Primary Investigator: Georgiy Zadvitskiy
Project: Reflectometry synthetic diagnostics for nuclear fusion plasmas
Allocation: 862000 core hours
Abstract: Nuclear fusion is a very promising source of clean and sustainable energy. Magnetic confined fusion on the base of the tokamak device has shown the most advanced results. In order to produce sustainable reaction which will provide strong power output one should minimize plasma power losses. One of the dominant mechanism which enhances energy and particle transport is turbulence. Based on radar technique, microwave reflectometry diagnostics are powerful tools that can provide an information about plasma turbulence with a good time and spacial resolution. However, an interpretation of signals of these diagnostics is usually very tricky. Reflectometry synthetic diagnostic code will be used to help with experimental data analysis. Using close loop iterative methods diagnostics signals can be connected with turbulence properties. This data will be then used for turbulence models validation, study of the transport and transition to advanced confinement regime. COMPASS is a Czech tokamak that was operating from 2008 in Prague. Recently, fast swept frequency reflectometer (FSR) was installed to the machine. The main propose of this diagnostic is provide fast measurements of the electron density profile. However, FSR can be also used for a turbulence study. Using synthetic diagnostics and FSR data it is possible to measure turbulence amplitude as well as turbulence wavenumber spectra. Reflectometry synthetic diagnostics will be also used for COMPASS Upgrade tokamak reflectometer design. The beginning of COMPASS Upgrade (Compass-U) operation is planned in 2022.

 

Primary Investigator: Matus Dubecky
Project: Accuracy limits of quantum Monte Carlo in weak-interaction limit III.
Allocation: 4321000 core hours
Abstract: Stochastic electronic structure fixed-node diffusion Monte Carlo (FNDMC) method gains momentum as a quantum many-body method suitable for reference computations of large (possibly extended) systems, and, at the same time, it is well suited for supercomputer applications for its trivial intrinsic massive parallelism. FNDMC has recently become a promising choice for noncovalent systems as well, as it overcomes some of the limits of more traditional approaches like coupled-cluster, if combined with 1-determinant trial wave functions (e.g., steep scaling bottleneck, or, missing treatment of periodic boundary conditions). In this project, the last one in the series, we plan to undertake a final benchmark study of the best-identified FNDMC protocol following upon our previous screening and benchmark studies, and, its extensive applications in low-dimensional materials interactions (e.g., molecules or wires on 2D materials). Successful accomplishment of this project will facilitate usage of an outstanding FNDMC method in reference computations of noncovalent systems in circumstances where other reference methods are unavailable.

 

Primary Investigator: David Wagenknecht
Project: Theory of spintronic materials at finite temperatures
Allocation: 1177000 core hours
Abstract: In spintronic materials, a manipulation of electron’s internal degree of freedom – spin – opens additional possibilities in comparison to classical electrical devices, where the main objective is a detection of presence of electrons (electrical current). Even in common metals, description of finite temperatures (especially phonons and magnons) is a challenging task, especially because of numerical expenses. Our group is focused on development of ab initio approaches in bulk solids, we have incorporated a description of phonons and magnons within our first-principles codes recently, and we have proved robustness and efficiency of our methods. We would like to use computer hours of this project to continue in our effort and to describe advanced phenomena such as Gilbert damping or spin orbit torques at finite temperatures. Such development highly-rewarded work and it is of extreme importance for a purpose of designing future devices. Prediction of real material behavior is essential and despite the fact that testing samples of, e.g., antiferromagnetic memories have been already created, underlying physical phenomena of observed effects are not completely know, especially at nonzero temperatures, which may be a huge drawback for an utilization of the principles in novel devices. Because of it, the proposed project aims on brocading horizons of a basic science, but it has also wide range of potential applications.

 

Primary Investigator: Tomas Karasek
Project: Simulation of complex forming processes
Allocation: 938000 core hours at first period
Abstract: Objective of this project is development of prototype of asynchronous electric motor. During the development Digital Twin of electric motor based on complex numerical model will be created. This Digital Twin will be later on used for more efficient design of new generation of asynchronous electric motors. Implementation of Digital Twin methodology into the design process will allow to intercorporate (i) changes in international standards (ii) customer requirements (iii) lower the consumption of electrical energy. Digital Twin will help to reduce energy losses because multi-physical model of the electrical engine will provide better insight into (i) electrical losses in the conductors and conductive parts of the machine, (ii) magnetic losses in ferromagnetic parts of the machine, (iii) dielectric losses in insulation, (iv) mechanical losses from rotor friction with air and friction in contact surfaces and (v) ventilation losses due to changes in loading characteristic. Digital Twin will also help to assess the effect of the additional vortex losses caused by variations in the magnetic flux due to the unevenness of the air gap caused by the grooving.

 

Primary Investigator: Zdeněk Mašín
Project: Formation of temporary negative ions in low-energy electron collisions with the subunits of DNA
Allocation: 345000 core hours
Abstract: Radiation in the form of particles and photons can damage the DNA in our cells and can lead to cell death and mutations with a potential carcinogenic effect. Along its track in the body the primary radiation produces a chain of secondary particles. Among the secondary products most lethal to DNA are the OH radical and low-energy (< 30 eV) electrons. The role of electrons with energies below 10 eV is especially important since they carry a large proportion (up to approx. 80%) of energy of the primary radiation. These electrons damage the DNA via formation of temporary negative ions also known as resonances. The goal of this project is to study resonance formation in molecular dimers and monomers which can be used as models for the pyrimidinic subunits of DNA. Concretely, we will study resonance formation in pyrimidinic dimers and in pyrrole monomer. The expected outcome will be the first theoretical study of the effect of base stacking on resonance formation in DNA and a detailed insight into dissociative electron attachment process in pyrimidinic nucleobases. Finally, we will study photoionization of ethylene by ultraviolet light. Ethylene can be thought of as the minimal model for photon interactions with nucleobases. The calculations will be performed with the established UKRmol+ and RMT suites of codes of which the PI has been one of the main developers.

 

Primary Investigator: Santiago Alonso
Project: Catalytic properties of [Fe4S4]-dependent metalloenzymes.
Allocation: 319000 core hours
Abstract: [Fe4S4]-based radical S-adenosylmethionine (SAM) enzymes belongs to a huge superfamily with more than 100,000 members and carrying out more than 70 different radical-mediated reactions. In radical SAM enzymology, the preparatory stage of catalysis involves the activation of SAM through the reductive cleavage of the SAM C-S bond, which leads to the radical intermediate. Recently, the existence of another catalytically competent organometallic intermediate (so called Ω) was observed for several members of superfamily. However, the geometric and electronic structure of Ω remains unknown. Besides that, some other radical SAM enzymes are puzzling for their substrate promiscuity or for a different modus operandi of the activation of the SAM cofactor (activation of different C-S bonds). For these reasons, our goals are to investigate (i) a mechanism of interconversion between the radical and the organometallic intermediates and reveal the function of Ω, (ii) a mechanism of the selective C-S bond activation in SAM and (iii) a mechanism of selective activation of substrate by the enzymatic radical intermediate. To accomplish these goals, we plan to use DFT-based methods and to apply the broken-symmetry strategy to find a proper electronic configuration for the proposed systems.

 

Primary Investigator: Petr Strakos
Project: Research and Development of Libraries and Tools in the INFRA Lab II
Allocation: 1437000 core hours at first period
Abstract: As the members of the Infrastructure research laboratory our goal is to bring improvements and extensions of available tools that support the users of the IT4I clusters and their research. The key topics of our research are Energy-efficiency, improvements of the ESPRESO numerical library and development of Visualization tools. In addition, the resources will be used to provide high level support to other users of the IT4I infrastructure. The energy-efficiency topic focuses on the measurement and tuning of the HPC applications in terms of the possible energy savings. The ESPRESO team will provide improvements and new extensions of the ESPRESO library while in the development of the visualization tools a suitable workflow for the scientific visualizations of small to large datasets within Blender 2.8 will be created.

 

Primary Investigator: Mojmir Sob
Project: The entropy-driven segregation of impurities at grain boundaries
Allocation: 6366000 core hours at first period
Abstract: Despite of clear importance of entropy in numerous phenomena in materials science, this quantity is neglected in their quantification in majority of cases due to very high computational costs related to its evaluation. The negligence of entropy results in inaccurate quantitative values and – in the case of generalization – in incorrect prediction and interpretation of the studied effects. In this project, we propose to develop the procedure for computation of entropy for the case of the grain boundary segregation, which is of very high technological importance, and compare the calculated data with the experimental values. Once obtained, the values of calculated segregation entropy will be discussed from the viewpoint of their reliability and applied to interpretation of the structure/property relationship in grain boundary segregation.

