Abstract:
Climate extremes directly strike society, infrastructure and the environment. At global scales, they have become more frequent, intense and longer over the last decades. In the context of climate change, this trend is expected to continue, albeit with large regional contrasts. While there is a general agreement that the western Mediterranean is undergoing significant warming and drying, there are still large uncertainties regarding changes in heavy rainfall events. This activity will use an ocean-atmosphere coupled regional to advance our understanding of rainfall extremes in the region and the role of fine-scale air-sea interactions. The proposed research will enable the study of heavy rainfall events from an interdisciplinary perspective and will help determine their coastal impacts

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 300

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and agriculture 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality using WRF-Chem models.

Area: Astronomy, Space and Earth Sciences
Title: Gravitational-wave parameter estimation and identifying candidates for gravitational lensing
Leader: David Keitel
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1700

Abstract:
With the first detection of gravitational waves, one of the most spectacular predictions of Einstein’s theory of general relativity has been realised. Another such prediction was gravitational lensing – the bending of astronomical signals by heavy masses – and this has already been a fruitful tool in electromagnetic astronomy for decades. Now, with almost a hundred gravitational-wave events detected, our chances are growing to detect lensing of these waves themselves, thus bringing together the two predictions and enabling deeper studies of our cosmos. We will use RES supercomputers to improve tools for estimating the parameters of gravitational-wave events, to identify those that could be lensed, and to verify the robustness of these methods given uncertainties in the modelling of gravitational waveforms.

Area: Life and Health Sciences
Title: Exploring medium-size membrane-containing viruses by high-resolution cryo-electron microscopy
Leader: Nicola GA Abrescia
Institution: Center for Cooperative Research in Biosciences (CIC bioGUNE)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1267.2

Abstract:
We know only an infinitesimal part of the viruses populating our biosphere – and only two single-stranded DNA bacteriophages with an internal membrane have been elucidated structurally: FLiP and ΦCjT23. Accumulating structural information allows us to establish viral structure-based relationships not seen before across viruses apparently not related by primary sequence. The ultimate goal is to expand our knowledge on membrane-containing viruses with ssDNA genome and understanding their assembly mechanism and the role played in morphogenesis by the internal membrane. Further, the ability of structurally correlating viruses not strictly related by the current taxonomy offers the possibility of exporting strategies used against one virus to another virus.

Area: Physics
Title: Phonon-assisted ballistic current in photovoltaic topological materials
Leader: Juan José Palacios Burgos
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1500

Abstract:
Electron-phonon interactions are one of the main sources of many-body effects which determine certain quantum properties of materials, particularly at room and high temperatures. A remarkable example is the phonon-assisted ballistic current, occuring in some asymmetric crystalline solids as part of the bulk photovoltaic effect, a non-linear optical response by which a direct current is induced in the uniform material under an oscillating light field (such as sunlight). Besides its inherent theoretical interest, this effect is currently regarded as a core technology for new or alternative photovoltaic applications. A proper characterization of suitable materials requires including the contribution from lattice vibrations (phonons), induced by temperature. This is a computationally demanding task, perfectly suited for the RES facilities.

Area: Physics
Title: Thermal conductivity of paramagnetic systems
Leader: Riccardo Rurali
Institution: Institute of Materials Science of Barcelona (ICMAB)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 4608

Abstract:
We are interested in strategies that allow dynamically tuning the thermal conductivity of a material, an achievement that would pave the way to the design of phononic devices, where heat, rather than charge carriers, is used to encode and carry information. In this activity, we focus on the magnetic phase-transition between the antiferromagnetic and the paramagnetic phase of CrN, which occurs near room temperature and which can be triggered with a moderate magnetic field. To this end we create an extensive density-functional database that we use to train a machine learning potential and then compute the thermal conductivity of both phases.

Area: Physics
Title: Electron Irradiation of water by first-principles simulations
Leader: Daniel Muñoz Santiburcio
Institution: Instituto de Fusión Nuclear

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1728

Abstract:
Studying the interaction of fast charged particles with water is determinant for understanding the radiation damage of living tissues. In particular, electron irradiation of water can result in the ionization/fragmentation of the water molecules, which may cause damage in the biomolecules of the tissue via different mechanisms (e.g. attack of free radicals). In this project, we will use first-principles simulations to study the process of the irradiation of water by highly energetic electrons. The findings will have applications in radiation protection technologies, radiation damage mitigation strategies and radiation cancer therapy, among other fields.

Area: Physics
Title: Critical Phenomena in the collapse of vacuum gravitational waves.
Leader: Isabel Suárez Fernández
Institution: University of the Balearic Islands

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 300

Abstract:
Despite recent progress, our understanding of extreme dynamical vacuum spacetimes at the threshold of black hole formation is limited. There are numerous reasons for this, but the key issue is the immense challenge that their numerical treatment represents. Consequently, in the past, different groups studying these spacetimes have obtained wildly divergent results. For the first time, in this community project, results obtained with all of the active independently developed codes and numerical methods will be compared systematically. Our concrete task is to perform evolutions with the pseudospectral, adaptive mesh code BAMPS for this community project.

Area: Engineering and Mathematics
Title: Inertial Confinement Fusion and Astrophysics Laboratory targets simulations
Leader: Pedro Velarde Mayol
Institution: Instituto de Fusión Nuclear

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1200

Abstract:
We peroform numerical simulations of ICF and AstroLab targets with impreved in house codes Arwen and Bigbart. It will test the new algoritms implemented in these codes and we plan to design new targets for the new ICF lasers facilities that are being designed for the next 10 years. We want to redesign an Astrophysical Laboratory experiment taking in account more physical effects and the new diagnosis platforms developed at NIF (LLNL, USA) . Furthermore, we plan to simulate targets for an EU-XFEL experimental proposal on time depedent radiation emission.

Area: Engineering and Mathematics
Title: Development and Evaluation of Ad-hoc Storage Parallel File systems II
Leader: Felix Garcia Carballeira
Institution: Universidad Carlos III de Madrid

Assigned machine(s): MareNostrum (BSC) Picasso (UMA) CTE-ARM (BSC)
Assigned khours with priority: 1426

Abstract:
This activity is part of the European ADMIRE project (956748 H2020-JTI-EuroHPC-2019-1). The main objective of the ADMIRE project is creating an active I/O stack that dynamically adjusts computation and storage requirements through intelligent global coordination, malleability of computation and I/O, and the scheduling of storage resources along all levels of the storage hierarchy. To achieve this, the project will develop a software-defined framework based on ad-hoc parallel file systems. The objective of the request for computing resources is evaluate the performance and scalability of the ad-hoc storage systems developed in the project to identify bottlenecks to optimize and improve the scalability the ad-hoc storage systems.

Area: Engineering and Mathematics
Title: Influence of free-stream turbulence on the aerodynamics of flapping wings
Leader: Stefano Olivieri
Institution: Universidad Carlos III de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1080

Abstract:
Bio-inspired micro-aerial vehicles (MAVs) are an attractive concept in low-to-moderate Reynolds number aerodynamics with applications, e.g., in remote environmental monitoring. However, our current knowledge of flapping flight is essentially limited to configurations where the incoming flow is laminar and unperturbed, even though MAVs typically operate within the atmospheric boundary layer at low flight velocities, thus experiencing turbulent fluctuations with characteristic lengthscales and velocities comparables to those of the MAV itself. The goal of this activity is to generate novel insight into the impact of these turbulent perturbations on the aerodynamic performance of flapping wings, by means of high-fidelity direct numerical simulations and a physically-based (i.e., grid-induced turbulence) approach.

Area: Homogeneous Chemistry
Title: A new twist to an old story: reactivity of the first characterized high-valent metal-oxo species
Leader: Marcel Swart
Institution: Universidad de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 864

Abstract:
Twenty years after the discovery of the first high-valent Fe(IV)-oxo complex based on the TMC ligand, there are many aspects of oxidation chemistry which are poorly understood, such as for instance the role of spin states, the ligand, the driving force, etc.Here we investigate hydrogen-atom transfer and oxygen-atom transfer reactions with all different isomers of the prototype [Fe(IV)(O)(TMC)](2+) complex that was discovered in 2003, which set off the field of biomimetic chemistry in new directions.

Area: Homogeneous Chemistry
Title: Metal-metal bonds waiting to be discovered
Leader: Marcel Swart
Institution: Universidad de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 272.16

Abstract:
Metal-metal bonds are difficult to gauge and even more difficult to predict. Through a combination of experiment and calculations here we explore the valence-(de)localization in a series of di-Ru paddlewheel compounds, based on geometric structure, absorption and vibrational spectroscopy, and chemical bonding analysis.

Period 2022-3 (November 1st - February 28st)

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 450

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and agriculture 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality using WRF-Chem models.

Area: Astronomy, Space and Earth Sciences
Title: Mesoscale air-ocean interactions and their role in precipitation extremes over the western Mediterranean
Leader: Daniel Argüeso
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1840

Abstract:
Climate extremes directly strike society, infrastructure and the environment. At global scales, they have become more frequent, intense and longer over the last decades. In the context of climate change, this trend is expected to continue, albeit with large regional contrasts. While there is a general agreement that the western Mediterranean is undergoing significant warming and drying, there are still large uncertainties regarding changes in heavy rainfall events. This activity will use an ocean-atmosphere coupled regional to advance our understanding of rainfall extremes in the region and the role of fine-scale air-sea interactions. The proposed research will enable the study of heavy rainfall events from an interdisciplinary perspective and will help determine their coastal impacts.

Area: Astronomy, Space and Earth Sciences
Title: Studies In Theoretical Astrophysics and General Relativity
Leader: Milton Ruiz
Institution: University of Valencia

Assigned machine(s): MareNostrum (BSC) Altamira (UC) Picasso (UMA)
Assigned khours with priority: 2760

Abstract:
We tackle several large-scale, long-standing, unsolved problems in theoretical astrophysics and numerical relativity. We numerically solve the Einstein field equations coupled to the relativistic magnetohydrodynamic equations and the equations of radiation transport to simulate neutron stars, white dwarf stars, black holes, and accretion disks, in isolation or in binary systems. We are interested in the study of gravitational and EM radiation generated from these sources (multimessenger astronomy); our numerical studies address fundamental questions dealing with strong-field gravitation and focus on problems that are motivated by current and future observations of gravitational waves by aLIGO/VIRGO/KAGRA and other interferometers under development. Our simulations also model promising gamma-ray burst sources observed by ESA satellites.

Area: Astronomy, Space and Earth Sciences
Title: Preparing for the fourth observation run of gravitational wave detectors
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 11100

Abstract:
In the first three observation runs of the international network of gravitational wave detectors, gravitational waves from 90 compact binary coalescences of black holes and neutron stars have been detected. In December 2022 the fourth observation run will finally reach design sensitivity and is foreseen to detect hundreds of gravitational wave events. In this project we finalise our preparations to develop waveform models that are sufficiently accurate and computationally efficient so that they can be used by the LIGO-Virgo-KAGRA collaboration and eventually the general gravitational wave community to analyse all events to be detected in O4. To this end we perform numerical relativity simulations of high mass ratio precessing binaries and parameter estimation with our upgraded waveform models to map out systematic errors in our models.

Area: Astronomy, Space and Earth Sciences
Title: Climate change impacts on extreme precipitation events in Andalusia by using regional modelling at very high resolution. Evaluation of land-atmosphere feedbacks
Leader: Sonia Gámiz-Fortis
Institution: University of Granada

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2711.5

Abstract:
The aim of this project is to conduct dynamical downscaling simulations over Andalusia, analyzing the potential improvement of the regionalized product by including convection-permitting models instead the use of parametrizations. For this end, the ICTP Regional Climate Model (RegCM) model is used to downscale ERA5 large scale experiments using two nested domains with 5 and 1 km spatial resolution. After evaluating the prediction skill of the regionalized simulations and the added value from resolving explicitly the convection processes, an ensemble of climate simulations within the CMIP6 initiative using a pseudo-global warming (PWG) strategy will be conducted to regionalize projections of climate change along two future periods, near (2036-2050) and far (2085-2099), under the SSP5-8.5 scenario

Area: Astronomy, Space and Earth Sciences
Title: Cosmological mock datasets for WEAVE-QSO
Leader: Jose Oñorbe Bernis
Institution: Universidad de Sevilla

Assigned machine(s): MareNostrum (BSC) Picasso (UMA) Canigo (CSUC) Xula (CIEMAT) Finisterrae3 (CESGA)
Assigned khours with priority: 100

Abstract:
The WEAVE-QSO survey will observe around 450.000 high-redshift quasars over an area of up to 10.000 deg2 providing an incredible scientific dataset that will allow to study the expansion of the universe and elucidate the nature of dark energy as well as to also shed light on galaxy formation via study of the properties of inflowing/outflowing gas associated with nearby galaxies. Testing how the analysis pipelines, secondary astrophysical effects and observational errors will impact upon different precise measurements and vice versa will be crucial to guarantee the scientific success of the survey. The best way to carry out these tests is through the use of mock datasets. The goal of this Test Activity validate the mock creation pipeline created by our group at different HPC RES systems and perform scalability tests for future applications

Area: Life and Health Sciences
Title: Cryo-EM 3D reconstruction of a novel giant virus
Leader: Nicola GA Abrescia
Institution: Center for Cooperative Research in Biosciences (CIC bioGUNE)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2300

Abstract:
Viruses defy paradigms of classical biology and are agents of change and innovation. Hidden in plain sight for over a century, giant viruses were evading discovery. Common features of double-stranded DNA genome viruses are the similarity in a few core genes, relative independence of host transcription machinery, cytoplasmic replication, and formation of viral factories, which classify them in the nucleo-cytoplasmic large DNA viruses (NCLDVs) group. This novel dsDNA virus > 2,000 Å in diameter characterized via means of cryo-EM helps give light to these double jelly-roll virus MCP structures as only a few other giant viral structures have been published so far, helping place this virus in its corresponding structure-based viral lineage.

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 450

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and agriculture 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality using WRF-Chem models.

Area: Astronomy, Space and Earth Sciences
Title: Mesoscale air-ocean interactions and their role in precipitation extremes over the western Mediterranean
Leader: Daniel Argüeso
Institution: Universitat de les Illes Balears

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1840

Abstract:
Climate extremes directly strike society, infrastructure and the environment. At global scales, they have become more frequent, intense and longer over the last decades. In the context of climate change, this trend is expected to continue, albeit with large regional contrasts. While there is a general agreement that the western Mediterranean is undergoing significant warming and drying, there are still large uncertainties regarding changes in heavy rainfall events. This activity will use an ocean-atmosphere coupled regional to advance our understanding of rainfall extremes in the region and the role of fine-scale air-sea interactions. The proposed research will enable the study of heavy rainfall events from an interdisciplinary perspective and will help determine their coastal impacts.

Area: Homogeneous Chemistry
Title: Computational exploration and design of squalene-hopene cyclases for efficient cationic cyclizations
Leader: Silvia Osuna
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2500

Abstract:
Life could not be sustained without the presence of enzymes, which are responsible for accelerating the chemical reactions in a biologically compatible timescale. Enzymes present other advantageous features such as high specificity and selectivity, plus they operate under very mild biological conditions. Inspired by these extraordinary characteristics, many scientists wondered about the possibility of engineering new enzymes for industrially-relevant targets. In this project, free energy surfaces will be estimated using QM/MM metadynamics to provide a rationale for the experimentally observed selectivity of some engineered squalene-hopene cyclases towards the production of different industrially-relevant monoterpenes such as camphene, pinene or limonene.

Period 2022-2 (July 1st - October 31st)

Area: Physics
Title: Fast ignition of inertial confinement fusion targets driven by ion beams
Leader: Javier Honrubia
Institution: Universidad Politécnica de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500

Abstract:
Proton fast ignition of inertial confinement fusion targets intends to get ignition with a substantial reduction of the laser energy requirements. The protons are generated by multi-petawatt, multi-picosecond laser beams at relativistic intensities (10^20 W/cm^2) and deposit their energy in the compressed core, igniting the thermonuclear fuel. This project aims to optimise the proton beam generation in hollow cones and its application to the ignition of pre-compressed fuels. The combination of multidimensional PIC, radiation-hydrodynamic and hybrid simulations will be carried out to reach that goal. The outcome will be a realistic estimation of the laser energy requirements for proton fast ignition as an alternative to the standard central ignition scheme used at the large scale facilities NIF and LMJ.

Area: Physics
Title: Identifying mechanisms of activation and signalling of oncogenic proteins in cell membranes for tumour blocking
Leader: Jordi Marti
Institution: Universitat Politècnica de Catalunya

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 6000

Abstract:
Molecular Dynamics and Metadynamics simulations will be applied to study the binding of the oncogene KRas4B protein on DOPC/DOPS/cholesterol lipid membranes and in ionic aqueous solution. Free energy landscapes of KRas at membrane surfaces will be constructed after relevant collective variables of the dynamics are identified. This is a pioneering work on the study of the interactions between SOS1 and KRas in biological membranes at the all-atom level, what will lead us to the unveiling of the microscopic mechanisms regulating activation and signalling of the oncogenes, in order to develop drugs or procedures capable to control these mechanisms and eventually block the formation and development of tumors. All simulations will be performed at the MareNostrum4 BSC-CNS supercomputer using open source codes NAMD2, AMBER, GROMACS and PLUMED2.

Area: Astronomy, Space and Earth Sciences
Title: The Origin of the Basal Stellar Magnetic Fields with realistic 3D MHD Simulations of Cool Stars
Leader: Andrea Perdomo García
Institution: Instituto de Astrofísica de Canarias

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2500

Abstract:
Given their abundance in the universe, their tendency to host exoplanets and the fact that they are some of the best laboratories for plasma physics, cool stars are now more than ever an essential topic in astrophysics. Nevertheless, it is technically impossible to resolve their surface with direct observations, thus, simulations are undoubtedly one of the best tools to study in detail the structure and dynamics of their atmospheres. We employ state-of-the-art code MANCHA3D to perform realistic 3D radiative MHD simulations of the magnetic field amplification in the near-surface convection of the cool stars due to action of the local small-scale dynamo. We intend to shed a new light on the origin and properties of their basal magnetic field, which is well known in the solar case, while has never been studied in other cool stars.

Area: Astronomy, Space and Earth Sciences
Title: Preparing for the fourth observation run of gravitational wave detectors
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 9900

Abstract:
In the first three observation runs of the international network of gravitational wave detectors, gravitational waves from 90 compact binary coalescences of black holes and neutron stars have been detected. In December 2022 the fourth observation run will finally reach design sensitivity and is foreseen to detect hundreds of gravitational wave events. In this project we finalise our preparations to develop waveform models that are sufficiently accurate and computationally efficient so that they can be used by the LIGO-Virgo-KAGRA collaboration and eventually the general gravitational wave community to analyse all events to be detected in O4. To this end we perform numerical relativity simulations of high mass ratio precessing binaries and parameter estimation with our upgraded waveform models to map out systematic errors in our models.

Area: Astronomy, Space and Earth Sciences
Title: Climate change impacts on extreme precipitation events in Andalusia by using regional modelling at very high resolution. Evaluation of land-atmosphere feedbacks
Leader: Sonia Gámiz-Fortis
Institution: University of Granada

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 1200

Abstract:
The aim of this project is to conduct dynamical downscaling simulations over Andalusia, analyzing the potential improvement of the regionalized product by including convection-permitting models instead the use of parametrizations. For this end, the ICTP Regional Climate Model (RegCM) model is used to downscale ERA5 large scale experiments using two nested domains with 5 and 1 km spatial resolution. After evaluating the prediction skill of the regionalized simulations and the added value from resolving explicitly the convection processes, an ensemble of climate simulations within the CMIP6 initiative using a pseudo-global warming (PWG) strategy will be conducted to regionalize projections of climate change along two future periods, near (2036-2050) and far (2085-2099), under the SSP5-8.5 scenario.

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 450

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and Agriculture 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality using WRF-Chem models.

