Project: The effect of lattice defects on structure and technologically important properties of ferromagnetic nickel
Allocation: 6298000 core hours
Abstract: Our modern society based on utilisation of advanced materials requires the development of new materials. Nevertheless, their properties are significantly influenced by various crystal defects such as impurities, vacancies and grain boundaries. The proposed project is aimed to the understanding how these defects can influence the stability of material and its magnetic properties, therefore the fcc Ni was chosen as the model system. We also intend to clarify the relations between the above mentioned defects and their stability. Unfortunately, these relations very often include aspects that are experimentally inaccessible. Fortunately, they can be studied by means of theoretical approaches such as computational modelling, as planned in this project.
Primary Investigator: Vladimír Lukeš
Project: Numerical modelling of scattered acoustic fields in waveguides and porous structures
Allocation: 250000 core hours
Abstract: The noise and vibration reduction belong to important issues in design of structures used in the automotive industry or civil engineering. The engine silencer used to reduce the noise emitted by the exhaust gas presents an important and well-known example. However, there are many similar structures which can influence the acoustic wave propagation. Usually they involve porous or perforated plates and panels, such that they are permeable for the gas flow. The straightforward approach to modelling the acoustic wave propagation through vibrating perforated plates consists in solving directly the vibroacoustic problem with a 3D elastic structure describing the plate. However, its numerical treatment using the finite element method can lead to an intractable problem because of the prohibitive number of DOFs corresponding to the geometric complexity of the perforated structure. Therefore, it is reasonable to replace the elastic plate by an interface on which coupling transmission conditions are prescribed. In this project we propose to study numerical features of the solution to such problems obtained alternatively using the finite and boundary element methods in tight cooperation with the BEM4I developers at IT4Innovations.
Primary Investigator: Michal Podhoranyi
Allocation: 300000 core hours
Abstract: During the past decade, one of the main topics in reactive transport modelling has been the ongoing global search for strategies of safe nuclear waste disposal (Parhurst and Wissmeier 2015, Cochepin et al. 2008, Montarnal et al. 2007). Reactive transport modelling (Fig.1) can provide crucial information about the evolution of contaminant plumes over long time scales, and information about near-field processes, which are used to improve safety in the design of confining structures and containers (Parhurst and Wissmeier 2015). Globally, there are two commonly accepted disposal options – near surface disposal and deep geological disposal (WNA 2017). Near-surface disposal at ground level, or in caverns below ground level (at depths of tens meters) is implemented in many countries including the Czech Republic. The aim of the project is to improve the possibilities of a potential risk analysis of environmental contamination due to the long-term radioactive species spread around a deep radioactive waste repository. This aim will be made by integrating HPC infrastructure into the process of the reactive transport modelling. The solution is complicated by a low accuracy of known rock medium parameters values in large depths and in far future. The sensitivity analysis using numerical simulation computations is then very computationally consuming. Also, the individual reaction-transport simulations themselves are computationally consuming and their parallelization and using of HPC (High-Performance Computing) allow performing of the simulations in real size and available time.
Primary Investigator: Michal Krumnikl
Project: Fiji Bioimage Informatics on HPC – „Path to Exascale“
Allocation: 400000 core hours
Abstract: “Bioimage Informatics on HPC” allows IT4Innovations to be involved in research on a completely new topical area of big biological image data processing on HPC. This specific research is focused on parallelization of key steps in lightsheet microscopy data processing as well as analysis of big data generated from other microscopic modalities. Particularly, multi-dimensional microscopy acquisitions present one of the main primary data sources in modern biological sciences and deployment of HPC in these areas is a necessary condition for making biologically meaningful conclusions. This project is a continuation of the previous OPEN-12-20 call, solving particular VP3 subtasks of the Path to Exascale project. In the previous period, SPIM Workflow Manager was developed and published under Apache License. This project aims at further development and dissemination of HPC-aware plugins for the Fiji community.
Primary Investigator: Petr Sulc
Project: Numerical study of dynamics of 3D FE blade cascade model with inter-blade dry-friction contacts – II. phase
Allocation: 200000 core hours
Abstract: This proposed project is the second phase of the last project Numerical study of dynamics of 3D FE blade cascade model with inter-blade dry-friction contacts solved in 2018. In the first phase of the solution, valuable results were obtained on the dynamic behavior of turbine blade with dry-friction couplings in a bundle of triple blades. It enabled to make a dynamical study of the damping and stiffening effects of these mechanical systems due to dry friction contacts.