 

Primary Investigator: Pavel Jungwirth
Project: Benzene radical anion as a reagent in the Birch reduction: electronic structure and chemical reactivity
Allocation: 571000 core hours
Abstract: The Birch reaction uses solvated electrons generated in situ by dissolving alkali metals in liquid ammonia to reduce aromatic compounds. Specifically, the solvated electron binds to an aromatic compound forming a radical anion species. The radical anion is then protonated via a proton abstraction from an alcohol, which must be added to the reaction mixture as a proton source. Reactions involving solvated electrons interested scientists since their discovery and gained a significant industrial relevance due to their synthetic flexibility. Despite the vast experimental interest in the Birch reduction, there is a relatively modest amount of work done theoretically. In a previous project (OPEN-14-41), we calculated hybrid ab initio molecular dynamics (AIMD) trajectories of the benzene radical anion and described its quantum mechanical properties. Interestingly, we implicitly show that the benzene radical anion is stabilized by the solvated environment of liquid ammonia. In this project, we would like to make this claim explicit by calculating the density of electronic states of the solvated benzene radical anion that is directly comparable to experimental X-ray photoelectron spectra (XPS). Moreover, we are interested in extending the investigation of the Birch reduction further by employing the methods of AIMD to study the protonation of the benzene radical anion by the proton source (methanol).

 

Primary Investigator: Robert Vacha
Project: Protein Affinity and Selectivity to Cellular Membranes
Allocation: 2927000 core hours at first period
Abstract: Spatial and temporal organisation of proteins in cell is a crucial aspect for understanding the complex machinery of living cells. Peripheral proteins are organised at membranes of specific organelles to perform specialized functions. However, the relationship between the protein sequence and its membrane preference is not yet known. The aim of the proposed project is to identify, quantify, and explain protein affinity for membranes with specific composition. We will develop a computational method to determine the binding free energy of proteins and their mutants to membranes with specific lipid composition. By application of this method we will provide molecular understanding of the protein affinity to specific membranes, which will allow us to determine the preferred localization of proteins in cells and develop new protein biomarkers, sensors, scaffolds, and drugs.

 

Primary Investigator: Judita Nagyova
Project: Revised dynamics of the Belousov-Zhabotinsky reaction model
Allocation: 20000 core hours
Abstract: The main aim of this project is to investigate the dynamics of the Belousov-Zhabotinsky reaction simulated by the Györgyi-Field model. Its dynamic is governed by a set of three nonlinear ordinary differential equations. The model exhibits regular and chaotic movement for different choices of the flow rate parameter. It is possible to observe isolated values of this parameter in the chaotic region, for which regular movement occurs, even after zooming in by constructing nested subintervals of flow rates. This leads us to the idea of a fractal structure in the set of the observed parameters.

 

Primary Investigator: Mauricio Maldonado Dominguez
Project: Electron-Proton Transfer in Biomimetic Binuclear Transition-Metal Active Sites
Allocation: 805000 core hours
Abstract: Our goal is to develop a methodology to accurately reproduce the experimental redox potentials and acidity constants of binuclear Fe2S2 clusters reported for bioinspired complexes related to the Rieske and mitoNEET proteins. The latter is of special interest since only recent studies have begun to unravel its actual significance to human health and the treatment of diseases and is currently becoming a target for the alleviation of cancer and diabetes. We will then study their H-atom transfer (HAA) reactivity, specifically the dependence of the activation barriers with the asynchronicity of the HAA step and the kinetic energy distribution at the HAA transition states between these complexes and TEMPO-H, a model substrate. We will apply standard DFT combined with multireference quantum-chemical methods to achieve these goals. The calibrated protocol will serve as a cornerstone for the posterior investigation of Fe2S2 containing proteins, aiming to better understand this emerging family of proteins. Further, the projected results hold potential to be translated into functional and stable bioinspired catalysts for the efficient production and derivatization of molecular targets.

 

Primary Investigator: Sergiu Arapan
Project: Predicting the finite temperature phase diagram of Sn from first-principles
Allocation: 2254000 core hours
Abstract: Sn (tin) is an important chemical element for many technological applications due to low toxicity and anti-corrosive properties. It is an alloy component used in soft solders, food can industry and optoelectronics. The first large scale use of tin was the bronze alloy about 3000 BC. Fe-Sn binary systems are now extensively studied as candidates for the rare-earth free permanent magnets. Relevant magnetic phases are obtained at elevated temperatures, which reveals the important role of lattice dynamics and anharmonic effects in stabilizing these structures. To predict the temperature stability range of Fe-Sn binaries one must have an accurate finite temperature phase diagram of Sn. However, DFT calculations with the contribution of quasi-harmonic lattice fail to predict accurate temperature phase transitions of Sn. In this study, we aim to go beyond the standard DFT calculations and use anharmonic phonon contributions to calculate the α-Sn to β-Sn transition temperature, and thermodynamic integration for predicting the melting temperature of tin.

 

Primary Investigator: Martin Jirka
Project: Gamma radiation and pair production in laser-electron collision
Allocation: 200000 core hours
Abstract: With the advent of 10 PW-class laser facilities, a new regime of laser-matter interaction is opening since quantum electrodynamics effects, such as pair production and cascade development, start to be important and affect the interaction. To study this new regime of interaction, numerical simulations are required. With their help, it is possible to predict and study quantum effects which may occur in future experiments at modern laser facilities. The aim of this work is to study a particular interaction setup when an ultra-intense laser pulse collides head-on with an energetic electron bunch. As a result, a huge number of gamma photons is emitted. However, the number and energy distribution of created particles strongly depends on whether or not quantum effects are employed. Going to higher laser intensities or electron energies, the quantum effects cannot be further neglected and strongly affect the interaction dynamics. Therefore, the aim is to assess their role and predict the outcome of such an interaction in terms of the energy distribution of created particles.

 

Primary Investigator: Pavel Hobza
Project: IN SILICO DRUG DESIGN
Allocation: 6106000 core hours
Abstract: Modern drug design is based on the detail understanding of diseases in molecular basis. Drugs bind to their biological targets to modulate their functions. Reliable prediction of drug affinities is critically dependent on the description of noncovalent interactions. An accurate description requires the use of quantum mechanics (QM), which is however computationally very demanding. The use of semiempirical QM (SQM) methods can make the QM description of large protein-ligand complexes feasible. However, the quality of original SQM methods (such as PM6) was low. We have developed1-4 the corrected SQM methods (e.g. PM6-D3H4X) for accurate description of protein-ligand interactions. We have successfully applied5-16 the corrected SQM methods for accurate description of protein-ligand interactions. We have been developing the Computer-aided drug design framework that aims to reduce the amount of experimental work by prioritizing compounds for synthesis and biological screening with a higher success. We have ascertained that a SQM based approach outperforms classically used scoring functions in both ligand ranking16 and identifying the ligand native pose in cognate docking.15,19,20 To further improve and validate our methodology, we are carrying out large-scale virtual screening studies using extended databases of therapeutically relevant targets with active molecules and decoys. Currently, we are evaluating how this methodology improve “enrichment” in screening studies.

 

Primary Investigator: Ondrej Vlcek
Project: Finalization of the PALM-4U model validation against observation campaign in Prague-Dejvice
Allocation: 915000 core hours
Abstract: The newly developed urban model PALM-4U (www.palm4u.org) allows to perform detailed simulations of meteorological and air quality conditions in urban areas. The significantly enhanced version 6.0 of the model has been released recently. Our team has strongly contributed to its development (see references) and we intensively collaborate with our German partners connected within the MOSAIK project. Our collaboration includes also the study proposed in this project. The goal of the proposed project is to perform detailed validation of the model against the observation campaign done in Praha-Dejvice area within Urbi Pragensi project. Our team was invited to publish this validation in the special issue of GMD journal dedicated to the new version 6.0 of PALM-4U. Part of these simulations is performed in the Czech Republic the other part in Germany. Due to computational demands, Salomon is the only publicly available Czech IT infrastructure capable of supporting this task.