Area: Engineering and Mathematics
Title: Numerical study on the effect of hydrogen enrichment of a lean natural gas flame in a gas turbine model combustor
Leader: Leonardo Pachano
Institution: Barcelona Supercomputing Center

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2000

Abstract:
This RES project aims at studying the effect of hydrogen enrichment of a lean natural gas technically premixed flame by means of high-fidelity Large Eddy Simulations. A swirl-stabilized gas turbine model combustor is simulated at inert and reacting conditions with pure natural gas and mixtures of up to 50% of hydrogen in fuel per volume. Combustion modelling relies on the tabulation of laminar unstrained premixed flamelets and presumed-PDF integration to account for turbulence-chemistry-interaction. Numerical results are validated through comparison with a comprehensive experimental database comprising flow field Particle Image Velocimetry measurements, and flame topology OH* chemiluminescence and OH Planar Laser Induced measurements.

Area: Engineering and Mathematics
Title: Development and Evaluation of Ad-hoc Storage Parallel File systems
Leader: Felix Garcia Carballeira
Institution: Universidad Carlos III de Madrid

Assigned machine(s): MareNostrum (BSC) Picasso (UMA) CTE-ARM (BSC)
Assigned khours with priority: 212
Assigned khours without priority: 384

Abstract:
This activity is part of the European ADMIRE project (956748 H2020-JTI-EuroHPC-2019-1). The main objective of the ADMIRE project is creating an active I/O stack that dynamically adjusts computation and storage requirements through intelligent global coordination, malleability of computation and I/O, and the scheduling of storage resources along all levels of the storage hierarchy. To achieve this, the project will develop a software-defined framework based on ad-hoc parallel file systems. The objective of the request for computing resources is evaluate the performance and scalability of the ad-hoc storage systems developed in the project to identify bottlenecks to optimize and improve the scalability the ad-hoc storage systems.

Area: Homogeneous Chemistry
Title: Computational exploration and design of squalene-hopene cyclases for efficient cationic cyclizations
Leader: Silvia Osuna
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2500

Abstract:
Life could not be sustained without the presence of enzymes, which are responsible for accelerating the chemical reactions in a biologically compatible timescale. Enzymes present other advantageous features such as high specificity and selectivity, plus they operate under very mild biological conditions. Inspired by these extraordinary characteristics, many scientists wondered about the possibility of engineering new enzymes for industrially-relevant targets. In this project, free energy surfaces will be estimated using QM/MM metadynamics to provide a rationale for the experimentally observed selectivity of some engineered squalene-hopene cyclases towards the production of different industrially-relevant monoterpenes such as camphene, pinene or limonene.

Area: Heterogeneous Chemistry and Solids
Title: Design of new catalysts for CO2 reduction by means of first principles simulations and elastic strain engineering
Leader: Javier LLorca
Institution: Technical University of Madrid & IMDEA Materials Institute

Assigned machine(s): Picasso (UMA) CTE-POWER (BSC)
Assigned khours with priority: 650

Abstract:
The objective of this investigation is to design new catalysts (based on transition metas and intermetallic compounds) capable to facilitate the transformation of CO2 into CH4. This will be achieved by a search for candidates whose electronic structure can be modified by the application of large elastic strains. The design of the optimum catalysts will be achieved through a high throughput strategy based on the combination of density functional theory calculations and the development of ad hoc neural networks to select the combination of material and strain state that better improves the kinetics of the corresponding reaction.

Period 2022-1 (March 1st - June 30th)

Area: Astronomy, Space and Earth Sciences
Title: Realistic 3D Radiative MHD Simulations of Cool Stars: The Origin of the Basal Stellar Magnetic Fields
Leader: Andrea Perdomo García
Institution: Instituto de Astrofísica de Canarias

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 3500

Abstract:
The cool stars are the most common main-sequence stars in the universe and the best candidates to host habitable planets. Realistic 3D radiative MHD simulations are essential tool to study the structure and dynamics of their convection zones and atmospheres. We employ state-of-the-art code MANCHA3D to perform high-resolution simulations of the magnetic field amplification in the near-surface convection of the cool stars due to action of the local small-scale dynamo. This action is well known in the solar case, but has never been studied in other main-sequence cool stars. The results will shed a new light on the origin of the magnetic field in the cool stars.

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 445.44

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and Agriculture 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality using WRF-Chem models.

Area: Astronomy, Space and Earth Sciences
Title: 3D RMHD simulations of subparsec jets in the microquasar SS433.
Leader: Jose López Miralles
Institution: Universitat de Valencia

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 4000

Abstract:
The microquasar SS433 is one of the most powerful and exotic star systems in our Galaxy. It is catalogued as a High-Mass X-ray Binary composed by a compact object (most likely a stellar-mass Black Hole) and a companion star. One of the main properties of this system is that it reveals the presence of bipolar, precessing mildly-relativistic jets at all energy wave-lengths, from radio to X-rays.In this activity, we will perform a series of specific numerical simulations using our proprietary 3D RMHD code Lóstrego. Our objectives are: (1) run the first numerical simulations of the SS433 precessing jets considering the dynamical evolution of magnetic fields, and (2) disentangle the physical processes behind the local reheating reported in a series of Chandra observations at arc-second scales (i.e., the extended X-ray jets).

Area: Astronomy, Space and Earth Sciences
Title: Near-term climate change: Regionalized decadal predictions over the Iberian Peninsula. An assessment of the influence of land-atmosphere interactions on water resources.
Leader: María Jesús Esteban Parra
Institution: Universidad de Granada

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 375

Abstract:
The aim of the project is to conduct dynamical downscaling simulations of CMIP5/6 global decadal predictions over the Iberian Peninsula and address the potential improvement of the regionalized product by including realistic initial soil conditions. The Weather Research & Forecasting model is used to regionalize a representative subensemble of decadal experiments from the Decadal Prediction Large Ensemble and non-initialized experiments from the CESM Large Ensemble. After evaluating the prediction skill of the decadal regionalized hindcasts and the added value of initialization, a set of simulations will be conducted to regionalize decadal forecasts along a future period.

Area: Astronomy, Space and Earth Sciences
Title: Compact binary models for the ground based gravitational wave detectors at design sensitivity
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 10680

Abstract:
Our research team plays a prominent role in the development of the waveform models that are used to identify the sources of gravitational wave events by the LIGO-Virgo-Kagra collaboration. This project has two goals: First, to perform numerical relativity simulations of merging spinning black hole systems which will inform upgrades of our waveform models to the requirements of the fourth observing run (O4), which will start in late summer or fall of 2022, and will finally achieve the design sensitivity of the detectors. Second, we will be able to provide parameter estimation results of astrophysical interest, focusing on improved estimates of orbital eccentricity, and taking advantage of the superior computational performance of our waveform models.

Area: Astronomy, Space and Earth Sciences
Title: Towards constraining neutrino mass from galaxy clustering measurements
Leader: Matteo Zennaro
Institution: DIPC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2400

Abstract:
We plan to run a set of simulations including the effects of massive neutrinos for a twofold purpose. On the one hand we intend to further improve the cosmology rescaling algorithm developed by our group: with this technique we can manipulate a small set of high-quality simulations to mimic nonlinear structure in any arbitrary cosmology; our set of main simulations does not include, at the moment, any cosmologies with massive neutrinos – thus limiting the parameter space we can cover to neutrino masses below 0.4 eV (while, for example, using data from CMB experiments alone, the total neutrino mass is bound at ~0.6 eV at the 2-sigma level). On the other hand, we mean to use these simulations to improve and extend the galaxy biasing model we recently developed, in order to accurately capture the effect of neutrinos on galaxy clustering.

Area: Physics
Title: Extreme Holography
Leader: David Mateos
Institution: University of Barcelona (UB)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 900
Assigned khours without priority: 1500

Abstract:
Over the next decade a new generation of heavy ion collision experiments will probe the properties of out-of-equilibrium, strongly interacting QCD matter at non-zero baryon density. In particular, they will search for the conjectured critical point in the phase diagram of QCD. Understanding the results of these experiments will pose a huge theoretical challenge. The only non-perturbative, first-principle tool to study QCD, namely its lattice formulation, is not well suited for real-time phenomena, let alone at non-zero baryon density. This offers a golden opportunity for holography. We will numerically simulate for the first time holographic collisions in gauge theories with a critical point in their phase diagram. This will provide invaluable insights on the dynamics relevant for the next generation of heavy ion collisions.

Area: Engineering and Mathematics
Title: COMBUSTION NOISE ASSESSMENT IN LDI COMBUSTORS OF GAS TURBINES
Leader: Alberto BROATCH
Institution: Universitat Politècnica de València

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 880

Abstract:
New emission standards are promoting the substitution of gas turbine diffusion-flame combustors with new technologies that fulfill these requirements i.e., lean direct injection. These new technologies seem to be inherently noisier due to the unsteady combustion and the inhomogeneities that appear in the flow field. Understanding the relation that combustion, hydrodynamics and acoustics have in these new systems has become crucial to reduce the level of acoustic emissions and avoid huge pressure oscillations that could induce a catastrophic engine failure. In this project, the capabilities of an HPC-intended code called Alya will be assessed for predicting combustion noise and thermoacoustic instabilities. The proposed methodology uses three different tools to do this job: LES simulations, Helmholtz solvers and reduction order models.

Area: Engineering and Mathematics
Title: Improving pollutant dispersion prediction in urban environments through the use of advanced deep learning techniques
Leader: Joan Calafell Sandiumenge
Institution: Barcelona Supercomputing Center-Centro Nacional de Supercomputación

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2160

Abstract:
The goal of this project is to create a reliable and accurate pollution map generator in such a way that it takes into account the influence of complex urban geometries in the dispersion of pollutants but at a reasonable computational cost. This project explores an innovative Deep Learning-based algorithm to generate the pollutant concentration maps, drastically reducing the computational requirements while maintaining high predicting accuracy. The approach is based Conditional Generative Adversarial Networks to reconstruct wind flow maps in urban areas. CFD simulations will be carried out on HPC to simulate the effect that urban geometries have in the micro-meteorology and dispersion (more than 50 different configurations). This dataset will be used to develop a real time model that will be validated real data obtained with a pilot test

Area: Engineering and Mathematics
Title: Simulation of failure across scales in thermoplastic composites
Leader: Israel García García
Institution: Universidad de Sevilla

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 360

Abstract:
The accurate simulation of fracture and fatigue of composite materials across the different length-scales provides a better understanding of their failure mechanisms and supports innovation to inhibit them. The intricate nature of these materials, involving heterogeneity and anisotropy, increases the complexity of making predictions about their response, even using advanced simulation tools. A highly accurate numerical simulation will be carried out, including an extremely detailed reproduction of the material’s microstructure. This model will be subjected to different static and fatigue loading to characterize the initiation of the different failure mechanisms observed in this type of composites. The detailed observation of the process will allow the understanding of the damage/failure progress across scales.

Period 2021-3 (November 1st - February 28th)

Area: Astronomy, Space and Earth Sciences
Title: Realistic 3D Radiative MHD Simulations of Cool Stars: The Origin of the Basal Stellar Magnetic Fields
Leader: Andrea Perdomo García
Institution: Instituto de Astrofísica de Canarias

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 3500

Abstract:
The cool stars are the most common main-sequence stars in the universe and the best candidates to host habitable planets. Realistic 3D radiative MHD simulations are essential tool to study the structure and dynamics of their convection zones and atmospheres. We employ state-of-the-art code MANCHA3D to perform high-resolution simulations of the magnetic field amplification in the near-surface convection of the cool stars due to action of the local small-scale dynamo. This action is well known in the solar case, but has never been studied in other main-sequence cool stars. The results will shed a new light on the origin of the magnetic field in the cool stars.

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change at the urban scale
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 445.44

Abstract:
The computational activity proposed takes place in the context of the ERC Consolidator project URBAG: Integrated System Analysis of Urban Vegetation and Agriculture 2019-2024). Given the need of cities to increment green areas and local agriculture to promote urban sustainability, URBAG aims to provide the knowledge and tools to evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of air quality, heat wave and climate change mitigation, as well as ecosystem services provided to urban dwellers. To do so, URBAG uses, develops, and improves atmospheric transport models at the urban scale with the aim to evaluate 1) the efficacy of green areas on heat wave episodes using WRF and 2) how urban and peri-urban agriculture and vegetation affect air quality using WRF-Chem models.

Area: Astronomy, Space and Earth Sciences
Title: 3D RMHD simulations of subparsec jets in the microquasar SS433.
Leader: Jose López Miralles
Institution: Universitat de Valencia

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 4000

Abstract:
The microquasar SS433 is one of the most powerful and exotic star systems in our Galaxy. It is catalogued as a High-Mass X-ray Binary composed by a compact object (most likely a stellar-mass Black Hole) and a companion star. One of the main properties of this system is that it reveals the presence of bipolar, precessing mildly-relativistic jets at all energy wave-lengths, from radio to X-rays.In this activity, we will perform a series of specific numerical simulations using our proprietary 3D RMHD code Lóstrego. Our objectives are: (1) run the first numerical simulations of the SS433 precessing jets considering the dynamical evolution of magnetic fields, and (2) disentangle the physical processes behind the local reheating reported in a series of Chandra observations at arc-second scales (i.e., the extended X-ray jets).

Area: Astronomy, Space and Earth Sciences
Title: Near-term climate change: Regionalized decadal predictions over the Iberian Peninsula. An assessment of the influence of land-atmosphere interactions on water resources.
Leader: María Jesús Esteban Parra
Institution: Universidad de Granada

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 375

Abstract:
The aim of the project is to conduct dynamical downscaling simulations of CMIP5/6 global decadal predictions over the Iberian Peninsula and address the potential improvement of the regionalized product by including realistic initial soil conditions. The Weather Research & Forecasting model is used to regionalize a representative subensemble of decadal experiments from the Decadal Prediction Large Ensemble and non-initialized experiments from the CESM Large Ensemble. After evaluating the prediction skill of the decadal regionalized hindcasts and the added value of initialization, a set of simulations will be conducted to regionalize decadal forecasts along a future period.

Area: Astronomy, Space and Earth Sciences
Title: Compact binary models for the ground based gravitational wave detectors at design sensitivity
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 10680

Abstract:
Our research team plays a prominent role in the development of the waveform models that are used to identify the sources of gravitational wave events by the LIGO-Virgo-Kagra collaboration. This project has two goals: First, to perform numerical relativity simulations of merging spinning black hole systems which will inform upgrades of our waveform models to the requirements of the fourth observing run (O4), which will start in late summer or fall of 2022, and will finally achieve the design sensitivity of the detectors. Second, we will be able to provide parameter estimation results of astrophysical interest, focusing on improved estimates of orbital eccentricity, and taking advantage of the superior computational performance of our waveform models.

Area: Astronomy, Space and Earth Sciences
Title: Towards constraining neutrino mass from galaxy clustering measurements
Leader: Matteo Zennaro
Institution: DIPC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2400

Abstract:
We plan to run a set of simulations including the effects of massive neutrinos for a twofold purpose. On the one hand we intend to further improve the cosmology rescaling algorithm developed by our group: with this technique we can manipulate a small set of high-quality simulations to mimic nonlinear structure in any arbitrary cosmology; our set of main simulations does not include, at the moment, any cosmologies with massive neutrinos – thus limiting the parameter space we can cover to neutrino masses below 0.4 eV (while, for example, using data from CMB experiments alone, the total neutrino mass is bound at ~0.6 eV at the 2-sigma level). On the other hand, we mean to use these simulations to improve and extend the galaxy biasing model we recently developed, in order to accurately capture the effect of neutrinos on galaxy clustering.

Area: Physics
Title: Extreme Holography
Leader: David Mateos
Institution: University of Barcelona (UB)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 900
Assigned khours without priority: 1500

Abstract:
Over the next decade a new generation of heavy ion collision experiments will probe the properties of out-of-equilibrium, strongly interacting QCD matter at non-zero baryon density. In particular, they will search for the conjectured critical point in the phase diagram of QCD. Understanding the results of these experiments will pose a huge theoretical challenge. The only non-perturbative, first-principle tool to study QCD, namely its lattice formulation, is not well suited for real-time phenomena, let alone at non-zero baryon density. This offers a golden opportunity for holography. We will numerically simulate for the first time holographic collisions in gauge theories with a critical point in their phase diagram. This will provide invaluable insights on the dynamics relevant for the next generation of heavy ion collisions.

Area: Engineering and Mathematics
Title: COMBUSTION NOISE ASSESSMENT IN LDI COMBUSTORS OF GAS TURBINES
Leader: Alberto BROATCH
Institution: Universitat Politècnica de València

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 880

Abstract:
New emission standards are promoting the substitution of gas turbine diffusion-flame combustors with new technologies that fulfill these requirements i.e., lean direct injection. These new technologies seem to be inherently noisier due to the unsteady combustion and the inhomogeneities that appear in the flow field. Understanding the relation that combustion, hydrodynamics and acoustics have in these new systems has become crucial to reduce the level of acoustic emissions and avoid huge pressure oscillations that could induce a catastrophic engine failure. In this project, the capabilities of an HPC-intended code called Alya will be assessed for predicting combustion noise and thermoacoustic instabilities. The proposed methodology uses three different tools to do this job: LES simulations, Helmholtz solvers and reduction order models.

Area: Engineering and Mathematics
Title: Improving pollutant dispersion prediction in urban environments through the use of advanced deep learning techniques
Leader: Joan Calafell Sandiumenge
Institution: Barcelona Supercomputing Center-Centro Nacional de Supercomputación

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2160

Abstract:
The goal of this project is to create a reliable and accurate pollution map generator in such a way that it takes into account the influence of complex urban geometries in the dispersion of pollutants but at a reasonable computational cost. This project explores an innovative Deep Learning-based algorithm to generate the pollutant concentration maps, drastically reducing the computational requirements while maintaining high predicting accuracy. The approach is based Conditional Generative Adversarial Networks to reconstruct wind flow maps in urban areas. CFD simulations will be carried out on HPC to simulate the effect that urban geometries have in the micro-meteorology and dispersion (more than 50 different configurations). This dataset will be used to develop a real time model that will be validated real data obtained with a pilot test.

Area: Engineering and Mathematics
Title: Simulation of failure across scales in thermoplastic composites
Leader: Israel García García
Institution: Universidad de Sevilla

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 360

Abstract:
The accurate simulation of fracture and fatigue of composite materials across the different length-scales provides a better understanding of their failure mechanisms and supports innovation to inhibit them. The intricate nature of these materials, involving heterogeneity and anisotropy, increases the complexity of making predictions about their response, even using advanced simulation tools. A highly accurate numerical simulation will be carried out, including an extremely detailed reproduction of the material’s microstructure. This model will be subjected to different static and fatigue loading to characterize the initiation of the different failure mechanisms observed in this type of composites. The detailed observation of the process will allow the understanding of the damage/failure progress across scales.

Period 2021-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: High-resolution WRF simulations for assessing low carbon power systems in Spain (HIGHWAYS)
Leader: David Pozo Vazquez
Institution: University of Jaén

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
The feasibility of low carbon power systems (LCPSs) for Spain is becoming no longer in question. Nevertheless, such systems still present serious challenges to become a reality. The major issue arises because they should be sustainable, reliable and economical, but these features are difficult to conciliate as the penetration of renewables increases. The models used in the design and simulation of LCPSs require appropriate solar and wind resources databases as a very key input. This project aims at contributing to the planning and development of an optimized LCPS in Spain by providing an enhanced and specialized historical solar and wind resources database. The database, obtained using a dynamical downscaling procedure based on the WRF model, will span multiple decades and will have a high temporal and spatial resolution.