Primary Investigator: David Wagenknecht
Project: Electrical transport in non-collinear magnetic structures from the first principles
Allocation: 2535000 core hours
Abstract: Electronic devices, that are essential for modern computers and gadgets, are based on a manipulation with transport of electric charge carries, i.e., electrons and holes (an absence of electrons). Thus, in electronics, a binary logic based on electric current level [electric current is detected (true) or not detected (false)] is widely used. In contrary, spintronics instead focuses on another electron’s attribute – spin – an internal degree of freedom having two possible values, usually denoted as “up” and ”down”. Therefore, in spintronics, logic operations may be based on a distinguishability of the up and down states. Since spin is an essence of magnetism, spintronics opens new possibilities for applications of magnetic materials in computer design and data processing. One of the most famous example are reading heads of hard-disk drives, where the giant magnetoresistance led to a huge increase in the storage capacity during 1990s (from tens to hundreds of GB). In the proposed project, we will investigate the influence of non-collinear magnetism in magnetic materials and layered magnetic structures on electronic transport. The ultimate goal of our research is to open new ways towards innovations in design of novel spintronic devices for advanced logic operations and data storage.
Primary Investigator: Jiri Klimes
Project: Accuracy and precision for extended systems
Allocation: 1120000 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 derivatives of 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: Stepan Sklenak
Project: Periodic DFT studies of zeolite-based catalysts
Allocation: 1019000 core hours
Abstract: Zeolite based catalysts are the most important industrial catalysts used mainly in petrochemistry (production of fuels, various hydrocarbons), and furthermore, for N2O decomposition and N2O selective catalytic reduction (SCR), for direct NO decomposition as well as for SCR of NOx using various reducing agents. In addition, zeolites are also employed as catalysts in synthesis of fine chemicals and as well as in the processing of biomass. Zeolites are also used as ion exchange agents (e.g. they replaced harmful phosphates in washing powder detergents). Zeolites are crystalline microporous aluminosilicates with a unique microporous nature, where the shape and size of a particular pore system exerts a steric influence on the reaction, controlling the access of reactants and products. Thus, zeolites are often said to act as shape-selective catalysts. Increasingly, attention has focused on fine-tuning the properties of zeolite catalysts in order to carry out very specific syntheses of high-value chemicals. Periodic DFT methods permit investigations of properties of zeolite-based catalysts which are needed for their fine-tuning. DFT calculations are complementary to experimental examinations and together they can provide more complex knowledge of the properties of the studied catalysts. We propose periodic DFT investigations of various properties of metal cation (Li+, Na+, Cs+, Fe2+, Co2+, and Cu2+) exchanged zeolites (e.g. ferrierite, ZSM-5, beta, mordenite, and TNU-9).
Primary Investigator: Mauricio Maldonado Dominguez
Project: Radical Catalysis by Biomimetic Polynuclear Transition-Metal Active Sites
Allocation: 571000 core hours
Abstract: Our first goal is to develop a methodology that accurately reproduces the available 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 the thermodynamic contributions (both the classical Bell-Evans Polanyi and a nonclassical component we recently proposed) to their reactivity, specifically the dependence of the rate constants with the free energy of reaction and asynchronicity factors for H-atom transfer between these complexes and model substrates. 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 and Fe4S4 containing proteins. The present project is predicted to significantly contribute to our understanding of the properties of Fe2S2 and Fe4S4-dependent radical enzymes and their selectivity, that would have a great potential to be translated into functional and stable bioinspired catalysts for the efficient production and derivatization of molecular targets.