 

Primary Investigator: Jan Premus
Project: Dynamic source inversion of 2014 Mw 6 South Napa, California, earthquake using realistic friction laws
Allocation: 279000 core hours
Abstract: Earthquakes are caused by sudden release of elastic energy that was accumulated on the fault plane due relative motion of the tectonic plates. To determine the source parameters of an earthquake, a large number of computational simulations with various input parameters are performed. In this project, we employ our recently developed code FD3D_TSN that solves dynamic rupture propagation on the fault with high accuracy and low computational demands. The solver is combined with random sampling optimization to derive the source parameters of 2014, South Napa earthquake. With magnitude 6.0 the earthquake counts as the largest in San Francisco Bay area in the last 25 years, causing 1 casualty, about 200 people injured and damage estimated up to $1 billion. The earthquake produced a significant surface rupture on ~12 km length, which occurred mainly aseismically within few days after the earthquake. To explain this behavior, a complex dynamic rupture model will be employed to obtain a unique dynamic earthquake source model.

 

Primary Investigator: Dominik Legut
Project: Strengthening and toughening w-BN by 3D networks of planar defects
Allocation: 6918000 core hours
Abstract: Recently, three-dimensional (3D) network of nanometer-spaced planar defects was found in superhard w-BN, which is constructed by a high density of intersecting (0001) stacking faults and {10-10} inversion domain boundaries (IDB). This 3D network of planar defects brings accordingly a scientific curiosity whether it can strengthen and toughen the nanostructured w-BN or not and whether there is the synergetic effect of the interface spacings of IDB and stacking faults. In this project, through the unique combination of ab initio derived ideal strength and Peierls stress, and large-scale molecular dynamics (MD) simulations of 3D polycrystal sample, we will study the strengthening and toughening of w-BN by 3D networks of planar defects with several aims: 1) stability of different types of IDB interface with different interface spacing; 2) ab initio derived ideal strength and Peierls stress of IDB interface model and the 3D network model consisting both IDB and stacking fault, and the corresponding electronic-scaled mechanism; 3) mechanical response of the 3D polycrystal w-BN sample consisting of 3D network of planar defect, and the corresponding atomic-scaled mechanism.

 

Primary Investigator: Ctirad Cervinka
Project: Glass Transition Temperatures of Ionic Liquids from Polarizable Molecular Dynamics Simulations
Allocation: 1410000 core hours
Abstract: Unique properties of ionic liquids (ILs), such as low volatility, high electrochemical stability or a boundless structural variability make these compounds promising for many applications in chemical processes − gas capture, energy storage, stabilization of nanoparticles etc. Prevailing higher cost of ILs, limited availability of their physico-chemical properties or an insufficient understanding of ILs-related phenomena at the atomic level still hinder massive spread of ILs in chemical industry to occur. Knowledge of the melting temperature is a key prerequisite for each compound that is to be used in the liquid phase for a given application. However, numerous ILs have been reported not to crystallize at all very often. Large cohesive forces among the individual ions render the fluid highly viscous, which impedes formation of a regular crystal lattice upon cooling. Instead, ILs typically exhibit massive supercooling of the liquid phase which undergoes a phase transition to an amorphous glass-like solid state at temperatures well below the true melting temperature. Knowledge of the respective glass transition temperature thus becomes of utmost importance in case of ILs. Molecular-dynamics (MD) simulations enable to calculate various structural, thermodynamic, or most importantly here, transport properties for condensed chaotic phases (such as liquid and glass). Analyzing the temperature trends of such properties enables to derive the glass transition temperatures from theory.

 

Primary Investigator: Radek Halfar
Project: Investigation of biological systems properties using chaos theory
Allocation: 10000 core hours
Abstract: The project is a continuation of long-term research dealing with the investigation of biological systems in terms of chaos theory, and its possibilities for detection and prediction of life-threatening conditions. The change of dynamical behavior can be seen in many biological systems. An example of a biological system where dynamical behavior is an important predictor of life-threatening conditions is the human brain. During an epileptic seizure, a reduction in the amount of chaos in the electrical activity of the human brain can be observed. Another example can be seen in a human heart because the fibrillation can be seen as a form of spatio-temporal chaos. In this project, the mathematical models, as well as measured data of various biological systems, will be investigated. For this purpose, modern techniques along with the state of the art tools are planned to apply.

 

Primary Investigator: Jiří Tomčala
Project: A new time series prediction method and its application to supercomputer energy consumption
Allocation: 80000 core hours
Abstract: The biggest challenge in the area of prediction methods is to create a method that is both accurate and fast. Simple and fast methods (e.g. Moving Average, Exponential Smoothing) are generally known, but they are inaccurate. On the other hand, methods with very accurate results have recently emerged (e.g. Extreme Gradient Boosting), but they are computationally demanding and slow. The aim of this project is to propose and test a new prediction method that would take the best of the existing prediction methods. The very next goal is then to compare this new method with the most commonly used methods in this area, especially in terms of accuracy and speed. Testing and comparison with other methods will be performed on artificial time series as well as on real-world complex time series, in this case the course of the IT4Innovations supercomputer infrastructure power consumption.

 

Primary Investigator: Irina Borodkina
Project: SOLPS-ITER simulations for COMPASS Upgrade divertor design
Allocation: 239000 core hours
Abstract: The COMPASS-Upgrade (COMPASS-U) project, which has been recently given funding from ESIF, is aiming at constructing a world-class fusion research facility. COMPASS-U is a medium-size, high-magnetic-field and high-density tokamak project with a flexible set of the poloidal field coils for generation of the single-null, double-null and snowflake divertor configurations. With its high plasma and neutral density, closed divertor and strong ITER-like target shaping, COMPASS-U is of particular interest for ITER in terms of similar divertor plasma and neutral parameters, as well as predicted power decay length and stationary power loads to the divertor targets [1]. The development of divertor design with a reliable solution for the power and impurity particle exhaust is one of the important challenge towards the realization of COMPASS-U project. It is essential to efficiently dissipate power in the divertor, probably necessitating operation in a detached regime, to ensure the maximum inter-ELM power load at the divertor target below 15 MW/m2 and to maintain a low electron temperature at the target plates in the range of 5-10 eV to suppress erosion. The numerical simulation can be an excellent tool for an elaboration of a tokamak divertor design by studying the effect of different divertor geometries on the divertor plasma parameters, estimating the radiation power fluxes on divertor targets, and therefore can contribute to the determination of the optimal operation regimes and design of COMPASS-U tokamak.

 

Primary Investigator: Ludek Pesek
Project: Numerical study of dynamics of 3D FE blade cascade model with inter-blade dry-friction contacts –phase III
Allocation: 60000 core hours
Abstract: In the latest years we deal with investigation of additional structural damping of complex blade systems due to inner couplings [1]. In frame of the project GACR 16-04546S the physical model of the blade disk with friction couplings between “blade tie-bosses” has been proposed and fabricated for experimental research. For numerical analysis of the dynamical behavior of the disk and its non-linear behavior the three-dimensional FE model with friction contacts has been developed in the program ANSYS [2]. The Augmented Lagrangian method is used to compute contact normal pressures and friction stresses. The friction coupling is modeled by the Isotropic Coulomb’s law. For a description of the friction coefficient, its dependence on relative velocity is considered. The damping ratio of the friction damping is evaluated from the envelope of free vibration attenuations after resonant excitation. Because of long computational times of the full bladed wheel in case of the non-linear solution due to the friction contacts, we decided to aim at the dynamics of bundle of three blades under very short (few periods) resonant excitation. Excitation force is applied at the head of the middle blade in direction perpendicular to a plane of the blade for both loading cases [3]. The calculations show that the contact states, i.e. stick, slip, stick-slip, vary significantly in time and space. It depends on the contact pre-stresses and size of excitation amplitudes. In most times the contact is concentrated in small areas of the contact surfaces and is in a slip state (sliding) due to large vibrational amplitudes and exceeding the adhesion in contact forces. The size of microslips and macroslips plays decisive role on the amount of damping and reduction of vibration amplitudes [1]. The numerical results are under experimental verification. The experiments confirmed that the dry friction damping effect is high and positively contributes to the decrease of vibration amplitudes. The values of eigen-frequency of blades in the triple, however, change in dependence on the prestress in the contacts and level of the excitation amplitudes Therefore, besides the damping the stiffening effect due to dry friction contacts will be also the topic of the research in this project. The calculations on the supercomputer allow us to calculate longer transient tasks, more contact prestress setups on the blade triple model for more accurate analysis of damping and stiffening effects by dry-friction contacts. Then we are going to apply the same numerical and analysis methods for evaluation of these effects on the whole blade disk. The obtained results will be used for the solution of the new GACR project no. 20-26779S.