Area: Astronomy, Space and Earth Sciences
Title: The long and winding road to black-hole formation in stellar core collapse
Leader: Martin Obergaulinger
Institution: Universitat de València

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2650

Abstract:
Stellar-mass black holes, as detected in gravitational waves by LIGO and Virgo, are formed as the final product of the evolution of some stars of more than 8 solar masses. Their formation can be accompanied by a collapsar, a particular type of long gamma-ray burst, a very energetic, relativistic explosion of the progenitor star. Special conditions are required to produce such an explosion, which only a subset of all stars fulfil. Most notably, rapid rotation and possibly strong magnetic fields need to be present. Even then, the success depends on the details of a long and complex evolution in which the gas flows, nuclear physics, neutrino emission, and magnetic fields all play an important role. This project uses simulations including all these processes to study the formation of black holes and the possible launching of a collapsar.

Area: Astronomy, Space and Earth Sciences
Title: Compact binary coalescence modelling toward LIGO/Virgo design sensitivity and next generation detectors
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 10750

Abstract:
This project continues our long-term program to model the gravitational wave signals emitted during the coalescence of astrophysical black hole binary systems, and to apply these models to measure the properties of the sources, such as the masses and spins of the components of the binary or its location, with the methods of Bayesian inference. The focus of the project is on high mass events, which are hard to distinguish from noise artefacts, and on precessing sources with mass or high mass ratio, which is a region of parameter space that is not yet well understood for gravitational wave data analysis, and where measuring the source parameters is particularly difficult.

Area: Life and Health Sciences
Title: Genomic analysis of 10,000 Next Genome Sequencing data sets for the diagnosis or rare disease patients
Leader: Dr. Sergi Beltran
Institution: CNAG-CRG

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 750

Abstract:
We wish to analyse 15,000 whole exome and whole genome datasets for rare disease, using the latest available resources. The datasets come from across Europe and have been shared as part of European projects such as Solve-RD, the European Joint Project on Rare Diseases and RD-Connect. We will align to the GRCh38 version of the genome, and perform variant calling using GATK4.0. The data will then be fully integrated into the the RD-Connect Genome-Phenome Analysis Platform (GPAP), an IRDiRC recognised resource, which is a resource freely accessible by any bona fide rare disease researcher. The GPAP has an extensive set of features allows the researcher to perform their own variant filtration and prioritisation on their case, and to attempt to identify similar cases, both within the system and through initiatives such as MatchmakerExchange.

Area: Engineering and Mathematics
Title: The effect of free-stream perturbations on wings at low Reynolds numbers.
Leader: Oscar Flores
Institution: Universidad Carlos III de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 400

Abstract:
This work aims to study the effect of free-stream perturbations on the aerodynamic performance of a wing, in the low Reynolds number regime characteristic of Micro Air Vehicles. To that end, Direct Numerical Simulations of a wing flying at constant speed and a fixed angle of attack will be performed, at a Reynolds number Re=5000. The wing will have a NACA0012 cross section and will be modelled as infinite along the span. The effect of the characteristic length of the free-stream perturbation will be analysed, keeping the turbulent intensity constant. The results will allow us to evaluate the impact of gusty environments on the aerodynamic response of Micro Air Vehicles, producing the necessary knowledge to derive control and gust mitigation strategies for these small fliers.

Period 2021-1 (March 1st - June 30st)

Area: Astronomy, Space and Earth Sciences
Title: High-resolution WRF simulations for assessing low carbon power systems in Spain (HIGHWAYS)
Leader: David Pozo Vazquez
Institution: University of Jaén

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1760

Abstract:
The feasibility of low carbon power systems (LCPSs) for Spain is becoming no longer in question. Nevertheless, such systems still present serious challenges to become a reality. The major issue arises because they should be sustainable, reliable and economical, but these features are difficult to conciliate as the penetration of renewables increases. The models used in the design and simulation of LCPSs require appropriate solar and wind resources databases as a very key input. This project aims at contributing to the planning and development of an optimized LCPS in Spain by providing an enhanced and specialized historical solar and wind resources database. The database, obtained using a dynamical downscaling procedure based on the WRF model, will span multiple decades and will have a high temporal and spatial resolution.

Area: Astronomy, Space and Earth Sciences
Title: Compact binary coalescence modelling toward LIGO/Virgo design sensitivity and next generation detectors
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 10750

Abstract:
This project continues our long-term program to model the gravitational wave signals emitted during the coalescence of astrophysical black hole binary systems, and to apply these models to measure the properties of the sources, such as the masses and spins of the components of the binary or its location, with the methods of Bayesian inference. The focus of the project is on high mass events, which are hard to distinguish from noise artefacts, and on and on precessing sources with high mass ratios, which is a region of parameter space that is not yet well understood, and where measuring the source parameters is particularly difficult for high mass systems, but also for unequal mass low mass systems, where an accurate determination of the mass of the lighter component is crucial to determine its character as a black hole or neutron star.

Area: Chemistry of Solids
Title: Formation and modification of single-atom sites on the surface of bimetallic catalysts
Leader: Konstantin Neyman
Institution: Universitat de Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 320

Abstract:
Nanoparticles exposing single atoms of a catalytically active metal dispersed in a more inert host metal comprise a novel, rapidly advancing class of so-called single-atom alloy (SAA) catalysts. These catalysts are characterized not only by higher activity and selectivity, but also by cost savings via lower usage of precious metals, improved resistance to poisoning, etc. Yet, the number and properties of the single-atom active sites often dynamically change in the presence of reaction media. Time-resolved monitoring of these changes notably affecting the catalytic performance is challenging. This computational project aims to provide backgrounds for a very promising vibrational spectroscopy technique to trace changes of active sites in SAA catalysts of Pd and Pt alloyed with Ag and Au depending on the exposition time to CO molecules.

Period 2020-3 (November 1st - February 28th)

Area: Astronomy, Space and Earth Sciences
Title: Modelling the impacts of green infrastructure on air quality and climate change
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 207.36

Abstract:
Urban and peri-urban agriculture have become a growing phenomenon worldwide over the last decades and covers a large variety of forms, such as vertical farming, greenhouse rooftops, local foodsheds, which together with green spaces, are referred to as green infrastructure. Green infrastructure can promote urban sustainability, such as reducing greenhouse gas emissions, improving local air quality, and optimizing its use of resources. Hence, this project will study the impacts of green infrastructure on air quality and climate change using the WRF and WRF-Chem models with multi-layer canopy model (BEP+BEM). Moreover, because high-resolution simulations require a lot of resources and computational time, this project is also focused on understanding the scalability of the models to reduce resources and computational time.

Area: Astronomy, Space and Earth Sciences
Title: The end of an era – analysing the last gravitational wave detections before LIGO-Virgo design sensitivity
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 9880

Abstract:
The advanced gravitational wave detector network is approaching its design sensitivity, providing a wealth of observations of binary black holes and other compact objects. Accurate and efficient modeling of these signals becomes ever more crucial to extract their full scientific content, as does the improvement and better understanding of Bayesian inference methods. This project continues the long-term program of waveform modeling at UIB, using numerical relativity simulations to develop increasingly precise and computationally efficient models for practical use in data analysis. We will cover an extended set of of precessing and eccentric binaries, further upgrade our phenomenological waveform family, and use it to study parameter estimation of the most challenging detected events on the home stretch to design sensitivity.

Area: Life and Health Sciences
Title: Rational hit-to-lead optimization of anti-PD-1 biological drugs
Leader: Ernest Giralt Lledó
Institution: Institute for Research in Biomedicine (IRB)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 150

Abstract:
Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-i3 and PD-i6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys.

Area: Physics
Title: Fully quantum mechanical simulations of an excess electron adsorbed in water clusters
Leader: Eduardo R. Hernández
Institution: Instituto de Ciencia de Materiales de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 750
Assigned khours without priority: 750

Abstract:
The solvated electron in water is a system that has intrigued scientists since its discovery in the early 1960s. Singly-charged water cluster anions have long been studied as a means to gain insight into the limiting case of the bulk solvated electron. In the past, several computational studies have considered such systems by a combined classical-quantum approach, neglecting the quantum effects in water dynamics. However it is to be expected that quantum effects be non-negligible, given the lightness of the atoms involved. Our aim in this project is to lift this approximation, by treating both water molecules and adsorbed electron fully quantum mechanically. This will be done by combining a Path Integral treatment of the water cluster with the numerical solution of the Schrödinger equation for the electron.

Area: Chemistry of Solids
Title: Assessment of quinoid-resonance structures in the electron transport through single molecule junctions
Leader: Sandra Rodriguez
Institution: Universidad de Málaga

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 392
Assigned khours without priority: 150

Abstract:
High-performance conducting polymers for organic electronics have been successfully designed through the use of the so-called “donor-acceptor” approach, whereby the bandgap is reduced. It could be thought that in the same way, the alternation of D and A building blocks along a π-conjugated molecule would be an effective strategy to engineer small HOMO-LUMO gap molecules, with remarkable and efficient charge transport in the molecular electronic field. Behind this approach, the role played by the quinoid-resonance structure is crucial; however, its analysis and/or study have been overlooked in the few published works on single D-A π-conjugated molecule junctions. In this project, will be evaluated the transport properties of a series of D-A π-conjugated molecules in their single molecule junctions considering the quinoid-resonace effect.

Area: Chemistry of Solids
Title: CO2 conversion into light fuels activated by H/H2 over transition metal encapsulated in MFI zeolites (TM@S-1)
Leader: Pablo Gamallo
Institution: Universitat de Barcelona (UB) and Institut de Química Teòrica i Computacional (IQTC)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 796
Assigned khours without priority: 120

Abstract:
The present study is focused on the DFT characterization of the mechanisms behind the catalytic hydrogenation of CO2 into chemical species such as methane and methanol. Specifically, we explore the effect of H/H2 in the activation of CO2 on single atom catalysts formed by transition metal atoms supported on MFI zeolites (TM@S-1). These novel class of catalysts exhibit exceptional activity and selectivity thanks to their easy tunability, and present optimal metal utilization. However, there remains a lack of information about the catalytic performance of many of these supported materials. The present project aims to screen the large search-space of TM atoms encapsulated on Silicalite-1 zeolite and find the best candidate for CO2 hydrogenation into valuable light fuels.

Period 2020-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: Modeling the urban atmosphere to determine the effect of green infrastructure on air quality and carbon footprint
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 150

Abstract:
Urban and peri-urban agriculture is currently experiencing rapid growth. This covers a variety of forms, such as vertical farming, greenhouse rooftops, local foodsheds, which together with green spaces, are referred to as green infrastructure. Often various types of green infrastructures are promoted equally in urban sustainability agendas, without existing studies clearly indicating the effectiveness of one or another better serving sustainability goals of the city, such as reducing greenhouse gas emissions, improving local air quality, and optimizing its use of resources. This project will evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of these local and global environmental impacts using the WRF and WRF-Chem models with multi-layer canopy model (BEP+BEM).

Area: Astronomy, Space and Earth Sciences
Title: The end of an era – analysing the last gravitational wave detections before LIGO-Virgo design sensitivity
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 10200

Abstract:
The advanced gravitational wave detector network is approaching its design sensitivity, providing a wealth of observations of binary black holes and other compact objects. Accurate and efficient modeling of these signals becomes ever more crucial to extract their full scientific content, as does the improvement and better understanding of Bayesian inference methods. This project continues the long-term program of waveform modeling at UIB, using numerical relativity simulations to develop increasingly precise and computationally efficient models for practical use in data analysis. We will cover an extended set of of precessing and eccentric binaries, further upgrade our phenomenological waveform family, and use it to study parameter estimation of the most challenging detected events on the home stretch to design sensitivity.

Area: Life and Health Sciences
Title: Rational structure-based design of anti-PD-1 biological peptides
Leader: Ernest Giralt Lledó
Institution: Institute for Research in Biomedicine (IRB)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1382

Abstract:
Peptides, together with antibodies, are among the most potent biochemical tools to modulate challenging protein-protein interactions. However, current structure-based methods are largely limited to natural peptides and are not suitable for designing target-specific binders with improved pharmaceutical properties, such as macrocyclic peptides. Here we report a general framework that leverages the computational power of Rosetta for large-scale backbone sampling and energy scoring, followed by side-chain composition, to design heterochiral cyclic peptides that bind to a protein surface of interest. To showcase the applicability of our approach, we identified two peptides (PD-i3 and PD-i6) that target PD-1, a key immune checkpoint, and work as protein ligand decoys.

Area: Physics
Title: ‘In silico’ seawater: evaluating for the first time the physical properties of seawater from molecular dynamics simulations
Leader: Carlos Vega de las Heras
Institution: UCM

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 648

Abstract:
Thermohaline circulation plays an essential role in regulating the Earth’s climate. It is driven by density gradients in oceans. Thus knowledge of the dependence of the physical properties of seawater on temperature and composition is fundamental. The complexity of seawater composition and the unavailability of forcefields have probably prevented until now the implementation of molecular simulation for seawater. We have recently shown that both problems can be overcome. The goal of this proposal is to carry out, for the first time, molecular dynamics simulations for seawater. Using a state of the art force field and a system representative of the standard seawater composition we intend to evaluate static, dynamical, structural and interfacial properties of seawater. This work could also be of help in the design of desalination processes.

Area: Chemistry of Solids
Title: Carbon Capture and Storage on Transition Metal Nitride and Nitride MXene Materials
Leader: Francesc Viñes Solana
Institution: Universitat de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 150
Assigned khours without priority: 150

Abstract:
The high concentration of CO2 in the Earth´s atmosphere correlates to global warming and non-sustainable anthropogenic emissions, mainly coming from the use of fossil fuels. Reducing the amount of this greenhouse gas has triggered research into CO2 abatement, e.g. using scrubber materials in carbon capture and storage technologies. This is hampered by the high stability of CO2, which requires the use of highly active materials, which, despite the intensive search by many groups worldwide, have not yet been found. The present activity investigates the performance of transition metal nitrides (TMNs) and novel two-dimensional TMNs and carbides, called MXenes, which have been recently synthesized and predicted to capture and activate CO2.

Period 2020-1 (March 1st - June 30th)

Area: Astronomy, Space and Earth Sciences
Title: Modeling the urban atmosphere to determine the effect of green infrastructure on air quality and carbon footprint
Leader: Gara Villalba Méndez
Institution: Associate professor at the Dept. of Chemical, Biological, and Environmental Engineering, Universitat Autònoma de Barcelona and senior researcher at the Institute of Environmental Science and Technology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1658.88

Abstract:
Urban and peri-urban agriculture is currently experiencing rapid growth. This covers a variety of forms, such as vertical farming, greenhouse rooftops, local foodsheds, which together with green spaces, are referred to as green infrastructure. Often various types of green infrastructures are promoted equally in urban sustainability agendas, without existing studies clearly indicating the effectiveness of one or another better serving sustainability goals of the city, such as reducing greenhouse gas emissions, improving local air quality, and optimizing its use of resources. This project will evaluate which combinations of urban/peri-urban agriculture and green spaces result in the best performance in terms of these local and global environmental impacts using the WRF and WRF-Chem models with multi-layer canopy model (BEP+BEM).

Area: Astronomy, Space and Earth Sciences
Title: Testing models for gravitational waves from coalescing black holes with generic configurations
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 8200

Abstract:
This project is part of the extension of the UIB long-term program to study the coalescence of binaries of black holes (BH) in general relativity and the gravitational wave (GW) signals emitted in the process to the more generic eccentric case. In this project we will produce the first generic (unequal mass, unequal spin, precessing and eccentric, and high mass ratio) complete waveforms (by connecting the numerical simulations of the last orbits to perturbative inspiral information) for the coalescence of black hole binaries. We will then inject these signals into simulated detector noise to test the parameter bias and efficiency of current waveform models when analysing generic signals.

Area: Physics
Title: Multiscale design of molecular materials for Neuromorphic Computing
Leader: Salvador Cardona
Institution: University of Valencia

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 516

Abstract:
Neuromorphic computing has been suggested as an efficient alternative to current computing as it can combine both memory and computation on the same location through an array of neuron-like elements with synapse-like connections. Designing suitable materials for hardware-based artificial neural networks is proposed to overcome this barrier and develop neuromorphic architectures. In this project we will study a key element, called memristor, that is being used as the main component for building neuron-like structures. We intend to design new molecular memristors by developing a theoretical methodology to understand the relation between molecular structure and memristive behavior.

Area: Chemistry of Solids
Title: Carbon Capture and Storage on Transition Metal Nitride and Nitride MXene Materials
Leader: Francesc Viñes Solana
Institution: Universitat de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 300

Abstract:
The high concentration of CO2 in the Earth´s atmosphere correlates to global warming and non-sustainable anthropogenic emissions, mainly coming from the use of fossil fuels. Reducing the amount of this greenhouse gas has triggered research into CO2 abatement, e.g. using scrubber materials in carbon capture and storage technologies. This is hampered by the high stability of CO2, which requires the use of highly active materials, which, despite the intensive search by many groups worldwide, have not yet been found. The present activity investigates the performance of transition metal nitrides (TMNs) and novel two-dimensional TMNs and carbides, called MXenes, which have been recently synthesized and predicted to capture and activate CO2.

Period 2019-3 (November 1st - February 29th)

Area: Astronomy, Space and Earth Sciences
Title: Testing models for gravitational waves from coalescing black holes with generic configurations
Leader: Sascha Husa
Institution: Universitat de les Illes Balears

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 8300

Abstract:
This project is part of the extension of the UIB long-term program to study the coalescence of binaries of black holes (BH) in general relativity and the gravitational wave (GW) signals emitted in the process to the more generic eccentric case. In this project we will produce the first generic (unequal mass, unequal spin, precessing and eccentric) complete waveforms (by connecting the numerical simulations of the last orbits to perturbative inspiral information) for the coalescence of black hole binaries. We will then inject these signals into simulated detector noise to test the parameter bias and efficiency of current waveform models when analysing generic signals.

Area: Physics
Title: Electro-hydrodynamic simulation of the streamer-to-leader transition in lightning and other long electric discharges: polarity asymmetry and the role of water
Leader: Alejandro Luque Estepa
Institution: Instituto de Astrofísica de Andalucía

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1948

Abstract:
The propagation of long electric discharges presents a polarity asymmetry. Positive discharges propagate rather smoothly while negative discharges propagate in sudden jumps. Recent observations show the stepping of positive leaders under highly humid environments, which suggests that we should include water chemistry in our models to fully address the stepping mechanism. Hence, we propose to study with numerical simulations the relevance of humidity in the propagation of long electric discharges.If successful, our project will have implications in the field of atmospheric electricity, perhaps shedding light on the mechanisms that in a thunderstorm accelerate particles up to energies above one megaelectronvolt. It may also have implications in technological applications of long discharges such as high-voltage switches.

Period 2019-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: Highly accurate generic black-hole binary simulations: exploring the highly eccentric precessing case
Leader: Antoni Ramos Buades
Institution: University of Balearic Islands

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 2685

Abstract:
This project is part of the extension of the UIB long-term program to study the coalescence of binaries of black holes (BH) in general relativity and the gravitational wave (GW) signals emitted in the process to the more generic eccentric case. Current gravitational waveform models used by the LIGO and Virgo collaborations to claim detections assume quasicircularity of the orbits of the two merging BHs. In this project we produce highly accurate solutions of the Einstein equations for highly eccentric systems with arbitrary spin oritentations, this is, highly eccentric precessing waveforms . These GW signals will serve to test the validity of key waveform approximations, well used in the precessing quasi-circular case, in the precessing high eccentric limit.

Area: Chemistry of Solids
Title: Developing Realistic Models of Titanium Carbide Nanoparticles
Leader: Stefan T. Bromley
Institution: University of Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 490

Abstract:
Titanium carbide (TiC) is an important transition metal carbide (TMC) material in catalysis, solid-state chemistry, and materials science. TMCs can often display catalytic activities similar to that of noble metals and are thus potential replacements for expensive late transitions metals based catalysts. Of particular environmental interest is the conversion of greenhouse gases such as CO2 into added-value greener products such as methanol. Although bulk TMCs and their surfaces are reasonably well understood, the nanoscale structure and properties of this important class of material is lacking. In this Activity we will develop realistic models of TiC nanoparticles (NPs) and use them to understand their structural, electronic and chemical properties.