Primary Investigator: Lubomir Rulisek
Project: Interactions of Macrocyclic Inhibitors with STING Protein – Novel Route to Treat Cancer and Chronic Hepatitis B
Allocation: 3119000 core hours
Abstract: Chronic Hepatitis B (CHB) is a major global health problem with treatment options limited to pegylated-interferon-alpha (PegIFN-α) or nucleos(t)ide analogues (NUC). While infection can be controlled with these antivirals, the development of efficient antiviral strategies to eliminate the virus and thus to cure infection remains a key unmet medical need. Here, we propose a computational and structural chemistry support for targeting of the pattern recognition receptor STING (stimulator of interferon genes) for treatment of CHB and cancer. STING has been shown to directly bind to a variety of different cyclic dinucleotides (CDNs) and induce transcription of the genes encoding type I IFNs and cytokines promoting intercellular host immune defence. A series of novel phospho(i)nate CDNs has been synthesized at IOCB with some of the compounds exhibiting nM activities which is very encouraging. To fine-tune their properties and explore fully the potential of these class of compounds, massive-scale computations are needed. The conformational sampling of the CDNs and other similar macrocycles will allow us to calculate ligand strain energy, one of the important components in the overall binding free energy. This may lead to further improvement of the compounds.
Primary Investigator: Michal Merta
Project: Development of parallel BEM-based solvers
Allocation: 350000 core hours
Abstract: One can choose from several numerical methods for modelling natural phenomena occurring in real world, let us mention, e.g., the finite element method or the finite volume method. The main features of the boundary element method (BEM) make it well suited for problems stated on unbounded domains (such as sound or electromagnetic wave scattering) or shape optimization problems. Within the previous projects, we have focused on optimization of BEM solvers for Haswell and Skylake microarchitecture and its acceleration using Intel Xeon Phi coprocessors which are installed at infrastructure of IT4Innovations National Supercomputing Center. The current project aims at their further optimization and at development of parallel solvers for time-dependent heat equation.
Primary Investigator: Fabien Jaulmes
Project: Computational modelling of ion orbits in tokamak plasmas
Allocation: 400000 core hours
Abstract: Nuclear fusion technology might enable us to generate energy without releasing large amounts of greenhouse gases into the atmosphere or leaving behind long lived radioactive waste. Among the approaches to fusion – tokamak (russian abrev.: ”toroidal chamber with magnetic coils”) seems to be the most promising one. The concept involves the use of large magnetic fields to confine plasma hot enough to sustain fusion within itself. Today, as a part of international project under the title ITER, a new tokamak is built in southern France with first plasma currently scheduled for December 2025. If successful, the device would be the first one of its kind to produce net energy. COMPASS is a small tokamak located in Prague, Czech Republic. It allows scientific investigation of various physics related to the operation of the future ITER. In particular, a new 80keV Neutral Beam Injection system is planned to be tested next year at Institute of Plasma Physics (IPP). The study and modelling of NBI-born particle behaviour is of great relevance and might impact future design of the system and its integration in COMPASS, as well as in the planned upgrade of the machine in 2022 (COMPASS-Upgrade).
Primary Investigator: Frantisek Gallovic
Project: Dynamic source inversion of the 2016 Mw6.5 Norcia earthquake
Allocation: 200000 core hours
Abstract: In 2016 three Mw>6 earthquakes associated with normal faulting struck Central Italy. The largest event of this sequence with Mw=6.5 happened close to the city of Norcia on October 30. According to the previous analyses, the characteristic property of this event is the rupture that reached the surface and a large slip on relatively small rupture area. In this project, we aim to interpret the inferred source properties in terms of earthquake physics, i.e. frictional processes with heterogeneous rheological parameters. We assume linear slip-weakening friction law, and thus we aim to infer the stress before and after the earthquake and the co-called critical slip distance. Building upon our previous applications to a community benchmark synthetic test and the 2016 Mw6.2 Amatrice earthquake, we will apply our highly efficient Bayesian dynamic inversion combining finite-difference forward dynamic solver and Parallel Tempering Monte Carlo algorithm. The resulting samples of the posterior probability density function provide us with estimates of the best fitting model and its uncertainty. Interpretation of the dynamic properties of the Norcia earthquake will help to understand earthquake physics of such surface-breaking events and its associated seismic hazard.
Primary Investigator: Petr Kovar
Project: Complementary graphs sharing cycle sounts
Allocation: 40000 core hours
Abstract: The problem to determine, whether two general graph are isomorphic, is known to be NP hard. Nonetheless, for specific classes there are faster algorithms. We attempt to disprove the correctness of one such algorithm for a specific class of highly symmetric graphs. At the same time we plan to construct an infinite class of highly symmetric graphs sharing the same cycle vector as a benchmark class.
Primary Investigator: Jan Hrusak
Project: Study of the creation of the long-chain nitrogen containing hydrocarbons in Titan’s upper atmosphere.