 

Primary Investigator: Martin Kolísko
Project: Comparative genomics of diplomonads as a model for understanding evolution of parasitic genomes
Allocation: 239000 core hours
Abstract: Most well-known microbial eukaryotes are devastating parasites of humans and animals; however, many other species are known to be host-associated, yet their pathogenicity remains unknown. Comparative genomics is a powerful tool for understanding parasite evolution, metabolism, and functionality on a genomic level. Diplomonads are a group of microbial eukaryotes that include medically and economically important parasites. Additionally, there are several putative secondarily free-living species and host-associated commensalic species. Here we propose a taxonomically wide comparative study of diplomonads, including well-studied parasites, primarily and secondarily free-living species, and commensals. The results will address some of the fundamental questions of biology, including the mechanisms of reversal from a free-living to parasitic lifestyle and whether it is possible to predict pathogenicity or host-associated lifestyle based on genomic information. Additionally, we will use phylogenomics to resolve the internal phylogeny of diplomonads in order to obtain a correct evolutionary framework for comparative analyses.

 

Primary Investigator: Jiří Kolafa
Project: Supersonic expansion of water vapor to a vacuum
Allocation: 96000 core hours
Abstract: The upper atmosphere (stratosphere) is very cold, but it is not empty. There are small frozen water particles in the form of the so called “polar stratospheric clouds”. Other molecules can adsorb on these icicles. These particles are irradiated by the Sun, which drives many important chemical reactions, the notorious ozone decomposition in particular. Since it is difficult to study these particles “in the wild”, model icicles are created in a laboratory. One possibility is supersonic expansion: Water vapor expands through a small orifice to a vacuum, reaches supersonic speeds, cools down, and eventually freezes. However, there is contradictory evidence about the shape of these particles: Cross-section measurements indicate irregular shapes, which is a bit against the common sense. Here molecular simulations may help. We have developed a method for direct simulation of the expansion. The results indicate spherical particles; however, because of computer limitations, we could simulate only small systems. We hope that with sufficient resources, we can simulate large enough systems to determine the shape of the icicles.

 

Primary Investigator: Jan Bohacek
Project: Centrum vyzkumu nizkouhlikovych materialovych technologii CZ.02.1.01/0.0/0.0/16_019/0000753
Allocation: 399000 core hours
Abstract: Shell-and-tube heat exchangers can be found in countless applications. Heat transfer surfaces are in many of them represented by a bank of tubes. The crossflow is subjected to a pressure drop, which is an essential parameter for an optimal design. For decades, a few empirical formulas from several handbooks have been continuously used by many engineers and researchers worldwide. The formulas were originally developed by fitting vast data collected from measurements with steel rods. Nowadays, the popularity of using non-metallic components such as those made of various plastics is on increase. Generally, they are significantly less stiff than metallic counterparts, which makes them more prone to vortex-induced vibrations. Self-exciting oscillations will result in remarkable increase in drag coefficients. Therefore, it is of urgent interest to revise the existing formulas for pressure drop.

 

Primary Investigator: Andrzej Kadzielawa
Project: Tailoring thermal stability of W-Cr based alloys for fusion applications
Allocation: 4297000 core hours at first period
Abstract: There is very little known about W-Cr system. Phase content of a W-Cr alloy was evaluated last in few papers from ’60s and ’70s. Back then tungsten-chromium alloys had no large-scale application; however, in the future \texttt{W-Cr} alloy is foreseen to cover hundreds of square meters of fusion reactor vessel. For example, International Thermonuclear Experimental Reactor that is currently under construction in Cadarache (France) has surface of 620 m2. Expected lifetime of one plasma facing component is 5 years. Within this time period it is expected that the armour material of the component, where a self-passivating tungsten alloy is foreseen, will not experience a significant change in microstructure, phase content, mechanical and oxidation behaviour. In the last two years, questions on thermal stability of W-Cr alloys has re-occurred in literature and conferences. The preliminary results show that the decomposition kinetics can be fast around the temperature of 1000C, i.e. around the accidental conditions. In such a case, changes in the phase content and degradation of oxidation performance is inevitable. Further, the decomposition rate decreases with decreasing temperature, thus it is very difficult to experimentally verify the lifetime of the component if the changes will be apparent after year-long heat treatment. This might be further complicated by the decomposition behaviour that might lead to very fine precipitates difficult to observe in conventional scanning electron microscopes. All this changes will significantly influence the oxidation performance of the alloy. Thus, it is of a prime importance to gain more knowledge about tungsten-alloys especially regarding thermal stability and stabilizing the saturated solid solution. The ab initio computational modelling methods have the potential to bring broader understanding of the W-Cr alloys system and help to answer following questions: (1) what are the mechanisms of W-Cr solid solution stabilization? (2) What is the formula describing the decomposition kinetics at lower temperatures? (3) Is different stabilization necessary for spinodal region and nucleation and growth region of the miscibility gap?

 

Primary Investigator: Vojta Kubac
Project: Endosomal Escape and the Biophysics of Membrane Fusion
Allocation: 359000 core hours
Abstract: Endosomal Escape and the Biophysics of Membrane Fusion After undergoing endocytosis, many bioconjugates and complex drugs remain trapped in endosomes, lowering their bioavailability. This problem has been particularly severe in the case of cell penetrating peptide based delivery systems and functionalized nanoparticles. The aim of this project is to investigate potential endosomal escape mechanisms, with a focus on escapce through membrane fusion. Our strategy is to selectively induce membrane restructuring of late endosomal lipids as well as make it predictable through the extraction of continuum properties. The resulting theoretical insights will provide a basis for the design of new endosomolytic agents as well as interfaces for therapeutic nanoparticles.

 

Primary Investigator: Jan Burjánek
Project: Modelling the ambient vibrations of local geological structures
Allocation: 375000 core hours
Abstract: Earthquakes are manifested by strong ground motions often affecting structures and consequently having strong social and economic impacts. Unconsolidated sediments and weathered rocks can significantly amplify the seismic motions resulting in a more severe damage. Physics based interpretation of local site effects plays a key role in seismic hazard assessment, as in imaging of subsurface geological structures. We aim at development of new non-invasive ambient-vibrations approaches based on numerical seismic wave-propagation modelling applied to complex geological structures. We will systematically simulate ambient vibrations of geological basins (e.g., Mýtina maar – volcanic body in West Bohemia) in order to isolate potential signatures of the local 3D structure in the synthetized wave field. The simulated ground motions will be compared with the observed data, and shall be a base for further development of existing portfolio of site specific earthquake hazard evaluation.

 

Primary Investigator: Ota Bludsky
Project: Exploring Zeolites with Nanoscale Architecture: Synergy Between Experiment and Theory
Allocation: 2195000 core hours at first period
Abstract: The zeolite-to-zeolite transformation with layered precursors as nanoscale building blocks has been identified as one of the most promising strategies for the preparation of novel 2D and 3D materials. Advances in the synthesis of new zeolites with the rational control of their composition, morphology, and functionalities have revealed the considerable potential for their application in adsorption, separation, and catalysis. An alternative, environment-conscious separation technique (with respect to energy-intensive cryogenic distillation) is the kinetic separation of hydrocarbons on small-pore zeolites with 8MR channels. Recent research has shown that the nominal crystallographic pore aperture size may not be decisive factor and that the lattice flexibility can have a significant impact on diffusivity assessment. This project focuses on this phenomenon promoted by zeolite flexibility and on predicting flexibility effects for zeolite frameworks with nanoscale architecture. Progress in this direction can lead to the discovery of new materials for efficient molecular separation.