Period 2019-1 (March 1st - June 30th)

Area: Chemistry and Materials Science and Technology
Title: Deoxygenation Reactions on Mo2C Based Catalysts
Leader: Francesc Viñes Solana
Institution: Universitat de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 651

Abstract:
The biofuel generation from biomass is needed to meet the energy requirements of our society. The initial biomass pyrolysis requires a deoxygenation treatment of the product species prior to the refinery process. Nowadays catalysts Ni and Co based have to be replaced by low-cost materials with improved catalytic activity. Experimental studies at Laval University on α- and β-Mo2C nanoislands grown on Cu reveal their excellent performance in the deoxygenation of textbook reactants. Atomistic information is required to interpret the IR and STM experiments and determine the key catalytic factors. The present project will computationally assist in the interpretation, determining the molecular reaction mechanism, ultimately discovering the underlying chemistry so as to foster the key catalytic aspects of the Mo2C catalyzed dexoygenation.

Area: Chemistry and Materials Science and Technology
Title: Multiscale Modelling of Precipitation Strengthening in Metallic Alloys
Leader: Javier LLorca
Institution: Technical University of Madrid & IMDEA Materials Institute

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1000

Abstract:
A multiscale modelling strategy based on atomistic simulations has been developed to study precipitation hardening in metallic alloys. The interaction between dislocations and precipitates was analyzed by means of atomistic simulations. The different thermodynamic functions that determine the features of these obstacles for the dislocation glide were computed using molecular statics, molecular dynamics and the nudged elastic band method. Predictions of the yield stress as a function of temperature were obtained from the atomistic simulations by means of the transition state theory. The methodology was applied to Al-Cu and Mg-Al alloys.

Area: Chemistry and Materials Science and Technology
Title: Understanding the structure and vibrational spectra of realistic silicate nanoparticles: linking theory and observation
Leader: Stefan T. Bromley
Institution: University of Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1040

Abstract:
Silicate nanoparticles are ubiquitous in the interstellar medium and in the Earth’s atmosphere/biosphere and are hugely important in materials science (e.g. formation of nanoporous materials, used in composite materials). Often overlooked are the properties of nano-silicates (diameter <2 nm) which are likely to be particularly numerous. Such small species are likely to have very different geometries from the bulk crystalline and surface structures, and thus have very distinct vibrational spectra not observed in crystalline material. Using quantum chemical density functional calculations we will study the structure and vibrational spectra of a varied set of olivinic and pyroxene nanoparticles with sizes up to 2000 atoms in order to provide insight for experimentalists.

Area: Chemistry and Materials Science and Technology
Title: Developing Realistic Models of Titanium Carbide Nanoparticles
Leader: Stefan T. Bromley
Institution: University of Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 490

Abstract:
Titanium carbide (TiC) is an important transition metal carbide (TMC) material in catalysis, solid-state chemistry, and materials science. TMCs can often display catalytic activities similar to that of noble metals and are thus potential replacements for expensive late transitions metals based catalysts. Of particular environmental interest is the conversion of greenhouse gases such as CO2 into added-value greener products such as methanol. Although bulk TMCs and their surfaces are reasonably well understood, the nanoscale structure and properties of this important class of material is lacking. In this Activity we will develop realistic models of TiC nanoparticles (NPs) and use them to understand their structural, electronic and chemical properties.

Period 2018-3 (November 1st - February 28th)

Area: Astronomy, Space and Earth Sciences
Title: Near-term climate change: Regionalized decadal prediction for the Iberian Peninsula. Soil-atmosphere interactions on water resources
Leader: María Jesús Esteban Parra
Institution: Universidad de Granada

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 475

Abstract:
This work aims to study the impact of high-resolution near-term climate change on Iberian Peninsula water resources. For this end, dynamical downscaling of the decadal predictions from the Coupled Model Intercomparison Project (CMIP), and the improvement by including initial soil conditions will be carried out. It will analyze whether an added value can also be found in the regionalized decadal predictions of hydroclimatic variables and if these can be improved by introducing initial soil conditions. To do this, we will use the Weather Research & Forecasting (WRF) model, obtaining hindcasts for several decades, to evaluate the predictive skill of the regionalization. Additionally, regionalized predictions will be made for decades 2016-2025 and 2020-2029, which will be used as input in the Variable Infiltration Capacity (VIC) model.

Area: Chemistry and Materials Science and Technology
Title: Understanding the mechanisms of permeation in K+ channels
Leader: Carmen Domene
Institution: University of Bath

Assigned machine(s): Picasso (UMA) MinoTauro (BSC)
Assigned khours with priority: 1050

Abstract:
The transport of ions and water across membrane cells and organelles is a prerequisite for many of life’s processes. Transport often involves very precise selectivity for specific particles. For example, cell membranes present a serious energy barrier to an ion crossing it because ions are energetically more stable in water than in the hydrophobic membrane interior. Membrane proteins such as ion channels are used by the cell to transport ions and other metabolites across membranes.
Despite the large number of genes encoding membrane proteins, just about 0.9% of membrane protein structures are presently known at high resolution. Due to the inherent experimental difficulties in obtaining structural data, it is essential that we maximize our understanding of their structure/function relationships using computer simulation.

Area: Chemistry and Materials Science and Technology
Title: Hydrogen Dissociation and Evolution Catalyzed by MXenes
Leader: Francesc Viñes Solana
Institution: Universitat de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500

Abstract:
Two-dimensional transition metal carbides (TMCs) and nitrides, called MXenes, have been recently synthesized, and their possible uses are numerous. One appealing application is to benefit from the TMCs’ outstanding catalytic activity and large surface area. Here we evaluate a wide set of carbide MXenes for the textbook and industrially relevant H2 formation/dissociation, considering liquid/solid interfaces for catalytic hydrogen evolution, and hydrogen breaking in gas/solid. To do so, state-of-the-art DFT calculations including dispersive forces, temperature and pressure dependences, and solvation effects are conducted, inspecting the thermodynamics and kinetics of the processes. This will enable us to assess the materials capabilities and rationally guide subsequent experiments.

Area: Chemistry and Materials Science and Technology
Title: Multiscale Modelling of Precipitation Strengthening in Metallic Alloys
Leader: Javier LLorca
Institution: Technical University of Madrid & IMDEA Materials Institute

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1200

Abstract:
A multiscale modelling strategy based on atomistic simulations has been developed to study precipitation hardening in metallic alloys. The interaction between dislocations and precipitates was analyzed by means of atomistic simulations. The different thermodynamic functions that determine the features of these obstacles for the dislocation glide were computed using molecular statics, molecular dynamics and the nudged elastic band method. Predictions of the yield stress as a function of temperature were obtained from the atomistic simulations by means of the transition state theory. The methodology was applied to Al-Cu and Mg-Al alloys

Period 2018-2 (July 1st - October 31st)

Area: Mathematics, Physics and Engineering
Title: Quantum tetramers and hexamers
Leader: Grigory E. Astrakharchik
Institution: Universitat Politecnica de Catalunya

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500

Abstract:
We solve the three-boson problem with contact two- and three-body interactions in one dimension and analytically calculate the ground and excited trimer-state energies. Then, by using the diffusion Monte Carlo technique we calculate the binding energy of three dimers formed in a one-dimensional Bose-Bose or Fermi-Bose mixture with attractive inter- and repulsive intraspecies interactions. Combining these results with our three-body analytics we extract the three-dimer scattering length close to the dimer-dimer zero crossing. In both considered cases the three-dimer interaction turns out to be repulsive. Our results constitute a concrete proposal for obtaining a one-dimensional gas with a pure three-body repulsion

Area: Mathematics, Physics and Engineering
Title: DNS of large-amplitude transverse gusts on infinite wings at low Reynolds number
Leader: Manuel Moriche
Institution: Universidad Carlos III de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 575

Abstract:
In this activity we analyze the flow and the aerodynamic forces of large-amplitude, transverse, transient gusts. The Reynolds number based on the free stream velocity and the chord is 5000. The configuration under study is an infinite aspect ratio wing with NACA 0012 cross section.

Area: Chemistry and Materials Science and Technology
Title: Transition Metal Activity Towards Carbon
Leader: Francesc Viñes Solana
Institution: Universitat de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 300

Abstract:
The interaction of C with Transition Metals (TM) surfaces and nanoparticles is key in many research fields, including nanotechnology and heterogeneous catalysis, i.e. in graphene synthesis, formation of TM carbides, and C poisoning and catalytic promotion. An atomistic detail of the interaction at the surface (even subsurface) of TM surfaces and nanoparticles is a necessary point to understand the chemical modification, even to tailor it at will. The purpose of the present project is to gain this detailed knowledge by an exhaustive exploration of C atoms on a full set of TMs (27) and surfaces (81) by means of first-principles density functional calculations, as to gain the thermodynamics and kinetic stability of such moieties at sub/surface of surfaces and low-coordinated sites, supplying an elementary chart to guide experiments.

Area: Chemistry and Materials Science and Technology
Title: Rationalizing the shape of photocatalytically active gold nanoplatelets on graphene
Leader: Lluís Blancafort
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500

Abstract:
Gold nanoplatelets deposited on graphene have high catalytic activity in the light induced water splitting reaction, which is a potential source of clean hydrogen fuel, and in other gold catalyzed organic reactions such as Ullman-like homocoupling, N-C cross coupling and oxidative coupling. The reactivity is closely related to the morphology of the platelets (111 orientation of the faces), which are formed by pyrolysis of chitosan films containing Au(3+). This RES activity is the beginning of a long-term project which aims to elucidate the mechanism of these reactions, focusing on how it depends on the shape of the nanoplatelets. This knowledge will provide us with design principles for the optimization of the (photo)catalytic activity of these materials by alloying and doping

Area: Chemistry and Materials Science and Technology
Title: Modeling of RuO2 surface-liquid water and RuO2 nanoparticle–liquid water interfaces: Influence of surface morphology and nanoparticle size
Leader: Xavier Solans Monfort
Institution: Universitat Autònoma de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500

Abstract:
The production of clean energy is one of the most important scientific challenges of the 21st century. Nowadays, the global energy supply is mainly obtained by carbon-based energy sources, but there is a strong demand of clean and friendly carbon-neutral alternatives that have the ability to serve the energetic needs of present and future generations. One of these alternative energy sources is the splitting of water into O2 and H2, the most critical step of this process being the formation of oxygen.
Ruthenium oxide (RuO2) has been reported to be a very active water oxidation co-catalyst whose activity can be improved when used in the form nanoparticles. Present activity aims of understanding the structure of RuO2 – liquid water interface using ab-initio molecular dynamics simulations.

Area: Chemistry and Materials Science and Technology
Title: Understanding the mechanisms of permeation in K+ channels
Leader: Carmen Domene
Institution: University of Bath

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 800

Abstract:
The transport of ions and water across membrane cells and organelles is a prerequisite for many of life’s processes. Transport often involves very precise selectivity for specific particles. For example, cell membranes present a serious energy barrier to an ion crossing it because ions are energetically more stable in water than in the hydrophobic membrane interior. Membrane proteins such as ion channels are used by the cell to transport ions and other metabolites across membranes.
Despite the large number of genes encoding membrane proteins, just about 0.9% of membrane protein structures are presently known at high resolution. Due to the inherent experimental difficulties in obtaining structural data, it is essential that we maximize our understanding of their structure/function relationships using computer simulation.

Period 2018-1 (March 1st - June 30th)

Area: Astronomy, Space and Earth Sciences
Title: Chemo-dynamIcal propertiEs of gaLaxies and the cOsmic web – CIELO
Leader: Patricia B. Tissera
Institution: Universidad Andres Bello

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1200

Abstract:
We study the formation of galaxies using high resolution zoom-in haloes selected from a large volume consistent with the current cosmological model. This galaxy sample will allow us to address a variety of exciting open problems in galaxy astrophysics, such as environmental effects, the interplay between chemical and dynamical evolution, the role of inflows and outflows therein, the orbital satellite evolution and its links with gas acquisition.The experiments are designed to gain insight into the local Cosmic Web (CW) dynamics using zoom-in simulation binning in environmental properties independent of halo mass. This a new, original approach to analyse the links between high redshift CW properties and galaxy properties.

Area: Mathematics, Physics and Engineering
Title: Development of advanced LES spray combustion models for engine applications
Leader: Jose M García Oliver
Institution: Universitat Politècnica de València

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1000

Abstract:
The present activity aims at evaluating advanced atomization and combustion models for the prediction of liquid spray processes under Diesel engine conditions, which is a highly transient problem. The end goal is having a fully Eulerian model that overcome limitations of droplet ones, with tabulated chemistry to efficiently manage the computational demand due to the highly complicated chemistry of combustion. Realistic in-cylinder engine conditions are used from the standard Spray A defined by the Engine Combustion Network, for which experimental information is available. By means of the different calculation runs, the prediction capabilities of the different approaches will be assessed.

Area: Chemistry and Materials Science and Technology
Title: Transition Metal Activity Towards Carbon
Leader: Francesc Viñes Solana
Institution: Universitat de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 670

Abstract:
The interaction of C with Transition Metals (TM) surfaces and nanoparticles is key in many research fields, including nanotechnology and heterogeneous catalysis, i.e. in graphene synthesis, formation of TM carbides, and C poisoning and catalytic promotion. An atomistic detail of the interaction at the surface (even subsurface) of TM surfaces and nanoparticles is a necessary point to understand the chemical modification, even to tailor it at will. The purpose of the present project is to gain this detailed knowledge by an exhaustive exploration of C atoms on a full set of TMs (27) and surfaces (81) by means of first-principles density functional calculations, as to gain the thermodynamics and kinetic stability of such moieties at sub/surface of surfaces and low-coordinated sites, supplying an elementary chart to guide experiments.

Area: Chemistry and Materials Science and Technology
Title: Ab initio-based Scanning Tunnelling Microscope simulations of realistic MoS2 samples
Leader: Blanca Biel
Institution: Universidad de Granada

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 405

Abstract:
STM is a powerful tool to characterize and access the electronic structure of materials. Advanced STM simulations based on Density Functional Theory methods complement experimental studies and can help interpreting the experimental findings. The goal of the present activity is to acquire a deep knowledge of the modifications of the electronic properties of MoS2 in a realistic situation, namely in the presence of defects, strain or a metallic substrate, by means of such advanced STM simulations, working closely with an experimental team.

Period 2017-3 (November 1st - February 28th)

Area: Astronomy, Space and Earth Sciences
Title: Geodynamic modeling of the Westernmost Mediterranean and the Iberia Peninsula region
Leader: Ivone Jiménez-Munt
Institution: Instituto de Ciencias de la Tierra Jaume Almera

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 2017.54

Abstract:
The relative and complex motions of Iberia, Africa and Europe have given rise to numerous tectonic reconstructions of the Alpine Mediterranean region. According to these reconstructions, the northern convergence of Africa against Europe was accommodated by the development of two subduction zones affecting the northern and southeastern Iberian margins. Recently, it has been proposed a tectonic history of the Western Mediterranean since Cretaceous based on the interaction of two tectonic plates with opposite polarity. Several mechanisms have been proposed as responsible for the intraplate deformation of Iberia. The main objectives of this project is through numerical modeling, trying to explain the mechanisms that gave rise to the current relief of the Iberian Peninsula and analyze the dynamic evolution of a double subduction process.

Area: Chemistry and Materials Science and Technology
Title: Cooperativity Effects in Spin Crossover Complexes: Periodic Calculations and Entropic-Phonon Contributions
Leader: Eliseo RUIZ
Institution: Universitat de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1200

Abstract:
The use of magnetic molecules in electronic devices opens several possibilities in the field of Molecular Spintronics. Spin crossover systems show an appealing switching behavior and their main advantage, when compared with single-molecule magnet systems, is that such behavior may appear at room temperature. The theoretical prediction of the spin crossover properties is a difficult task because the switching process (high-low spin states) implies an important change in the electronic structure of the paramagnetic centers. Our study focus on an extension of some reported work in this field, most of them with discrete Fe(II) complexes, by performing periodic calculations to add the cooperativity effects, effect of solvent and cations, and the inclusion of the vibrational effects in the energy values of the periodic calculations.

Period 2017-2 (July 1st - October 31st)

Area: Life and Health Sciences
Title: Disorder effects on large domain dynamics of the scavenger decapping enzyme
Leader: Ramon Crehuet
Institution: Consejo Superior de Investigaciones Científicas (CSIC)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 450

Abstract:
The scavenger decapping enzyme hydrolyzes the protective cap of mRNA fragments. Previous NMR and crystallographic results by Remco Sprangers group have shows that the activity of this enzyme depends on its domain motions. When the flipping motions of the domains is too fast, the enzyme turnover is reduced.We will perform Monte Carlo simulations to unveil the relationship between two crucial processes at the interface of biochemistry and biophyiscs. First, how an intramolecular coupled folding and binding event takes place. And second, how this binding affects the enzyme turnover, through the modulation of the large scale enzyme dynamics.

Area: Life and Health Sciences
Title: PCNA sliding mechanism on DNA
Leader: Ramon Crehuet
Institution: Consejo Superior de Investigaciones Científicas (CSIC)

Assigned machine(s): Picasso (UMA) MinoTauro (BSC)
Assigned khours with priority: 994

Abstract:
PCNA is an essential protein in the replication and repair of DNA, which acts by recruiting polymerases and other enzymes to the replication fork. PCNA function is mediated by p15, a nuclear intrinsically disordered protein with oncogenic potential involved in replication and cell-cycle progression. Single molecule experiments have shown that PCNA has two different types of sliding onto DNA, but their mechanisms remain unknown.This proposal will simulate the sliding mechanisms of PCNA in the presence and absence of p15 with all-atom molecular dynamics and compare the results to NMR and crystallographic data from our team. Our aims are to understand the molecular details of the PCNA sliding as well as the role of p15 in modulating the PCNA-DNA binding and ultimately in altering the function of PCNA.

Period 2017-1 (March 1st - June 30th)

Area: Mathematics, Physics and Engineering
Title: Computing pixel base socio-economic measures to analyze economic development
Leader: Marta Reynal-Querol
Institution: Universitat Pompeu Fabra

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 800
Assigned khours without priority: 100

Abstract:
The study of the relative role of human capital and institutions in the explanation of the colonial origins of economic development has generated lengthy debate among economists that analyze the role of institutions and human capital in separate empirical frameworks.
The ERC project has three important contributions in this literature. First, I am going to analyze the two competing theories on the same empirical framework. Second, I am going to use measures of initial human capital and institutions at the initial stage of colonization. Third, I am going to use sub-national variation.

Area: Chemistry and Materials Science and Technology
Title: Development of New TiO2-SiO2 Mixed Oxide Materials: From Nanoscale to Bulk
Leader: Stefan T. Bromley
Institution: University of Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500
Assigned khours without priority: 100

Abstract:
Nanostructures and nanostructured materials based upon interfacing nano-TiO2 with nano-SiO2 have drawn much recent attention due to their huge potential for applications in a diverse range of important fields (e.g. gas sensing, (photo)catalysis, optical components). The nano-SiO2-TiO2 combination gives rise to new physical/chemical/optical properties which are quite distinct from, and usually superior to, either separate nanomaterial. To understand nano-SiO2-TiO2 systems it is imperative to control the manner by which the two oxides are interfaced together. Using computer modelling we will study: (i)the electronic/chemical/structural properties of nano-SiO2-TiO2 systems, and (ii) how nano-SiO2 and nano-TiO2 interface together at the atomic/nano scale.