Allocation: 407000 core hours
Abstract: The inspiration for this project arose from one of the very successful Cassini-Huygens mission to Saturn´s moon Titan. One of the most surprising results of this endeavor was the existence of large negative ions in Titan’s upper atmosphere revealed by Cassini Plasma Electron Spectrometer (CPPS) is one of the important discoveries of the mission. It also led to the inclusion of negative ion processes into models of the ionospheric chemistry of Titan [1-4]. Small anionic species can act as intermediates in the formation of the large observed negative ions, which are most likely the precursors to aerosols observed at the lower altitudes. The project aims for the theoretical treatment of selected important reactions of negatively charged molecular ions that can play a fundamental role in the creation of long- chain nitrogen containing hydrocarbons in the upper atmosphere of Titan. We will focus on the reactions of C2N- and C4N- with acetylene. These processes have already been studied experimentally with the guided beam apparatus at the J. Heyrovský Institute and the proposed calculations are necessary to rationalize the obtained findings and to suggest production pathways for the observed products.
Primary Investigator: Sami Kereche
Project: At the source of super power: The S-layer
Allocation: 200000 core hours
Abstract: Bacteria are present on Earth since more than 3 billion years and account for a biomass that exceeds the one of all plants and animal. In Extreme habitats, which are characterized by very hard conditions (temperatures, pressure, pHs etc.), bacteria are also present. These so called extremophilic bacteria share a similar cell envelope architecture. The most external coat of this envelope faces with the environment and is called Surface layer (S-layer). S-layers are composed of one or more proteins repeated in a regular fashion surrounding the cell. Interestingly, sometimes these structures appear to be related to the pathogenicity of infective bacterial species and their presence is diffused in pathogenic specie. Despite the fact that S-layers are broadly spread among bacteria, their function is mysterious and unknown. With the long term aim to uncover the mysterious functions associated to S-layers, we will work on Deinococcus radiodurans, a polyextremophile, which has been listed as the world’s toughest bacterium. It can withstand 1.5 million rads thus ̴3 000 times more than a human can survive. The aim of this project is to understand the structural organization of the S-layer protein DR_2577 by computations of three-dimensional (3D) structures from datasets acquired by cryo-electron microscopy (cryo-EM). We will process newly acquired cryoEM datasets of DR_2577, and attempt to reach the hallmark of 6Å resolution.
Primary Investigator: Vladislav Pokorny
Project: Spin-orbit coupling in molecular junctions and semiconducting nanowires: a step towards molecular spintronics
Allocation: 350000 core hours
Abstract: Miniaturization of the electronic circuits used in digital devices and the ever-increasing density of data stored on media are some of the driving forces behind the current technological revolution. A promising strategy is to employ atoms and molecules as efficient building blocks, replacing transistors, resistors or memory elements by objects as small as single or few atoms. This effort lead to the emergence of a new interdisciplinary research fields of molecular electronics and, recently, molecular spintronics. The challenge for the scientific community is now to understand the interplay among the various quantum-mechanical and relativistic effects, which constitute the basic laws that govern electron transport through nanoscopic devices. Supercomputers are now a necessary tool for simulating the prospective molecular devices, understanding the available experimental results and predicting their behavior.
Primary Investigator: Jan Zemen
Project: Computer modeling of twinning stress in Ni-Mn-Ga system
Allocation: 2133000 core hours
Abstract: The goal of the proposed theoretical investigation is to advance the fundamental understanding of twin boundary motion in Ni-Mn-Ga magnetic shape memory alloy, which has a large application potential in actuators, sensors, energy harvesters, and magnetic refrigeration systems. The low twinning stress of this alloy in combination with large magnetic anisotropy is responsible for easy reorientation of martensitic twins. It results in macroscopic deformation in external magnetic field, which can reach up to 12 %. The twining stress can be estimated by employing first-principles calculations in combination with an extended Peierls-Nabarro (P-N) model. In particular we aim to reveal the effects of exact chemical composition including the effects of adding extra elements (Cu, Co, Fe, Zn). The project results will provide guidelines for design of new alloy compositions with a high application potential.