 

Primary Investigator: Valeria Butera
Project: Investigations of Functional Waveguide Materials for MIR Sensors: a DFT study
Allocation: 612000 core hours
Abstract: Mid-infrared (MIR) based, monolithically integrated optical sensors are a recent and rapidly emerging research field. Recently, compact optoelectronic devices have been obtained by combining bi-functional quantum cascade lasers and detectors with optical interconnects. This study supports the development of the next-sensor generation by focusing on the adsorption and the related reactions of the analyte molecules on the waveguide surface in the interaction zone. In contrast to existing solutions, which perform the measurement in a liquid or gaseous analyte, the adsorbed molecules are predicted to have a different absorption footprint, which will be taken into account by quantum-chemical modeling within this project. Specifically, we will develop an adapted theoretical approach based on density functional theory (DFT) and periodic boundary condition (PBC) calculations to model the interaction of analytes with sensor surfaces. Our theoretical investigation address to identify the sites on the chemical sensor surface that target analyte molecules attached to and determine the respective binding energies and charge transfer. Furthermore, we will investigate the resulting shifts in the absorption spectra of analyte substances due to the consequent alteration of the geometric and electronic configuration of the analyte after their adsorption. Particularly, our research interest will be addressed to developing TiO2 based chemical sensors that is used for the detection of small sugar molecules with a potential application in medical sensing. Simultaneously, we will focus on environmental sensors for the CO2 detection and its conversion reactions into added-value products. The results obtained from our DFT investigations will be directly combined with the experimental findings gained in my host group to enable directed optimization of the sensing surface e.g. through engineered roughness or by exploiting field enhancement due to plasmonic near-field antennas. All components will be combined into advanced, fully-integrated prototype sensors, which open new opportunities for further application-oriented research.

 

Primary Investigator: Martin Zeleny
Project: Computer modeling of doped CoCrNi medium entropy alloys
Allocation: 3477000 core hours at first period
Abstract: The equimolar CoCrNi Medium-Entropy Alloy (MEA) exhibits a very significant strength-ductility-toughness combination due to its low energy of stacking fault resulting in twinning-induced plasticity. Exceptional properties of CoCrNi MEA with single FCC phase can be further tailored by change of composition or alloying with other elements. It can result even in stabilization of another type of structures, e.g. HCP, or in precipitation of a new phase. In the light of the following reasoning, we propose an ab initio investigation of the impact of compositional fluctuations or doping by Cu, Zn and Al additions on the phase stability and mechanical properties of CoCrNi MEA. In particular, we are going to estimate the stability of FCC, HCP and DHCP structures, stacking fault energies as well as mechanical properties represented by tensor of elastic constants as a function of concentration of each element. The project will provide guidelines for design of new alloy s with a high application potential.

 

Primary Investigator: Jiri Klimes
Project: Accuracy and precision for extended systems IV
Allocation: 2839000 core hours
Abstract: Materials bound by non-covalent interactions are important both in nature and industries. From methane clathrates at the bottom of the sea, over pharmaceuticals in pills, to layered systems such as graphite. Many of them have also some peculiar properties. For example, even at the same conditions, many pharmaceuticals can exist in different crystal structures, called polymorphs. One of these polymorphs is the most stable, but the others are usually very close in energy. One of the long term goals of our project is to develop a theoretical modelling scheme that would allow a reliable description of the stability of the different polymorphs or different phases of materials in general. The problem is that to get the tiny energy differences between different phases, we need to use quantum mechanics. Solving the equations of quantum mechanics is only possible for simple systems and for extended systems we need to use approximations. To reach our goal we want to combine one of the most accurate schemes currently available for the treatment of extended systems with a method used to calculate reference quality binding energies of molecules. Moreover, we want to develop methods that will ensure that our results are very precise and thus reproducible. This will enable us to obtain highly reliable binding energies of extended systems.

 

Primary Investigator: Roman Divis
Project: Innovative method for determining railway infrastructure capacity using nested simulations
Allocation: 359000 core hours
Abstract: Railway transport is used as a one of the dominant types of passenger and freight transport. Compared to road transport, rail infrastructure represents a more restricted environment with limited infrastructure. Unexpected events – train delays, malfunction of railway infrastructure devices – can greatly affect the quality and continuity of rail traffic operation. For these reasons, it is necessary to consider the capacity of the railway infrastructure when planning train schedules. Methods for assessing capacity aim to objectively quantify the utilization and quality of traffic on a given segment of the infrastructure. Methods are based on different approaches – analytical, graphical, graphical-analytical or experimental. Analytical methods define a mathematical apparatus that provides information about the capacity using data about traffic situation and infrastructure. The use of these methods is relatively simple, but the usefulness of the results is limited. However, today, the analytical methods represent dominant way of determining capacity. Experimental methods use computer simulations to perform stochastic experiments to obtain qualitative indicators of capacity. The aim of this project is to propose a new experimental methodology that uses computer simulations and specifically the technique of nested simulations. Such a methodology has a potential to provide better results and some new capacity indicators to improve train timetables planning.

 

Primary Investigator: Petr Valenta
Project: Relativistic Mirrors in Laser-Plasma Interaction III
Allocation: 645000 core hours
Abstract: A relativistic mirror may be defined as an object that reflects incoming radiation while moving at relativistic velocity. Due to the double Doppler effect, the reflected electromagnetic wave is compressed, amplified and its frequency is upshifted. The theory of light reflection from objects propagating in vacuum at arbitrary (subluminal) velocity was first formulated by Einstein in 1905. Later, it turned out that relativistic mirrors can be realized by irradiating plasma targets by intense laser pulses. Relativistic mirrors are currently studied in many different contexts because of their great potential for both fundamental science (e.g. light intensification towards the Schwinger limit, investigation of photon-photon and Delbruck scattering, detection of Hawking radiation) and practical applications (e.g. attosecond spectroscopy, molecular imaging, plasma diagnostics). In this project we plan to numerically investigate the properties of relativistic mirrors realized with strongly nonlinear Langmuir waves driven by intense laser pulses in plasma. We will be optimizing the reflection coefficient of the relativistic mirror as well as the factors of electric field amplification and frequency upshift of the reflected electromagnetic wave. We will be closely working with the experimental team in order to design a setup for upcoming experiments using the state-of-the-art laser systems currently being built at the ELI Beamlines facility. The ultimate goal of our research is to develop compact and tunable source of coherent high-brightness radiation with wavelengths ranging from x-rays to gamma-rays.

 

Primary Investigator: Michail Kourniotis
Project: Impact of massive stars on the composition of globular clusters
Allocation: 718000 core hours
Abstract: Globular clusters are spheroidal dense collections of old stars typically found in the halo of Milky Way and of other galaxies. They have total masses of 10^5 to 10^6 solar masses, an order of magnitude (or more) heavier than the young open clusters. Originally thought to comprise of stars with the same age, it is now well established that globular clusters host multiple generations of stars with different ages and chemical compositions. Their oldest components render their study critical for understanding star formation in the early Universe. Numerical methods for simulating the non-stationary wind of massive clusters are valuable for retrieving the gas dynamics and the thermal instabilities that potentially lead to newborn stars. The latest stellar evolutionary models can provide the essential input parameters in order to monitor the dynamical feedback from the stars. Additionally, individual, high energetic sources such as supernovae and the outbursts of distinct extreme stellar types need to be further accounted given that their high mass-loss output can dramatically modulate their gaseous surroundings. By accessing high resolution 3D simulations, we propose to establish a thorough picture on the formation of multiple stellar generations in globular clusters. In retrospect, our study would help to understand the role of extreme luminous sources on the evolution of the parent cluster wind as a function of environmental properties and spatial distribution within the cluster margins.

 

Primary Investigator: Marek Ingr
Project: Interactions of native and substituted hyaluronan with technologically relevant organic molecules
Allocation: 318000 core hours
Abstract: Hyaluronic acid (HA) is a natural polysaccharide contained by the extracellular matrix of connective tissues finding wide applications in medicine and cosmetics. It is used not only in its native state, but also in chemically modified forms, e.g. as a base of drug delivery systems or artificial tissues. It is therefore worthwhile to study its structure not only in aqueous solutions, but also in mixed solvents consisting of water and an organic solvent miscible with water which may be used for the processing and chemical modification of HA molecules. This project is concerned with molecular-dynamics simulations of native and modified HA molecules in such solvents. . Firstly, conformations of native HA oligosaccharides in mixed solvents and the structure of their solvation shells will be studied and compared with the same molecules in aqueous solutions. Furthermore, HA molecules modified by various substituents will be studied in order to determine their influence on the oligosaccharide structure in both aqueous and mixed solvents. Finally, interactions of native and modified HA oligosaccharides with dissolved organic molecules acting as reagents potentially modifying HA will be carried out in order to predict the interaction points of HA and these molecules, influence on the oligosaccharide structure and the regioselectivity of the following reaction. This study should thus provide information suitable in synthesis and processing of novel materials based on hyaluronic acid.