Period 2016-3 (November 1st - February 28th)

Area: Life and Health Sciences
Title: Structure of large viruses with a membrane studied by high-resolution cryo-electron microscopy
Leader: Nicola GA Abrescia
Institution: Center for Cooperative Research in Biosciences (CIC bioGUNE)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 132

Abstract:
Cryo-electron microscopy (cryo-EM) has entered in a new era thanks to the availability of powerful transmission electron microscopes equipped with direct detection cameras. Nowadays with cryo-EM it is possible to reach atomic resolution and to describe distinct conformational states adopted by the molecule/virus of interest.
Here, using high-resolution cryo-EM based image reconstruction techniques we aim to describe the three-dimensional structure and assembly of Haloarcula californiae icosahedral virus 1 (HCIV-1) eventually in different conformational states and that of the proteo-lipidic tube used by lipid-containing bacteriophage PRD1 to infect the host cell.
Both objectives will elucidate fundamental stages in the lifecycle of these viruses from assembly to genome delivery.

Area: Chemistry and Materials Science and Technology
Title: Evaluating the Potential Experimental Realisation of 2D Materials based on Radical Building Blocks
Leader: Stefan T. Bromley
Institution: University of Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 370

Abstract:
Two dimensional covalent organic frameworks (2D-COFs) are an exciting new class of planar ordered organic materials formed from the directed self-assembly of molecular building blocks. To date no 2D-COF has been reported based on open-shell molecules due to their inherent instability. Triarylmethyls (TAMs) are stable open-shell molecules that could be used to fill this gap. By means of accurate ab initio density functional calculations we have designed numerous TAM-based 2D-COFs. Further, by external strain, we show that the materials’ structures can be smoothly perturbed which, as we reported for single TAMs, gives rise to a predictable variance in spin localization. Consequently, other important magnetic, optical and electrical properties of the material can also be finely tuned.

Area: Chemistry and Materials Science and Technology
Title: Transport and structural properties of Van der Waals few layered A-RAM devices
Leader: Blanca Biel
Institution: Universidad de Granada

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 650

Abstract:
Due to their exceptional electronic properties, van der Waals materials show great potential as future active component in nanoscale electronic devices. The goal of this project is to use Density Functional Theory methods to assess the performance of such materials to build fully 2D non-volatile ARAM memory cells. Our results will not only help to the understanding of the fundamental properties of 2D heterostructures but will also contribute to the theoretical and experimental design of future memory devices developed within the frame of both national (TEC2014-59730-R) and European projects (REMINDER H2020-687931 and WAY-TO-GO-FAST H2020- ECSEL-2014-2-662175).

Period 2016-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: Stellar core collapse with rotation and magnetic fields
Leader: Martin Obergaulinger
Institution: Universitat de València

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 210
Assigned khours without priority: 50

Abstract:
We study the evolution of cores of evolved massive stars in fully self-consistent simulations employing a sophisticated neutrino-transport solver. These cores are the central engines of core-collapse supernovae and long gamma-ray bursts. Their dynamics is the result of a complex combination of physical effects such as nuclear physics, neutrino transport, fluid dynamics, magnetic fields, and relativistic gravity and may vary strongly across the wide range of stellar masses. Our goal is to investigate the explosion mechanism in the presence of rotation and magnetic fields, which currently is not well understood. Specific issues are the conditions for successful supernova explosions as opposed to secondary collapse to black holes and, in the latter case, the formation of an accretion disc and possible jet-like outflows.

Area: Life and Health Sciences
Title: Structure of large viruses with a membrane studied by high-resolution cryo-electron microscopy
Leader: Nicola GA Abrescia
Institution: Center for Cooperative Research in Biosciences (CIC bioGUNE)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 207.36

Abstract:
Cryo-electron microscopy (cryo-EM) has entered in a new era thanks to the availability of powerful transmission electron microscopes equipped with direct detection cameras. Nowadays with cryo-EM it is possible to reach atomic resolution and to describe distinct conformational states adopted by the molecule/virus of interest.
Here, using high-resolution cryo-EM based image reconstruction techniques we aim to describe the three-dimensional structure and assembly of Haloarcula californiae icosahedral virus 1 (HCIV-1) eventually in different conformational states and that of the proteo-lipidic tube used by lipid-containing bacteriophage PRD1 to infect the host cell.
Both objectives will elucidate fundamental stages in the lifecycle of these viruses from assembly to genome delivery.

Area: Chemistry and Materials Science and Technology
Title: Evaluating the Potential Experimental Realisation of 2D Materials based on Radical Building Blocks
Leader: Stefan T. Bromley
Institution: University of Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 737

Abstract:
Two dimensional covalent organic frameworks (2D-COFs) are an exciting new class of planar ordered organic materials formed from the directed self-assembly of molecular building blocks. To date no 2D-COF has been reported based on open-shell molecules due to their inherent instability. Triarylmethyls (TAMs) are stable open-shell molecules that could be used to fill this gap. By means of accurate ab initio density functional calculations we have designed numerous TAM-based 2D-COFs. Further, by external strain, we show that the materials’ structures can be smoothly perturbed which, as we reported for single TAMs, gives rise to a predictable variance in spin localization. Consequently, other important magnetic, optical and electrical properties of the material can also be finely tuned.

Period 2016-1 (March 1st - June 30th)

Area: Chemistry and Materials Science and Technology
Title: Toward rational design of Ni-ceria catalysts for increasing natural gas exploitation: the methane dry reforming reaction
Leader: M. Verónica Ganduglia-Pirovano
Institution: Instituto de Catálisis y Petroleoquímica

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 952

Abstract:
The aim of our theoretical work is to elucidate the dry reforming of methane reaction mechanism on ceria supported Ni nanoparticles as a model catalyst. The fundamental understanding of the reaction mechanisms, coupled to the detailed analysis of the configuration and properties of the active sites, is expected to help identify the key properties of a succesful new catalytic system for the conversion of natural gas to useable chemical fuel. The expected intense interplay between theory and our experimental collaborators at the Brookhaven Natl. Lab. will allow a great opportunity to explore implications of the results for applications. The calculations employ the DFT+U approach as implemented in the VASP code. Transition structures along reaction pathways are searched using the nudged elastic band method (NEB).

Area: Chemistry and Materials Science and Technology
Title: Modelling anion dissociation as a key step in organometallic catalysis
Leader: Gregori Ujaque
Institution: Universitat Autònoma de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
Anion dissociation processes are very common within homogeneous catalytic processes. They involve a charge generation process. In the case of a neutral complex, for instance, such ligand dissociation implies the generation of two charged species in solution: a positive organometallic complex and a negative anion. Such an apparently easy chemical transformation is shown to be hardly well reproduced by using the well established continuum models. In this project, the application of QM/MM-MD simulation techniques, that allow an explicit representation of the solvent, will be applied to a test case. This will allow us to check the appropriateness of these methods to investigate this type of processes.

Period 2015-3 (November 1st - February 29th)

Area: Life and Health Sciences
Title: High-resolution structures of whole viruses by cryo-electron microscopy techniques
Leader: Nicola GA Abrescia
Institution: Center for Cooperative Research in Biosciences (CIC bioGUNE)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 150

Abstract:
Structure-based approaches have revealed unexpected evolutionary relationships between viruses infecting organisms from different domains of cellular life.
Here, using high-resolution cryo-electron microscopy based image reconstruction techniques we aim to unravel the high-resolution three-dimensional structure and assembly of Haloarcula hispanica icosahedral virus 2 (HHIV-2) and Haloarcula californiae icosahedral virus 1 (HCIV-1).
The comparison of these euryarchaeal, halophilic, icosahedral, internal membrane-containing viruses to other viruses infecting organisms from the eukaryal and bacterial domains will inform us on the mechanisms of virus assembly and their relationship across evolution.

Area: Chemistry and Materials Science and Technology
Title: Stability of TiO2-SiO2 mixed oxide nanomaterials
Leader: Stefan T. Bromley
Institution: University of Barcelona & ICREA

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1000

Abstract:
Nanostructures and nanostructured materials based upon interfacing nano-TiO2 with nano-SiO2 have drawn much recent attention due to their huge potential for applications in a diverse range of important fields (e.g. gas sensing, (photo)catalysis, optical components). The nano-SiO2-TiO2 combination gives rise to new physical/chemical/optical properties which are quite distinct from, and usually superior to, either separate nanomaterial. To understand nano-SiO2-TiO2 systems it is imperative to control the manner by which the two oxides are interfaced together. Using computer modelling we will study: (i)the electronic/chemical/structural properties of nano-SiO2-TiO2 systems, and (ii) how nano-SiO2 and nano-TiO2 interface together at the atomic/nano scale.

Period 2015-2 (July 1st - October 31st)

Area: Life and Health Sciences
Title: High-resolution structures of whole viruses by cryo-electron microscopy techniques
Leader: Nicola GA Abrescia
Institution: Center for Cooperative Research in Biosciences (CIC bioGUNE)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 27

Abstract:
Structure-based approaches have revealed unexpected evolutionary relationships between viruses infecting organisms from different domains of cellular life.
Here, using high-resolution cryo-electron microscopy based image reconstruction techniques we aim to unravel the high-resolution three-dimensional structure and assembly of Haloarcula hispanica icosahedral virus 2 (HHIV-2) and Haloarcula californiae icosahedral virus 1 (HCIV-1).
The comparison of these euryarchaeal, halophilic, icosahedral, internal membrane-containing viruses to other viruses infecting organisms from the eukaryal and bacterial domains will inform us on the mechanisms of virus assembly and their relationship across evolution

Area: Mathematics, Physics and Engineering
Title: Fracture and hydrodynamics in curved and evolving surfaces
Leader: Marino Arroyo Balaguer
Institution: upc

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 80

Abstract:
Many phenomena in mechanics become more interesting when they take place in a curved and dynamical interface. In this proposal, examine computationally two such phenomena: fracture in thin sheets and hydrodynamics in fluid biomembranes. Both involve solving partial differential equations of evolving and curved surfaces, and both require high-­fidelity simulations to complement experiment. Using a common computational framework based on subdivision finite elements, we plan to study the interaction between curvature and crack propagation, and the dynamical behavior of curving proteins embedded in a fluid membrane.

Area: Chemistry and Materials Science and Technology
Title: Electronic and magnetic properties of molecules adsorbed on semi-infinite surfaces including spin-orbit coupling
Leader: Jorge Iribas Cerdá
Institution: ICMM-CSIC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 806

Abstract:
ab initio studies of spin-related and spin-orbit derived phenomena in magnetic molecules and/or layers adsorbed on semi-infinite surfaces: magnetic anisotropies, spin filters, spin torque, spin texture, magnetoresistance, etc.

Area: Chemistry and Materials Science and Technology
Title: Rational design of noble-metal free catalysts for the dry reforming of methane
Leader: M. Verónica Ganduglia-Pirovano
Institution: Instituto de Catálisis y Petroleoquímica

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 100

Abstract:
The aim of our theoretical work is to elucidate the dry reforming of methane reaction mechanism on ceria supported Ni nanoparticles as a model catalyst. The fundamental understanding of the reaction mechanisms, coupled to the detailed analysis of the configuration and properties of the active sites, is expected to help identify the key properties of a succesful new catalytic system for the conversion of natural gas to useable chemical fuel. The expected intense interplay between theory and our experimental collaborators at the Brookhaven Natl. Lab. will allow a great opportunity to explore implications of the results for applications. The calculations employ the DFT+U approach as implemented in the VASP code. Transition structures along reaction pathways are searched using the nudged elastic band method (NEB).

Area: Chemistry and Materials Science and Technology
Title: Understanding the water-gas shift reaction for hydrogen production on model Ni/ceria catalysts
Leader: M. Verónica Ganduglia-Pirovano
Institution: Instituto de Catálisis y Petroleoquímica

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 239

Abstract:
The aim of our theoretical work is to elucidate the full water-gas shift reaction mechanism on ceria supported 2D Ni nanoparticles as a model catalyst. The fundamental understanding of the reaction mechanisms, coupled to the detailed analysis of the configuration and properties of the active sites, is expected to help identify the key properties of a succesful new catalytic system for hydrogen production. The expected intense interplay between theory and our experimental collaborators at the Brookhaven Natl. Lab. will allow a great opportunity to explore implications of the results for applications. The calculations employed the DFT+U approach as implemented in the VASP code. Transition structures along reaction pathways are searched using the nudged elastic band method (NEB).

Period 2015-1 (March 1st - June 30th)

Area: Mathematics, Physics and Engineering
Title: Random Field Ising Model in four spatial dimensions and beyond
Leader: Victor Martin Mayor
Institution: Universidad Complutense de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 1120

Abstract:
The random-field Ising model (RFIM) is of paramount importance in the field of disordered systems. A plethora of problems, ranging from hysteresis in magnetic systems to random pinning of polymers and fluids in porous media, can be studied via the RFIM. As such, the RFIM is under intense research for more than 30 years now. Yet, surprisingly, some of its most fundamental questions remain unanswered. Our group, using powerful algorithms and statistical analysis tools from the pools of Statistical Physics and Computer
Science provided clear answers for the three-dimensional model. Nevertheless, a complete picture of the RFIM’s critical behavior requires the understanding of the role of the spatial dimensionality. The goal of the present proposal is to fill this gap by studying the model at four dimensions and beyond.

Period 2014-3 (November 1st - February 28th)

Area: Mathematics, Physics and Engineering
Title: Direct numerical simulations of Taylor-Couette flow for the Princeton experimental setup.
Leader: Francisco Marques Truyol
Institution: Universitat Politècnica de Catalunya

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 720
Assigned khours without priority: 80

Abstract:
The mechanisms triggering the outward angular momentum transport in accretion astrophysical flows are still unknown. The experimental outcomes attained so far have shown completely different results, thus providing opposite conclusions. Here we numerically compute the flow in the Princeton experimental setup at large Reynolds numbers. In this experiment the flow remains laminar in spite of the large Reynolds considered. Our goal is identifying the physical mechanisms responsible for the flow relaminarization. The high spatial resolution as well as the long simulation time needed make using HPC resources essential to deal with this problem.

Area: Mathematics, Physics and Engineering
Title: Molecular Kondo Project – III
Leader: Juan José Palacios Burgos
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 400
Assigned khours without priority: 50

Abstract:
The molecular Kondo project is an ambitious project that aims to contribute significantly to elucidate, calculate, and predict the Kondo-like resonances observed repeatedly in transport experiments on different organic molecules in recent years. All our effort is directed to the development of molecular effective Hamiltonians using DFT techniques and to correlate these Hamiltonians using a powerful computational tool known as impurity solver. The understanding of these many-body resonances in true complex system is especially important from a fundamental point of view, but also is important from a technological point of view as it enables applying this well-known quantum effect in nanoelectronic devices such as magnetic nanosensors.

Area: Chemistry and Materials Science and Technology
Title: Acid Gas Removal by Ionic Liquids: a Computational Approach
Leader: Santiago Aparicio
Institution: Universidad de Burgos

Assigned machine(s): Magerit (UPM) Picasso (UMA)
Assigned khours without priority: 53

Abstract:
The project studies the application of ILs to the acid gas capture processes, mainly for CO2 and SO2, based on the particular properties of these ILs. Comparing with the current methods for acid gases capture and separation, ILs have several advantages such as lower volatility, less thermal degradation during regeneration and the energy required for gas stripping being also lower that in the standard case. Likewise, the tunable properties of ILs, through a judicious combination of ions, would allow bottom-up approaches for designing suitable absorbents for acid gas capture. One of the main advantages of ILs is that their properties may be tuned (designer solvents) by a judicious combination of ions. Hence, a computational approach is proposed to find adequate ILs for acid gases removal

Period 2014-2 (July 1st - October 31st)

Area: Mathematics, Physics and Engineering
Title: Direct numerical simulations of Taylor-Couette flow for the Princeton experimental setup.
Leader: Francisco Marques Truyol
Institution: Universitat Politècnica de Catalunya

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500
Assigned khours without priority: 140

Abstract:
The mechanisms triggering the outward angular momentum transport inaccretion astrophysical flows are still unknown. The experimentaloutcomes attained so far have shown completely different results, thus providing opposite conclusions. Here we numerically compute the flow in the Princeton experimental setup at large Reynolds numbers. In thisexperiment the flow remains laminar in spite of the large Reynoldsconsidered. Our goal is identifying the physical mechanismsresponsible for the flow relaminarization. The high spatial resolution as well as the long simulation time needed make using HPC resources essential to deal with this problem.

Area: Mathematics, Physics and Engineering
Title: Molecular Kondo Project – II
Leader: Juan José Palacios Burgos
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500
Assigned khours without priority: 110

Abstract:
The molecular Kondo project is an ambitious project that aims to contribute significantly to elucidate, calculate, and predict the Kondo-like resonances observed repeatedly in transport experiments on different organic molecules in recent years. All our effort is directed to the development of molecular effective Hamiltonians using DFT techniques and to correlate these Hamiltonians using a powerful computational tool known as impurity solver. The understanding of these many-body resonances in true complex system is especially important from a fundamental point of view, but also is important from a technological point of view as it enables applying this well-known quantum effect in nanoelectronic devices such as magnetic nanosensors.

Area: Chemistry and Materials Science and Technology
Title: Hydrogen Spillover on Pd-doped Nanoporous Carbons and Catalytic Activity of Silver-Gold Nanoparticles
Leader: Iván Cabria
Institution: University of Valladolid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 102

Abstract:
First principles calculations of two of the most promising types of technologically interesting nanostructures will be carried out: Hydrogen spillover on palladium-doped nanoporous carbons and the Catalytic activity of silver-gold nanoparticles.Pd-doped nanoporous carbons have larger hydrogen storage capacities than pure nanoporous carbons. This increases is probably due to the spillover effect. First principles calculations will clarify the role of the spillover on the increase of the hydrogen storage capacities.Silver is an excellent material for the oxidation of etene. Mixing silver and gold, in the appropriate proportions could possibly yield a nanomaterial with improved catalytic properties. First principles calculations of propene interacting with silver-gold nanoparticles will explain their catalytic properties.

Period 2014-1 (March 1st - June 30th)

Area: Mathematics, Physics and Engineering
Title: Direct numerical simulations of Taylor-Couette flow for the Princeton experimental setup.
Leader: Francisco Marques Truyol
Institution: Universitat Politècnica de Catalunya

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 800

Abstract:
The mechanisms triggering the outward angular momentum transport inaccretion astrophysical flows are still unknown. The experimentaloutcomes attained so far have shown completely different results, thus providing opposite conclusions. Here we numerically compute the flow in the Princeton experimental setup at large Reynolds numbers. In thisexperiment the flow remains laminar in spite of the large Reynoldsconsidered. Our goal is identifying the physical mechanismsresponsible for the flow relaminarization. The high spatial resolution as well as the long simulation time needed make using HPC resources essential to deal with this problem.

Area: Chemistry and Materials Science and Technology
Title: Structure , reactivity and physical properties of polyoxometallates in solution
Leader: Prof. Dr. Josep M. Poblet
Institution: Universitat Rovira i Virgili

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200
Assigned khours without priority: 100

Abstract:
Polyoxometalates are primarily constituted of early-transition-metal elements in their highest oxidation states, a great majority of these structures are anionic and consequently salts with obligatory cations. Polyoxometalates, especially tungsto- and molybdophospates and silicates, are highly used in catalysis and in material science. The present project deals with the understanding and control of polyoxoanion transformations in solution, and is part of a collaborative research initiated in 2009 between the experimental group headed by Leroy Cronin at the Glasgow University, and the theoretical group of the University Rovira i Virgili of Tarragona. Both teams are interested in the understanding of complex chemical systems, either using synthetic and physical-chemistry techniques or computational tools.

Period 2013-3 (November 1st - February 28 th)

Area: Life and Health Sciences
Title: Exploring the Small Molecule Binding effects in protein folding equilibrium
Leader: Ramon Crehuet
Institution: Consejo Superior de Investigaciones Científicas (CSIC)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 250
Assigned khours without priority: 75

Abstract:
Intrinsically Disordered Proteins are an emerging family of proteins whose principal feature is that they do not exhibit a folded structure. Their role in cancer and neurodegenerative diseases suggests they should be preeminent drug targets. However very few studies have addressed the interaction and regulation of small-molecules with IDPs. The reason is the difficulty to study the interaction experimentally.Recent NMR and ICT results addressing the binding and folding of IDPs has given insight but still cannot resolve the full description of the binding process. Simulations are thus needed to give an explanation of the underlying molecular processes. PROFASI, is a protein simulator and aggregator program is a code well suited for this task.