Primary Investigator: Petr Kovar
Project: Tournament scheduling
Allocation: 10000 core hours
Abstract: Scheduling of sport tournaments can be easily described using graph labellings. The requirements and restrictions put on the tournament are reflected in both the graph structure and the properties of the specific graph labellings. The typical question is “Can we find a scheduling of a tournament of n teams under certain restrictions?” And the typical follow-up question is “For which values of n can we do so?”. To answer the question general theoretical methods have to be developed – typically based on graph labellings. A general construction is often based on induction, while “small” cases have to be found by brute force. We develop the theoretical methods and we need to find the starting cases using a solid computational power.
Primary Investigator: Martin Zeleny
Project: Computer modeling of impurities in medium entropy alloys
Allocation: 2921000 core hours
Abstract: Unique properties have been reported on the literature for equimolar CoCrNi Medium-Entropy Alloy (MEA) with very significant strength-ductility-toughness combination due to its twinning-induced plasticity ability. Exceptional properties of CoCrNi MEA with single FCC solid solution microstructure can be further enhanced by interstitials alloying similarly to other industrial materials, which can result in stabilization of another phase, e.g. HCP. In the light of the following reasoning, the ab initio calculations of the influence of dissolved nitrogen or carbon on phase stability and properties of CoCrNi MEA will be performed. In particular, we are going to estimate stability of FCC and HCP phases with different ordering of interstitials as well as their mechanical properties represented by tensor of elastic constants. The project results will provide guidelines for design of new alloy compositions with a high application potential.
Primary Investigator: Stanislav Polzer
Project: Computational modelling of abdominal aortic aneurysms
Allocation: 60000 core hours
Abstract: Abdominal Aortic aneurysm (AAA) is a permanent dilatation of abdominal aorta. Its rupture is a life-threatening event. On the other hand the non-ruptured AAA does not bring any complication to patient in most cases. Therefore the effort is in operating only cases with AAA close to rupture. So far the maximum diameter criterion is used. However it is not very accurate since not all large AAAs rupture while some small does. Therefore new criterions have been searched for some twenty years now. One of them is based on a wall stress analysis on the AAA. This project aims at analyzing of several material models which are commonly used in wall stress calculations in order to reveal model robustness in predicting aneurysm rupture.
Primary Investigator: Petr Strakos
Project: Research and Development of Libraries and Tools in the INFRA Lab
Allocation: 1471000 core hours
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 in the single node performance of the ESPRESO library while in the development of the visualization tools, we will create the workflow for the scientific visualizations using open source Blender 2.8.
Primary Investigator: Vojtěch Horný
Project: Laser wakefield acceleration with a transverse injection pulse
Allocation: 736000 core hours
Abstract: Laser wakefield acceleration after the interaction of the ultraintense ultrashort laser pulse with a gaseous target is a very promising mechanism to accelerate electron beams to the relativistic energies. The main advantages over conventional radiofrequency accelerators are financial affordability, smaller source size and shorter beam duration. However, electron bunches generated by plasma accelerator are still not stable and their properties are not reproducible. Also, lower values of bunch emittance, which is a crucial property required for certain practical applications, have not been reached yet. This parameter depends only on the injection process of electrons into the accelerating field. On that account, a new scheme of optical electron injection into the proper phase of the plasma wave was suggested by our group recently. Its principle is the introduction of the second, orthogonally crossing weaker injection pulse. Nevertheless, this scheme demands further investigation, as the effect of mutual polarization of both pulses, remains unclear. The preliminary 2D simulations anticipate the non-monotonic dependence of bunch parameters on injection pulse polarization vector. Moreover, in some configurations, the generation of attosecond electron bunches is predicted. Such bunches could be used as a seed for the all-optical X-ray free electron laser, among other applications in the medical treatment and diagnostics, industry, public security or fundamental research. The set of 3D particle-in-cell simulations is required to confirm these conclusions.
Primary Investigator: Ales Podolnik
Project: Understanding of Probe Measurements at Tokamak COMPASS-U
Allocation: 400000 core hours
Abstract: The capabilities of nuclear fusion research in Czech Republic will be soon expanded when the state-of-the-art tokamak COMPASS-Upgrade will be put into operation. This device with high magnetic field will be a unique experiment worldwide. Aimed at research of the plasma in different confinement modes, this device will require thorough diagnostics. One of such diagnostics are Langmuir probes serving as an inspection tool for the edge plasma experiments. Although being developed in 1920s, they perform as most versatile instruments for determining important plasma parameters, such as electron temperature and density, which are necessary to calculate the incidental heat flux at plasma-facing components. This is crucial for operation of future devices, since it enables us to predict heat loads present in machines such as ITER, and with increasing importance, the demonstration fusion power plant, DEMO. This project aims at proper understanding and calibration of Langmuir probes undergoing design phase at IPP CAS, increasing their precision and reliability.