 

Primary Investigator: Vaclav Bazgier
Project: Virtual screening of human and plant hormones 2
Allocation: 2814000 core hours
Abstract: Virtual screening is a computational method that allows to discover potentially new chemical compounds based on structures of biological macromolecules. This project is a continuation of the already running project project OPEN-16-30 where we are looking for new potentially new derivatives in relation to hormones and other biologically active compounds. In this new project we would like to focus on design of new chemical compounds and their derivatives in relation to hormones and other biologically active compounds against and we would use more publicly available datasets of small compounds. In general, hormones plays crucial role in human, animal and plant life and are responsible for a number of biological interest processes and nowadays it is very useful to study the issue. The design of new compounds will be provided by the molecular modelling called molecular docking technique. This technique allows to run virtual screening of proposed molecules over multiple targets to select potential compounds for further in-vitro or in-vivo testing and thus to help in the design of new derivatives of drugs or fertilizers.

 

Primary Investigator: Ondrej Chrenko
Project: Planet formation after pebble isolation
Allocation: 611000 core hours
Abstract: Modern scenarios of planet formation suggest that planets form by accretion of cm- to m-sized solid particles—referred to as pebbles—which are subject to the aerodynamic drag in protoplanetary disks. The drag has two dynamical consequences: (i) it forces pebbles to radially drift through the disk; (ii) it enhances the cross-section of gravitational capture of pebbles by planetary embryos. However, pebble accretion is not without limits. Once the mass of a growing protoplanet exceeds a certain threshold, a pressure bump is formed in the gas outside the planetary orbit. The bump then starts to trap the drifting pebbles and isolates them from the protoplanet. This process—known as the pebble isolation—therefore sets the final mass that a single protoplanet can reach by pebble accretion. In this project, we aim to investigate the evolution of pebbles which gradually accumulate within the pebble isolation. As the solid-to-gas ratio locally increases, it might be possible that the respective region of the disk becomes prone to hydrodynamic instabilities, and pebbles become concentrated into clumps which might undergo a gravitational collapse, thus forming a new planetary embryo. We will use two-fluid hydrodynamic simulations (with one fluid for the gas and one for the pebbles) in 2D and 3D to explore this possibility. The results will help to explain the origin of planetary systems.

 

Primary Investigator: David Tskhakaya
Project: PIC modelling of the COMPASS-U plasma edge
Allocation: 720000 core hours
Abstract: Kinetic study of the plasma edge is one of the hottest topics in fusion plasma research. Kinetic effects play important role in plasma transport at the edge and plasma surface interaction processes, affecting overall performance of the plasma discharge as well as life-time of plasma facing components. Such effects expected to become essential in next generation fusion plasma devices. Due to complexity of the problem, quantitative kinetic study of the plasma edge can be performed only via sophisticated numerical tools. The aim of the proposed project is to perform first predictive kinetic modelling of the COMPASS-Upgrade tokamak to be built in Prague. We consider different discharge configurations and find corresponding limiting values of the power and heat loads to the most critical PFC elements, so called divertor plates, as well as estimate effective impurity sputtering yields. This findings will be used for optimizing plasma discharges at COMPASS-U and in general, in magnetic confinement fusion research.

 

Primary Investigator: Jakub Velimsky
Project: Three-dimensional electrical conductivity in the Earth’s mantle recovered from geomagnetic variations of magnetospheric, ionospheric, and tidal origin
Allocation: 151000 core hours at first period
Abstract: The electrical conductivity is an important geophysical parameter connected to the thermal, chemical, and mineralogical state of the Earth’s mantle. A traditional technique to study the distribution of electrical conductivity in deep regions of the Earth is the electromagnetic induction method, driven by the geomagnetic variations in the ionosphere, the magnetosphere, and recently also by ocean tides. Accurate data from the Swarm satellite mission by the European Space Agency, and from the global ground observatory network are now available. In this project, we plan to implement three-dimensional inversions of satellite and observatory data in all three basic configurations, providing complementary resolutions and sensitivities, yet requiring different numerical modelling and data processing techniques. We will thus obtain a three-dimensional model of electrical conductivity in the Earth’s mantle that we will further interpret in terms of mantle state using thermodynamical modelling.

 

Primary Investigator: Jiri Jaros
Project: Photoacoustic tomography of the breast II
Allocation: 296000 core hours
Abstract: Photoacoustic tomography (PAT) is a biomedical imaging modality based on the photoacoustic effect. In PAT, non-ionizing laser pulses are delivered into biological tissues. Some of the delivered energy will be absorbed and converted into heat, leading to transient thermoelastic expansion and thus wideband ultrasonic emission in the low MHz range. The generated ultrasonic waves are detected by ultrasonic transducers and then analyzed to produce images. Since the optical absorption is closely associated with physiological properties, such as hemoglobin concentration and oxygen saturation, the PAT is used to visualize vasculature inside tumors with a very high resolution. This simulation study is focused on the optimization and validation of the PAT software being developed as part of the H2020 project Pammoth on a set of breast phantoms. The resolution, accuracy, sharpness, motion and noise artifact, and the depth of penetration will be investigated and optimized. This study moves us towards the deployment in a real PAT system for breast mammography.

 

Primary Investigator: Jakub Sebesta
Project: Magnetic Ordering in High Entropy Alloys
Allocation: 140000 core hours
Abstract: High entropy alloys (HEAs) are multi-principal element alloys, which stands for a promising group of material with a wide range of application especially in the mechanical engineering. One can mention attractive physical properties as extreme tensile strength, high hardness or great ductility. A high number of constituents, originally at least five but one deals also with four-pricialelement alloys, not only does it allow possible variation of their properties, but primarily it brings a stabilization of the high temperature phase thanks to the significant entropy term. We deal with the magnetic properties of the four- and five- principal element alloys based on the 3d elements. Magnetism is not important by itself, but it influence e.g. the mechanical properties as well. We focus on the magnetic properties of the ground state and the relation between the magnetic properties and the composition in order to enhance.

 

Primary Investigator: Ales Podolnik
Project: Simulation of probe diagnostics for COMPASS-Upgrade
Allocation: 1024000 core hours
Abstract: The COMPASS-Upgrade project, which has been recently given funding from ESIF, is aiming at constructing a world-class fusion research facility. This high-field and high density device is going to produce plasmas relevant to both future ITER and DEMO fusion reactors. To study such plasmas, existing diagnostics will be reused as well as there is need to adapt others to the harsh environment of scrape-off layer plasma in direct contact with plasma facing components. One of such diagnostics are Langmuir probes that in proper setup can measure electron temperature and density as well as floating potential. However, to accommodate them to such device takes significant effort. Design of a new fusion devce requires investigation of possible concepts of diagnostic equipment. In this project, we aim to simulate probes that would be accomodated to various plasma facing component variants, mainly different shaping options. As shown in previous results, proper probe design can be beneficial not only from the operational point of view, for example to avoid melting of the probe, but it also can compensate for various effects negatively affecting the accuracy of obtained physical data.

 

Primary Investigator: Pablo Nieves
Project: Computational design of novel materials with giant magnetocaloric effect for magnetic refrigeration technology
Allocation: 4230000 core hours
Abstract: Magnetic cooling could be an environmental friendly energy solution substituting conventional vapour compression refrigeration in the future. This new technology is based on the magnetocaloric effect (MCE) in which the temperature of magnetic materials increases when they are placed in a magnetic field and cool down when they are removed. This thermal response is maximized when the solid is near its magnetic ordering temperature. Thus, the materials considered for magnetic refrigeration devices should be magnetic materials with a magnetic or magnetostructural phase transition temperature near the temperature region of interest. For refrigerators that could be used in the home, this temperature is room temperature. In the last decade, first commercial prototypes have been developed as the one made by Cooltech Applications in 2016. However, thermal and magnetic hysteresis problems remain to be solved for first-order phase transition materials that exhibit the giant magnetocaloric effect (GMCE). Gadolinium and its alloys undergo second-order phase transitions that have no magnetic or thermal hysteresis. However, the use of rare earth elements makes these materials very expensive. Ni2Mn-X (X = Ga, Co, In, Al, Sb) Heusler alloys are also promising candidates for magnetic cooling applications because they have Curie temperatures near room temperature and, depending on composition, can have martensitic phase transformations near room temperature. From the theoretical point of view, modelling of GMCE is quite challenging since it involves the finite temperature dynamics of both lattice and spins. Within current proposal we intend to combine novel advanced computational methods to simulate and design promising Rare-Earth-free alloys with GMCE. In particular, we aim to study Mn-based materials where GMCE is due to the magnetic transition temperature (second-order transition) like Mn5Ge3 or magnetostructural coupling transition temperature (first-order transition) like MnAs.