Area: Life and Health Sciences
Title: Exploration of the unsual biophysics of Intrinsically Disordered Proteins using Monte Carlo simulations
Leader: Ramon Crehuet
Institution: Consejo Superior de Investigaciones Científicas (CSIC)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 250
Assigned khours without priority: 75

Abstract:
Intrinsically Disordered Proteins (IDPs) are an emerging family of proteins whose principal feature is that they do not exhibit a folded structure and thus challenge the sequence-structure-function paradigm. They perform crucial roles in the cell, determined by their dynamical behavior. They are key agents in some diseases.Several experimental techniques (NMR, CD or SAXS) can give information on their structural ensembles, but are unable to fully determine their conformational distributions. Therefore, the role of the models used to interpret the data is crucial. Current models are very simple and their predictive value is low. An important aspect is the development of computational tools to better understand IDPs ensembles.PROFASI is one of them. In this project, we will use it to show its unusual biophysical characteristics

Area: Chemistry and Materials Science and Technology
Title: Reveling insulator-to-metal transition in Mott materials with delocalization measures
Leader: Ángel Martín Pendás
Institution:

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 480
Assigned khours without priority: 120

Abstract:
Transition Metal Oxides (TMOs) are prototypical Mott insulators, that unlike usual metals are predicted to be insulators at standard conditions and
undergo an insulator-to-metal transition when put under pressure. Although standard ab initio methods fail to predict the insulating nature of TMOs as well as to describe the electronic transition they suffer, the recently developed Reduced Density Matrix Functional Theory (RDMFT) is expected to correctly capture it. Localization (LI) and Delocalization Indices (DI) measure to what extent the electrons confined to a finite region of the space can be found out of that region. Once the RDMFT calculations done with Elk successfully predict the behaviour of the TMOs, inspection of LI/DI evaluated with DGrid are expected to yield an accurate description of the problem.

Period 2013-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: Dust Effects on the Spectral Energy Distribution of Galaxies
Leader: Rosa Domínguez
Institution: Univ Autonoma Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 248

Abstract:
The aim of the application is to calculate dust effects in the SEDs of simulated galaxies on scales 50 – 100 kpc, i.e., larger than the galaxy size. These effects could be particularly important in star-forming proto-galaxies at high redshift, where star formation occurs enshrouded within infalling gaseous filaments, possibly metal enriched by previous violent events. To this end, a MPI code to solve radiative transfer in dust for systems of any geometry, as proto-galaxies or proto-groups of galaxies at high z, has been written: GRASIL-3D. We plan to calculate the SEDs and 2D images (at different angles) of a variety of simulated proto-galaxies from the UV to mm, as well as their evolution, to find out whether dust effects when the surrounding dust distribution is considered could have observable implications.

Area: Mathematics, Physics and Engineering
Title: Simulation of the negative electron compressibility in LaAlO3/SrTiO3 interfaces
Leader: Javier Junquera
Institution: Universidad de Cantabria

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
We propose studying the origin of the negative electron compressibility appearing at the LaAlO3/SrTiO3 interface when the conducting charge is almost depleted. In order to achieve this goal it is necessary to perform calculations in systems with many atoms to allow for a small electron density and possible localization of the electron. Due to the extremely high number of atoms (tens of thousands) we propose to use a Tight-Binding model which was previously fitted to ab initio calculations to obtain the electron distribution and the variation of the Fermi energy with the electron density in the heterostructure.

Area: Chemistry and Materials Science and Technology
Title: Dielectric Losses Caused by Jahn-Teller Phonons in LaCoO3 Perovskite Nanoparticles
Leader: Jose Gracia
Institution: UNIZAR

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 150

Abstract:
Jahn-Teller interaction, strong electron-phonon interaction, lifts the degeneracy of the energy of orbitals, while preserving the total orbital energy. Jahn-Teller interaction is accompanied by the distortion of the crystal structure and results in bucking the octahedral network. This leads to altering the M-O-M bond angle and distance. Temperature induces changes in the crystal structure of Cobalnites, the unit cell becomes more cubic what reduces the electron-phonon coupling. At temperature enough to the semiconductor to metal transition the softening of Jahn-Teller distortions leads to the frequency drop of the octahedral bending and stretching modes.Softening of the octahedral bending and stretching modes drives to colossal dielectric losses.

Area: Chemistry and Materials Science and Technology
Title: High level QM/MM Free Energy Surfaces of enzyme catalyzed reactions by FEP methods
Leader: Vicent Moliner
Institution: Universitat Jaume I

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 15

Abstract:
The present project is devoted to the computational description of catalysis phenomena in biologi systems by exploration of free energy surfaces with high level QM/MM potentials. In particular, free energy perturbation (FEP) methods will be obtain for the chemical step of enzyme catalyzed reactions which will allow obtaining valuable information to design new chemicals with medical applications.
The two selected systems are the Aromatase and the Lactate dehydrogenase. Inhibition of the former is indeed an effective molecular target for the development of new treatment for hormone dependent breast cancer. LDH is another complex system with a chemical step involving two proton transfers. Measuring LDH levels can be helpful in monitoring treatment for cancer, heart failure, hypothyroidism, anemia, and lung or liver disease.

Period 2013-1 (Match 1st - June 30th)

Area: Life and Health Sciences
Title: Understanding the binding kinetics of Acetylcholine Binding Protein (AChBP) inhibitors
Leader: Xavier Barril
Institution: University of Barcelona

Assigned machine(s): MareNostrum (BSC) Picasso (UMA)
Assigned khours with priority: 192

Abstract:
In this study, we would like to investigate the mechanism by which small molecules influence the action of acetylcholine-binding proteins (AChBP). These proteins serve as model systems for nicotinic acetylcholine receptors, which are highly expressed in the central nervous system and are important drug targets for different neurodegenerative diseases and nicotine addiction. Particularly, we are interested in kinetic aspects of ligand binding and its potential relationship with the opening of a ligand-inducible subpocket. This is part of a collaborative project and we will compare our results with the experimentally determined kinetic and thermodynamic data. With this approach, we expect to contribute to a better understanding of kinetics-structure relationships at an atomistic level.

Area: Mathematics, Physics and Engineering
Title: Simulation of the negative electron compressibility in LaAlO3/SrTiO3 interfaces
Leader: Javier Junquera
Institution: Universidad de Cantabria

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
We propose studying the origin of the negative electron compressibility appearing at the LaAlO3/SrTiO3 interface when the conducting charge is almost depleted. In order to achieve this goal it is necessary to perform calculations in systems with many atoms to allow for a small electron density and possible localization of the electron. Due to the extremely high number of atoms (tens of thousands) we propose to use a Tight-Binding model which was previously fitted to ab initio calculations to obtain the electron distribution and the variation of the Fermi energy with the electron density in the heterostructure.

Area: Chemistry and Materials Science and Technology
Title: Elucidating the mechanism of formation of the enamine intermediate in proline catalyzed aldol reactions in water
Leader: Jordi Ribas Ariño
Institution: University of Barcelona

Assigned machine(s): Picasso (UMA) Tirant (UV)
Assigned khours with priority: 436.667

Abstract:
In the drive towards green chemistry, organocatalytic reactions carried out in aqueous media have recently received a great deal of attention. The proline amide catalyzed self aldol reaction of propionaldehyde in water constitutes the first organocatalytic aldol reaction that proceeds with the reagents homogeneously dissolved in water and that affords the products with good enantioselectivity.
Having already disclosed the origin of such good enantioselectivity (Chem. Eur. J. 2012,18,15868), the purpose of the proposed Activity is to elucidate the mechanism of formation of the enamine intermediate in this key reaction on the basis of first principles molecular dynamics simulations in the condensed phase. This study will thus result in a detailed understanding of the full catalytic cycle of this reaction.

Period 2012-3 (November 1st - February 28th)

Period 2012-2 (July 1st - October 31th)

Area: Astronomy, Space and Earth Sciences
Title: Imaging fields for time reversal in seismology
Leader: Daniel Stich
Institution: Instituto Andaluz de Geofísica

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 5

Abstract:
Besides the classic forward and inverse problems, a third and more exotic flavour of modelling has appeared in seismology: Time reversal of the seismic wavefield. It’s a forward problem mathematically, but an inverse problem conceptually, with the difference that no model parameterisation is required. When applied to complex waveforms, time reversal is able to locate complexity of the propagation medium, like mountain roots or sedimentary basins. However, a benchmarking exercise using appropriate forward models and different imaging fields is a pending assignment in the earthquake community. In our case, it’s directed at understanding the imaging capabilities of time reversal for the purpose of investigating Earth structure, and learning how quantitative estimates can be extracted despite the lack of parameterisation.

Area: Life and Health Sciences
Title: Evidence of Conformational Selection in a Glycosyltransferase Structure?
Leader: Antoni Planas
Institution: Laboratory of Biochemistry. IQS – Universitat Ramon Llull

Assigned machine(s): Magerit (UPM) Picasso (UMA)
Assigned khours with priority: 650

Abstract:
The interaction of enzymes with their natural substrates usually leads to substantial changes in protein structure. This has traditionally been regarded as the induced fit effect which overrides the static lock and key model. Recently, the conformational selection concept is also being considered. According to this, the protein structure itself is present in equilibrium of two or more conformations, and the substrate “selects” only the active one. By means of molecular dynamics and metadynamics, we are going to address the key question about how enzyme-substrate complex is formed: induced fit mechanism versus conformational selection. In particular we will focus in a recently solved glycosyltransferase structure, which shows the coexistence of two protein conformations, suggesting conformational selection may apply to this enzyme.

Area: Mathematics, Physics and Engineering
Title: Interface engineering in multifunctional oxides
Leader: Jorge Iniquez
Institution: Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
We will study a family of nano-structured oxides with great potential for the engineering of electronic effects. More precisely, we will consider super-lattices that combine two types of transition-metal oxides, nickelates with manganites, and run quantum simulations to check whether the chemical heterogeneity at the interfaces allows control of their charge and spin state. That would open the door to many interesting effects: For example, we will investigate whether the properties of the manganite layers can be manipulated, and whether interlayer couplings can be induced and controlled. Note that, on top of their fundamental appeal, effects of this type attract great interest in the field of oxide-based electronics and spintronics. Experimental collaborators will try to realize the most promising theoretical predictions.

Area: Mathematics, Physics and Engineering
Title: GridTDSE: direct numerical resolution of TDSE in atomic and molecular collisions
Leader: Luis Errea
Institution: Universidad Autonoma de Madrid, Dpto Quimica C-13

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 48

Abstract:
Excitation, ionization and charge transfer cross sections for inelastic collisions of ions on atoms and small molecules will be calculated by direct solution of the Time Dependent Schrödinger equation. The GridTDSE parallel code employed uses Grid schemes and Finite Difference approximations to evaluate the Hamiltonian on the total wavefunction characteristic of the collision. 3- and 6- cartesian coordinate systems will be employed for the semi-classical (the nuclei describe classical rectilinear trajectories) and fully-quantum (electron and atoms represented in quantum formalism) calculations. Full data base for Ne^{10+} and Ar^{18+} projectiles colliding on atomic hydrogen targets (in the fundamental and excited states) and on water molecules will be obtained in the low-intermediate-high impact energy range.

Period 2012-1 (March 1st - June 30th)

Area: Astronomy, Space and Earth Sciences
Title: Time reversal imaging of continuous seismic sources
Leader: Daniel Stich
Institution: Instituto Andaluz de Geofísica

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 18

Abstract:
Most laws in physics, including the elastodynamic wave equation, are time reversal invariant. While the direction of processes in nature is prescribed by the 2nd principle of thermodynamics, in numerical simulations the direction can be inverted. In earthquake seismology, time reversal approaches have been used recently to image characteristics of tectonic earthquakes as well as more exotic seismic sources by numerically back-propagating recorded wavefields. Unlike proper inversion, time reversal needs virtually no a priory assumptions of the processes involved. Here we apply time reversal to elucidate the nature of peculiar propagation effects on surface waves in the Gibraltar Arc area, focusing on resonance effects in deep sedimentary basins that act as continuous secondary sources contributing to the complexity in recorded seismograms.

Area: Life and Health Sciences
Title: Reverse-engineering mutant gene regulatory networks in Drosophila
Leader: Johannes Jaeger
Institution: EMBL/CRG Research Unit in Systems Biology

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 350

Abstract:
We want to understand the role of developmental gene regulatory networks in animal development and pattern formation. As a case study, we investigate the gap gene network of the fruit fly, Drosophila melanogaster. We use a systems-level approach to reconstitute the gap gene system in silico, by fitting gene network model to quantitative, spatio-temporal gene expression data. This computationally intensive procedure requires a supercomputer such as Mare Nostrum. In particular, we use this reverse engineering method to study gene expression in mutants of the terminal gap gene tailless. These mutants show significantly increased variability of gene expression between individuals. The models we will obtain by fitting will help us understand the sensitivity in the system that causes this increased variability.

Area: Chemistry and Materials Science and Technology
Title: Structures, energetics, and phase transitions of self-assembled monolayers of alkylthiolates on various metal surfaces
Leader: Yang
Institution: Wang

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 80

Abstract:
Self-assembled monolayers (SAMs) of alkylthiolates on surfaces are of great interest due to their potential applications. The different behaviors of alkylthiolates SAMs on various surfaces are not fully understood and require sophisticated studies. This study focuses on the systematic investigation on the adsorption, self-assembly and phase transitions of alkylthiols on various reconstructed and unconstructed Au(111), Ag(111) and Pt(111) surfaces, based on first-principles density functional theory and molecular dynamics. This would provide a new insight into surface physics and supermolecular chemistry.

Period 2011-3 (November 1st - February 29th)

Area: Astronomy, Space and Earth Sciences
Title: Time reversal imaging of continuous seismic sources
Leader: Daniel Stich
Institution: Instituto Andaluz de Geofísica

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 18

Abstract:
Most laws in physics, including the elastodynamic wave equation, are time reversal invariant. While the direction of processes in nature is prescribed by the 2nd principle of thermodynamics, in numerical simulations the direction can be inverted. In earthquake seismology, time reversal approaches have been used recently to image characteristics of tectonic earthquakes as well as more exotic seismic sources by numerically back-propagating recorded wavefields. Unlike proper inversion, time reversal needs virtually no a priory assumptions of the processes involved. Here we apply time reversal to elucidate the nature of peculiar propagation effects on surface waves in the Gibraltar Arc area, focusing on resonance effects in deep sedimentary basins that act as continuous secondary sources contributing to the complexity in recorded seismograms.

Area: Life and Health Sciences
Title: The structure and dynamics of neuropeptides in cell membranes
Leader: Slawomir Filipek
Institution: University of Warsaw, Faculty of Chemistry

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 499.2

Abstract:
Neuropeptides are neuronal signaling molecules which influence the activity of the brain and are involved in numerous brain functions, like analgesia, reward, learning and memory, but also participate in controling pain and stress, modulating immune responses and developing addiction. Neuropeptides are ligands of G-protein-coupled receptors (GPCRs) and among large number of them we will investigate ligands of neurokinin receptors, opioid receptors and formyl peptide receptors. Neuropeptides interact with cell membrane what can directly influence binding to the receptor. Our research aims at structure and dynamics of selected neuropeptides in contact with membrane. The obtained data will be used to investigate the mechanism of binding of neuropeptides to GPCRs and their activation.

Area: Life and Health Sciences
Title: Generating a design space for somitogenesis
Leader: James Sharpe
Institution: Center for Genomic Regulation

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 300

Abstract:
The main head to tail axis of the vertebrate body plan is segmented during a process called somitogenesis. The vast majority of researchers in the field of somitogenesis have been interpreting their experimental results under the framework of a kinematic FGF threshold mechanism for this process for the last 15 years. We have employed a modern systems biology design space approach to uncover a new ‘propagatory wave’ mechanism for somitogenesis which also fits all of this previously published research and new experimental data that we have generated.With the aid of Mare Nostrum we can include in this work a fully sampled design space for this somitogenesis function assuring that no other potential mechanisms are missed.

Area: Chemistry and Materials Science and Technology
Title: Tailoring molecular reactivity on monolayers of Cu adsorbed on Ru(0001)
Leader: Yang
Institution: Wang

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 40

Abstract:
Bimetallic surface alloys offer a fascinating scenario to tune the reactivity of a given surface by adding small amounts of atoms of a different species on them. We propose a combined electronic structure and molecular dynamics study, based on density functional theory (DFT), to investigate the enhancement of the catalytic power of Cu adsorbed on Ru(0001) after evaporation of Pd atoms on the system. Specifically, we will investigate the change on the reactivity of H2 on a 2 monolayers of Cu (with a 16xSQRT(3) reconstructed structure) adsorbed on Ru(0001) in the presence of Pd atoms.

Period 2011-2 (July 1st - October 31st)

Area: Astronomy, Space and Earth Sciences
Title: Time reversal imaging of continuous seismic sources
Leader: Daniel Stich
Institution: Instituto Andaluz de Geofísica

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 18

Abstract:
Most laws in physics, including the elastodynamic wave equation, are time reversal invariant. While the direction of processes in nature is prescribed by the 2nd principle of thermodynamics, in numerical simulations the direction can be inverted. In earthquake seismology, time reversal approaches have been used recently to image characteristics of tectonic earthquakes as well as more exotic seismic sources by numerically back-propagating recorded wavefields. Unlike proper inversion, time reversal needs virtually no a priory assumptions of the processes involved. Here we apply time reversal to elucidate the nature of peculiar propagation effects on surface waves in the Gibraltar Arc area, focusing on resonance effects in deep sedimentary basins that act as continuous secondary sources contributing to the complexity in recorded seismograms.

Area: Life and Health Sciences
Title: Model refinement of Mycoplasma genitalium glycosyltransferase structure by microsecond molecular dynamics simulations
Leader: Antoni Planas
Institution: Laboratory of Biochemistry. IQS – Universitat Ramon Llull

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 400

Abstract:
Structural Models of Mycoplasma genitalium glycosyltransferase (GT-MG517) will be refined by means of microsecond long molecular dynamics simulations. The final curated structural model that we will obtain for this enzyme will allow us to investigate, in the future, the presence, shape and relative orientation of plausible binding pockets for the substrates of this enzyme. Biochemical and structural knowledge of GT-MG517 mechanism of action will be used for the rational design of enzyme inhibitors as novel potential antibiotics against mycoplasma infections.

Area: Mathematics, Physics and Engineering
Title: Extending Parallel CFD capabilities of Kratos, a general purpose FE solver.
Leader: Riccardo Rossi
Institution: UPC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 21.5

Abstract:
The proposed research aims to the validation of a parallel level-set solver allowing the simulation of the flow of a fluid inside and in the surroundings of a rock-fill dam. The ultimate goal is the definition of a robust tool to be used in the assessment of civil engineering structure under extreme conditions.
The complexity of the problem to be faced makes fundamental the use of HPC facilities which provide an enabling tool for the research. In order to obtain maximal performance, the solver will be tested for scalability over the Mare-Nostrum hardware. A number of different benchmark examples will be considered including both free-surface problems and simpler eulerian one-field problems.

Area: Chemistry and Materials Science and Technology
Title: New concept solar cells: understanding doping at nanoscale
Leader: Michele Amato
Institution: Université Paris-Sud

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 153

Abstract:
Silicon Nanowires solar cells are very attractive candidates for renewable power sources and many efforts have been dedicating in order to reduce both cost and size and to improve their efficiency. Recently it has been demonstrated that doping efficiency can be really improved using a Silicon-Germanium NW instead than a pure one. Nevertheless it is not yet understood, both theoretically and experimentally, how electrical properties depend on the doping level of the material. The comprehension of doping mechanism in these materials seems to be crucial for the further development of NW-based solar cell, and therefore a whole theoretical characterization of the problem is required. Our aim is to obtain, trough ab-initio Density Functional Theory methods, a description of the electronic properties of single-doped and co-doped SiGe NWs.

Area: Chemistry and Materials Science and Technology
Title: Assembly of large molecular complexes on metals from DFT
Leader: Valerio Bellini
Institution: CNR-Nano-S3

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 90

Abstract:
In the latter years, one of the main challenges was to find ways to graft, in a controlled way, molecular magnets on the surface of materials, and eventually to assembly them in an ordered way. Complex assemblies can be obtained on surfaces by using simple molecular bricks in UHV conditions. The interest is now focused on large molecules that exhibit special functionalities as single units. Molecular nanomagnets have recently shown great potentialities for the storage and processing of information at molecular level and, some of them has shown suitable features for qubit encoding. We are interested in the simulation by density-functional methods of the adsorption and assembly of large polynuclear magnetic complexes on metal surfaces, whose behavior depends critically on the eventual functionalization as evidenced in recent experiments.

Area: Chemistry and Materials Science and Technology
Title: Self-assembly of alkylthiolates on gold and silver surfaces
Leader: Yang
Institution: Wang

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 175

Abstract:
The main objective of the present project is to study the self-assembly of alkylthiolates on gold and silver surfaces. First-principle simulations will be performed to characterize the supramolecular structures formed on the surfaces, to compare them with the observed patterns in STM experiments and to understand the factors governing the self-assembly process.The present study has a large interest since the self-assembly of alkylthiolate molecules has practical applications in many areas, such as corrosion prevention, wear protection and sensor devices.

Area: Chemistry and Materials Science and Technology
Title: Interferometric structural characterization of polyatomic molecules in high-energy photoionization
Leader: Luca Argenti
Institution: Universidad Autónoma de Madrid

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
High-resolution soft x-ray synchrotron sources, and ultra-short intense XUV pulses from free-electron lasers open new ways to the monitoring of nuclear dynamics in polyatomic molecules. Nuclear positions are encoded in the high-energy photoelectron spectra due to multicenter interferences, intramolecular scattering and nuclear recoil processes that accompany ionization. To extract these structural informations, a solid theory is essential. A DFT method which proved successful for the photoionization of diatomic molecules is applied to the time independent and time dependent photoionization of polyatomic molecules. Vibrationally resolved photoionization cross sections of CH4, CF4, C2H2 and BF3, for which experimental data exist, are computed and the interaction between one of those molecules and XUV femtosecond pulses is simulated.

Period 2011-1 (March 1st - June 30th)

Area: Life and Health Sciences
Title: Model refinement of Mycoplasma genitalium glycosyltransferase structure by microsecond molecular dynamics simulations
Leader: Antoni Planas
Institution: Laboratory of Biochemistry. IQS – Universitat Ramon Llull

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 400

Abstract:
Structural Models of Mycoplasma genitalium glycosyltransferase (GT-MG517) will be refined by means of microsecond long molecular dynamics simulations. The final curated structural model that we will obtain for this enzyme will allow us to investigate, in the future, the presence, shape and relative orientation of plausible binding pockets for the substrates of this enzyme. Biochemical and structural knowledge of GT-MG517 mechanism of action will be used for the rational design of enzyme inhibitors as novel potential antibiotics against mycoplasma infections.

Area: Mathematics, Physics and Engineering
Title: Interface engineering in multifunctional oxides
Leader: Jorge Iniquez
Institution: Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 350

Abstract:
We will study a family of nano-structured oxides with great potential for the engineering of electronic effects. More precisely, we will consider super-lattices that combine nickelates with other transition-metal oxides, and run quantum simulations to check whether the chemical heterogeneity at the interfaces allows control of their charge and spin state. That would open the door to many interesting effects: For example, we will try to produce heterostructures in which insulating interfaces separate metallic layers, to thus form confined electron gases, or induce large magnetoelectric effects. Note that, on top of their fundamental appeal, effects of this type attract great interest in the field of oxide-based electronics and spintronics. Experimental collaborators will try to realize the most promising theoretical predictions.

Area: Chemistry and Materials Science and Technology
Title: Self-assembly of molecules on surfaces.
Leader: Manuel Alcami
Institution: UAM

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 165

Abstract:
The main objective of the present project is to study the self-assembly of molecules on surfaces. First-principle simulations will be used to characterize the supramolecular structures formed on the surfaces, to compare them with the observed patterns in STM experiments and to understand the factors governing the self-assembly process.The present study has a large interest since self-assembly of molecules with large acceptor or a donor capabilities is expected to increase the efficiency of organic solar cells.

Area: Chemistry and Materials Science and Technology
Title: QM/MM simulations of protein immobilization on surfaces via metallic clusters
Leader: Carlos Sanz
Institution: Centre d’Investigació en Nanociència i Nanotecnologia (CIN2-CSIC/ICN)

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 20

Abstract:
The stable immobilization of proteins on surfaces is a key issue for a new generation of bioelectronic devices [Trends Biotechnol. 19 222 (2001)]. We employ a QM/MM approach developed by us [J. Phys. Chem. B 107, 13728 (2003)] that combines the SIESTA methodology (DFT approach) with an empirical force field to simulate the adsorption of a human oncostatin M (OSM) molecule on the surface of a 75-atom gold cluster. Such Au75 cluster is previously pinned on a graphite surface. We address the nature of the interaction between the OSM protein and the Au75 cluster as well as the orientation and ultimate structure of the adsorbed protein. The QM/MM results are compared with experimental data available in our group.

Period 2010-3 (November 1st - February 28th)

Area: Life and Health Sciences
Title: New applications for known drugs
Leader: Raul Insa
Institution: SOM Biotech SL

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
In-silico drug repositioning is a great advantage over experimental fishing methods or target oriented binding programs to detect new indications or uses of approved medicines. The present project objectives are to identify nine drug repositioning uses through bio-informatics software using supercomputing resources and managed by a start-up biotech established at the Bioincubadora-PCB, University of Barcelona. Social benefit of these findings, (in terms of intellectual property, places of work and experimental out-sourcing), are also expected.

Area: Chemistry and Materials Science and Technology
Title: The stability of Metal Organic Framework structures under water: an ab initio molecular dynamics study (1st. period)
Leader: Nuria Lopez
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 400

Abstract:
The stability of metal-organic frameworks constitutes a drawback for their implementation in industry as absorbers and catalysts. We will employ ab initio molecular simulations to identify the mechanisms responsible for lattice disruption in the presence of water and analyze possible synthetic solutions for the problem.

Area: Chemistry and Materials Science and Technology
Title: Self-assembly of molecules on surfaces.
Leader: Manuel Alcami
Institution: UAM

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
The main objective of the present project is to study the self-assembly of molecules on surfaces. First-principle simulations will be used to characterize the supramolecular structures formed on the surfaces, to compare them with the observed patterns in STM experiments and to understand the factors governing the self-assembly process.The present study has a large interest since self-assembly of molecules with large acceptor or a donor capabilities is expected to increase the efficiency of organic solar cells.

Area: Chemistry and Materials Science and Technology
Title: QM/MM simulations of protein immobilization on surfaces via metallic clusters
Leader: Carlos Sanz
Institution: Centre d’Investigació en Nanociència i Nanotecnologia (CIN2-CSIC/ICN)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
The stable immobilization of proteins on surfaces is a key issue for a new generation of bioelectronic devices [Trends Biotechnol. 19 222 (2001)]. We employ a QM/MM approach developed by us [J. Phys. Chem. B 107, 13728 (2003)] that combines the SIESTA methodology (DFT approach) with an empirical force field to simulate the adsorption of a human oncostatin M (OSM) molecule on the surface of a 75-atom gold cluster. Such Au75 cluster is previously pinned on a graphite surface. We address the nature of the interaction between the OSM protein and the Au75 cluster as well as the orientation and ultimate structure of the adsorbed protein. The QM/MM results are compared with experimental data available in our group.

Period 2010-2 (July 1st - October 31st)

Area: Chemistry and Materials Science and Technology
Title: QM/MM simulations of protein immobilization on surfaces via metallic clusters
Leader: Carlos Sanz
Institution: Centre d’Investigació en Nanociència i Nanotecnologia (CIN2-CSIC/ICN)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
The stable immobilization of proteins on surfaces is a key issue for a new generation of bioelectronic devices [Trends Biotechnol. 19 222 (2001)]. We employ a QM/MM approach developed by us [J. Phys. Chem. B 107, 13728 (2003)] that combines the SIESTA methodology (DFT approach) with an empirical force field to simulate the adsorption of a human oncostatin M (OSM) molecule on the surface of a 75-atom gold cluster. Such Au75 cluster is previously pinned on a graphite surface. We address the nature of the interaction between the OSM protein and the Au75 cluster as well as the orientation and ultimate structure of the adsorbed protein. The QM/MM results are compared with experimental data available in our group.

Area: Chemistry and Materials Science and Technology
Title: Self-assembly of molecules on surfaces.
Leader: Manuel Alcami
Institution: UAM

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
The main objective of the present project is to study the self-assembly of molecules on surfaces. First-principle simulations will be used to characterize the supramolecular structures formed on the surfaces, to compare them with the observed patterns in STM experiments and to understand the factors governing the self-assembly process.The present study has a large interest since self-assembly of molecules with large acceptor or a donor capabilities is expected to increase the efficiency of organic solar cells.

Area: Astronomy, Space and Earth Sciences
Title: IBERREF: A 3D seismic reference model for the Iberian lithosphere
Leader: Daniel Stich
Institution: Instituto Andaluz de Geofísica

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 20

Abstract:
The availability of powerful parallel computers brought into reach sophisticated numerical methods to model 3D seismic wave propagation in heterogeneous Earth structures. At the same time, the important densification of seismic broadband networks improves our abilities to follow the evolution of earthquake’s wavefields in situ. In this ambit, this study pretends to construct an appropriate 3D reference Earth model for the Iberia-Maghreb region, for future applications of earthquake source inversion and seismic tomography. In an iterative procedure we will design an a priori Earth model according to available results on deep Earth structure, and validate its performance by comparing observed seismograms from major regional earthquakes to 3D numerical simulations of waveforms using a parallel implementation of the spectral element method.

Area: Chemistry and Materials Science and Technology
Title: HCN synthesis on metals and complex materials: a Density Functional Theory approach: Third period
Leader: Nuria Lopez
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 550

Abstract:
HCN is a major chemical intermediate. It is produced from methane and ammonia however the reaction mechanism is not known. Our aim is to determine the reaction network over a series of new complex materials that can substitute the present Pt-based catalyst.

Period 2010-1 (March 1st - June 30th)

Area: Astronomy, Space and Earth Sciences
Title: IBERREF: A 3D seismic reference model for the Iberian lithosphere
Leader: Daniel Stich
Institution: Instituto Andaluz de Geofísica

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 30

Abstract:
The availability of powerful parallel computers brought into reach sophisticated numerical methods to model 3D seismic wave propagation in heterogeneous Earth structures. At the same time, the important densification of seismic broadband networks improves our abilities to follow the evolution of earthquake’s wavefields in situ. In this ambit, this study pretends to construct an appropriate 3D reference Earth model for the Iberia-Maghreb region, for future applications of earthquake source inversion and seismic tomography. In an iterative procedure we will design an a priori Earth model according to available results on deep Earth structure, and validate its performance by comparing observed seismograms from major regional earthquakes to 3D numerical simulations of waveforms using a parallel implementation of the spectral element method.

Area: Life and Health Sciences
Title: Biomedical repositioning of active compounds
Leader: Raul Insa
Institution: SOM Biotech SL

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 50

Abstract:
In-silico drug repositioning is a great advantage over experimental fishing methods or target oriented binding programs to detect new indications or uses of approved medicines. The present project objectives are to identify fifteen drug repositioning uses through bio-informatics software using supercomputing resources and managed by a start-up biotech established at the Bioincubadora-PCB, University of Barcelona. Social benefit of these findings, (in terms of intellectual property, places of work and experimental out-sourcing), are also expected.

Area: Chemistry and Materials Science and Technology
Title: Implementation of a time-independent quantum reactive scattering program
Leader: Ernesto Garcia
Institution: ehu

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 50

Abstract:
Detailed properties, like state-to-state cross sections and rate coefficients, of elementary reactions are of key importance in plasma, combustion and atmospheric chemistry modeling. The exact calculation of these properties requires the integration of the full dimensional Schrodinger equation for the nuclear motion of the atoms involved in the reaction. We shall tackle this problem using a program based on a time-independent method. The program needs to be run for a wide range of energies and up to a high value of the total angular momentum for which a massive allocation of supercomputer time is requested. The prototype H + H2 reaction will be used as a benchmark.

Area: Chemistry and Materials Science and Technology
Title: Self-assembly of molecules on surfaces.
Leader: Manuel Alcami
Institution: UAM

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
The main objective of the present project is to study the self-assembly of molecules on surfaces. First-principle simulations will be used to characterize the supramolecular structures formed on the surfaces, to compare them with the observed patterns in STM experiments and to understand the factors governing the self-assembly process.The present study has a large interest since self-assembly of molecules with large acceptor or a donor capabilities is expected to increase the efficiency of organic solar cells.

Area: Chemistry and Materials Science and Technology
Title: HCN synthesis on metals and complex materials: a Density Functional Theory approach: Second period
Leader: Nuria Lopez
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 600

Abstract:
HCN is a major chemical intermediate. It is produced from methane and ammonia however the reaction mechanism is not known. Our aim is to determine the reaction network over a series of new complex materials that can substitute the present Pt-based catalyst

Period 2009-3 (November 1st - February 28th)

Area: Astronomy, Space and Earth Sciences
Title: IBERREF: A 3D seismic reference model for the Iberian lithosphere
Leader: Daniel Stich
Institution: Instituto Andaluz de Geofísica

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 10.4

Abstract:
The availability of powerful parallel computers brought into reach sophisticated numerical methods to model 3D seismic wave propagation in heterogeneous Earth structures. At the same time, the important densification of seismic broadband networks improves our abilities to follow the evolution of earthquake’s wavefields in situ. In this ambit, this study pretends to construct an appropriate 3D reference Earth model for the Iberia-Maghreb region, for future applications of earthquake source inversion and seismic tomography. In an iterative procedure we will design an a priori Earth model according to available results on deep Earth structure, and validate its performance by comparing observed seismograms from major regional earthquakes to 3D numerical simulations of waveforms using a parallel implementation of the spectral element method.

Area: Chemistry and Materials Science and Technology
Title: Study of the exohedral reactivity of X3N@Ih-C80 (X=Sc, Lu, Gd)
Leader: dr. M. Swart
Institution: Institute de Quimica Computacional (IQC), Universitat de Girona (UdG)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 230

Abstract:
The aim of this activity is to study the exohedral reactivity of the TNT endohedral metallofullerenes X3N@Ih-C80 (X=Sc, Lu, Gd). The study of the reaction over all possible isomers is a key factor, as different orientations of the TNT unit have been observed experimentally. In particular, we will study the Diels-Alder cycloaddition for all non-equivalent bonds and isomers in the case of Sc3N@Ih-C80, Lu3N@Ih-C80 and Gd3N@Ih-C80. The lutetium and gadolinium based endohedral metallofullerenes are very interesting for medical applications. Gd3N@C80 might be the precursor of the current MRI contrast agents, and the equivalent lutetium based compound Lu3N@C80 could be used in cancer therapies. However, before all these compounds are used in medical applications, the exohedral reactivity of these cages must be intensely explored.

Area: Chemistry and Materials Science and Technology
Title: HCN synthesis on metals and complex materials: a Density Functional Theory approach
Leader: Nuria Lopez
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 600

Abstract:
HCN is a major chemical intermediate. It is produced from methane and ammonia however the reaction mechanism is not known. Our aim is to understand the chemistry taking place at the platinum catalyst in order to reduce the amount of novel metal employed in the system.

Period 2009-2 (June 1st - October 31st)

Area: Chemistry and Materials Science and Technology
Title: Cubic Molecular Nano-Containers as Selective Fullerene Hosts
Leader: Josep M. Luis
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 100

Abstract:
Size-selective fullerene recognition and host inside porphyrin-based supramolecular cubes is targeted. We have prepared porphyrin-based molecular cubes with large void inner spaces. Our interest is focused in their capability to selectively host a fullerene molecule (C20, C30, C40, C60, C70, C72, C76, C80,…) on the basis of size and affinity discrimination. Our synthetic strategy allows wide tuning of the nano-cube dimensions. One goal of this project is the design of new nano-containers and the theoretical study of their structure using a DFT approach. A second goal is the study of the selective inclusion of different fullerenes inside the nano-containers. The third goal is the exploration of changes in the electronic structure of hosted fullerenes as a first step towards their host-directed chemo and regioselective functionalization.

Area: Chemistry and Materials Science and Technology
Title: Study of the exohedral reactivity of X3N@Ih-C80 (X=Sc, Lu, Gd)
Leader: dr. M. Swart
Institution: Institute de Quimica Computacional (IQC), Universitat de Girona (UdG)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 326.4

Abstract:
The aim of this activity is to study the exohedral reactivity of the TNT endohedral metallofullerenes X3N@Ih-C80 (X=Sc, Lu, Gd). The study of the reaction over all possible isomers is a key factor, as different orientations of the TNT unit have been observed experimentally. In particular, we will study the Diels-Alder cycloaddition for all non-equivalent bonds and isomers in the case of Sc3N@Ih-C80, Lu3N@Ih-C80 and Gd3N@Ih-C80. The lutetium and gadolinium based endohedral metallofullerenes are very interesting for medical applications. Gd3N@C80 might be the precursor of the current MRI contrast agents, and the equivalent lutetium based compound Lu3N@C80 could be used in cancer therapies. However, before all these compounds are used in medical applications, the exohedral reactivity of these cages must be intensely explored.

Area: Chemistry and Materials Science and Technology
Title: First principles study on the activity and selectivity of Pd-Au alloys: 3rd application period
Leader: Nuria Lopez
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 800

Abstract:
PdAu alloys have been proposed as active and ultraselective for several chemical applications. The aim of our project is to understand what makes PdAu systems interesting from a catalytic point of view and why this combination of metals is not only suitable for oxidation chemistry but also for hydrogenations and C-O bond formation.

Period 2009-1 (February 1st - May 31st)

Area: Astronomy, Space and Earth Sciences
Title: Seismic Oceanography: high-resolution numerical simulations of the ocean circulation off Iberia
Leader: Nuno Serra
Institution: University of Hamburg

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 300

Abstract:
The boundaries between the Mediterranean Water (MW) and the surrounding Atlantic water present conditions to form thermohaline fine-structure due to double diffusion and intrusions. These small-scale processes play a yet not fully understood role in the mixing of MW and in the decay of MW eddies, forming at depth off Iberia. Conventional in situ measurements can only resolve these phenomena vertically. Seismic reflection measurements were shown to horizontally image small scales in the ocean (order of 10m), however, the lack of direct observations or detailed simulations renders the seismic interpretation difficult. An ocean model forced by wind and tides is applied at unprecedented high-resolution to the ocean off Iberia. The simulations will enable understanding the mixing processes that can be mapped by the seismic method.

Area: Astronomy, Space and Earth Sciences
Title: Light scattering properties of nonspherical atmospheric aerosols for radiative transfer applications: the ALFA database
Leader: Francisco José Olmo Reyes
Institution: Univeristy of Granada

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 50

Abstract:
The study of atmospheric aerosols and its impact on the Earth radiation budget requires the calculation and use of an extensive database of inherent optical properties for nonspherical particles. Such database (ALFA) will allow for the comparison of experimental data (from in-situ to satellite measurements) and calculations from direct and inverse models. This will be particularly valuable to understand the influence of Saharan aerosols in SE Spain skies. Applications will also include global-scale study of aerosol concentration due to anthropogenic effects.