 

Primary Investigator: Victor Emile Phillippe Claerbout
Project: Modelling Transition Metal Dichalcogenide Bilayer Heterostructures (MoTion)
Allocation: 2387000 core hours at first period
Abstract: Transition-metal dichalcogenides (TMDs) can be denoted as MX2, where M is a transition metal which is sandwiched between two planes of chalcogen X atoms to form an MX2 monolayer. The MX2 monolayers are held together by van der Waals (vdW) forces to form the three-dimensional structure. Although bulk TMDs were known for decades, studies on two-dimensional forms started only recently, showing very different properties than their bulk counterparts, such as the nature and the value of the band gaps and the excitonic properties. Two dimensional TMDs can be metallic, half-metallic or semiconducting depending on the chalcogen atom and the geometry. By stacking together monolayers of dissimilar TMDs, one can obtain TMD heterostructures with various properties. In this project, we are going to investigate the properties of TMD bilayer heterostructures (TMDbh) both with small and large lattice mismatch between the monolayers. We have four main goals: 1) to obtain classical molecular dynamics potentials that are non-existent in the literature thus beneficial to all the scientific community dedicated to the study of these materials, 2) to determine which kind of structure has the lowest friction by exploring the effect of the lattice mismatch, twist angle, transition metal atom and geometry, 3) to tune the band structure (band alignment, band gap and shape, charge transfer) to use them for energy harvesting or the production of devices such as sensors, transistors and lasers among others, and 4) to make this project a first step for a systematic investigation of mechanical and electronic properties of all possible TMDbh.

 

Primary Investigator: Petr Slavicek
Project: Accurate Computational Spectroscopy with Machine Learning
Allocation: 479000 core hours at first period
Abstract: The project aims at incorporating machine learning techniques to electronic spectra modelling in various energy domains, including time-resolved spectroscopies in order to provide quantitative spectroscopic data at an affordable computational price. Our goal is to accurately model all spectral characteristics (peak positions, shapes, widths and absolute intensities) at quantitative level so that the calculations could navigate the experiment. We will use various approaches to spectra modelling with a particular emphasis on the nuclear ensemble method and methods based on phase averaging of semiclassical trajectories. Machine learning and other statistical techniques allow us to increase the efficiency of the modelling process and, therefore, go beyond the standard level of accuracy. We will also investigate the role of both systematic and random errors which we see as currently underestimated in the field of computational chemistry.

 

Primary Investigator: Tomas Blejchar
Project: CFD simulation of flow and heat transfer in heat exchanger
Allocation: 60000 core hours
Abstract: Project is focused on optimization of hot water boiler. The hot water boiler will be equipped with heating resistive elements. The heating resistive elements can be used for water heating when surplus electricity is in the grid. Excessive electricity power is stored as a heat in hot water and the heat can be released when the consumption of electricity is high. The electric boiler in the basic design is designed to work in a stand-alone mode, but due to the used resistance heating elements it can be advantageously used also as a part of a cogeneration source with a steam turbine. The hot water produced in the boiler is taken to the district heating system, where it is used for heat supply.

 

Primary Investigator: Michal Novotny
Project: High accuracy calculation of absorption spectra of small mercury clusters
Allocation: 120000 core hours
Abstract: Mercury and its small molecular clusters are of high interest to the fundamental understanding of chemical bonding. An ab-initio approach is required to provide accurate data of its electronic structure, be it in the ground state or excited states. High accuracy methods such as CCSD(T) (coupled clusters with singles doubles and iterative triples) and EOM-CCSD (equation of motion coupled clusters) are applicable only to the smallest sizes of such clusters (2-5 atoms) and therefore a cheaper yet still accurate method needs to found to properly interpret experimental data as well as provide insight into the metallic transition of such clusters. Here we propose a quantum mechanical study to benchmark an appropriate DFT method as well as provide accurate absorption spectra of small mercury clusters.

 

Primary Investigator: Martin Mrovec
Project: Global Optimization Methods on Grassmann Manifolds for Electronic Structure Calculations based on the Hartree-Fock and the Generalized Kohn-Sham Theory
Allocation: 223000 core hours
Abstract: Quantum Chemistry calculations have a broad area of applications. For example, they are of a great importance in the pharmaceutical research or in the material engineering. However, they belong to the most time-consuming tasks solved on large supercomputers. One of the tasks is a searching of minimal (Ground State) energy of a system of electrons and nuclei. The solution is searched usually by iterative methods where an initial guess is chosen and then a given procedure is repeatedly performed until the convergence is reached. There are known molecular systems where the most commonly used methods fail to converge or they find a local minimum which does not represent the Ground State. Our intention is to develop alternative methods with a higher reliability. We are currently interested in minimization methods that are inspired by processes observed in the nature. The algorithms simulate a collective behavior of a swarm of animals searching a food. The value of the energy can be understood as a quality of food at a given point – lower energy corresponds to a better food quality. The points in a studied space represent individual animals. The purpose of the swarm is to find the point where the energy is globally minimal. As an advantage of swarm methods we should emphasize the ability of avoiding areas where the energy is minimal locally but not globally which is a common weakness of standard local optimization methods.

 

Primary Investigator: Miroslav Krůs
Project: Enhancing electron beam quality in laser wakefield accelerators by tailoring the injection phase space volume
Allocation: 1221000 core hours
Abstract: Plasma-wave-based electron accelerators, driven either by an ultrashort laser pulse or by particle beams, represent a promising concept of the next generation accelerators as it was demonstrated within last few decades [1]. In experiments, similar beam parameters (e.g. charge, emittance, dura-tion) as in conventional radiofrequency accelerators have been attained [2,3,4]. However, in plasma-based accelerators, these parameters have not been reached simultaneously yet. One of the fundamental particle beam parameters determining the overall beam quality is represented by the beam emittance, both transversal and longitudinal, related to beam focusability and beam energy spread, respectively. The beam emittance is influenced by the beam injection into the accelerating plasma structure at the beginning of the acceleration, as well as the evolution of the plasma wave during the acceleration process. The electron beam injection into the plasma-wave-based accelerator therefore represents a crucial issue of the entire acceleration process. The presented project aims at the generation of low-emittance electron beams. Low emittance can be reached via injection space and phase space manipulation, e.g. by the interaction of several overlapped laser pulses. The re-search will be carried out by particle-in-cell simulations for standard parameters feasible with current sub-100 TW laser systems. This approach enables better understanding of the acceleration process and optimizing the design of future plasma-based accelerators.

 

Primary Investigator: Jan Geletic
Project: Practical implementation of PALM-4U in urban planning (case study of Hradebni korzo)
Allocation: 852000 core hours
Abstract: The newly developed urban climate model PALM-4U (www.palm4u.org) allows to perform detailed simulations of conditions in urban areas, mainly with respect to phenomena of urban heating island and air quality. We have significantly contributed to the model development and we are using it for testing the efficiency of urban climate adaptation measures. Local municipalities as well as some departments of the Czech Government (esp. Prague Institute of Planning and Development) are interested in results of this modelling. The main objective of the project is to assess the impact of the planned adaptation measures in the area of the Hradebni korzo. The planned measures will focus on the implementation of blue and green infrastructure at street level. The impact of individual measures will be assessed at the end of the project. The project will focus on the development of practical cooperation between the professional and application spheres.

 

Primary Investigator: Wenda Zhang
Project: Spectral and polarimetric properties of corona in Active Galactic Nuclei
Allocation: 695000 core hours
Abstract: Black holes are the densest objects in the Universe that, according to Einstein’s General Relativity, induce so strong gravity that they can even distort the space-time itself. In the very centre of every galaxy there resides a supermassive black hole that can be as heavy as million or even billion Suns put together. Some of these black holes are very active, meaning that they are “swallowing” material from their surroundings, and produce extremely bright and variable radiation, even in the X-ray band. They are called Active Galactic Nuclei (AGN). The high energy X-ray photons in these objects are emitted by a “corona” – an extremely hot gas heated to more than billion degrees. This X-ray corona is located in the close vicinity of the central black hole, thus experiencing ultra-strong gravitational field. The properties of the corona, especially its shape, size and location are still unknown. We propose to utilize IT4I facilities to compute theoretical energy and polarization spectra for different coronal parameters using a state of the art numerical code MONK developed by our group. By comparing observations with these spectra, we will be able to put constraints on the geometry of corona and gain a better understanding of the physical processes in AGN. Our results will be stored as tables in a standard format to be used by an X-ray astronomical AGN community with data observed with past and current X-ray spectral missions as well as future X-ray polarimetric missions.