Area: Chemistry and Materials Science and Technology
Title: First principles study on the activity and selectivity of Pd-Au alloys: 2nd application period
Leader: Nuria Lopez
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 400

Abstract:
PdAu alloys have been proposed as active and ultraselective for several chemical applications. The aim of our project is to understand what makes PdAu systems interesting from a catalytic point of view and why this combination of metals is not only suitable for oxidation chemistry but also for hydrogenations and C-O bond formation.

Area: Chemistry and Materials Science and Technology
Title: Cubic Molecular Nano-Containers as Selective Fullerene Hosts
Leader: Josep M. Luis
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 100

Abstract:
Size-selective fullerene recognition and host inside porphyrin-based supramolecular cubes is targeted. We have prepared porphyrin-based molecular cubes with large void inner spaces. Our interest is focused in their capability to selectively host a fullerene molecule (C20, C30, C40, C60, C70, C72, C76, C80,…) on the basis of size and affinity discrimination. Our synthetic strategy allows wide tuning of the nano-cube dimensions. One goal of this project is the design of new nano-containers and the theoretical study of their structure using a DFT approach. A second goal is the study of the selective inclusion of different fullerenes inside the nano-containers. The third goal is the exploration of changes in the electronic structure of hosted fullerenes as a first step towards their host-directed chemo and regioselective functionalization.

Area: Chemistry and Materials Science and Technology
Title: Montmorillonite clay catalyzed synthesis of RNA oligomers.
Leader: Mariona Sodupe Roure
Institution: Universitat Autònoma de Barcelona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 175

Abstract:
Montmorillonite has been recognized as a potential prebiotic catalyst in the formation of RNA oligonucleotides. In order to understand the role of montmorillonite in the polymerization process of nucleotides, it is important to know how nucleotides and,in particular, nucleobases, bind in the interlayer. The present proposal aims to get a deep understanding, at a molecular level, of the interaction between adenine and guanine with hydrated Na+-montmorillonite. Several adsorption modes as well as the influence of the interlayer length will be analyzed.

Period 2008-3 (October 1st -January 31st)

Area: Chemistry and Materials Science and Technology
Title: Phase Change Materials from First Principles
Leader: Marco Bernasconi
Institution: Department of Material Science, University of Milano-Bicocca

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 80

Abstract:
Phase change materials are widely used in optical information storage (DVD) and are the active part of the most promising non-volatile memories of new concept, the Phase Change Memory (PCM) device, which exploits the large change in conductivity between the crystalline metallic phase and the insulating amorphous phase of a chalcogenide film. In spite of the great technological importance this class of materials, their microscopic structures and the detailed mechanism of the phase transformation are largely unknown. In this project, we plan to perform ab-initio molecular dynamics (MD) simulations for Ge2Sb2Te5 (GST), the prototypical material in this class, and related binary compounds, aiming at elucidating the structure of the amorphous phases. Density functional based MD simulations will be performed with the code QUICKSTEP as implemented in the CP2K suit of program. In particular, we will make use of a new MD technique recently developed by the proponents (T. Kühne et al., Phys. Rev. Lett. 98, 066401 (2007)). GST, GeTe, GeSb, and Sb2Te3 pure or doped with N and Si will be modelled by supercells containing up to 500 atoms with 3D periodic boundary conditions. Amorphous models will be produced by quenching from melt. The pressure induced amorphization of GST will be simulated as well. The research will provide precious insight on the properties of the amorphous phases and shed light on the mechanisms of the reversible crystal-to-amorphous transition underlying the technological applications of this class of materials. The availability of a microscopic model of the amorphous phase will also aid clarifying the origin of the large change in the electrical properties across the phase change exploited in the memory devices.

Area: Chemistry and Materials Science and Technology
Title: First principles study on the activity and selectivity of Pd-Au alloys
Leader: Nuria Lopez
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 450

Abstract:
PdAu alloys have been proposed as active and ultraselective for several chemical applications. The aim of our project is to understand what makes PdAu systems interesting from a catalytic point of view and why this combination of metals is not only suitable for oxidation chemistry but also for hydrogenations and C-O bond formation.

Area: Chemistry and Materials Science and Technology
Title: Design of fullerene-based materials for photonic applications
Leader: Manthos G. Papadopoulos
Institution: National Hellenic Research Foundation

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 150

Abstract:
The goal of this project is the design of fullerene-based materials for photonic applications. Key parameters for such a design are the nonlinear optical properties (NLO). Since the systems of interest are large, they involve hundreds of atoms and thousands of basis functions, we shall employ efficient computational techniques for the computation of the NLO properties. The proposed calculations involve: (i) Optimization of the geometry of the designed structures, (ii) Computation of the electronic and vibrational contributions to the linear and NLO properties, and (iii) Computation of the two-photon absorption (TPA) cross section. For the computations a systematic series of basis sets and a hierarchy methods for taking into account correlation (e.g. MP2, DFT etc) will be employed.

Area: Chemistry and Materials Science and Technology
Title: Cubic Molecular Nano-Containers as Selective Fullerene Hosts
Leader: Josep M. Luis
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 250

Abstract:
Size-selective fullerene purification benefiting from supramolecular fullerene-porphyrin interactions is targeted. We have prepared polyfunctional porphyrin-based molecular cubes with large void inner spaces. Our interest is focused in their capability to selectively host a unique fullerene molecule (C20, C30, C40, C60, C70, C72, C76, C80, C84,…) upon size discrimination. Our strategy allows wide tuning of the nano-cube dimensions by changing: i) the length of the macrocycle; ii) the transition metal bound into the macrocycle; iii) and the transition metal coordinated to the porphyrin moieties. One goal of this project is the design of new nano-containers and the theoretical study of their structure using a QM/QM approach. A second goal is the study of the selective inclusion of different fullerenes inside the nano-containers.

Area: Chemistry and Materials Science and Technology
Title: Supported metal nanoparticles as chemoselective hydrogenation catalysts
Leader: Avelino Corma Canós
Institution: Instituto de Tecnología Química UPV-CSIC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
Selective hydrogenation of multifunctional molecules is an an important target for the research in catalysis and the industrial production of fine chemicals. While gold nanoparticles supported on TiO2 are highly chemoselective for the hydrogenation of the nitro group in substituted nitroaromatics, platinum nanoparticles supported on TiO2 are highly active but not chemoselective. High selectivity is only achieved when the surface of the Pt nanoparticles is decorated with partly reduced oxide particles (TiOx) that are formed as a result of high-temperature reduction pretreatment. The nature of these TiOx particles and the mechanism of selective hydrogenation of the nitro group of nitrostyrene on these decorated Pt catalysts is being investigated from a theoretical point of view.

Period 2008-2 (June 1st - September 31st)

Area: Life and Health Sciences
Title: The 3D code of DNA: understanding apparition of curvature from atomic detail to gene scale
Leader: Agnes Noy
Institution: IRB-BSC/Sheffield University

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 210

Abstract:
Recent experimental studies have suggested flexibility is crucial in gene regulation, thus, the idea that DNA genetic information might also be encoded through its 3D shape has appeared. Because DNA is a very long polymer, this question should be tackled from different scales. X-ray and NMR structures as well as atomic models are able to give detail but they are limited in 10-100 bp while genes are in 3-50 kbp range and follow Worm-like Chain (WLC) model as is shown by single molecule experiments. Our research objective is to bring together the two kinds of data developing a more sophisticated model (Generalized WLC) were sequence is considered and global mechanical properties are explained.

Area: Chemistry and Materials Science and Technology
Title: Supported metal nanoparticles as chemoselective hydrogenation catalysts
Leader: Avelino Corma Canós
Institution: Instituto de Tecnología Química UPV-CSIC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 200

Abstract:
Selective hydrogenation of multifunctional molecules is an an important target for the research in catalysis and the industrial production of fine chemicals. We have recently shown that gold nanoparticles supported on TiO2 are highly chemoselective for the hydrogenation of the nitro group in substituted nitroaromatics, and that this unique catalytic behaviour can be attributed to a cooperation between the gold nanoparticle and the support that preferentially activates the nitro group. We intend to apply this knowledge to predict the way in which a Pt based catalyst, highly active for hydrogenation, can be done chemoselective. We shall investigate two possibilities: a) to increase the number of metal atoms in the nanoparticle edge by reducing the metal nanoparticle size, and b) to decorate the surface of the metal phase with partly reduced oxide particles (TiOx) that are formed as a result of high-temperature reduction pretreatment. This particles contain Lewis sites that preferentially coordinate the carbonyl and the nitro groups, therefore improving the hydrogenation selectivity.

Area: Chemistry and Materials Science and Technology
Title: Cubic Molecular Nano-Containers as Selective Fullerene Hosts
Leader: Josep M. Luis
Institution: Universitat de Girona

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500

Abstract:
Size-selective fullerene purification benefiting from supramolecular fullerene-porphyrin interactions is targeted. We have prepared polyfunctional porphyrin-based molecular cubes with large void inner spaces. Our interest is focused in their capability to selectively host a unique fullerene molecule (C20, C30, C40, C60, C70, C72, C76, C80, C84,…) upon size discrimination. Our strategy allows wide tuning of the nano-cube dimensions by changing: i) the length of the macrocycle; ii) the transition metal bound into the macrocycle; iii) and the transition metal coordinated to the porphyrin moieties. One goal of this project is the design of new nano-containers and the theoretical study of their structure using a QM/QM approach. A second goal is the study of the selective inclusion of different fullerenes inside the nano-containers.

Area: Chemistry and Materials Science and Technology
Title: Phase Change Materials from First Principles
Leader: Marco Bernasconi
Institution: Department of Material Science, University of Milano-Bicocca

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 100

Abstract:
Phase change materials are widely used in optical information storage (DVD) and are the active part of the most promising non-volatile memories of new concept, the Phase Change Memory (PCM) device, which exploits the large change in conductivity between the crystalline metallic phase and the insulating amorphous phase of a chalcogenide film. In spite of the great technological importance this class of materials, their microscopic structures and the detailed mechanism of the phase transformation are largely unknown. In this project, we plan to perform ab-initio molecular dynamics (MD) simulations for Ge2Sb2Te5 (GST), the prototypical material in this class, and related binary compounds, aiming at elucidating the structure of the amorphous phases. Density functional based MD simulations will be performed with the code QUICKSTEP as implemented in the CP2K suit of program. In particular, we will make use of a new MD technique recently developed by the proponents (T. Kühne et al., Phys. Rev. Lett. 98, 066401 (2007)). GST, GeTe, GeSb, and Sb2Te3 pure or doped with N and Si will be modelled by supercells containing up to 500 atoms with 3D periodic boundary conditions. Amorphous models will be produced by quenching from melt. The pressure induced amorphization of GST will be simulated as well. The research will provide precious insight on the properties of the amorphous phases and shed light on the mechanisms of the reversible crystal-to-amorphous transition underlying the technological applications of this class of materials. The availability of a microscopic model of the amorphous phase will also aid clarifying the origin of the large change in the electrical properties across the phase change exploited in the memory devices.

Area: Chemistry and Materials Science and Technology
Title: Design of fullerene-based materials for photonic applications
Leader: Manthos G. Papadopoulos
Institution: National Hellenic Research Foundation

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 150

Abstract:
The goal of this project is the design of fullerene-based materials for photonic applications. Key parameters for such a design are the nonlinear optical properties (NLO). Since the systems of interest are large, they involve hundreds of atoms and thousands of basis functions, we shall employ efficient computational techniques for the computation of the NLO properties. The proposed calculations involve: (i) Optimization of the geometry of the designed structures, (ii) Computation of the electronic and vibrational contributions to the linear and NLO properties, and (iii) Computation of the two-photon absorption (TPA) cross section. For the computations a systematic series of basis sets and a hierarchy methods for taking into account correlation (e.g. MP2, DFT etc) will be employed.

Area: Chemistry and Materials Science and Technology
Title: Reactivity of organic and organometallic molecules inside nano-sized molecular vessels
Leader: Carles Bo Jane
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 50

Abstract:
The use of molecular vessels and supramolecular assemblies to include or encapsulate transition metal complexes is attracting considerable attention because encapsulation of the catalyst may lead to significantly changes in its stability, activity and/or selectivity. We plan to investigate resocin[4]arene-based cavitands and its catalytic effect on some reactions involving transition metal complexes. For these reactions, we would like to ascertain the origin of the rate-accelerating effect of the cavitands on the reaction.

Period 2008-1 (February 1st - May 31st)

Area: Life and Health Sciences
Title: Exploring the topology space for gene regulatory networks
Leader: James Sharpe
Institution: Center for Genomic Regulation

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 320

Abstract:
Systems biology approaches have helped us to understand a number of specific biological processes. Due to the advent of more powerful computers, we now believe systems biology can go much further. By mapping out the space of possibilities for a given system it is hoped that fundamental design principles can be extracted. We are exploring this approach in the field of developmental patterning. By modeling all possible gene regulatory networks (GRNs) in a spatial context we are exploring how network structure relates to the possible gene expression patterns. Previously, we have performed this analysis on all GRNs up to 3 genes in complexity. With the advantage of Mare Nostrum, we are now able to perform the same analysis on GRNs up to 4 genes in complexity extending our work to the realm of more complex and biological realistic networks.

Area: Chemistry and Materials Science and Technology
Title: Phase Change Materials from First Principles
Leader: Marco Bernasconi
Institution: Department of Material Science, University of Milano-Bicocca

Assigned machine(s): Picasso (UMA)
Assigned khours without priority: 80

Abstract:
Phase change materials are widely used in optical information storage (DVD) and are the active part of the most promising non-volatile memories of new concept, the Phase Change Memory (PCM) device, which exploits the large change in conductivity between the crystalline metallic phase and the insulating amorphous phase of a chalcogenide film. In spite of the great technological importance this class of materials, their microscopic structures and the detailed mechanism of the phase transformation are largely unknown. In this project, we plan to perform ab-initio molecular dynamics (MD) simulations for Ge2Sb2Te5 (GST), the prototypical material in this class, and related binary compounds, aiming at elucidating the structure of the amorphous phases. Density functional based MD simulations will be performed with the code QUICKSTEP as implemented in the CP2K suit of program. In particular, we will make use of a new MD technique recently developed by the proponents (T. Kühne et al., Phys. Rev. Lett. 98, 066401 (2007)). GST, GeTe, GeSb, and Sb2Te3 pure or doped with N and Si will be modelled by supercells containing up to 500 atoms with 3D periodic boundary conditions. Amorphous models will be produced by quenching from melt. The pressure induced amorphization of GST will be simulated as well. The research will provide precious insight on the properties of the amorphous phases and shed light on the mechanisms of the reversible crystal-to-amorphous transition underlying the technological applications of this class of materials. The availability of a microscopic model of the amorphous phase will also aid clarifying the origin of the large change in the electrical properties across the phase change exploited in the memory devices.

Area: Chemistry and Materials Science and Technology
Title: Design of fullerene-based materials for photonic applications
Leader: Manthos G. Papadopoulos
Institution: National Hellenic Research Foundation

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
The goal of this project is the design of fullerene-based materials for photonic applications. Key parameters for such a design are the nonlinear optical properties (NLO). Since the systems of interest are large, they involve hundreds of atoms and thousands of basis functions, we shall employ efficient computational techniques for the computation of the NLO properties. The proposed calculations involve: (i) Optimization of the geometry of the designed structures, (ii) Computation of the electronic and vibrational contributions to the linear and NLO properties, and (iii) Computation of the two-photon absorption (TPA) cross section. For the computations a systematic series of basis sets and a hierarchy methods for taking into account correlation (e.g. MP2, DFT etc) will be employed.

Area: Chemistry and Materials Science and Technology
Title: Supported metal nanoparticles as chemoselective hydrogenation catalysts
Leader: Avelino Corma Canós
Institution: Instituto de Tecnología Química UPV-CSIC

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
Selective hydrogenation of multifunctional molecules is an an important target for the research in catalysis and the industrial production of fine chemicals. We have recently shown that gold nanoparticles supported on TiO2 are highly chemoselective for the hydrogenation of the nitro group in substituted nitroaromatics, and that this unique catalytic behaviour can be attributed to a cooperation between the gold nanoparticle and the support that preferentially activates the nitro group. We intend to apply this knowledge to predict the way in which a Pt based catalyst, highly active for hydrogenation, can be done chemoselective. We shall investigate two possibilities: a) to increase the number of metal atoms in the nanoparticle edge by reducing the metal nanoparticle size, and b) to decorate the surface of the metal phase with partly reduced oxide particles (TiOx) that are formed as a result of high-temperature reduction pretreatment. This particles contain Lewis sites that preferentially coordinate the carbonyl and the nitro groups, therefore improving the hydrogenation selectivity.

Area: Chemistry and Materials Science and Technology
Title: Reactivity of organic and organometallic molecules inside nano-sized molecular vessels
Leader: Carles Bo Jane
Institution: ICIQ

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 400

Abstract:
The use of molecular vessels and supramolecular assemblies to include or encapsulate transition metal complexes is attracting considerable attention because encapsulation of the catalyst may lead to significantly changes in its stability, activity and/or selectivity. We plan to investigate resocin[4]arene-based cavitands and its catalytic effect on the aza-claisen rearrangement and the nucleophillic aromatic substitution reaction. For these reactions, we would like to ascertain the origin of the rate-accelerating effect of the cavitands on the reaction. The reactivity of different late-transition metal complexes based on rhodium and palladium inside cavitands will be explored.

Period 2007-3 (October 1st - January 31st)

Area: Chemistry and Materials Science and Technology
Title: Computational study on the reaction mechanism of the selective oxygenation of saturated C-H bonds by a dimanganese catalyst
Leader: Odile Eisenstein
Institution: Institut Charles Gerhardt (University of Montpellier 2)

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 144

Abstract:

Area: Chemistry and Materials Science and Technology
Title: Phase Change Materials from First Principles
Leader: Marco Bernasconi
Institution: Department of Material Science, University of Milano-Bicocca

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:
Phase change materials are widely used in optical information storage (DVD) and are the active part of the most promising non-volatile memories of new concept, the Phase Change Memory (PCM) device, which exploits the large change in conductivity between the crystalline metallic phase and the insulating amorphous phase of a chalcogenide film. In spite of the great technological importance this class of materials, their microscopic structures and the detailed mechanism of the phase transformation are largely unknown. In this project, we plan to perform ab-initio molecular dynamics (MD) simulations for Ge2Sb2Te5 (GST), the prototypical material in this class, and related binary compounds, aiming at elucidating the structure of the amorphous phases. Density functional based MD simulations will be performed with the code QUICKSTEP as implemented in the CP2K suit of program. In particular, we will make use of a new MD technique recently developed by the proponents (T. Kühne et al., Phys. Rev. Lett. 98, 066401 (2007)). GST, GeTe, GeSb, and Sb2Te3 pure or doped with N and Si will be modelled by supercells containing up to 500 atoms with 3D periodic boundary conditions. Amorphous models will be produced by quenching from melt. The pressure induced amorphization of GST will be simulated as well. The research will provide precious insight on the properties of the amorphous phases and shed light on the mechanisms of the reversible crystal-to-amorphous transition underlying the technological applications of this class of materials. The availability of a microscopic model of the amorphous phase will also aid clarifying the origin of the large change in the electrical properties across the phase change exploited in the memory devices.

Period 2007-2 (June 1st - September 30th)

Area: Mathematics, Physics and Engineering
Title: Statistical mechanics of ionic liquids under confinement: molecular simulations
Leader: Jordi Faraudo
Institution: uab

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 100

Abstract:

Area: Life and Health Sciences
Title: From Historical Gene Pattern to Darwinian Molecular Processes. Towards a complete catalogue of adaptive events occurring after gene duplication.
Leader: Hernan Dopazo
Institution: cipf

Assigned machine(s): Picasso (UMA)
Assigned khours with priority: 500

Abstract:

Supercomputing and Bioinnovation Center

Address

Edificio de Bioinnovación
C/ Severo Ochoa 34
Parque Tecnológico de Andalucía
29590 Málaga, Spain

Contact

Phone number
+34 951 952 790
Email
soporte@scbi.uma.es