 

Primary Investigator: Eren Yuncu
Project: Extensive Genetic Analysis of Human Populations in Papua New Guinea
Allocation: 319000 core hours
Abstract: Papua New Guinea harbors great cultural and linguistic diversity and went through an independent Neolithization process. A previous study showed a sharp genetic differentiation between Papuan lowlanders and no non-Papuan admixture in highlander groups which also went through major population growth within last 10 thousand years. This study suggest Neolithization process re-shaped genetic diversity and spread by movement of people, similar to the Neolithization process in Eurasia and Africa but high level of genetic differentiation shows genetic, cultural and linguistic diversity is preserved during Neolithization, unlike Eurasia and Africa. In this project we will analyze admixture events that shaped present day Papuan populations by using qpGraph method and create a complex model showing admixture events between different language families within lowlands and highlands, in order to understand Neolithization process and history of Papua New Guinea in detail.

 

Primary Investigator: Jan Martinovic
Project: Support of Open Call of Lexis project
Allocation: 200000 core hours at first period
Abstract: LEXIS (Large-scale EXecution for Industry & Society) project will build an advanced engineering platform at the confluence of HPC, Cloud and Big Data which will leverage large-scale geographically-distributed resources from existing HPC infrastructure, employ Big Data analytics solutions and augment them with Cloud services. Driven by the requirements of the pilots, the LEXIS platform will build on best of breed data management solutions (EUDAT) and advanced, distributed orchestration solutions (TOSCA), augmenting them with new efficient hardware capabilities in the form of Data Nodes and federation, usage monitoring and accounting/billing supports to realize an innovative solution. The consortium will develop a demonstrator with a significant Open Source dimension including validation, test and documentation. It will be validated in the pilots – in the industrial and scientific sectors (Aeronautics, Earthquake and Tsunami, Weather and Climate). One of the important objective of the LEXIS project is to create Open Calls mainly to key industrial sectors (e.g. healthcare, manufacturing, energy). The task will include an evaluation of the likely impact at both the initial receipt of applications, along with ongoing monitoring and support of the participants during the life of the call duration. Our plan is to support more than five application experiments which will be selected within LEXIS project Open Call.

 

Primary Investigator: Michael Komm
Project: Particle-in-cell simulations of combined thermionic and secondary electron emission
Allocation: 479000 core hours
Abstract: One of the outstanding issues on the way towards power harnessing from nuclear fusion reactions is the problem of power exhaust – how to effectively remove the heat delivered by hot plasma to the plasma-facing components (PFCs) of the reactor. The interaction of plasma particles with solid surface of the PFCs is complex, especially in case of tungsten surface at temperatures close to the melting point, where thermionic emission occurs and where also secondary emission and electron back-scattering can become significant. The objective of our project is to study such interaction by means of particle-in-cell modelling in order to predict he behavior of the real PFCs. Application towards the interpretation of Langmuir probes are also expected.

 

Primary Investigator: Martin Matys
Project: Laser-driven ion acceleration using structured targets
Allocation: 559000 core hours
Abstract: Laser-plasma ion accelerators are currently receiving particular scientific attention as promising source of accelerated charged particles, since they are able to generate much stronger electric fields in comparison with conventional accelerators and can possibly replace them in future in several impressive applications, including proton therapy for the treatment of the cancer cells, production of PET (positron emission tomography) medical isotopes, generation of ultrashort neutron pulses, etc. Currently, laser-driven ion acceleration still needs to face several chalenges, like further improvement of produced particle beam quality and properties. Therefore, novel scheme for ion acceleration is proposed in this project. Interaction of high-intensity laser pulse with thin overdense double layer targets with initial corrugation on the interface, results into controlled rupturing of the foil. The remaining bunches are then accelerated as whole well-collimated structures, exhibiting monoenergetic behavior. Results from our demanding 2D and 3D simulations will also be visualized in 3D virtual reality web application to understand the whole picture of multidimensional effects and used for promotion of laser-plasma physics to the general public.

 

Primary Investigator: David Barina
Project: Convergence Verification of Collatz Problem
Allocation: 4215000 core hours
Abstract: One of the most famous problems in mathematics that remains unsolved is the Collatz conjecture, which asserts that, for arbitrary positive integer n, a sequence defined by repeatedly applying the function f(n) = 3n+1 if n is odd, or f(n) = n/2 if n is even will always converge to the cycle passing through the number 1. The terms of such sequence typically rise and fall repeatedly, oscillate wildly, and grow at a dizzying pace. The conjecture has never been proven. There are however experimental evidence and heuristic arguments that support it. As of 2019, the conjecture has been checked by computer for all starting values up to 10^20 [Hercher2018]. Our project aims to extend the computational records to higher values, and possibly to find some interesting results (numbers with extraordinary expansion factors, climbing to extremely high values, an iteration length that is strongly outside the expected distribution, a counterexample, etc.)

 

Primary Investigator: Jan Vicha
Project: Development of fully-relativistic and exact-two component relativistic density functional approaches for calculations of X-ray absorption spectra.
Allocation: 573000 core hours
Abstract: X-ray absorption spectroscopy (XAS) can provide important information about electronic structure of transition metal complexes. Nowadays, the assignment of XAS spectra relies on assistance of theoretical methods such as Time Dependent Density Functional Theory (TDDFT), which is however often neglecting the role of spin-orbit (SO) relativistic effects essential for understanding to the XAS spectra of heavier elements (4th-7th period) and particularly those near L- and M-edges that arise from core-ionized SO-split states. Since the computational cost of the conventional eigenvalue TDDFT increases with the number of eigenvalues, its application in high-density and high-frequency X-ray spectral regions is computationally expensive. Recently, we have reported a first relativistic four-component implementation of damped-response TDDFT (DR-TDDFT) for closed-shell systems, that is capable of a direct consignment of XAS spectral functions in user-selected frequency windows. Here, we aim for further broadening of the DR-TDDFT approach towards open-shell systems using relativistic two-component X2C Hamiltonian. In addition, an extensive benchmark study of XAS near L- and M-edges is also proposed for a wide variety of heavy-element complexes across the periodic table.

 

Primary Investigator: Jan Psikal
Project: Studies of laser-driven acceleration of charged particles with particle-in-cell code SMILEI
Allocation: 266000 core hours
Abstract: Since the plasma provides much stronger electric fields compared with conventional particle accelerators (more than four orders of magnitude), acceleration of charged particles from plasmas produced by intense laser pulses is intensively studied in last decades. With the continuous development of laser technology, laser facilities delivering femtosecond pulses (with pulse duration in tens of femtoseconds) of ultra-high peak power of several petawatts (PWs) have been constructed. These laser installations should enable to accelerate ions to energies about several hundreds of megaelectronvolt (MeV) per nucleon and electrons to energies exceeding a few GeVs, suitable for many applications. The main laser pulse interaction with almost instantaneously ionized targets occurs during several tens of femtoseconds and experimental measurements cannot well resolve all processes during such short time interval. Thus, numerical simulations are indispensable tool for this scientific research. However, such simulations in real 3D geometry, which enables to assess important multidimensional effects, are very demanding on computational resources. To investigate acceleration regimes in detail, we plan to use particle tracking in our multidimensional simulations.

 

Press Release: The Digital Innovation Hub Ostrava is being set up
The Digital Innovation Hub Ostrava is being set up
19th Open Access Grant Competition
19th Open Access Grant Competition
Invitation to the course Energy Efficiency in HPC (29-30/01/2020)
When: Wednesday 29 January 2020 9.00am – Thursday 30 January 2020, 3.30pm Where: campus VŠB-TUO […]
IT4Innovations Newsletter Q3/2019
IT4Innovations Newsletter Q3/2019
Press Release: 2nd Project Face to Face Meeting LINKS Foundation in Turin
2nd Project Face to Face Meeting LINKS Foundation in Turin
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