Primary Investigator: Styliani Skiadopoulou
Project: Magnetoelectricity in Ni-based Tellurates
Allocation: 1716000 core hours
Abstract: The celebrated era of Moore’s law in microelectronics, predicting the increase of the number of transistors on a single chip by decreasing their size, is coming to an end. Functional diversification (More than Moore) and new concepts in physics (Beyond Moore) aspire to extend the limitations that are imposed by merely scaling-down the electronic components. Multiferroics (MFs) are materials that can combine at least two primary ferroic properties: ferromagnetism, ferroelectricity and ferroelasticity. In the case of magnetoelectric (ME) MFs, coupling between ferroelectricity and ferromagnetism occurs. This interplay between dielectric and magnetic properties endows them with the utmost desiring multifunctionality, required to overcome the scaling-down barrier. A wide range of novel hybrid technological applications, such as sensing, photovoltaics, data storage, and spintronics, await material candidates with such multifunctionalities. The understanding of the underlying quantum-level microscopic mechanisms that lead to ME coupling is essential for the engineering of novel ME MFs, since the ones already existing in nature are very limited. A solid theoretical approach is essential for further insight in the fundamental physics hidden behind magnetoelectricity. On these grounds, we propose a combination of first principles calculations of electronic and magnetic structure and lattice dynamics calculations, to complementary experimental spectroscopic investigation, for a series of novel ME MF materials.
Primary Investigator: Jan Vicha
Project: X-ray absorption spectroscopy calculations using fully relativistic density functional theory.
Allocation: 400000 core hours
Abstract: The X-ray absorption spectroscopy (XAS) can provide important information about electronic structure of variety of compounds, from 4th row transition metal complexes to heaviest actinides. Some of these information, such as oxidation state of the central atom, orbital occupation in open-shell systems or the covalence of metal-ligand bond, are nearly impossible to determine using other non-destructive methods. Yet, their knowledge is a key for better understanding of the chemistry of the molecules in question. Nowadays, the assignment of XAS spectra in heavier elements rely on assistance of theoretical methods such as Time Dependent density functional theory (TDDFT). However, these calculations often neglect the role of spin-orbit relativistic effects, which are essential for description of heavy element complexes (particularly those of 6th and 7th period). Hence, while there is satisfactory agreement between theory and experiment for lighter elements (3d metals), prediction of XAS spectra of heavier elements remains highly challenging task. During this project, we aim to implement novel fully relativistic real-time TDDFT (RT-TDDFT) approach into the Relativistic Spectroscopy (ReSpect) code. In the second part, we will calculate 4c relativistic XAS spectra of K, L and M edges for variety of 4th to 7th period complexes and rigorously evaluate the role of spin-orbit interaction. This will be the first step in development of a new methodology for calculations of X-ray absorption spectra.
Primary Investigator: Yanjun Gu
Project: Simulations of collective absorption of laser-plasma interaction in the context of shock ignition in ICF
Allocation: 1231000 core hours
Abstract: One of the failure reasons of the recent National Ignition Campaign performed on the NIF in the US is an unexpected large impact of parametric instabilities (especially Stimulated Raman Scattering) in the gas filled hohlraum. Other alternative ignition approaches which has been proposed in the past (e.g. fast and shock ignition) have the advantage of being compatible with present-day laser technology. The shock ignition scheme is in particular interesting because it does not involve PW lasers and relativistic laser-plasma interaction. However, the parametric instabilities are not sufficiently understood in this context. Recent experimental campaigns on large laser facilities concentrate on this topic including the PALS laser in Prague. These results require theoretical description or model to be developed based on numerical simulations. Our previous project (OPEN-12-23) investigated the collective absorption of the laser in the sub-relativistic intensities. The mechanisms of different instabilities for hot electron generation become clear. Due to the limit of the simulations, the plane wave assumption is used. The aim of this project is to model the full laser speckle in order to include the effects of side scattering and provide a better understanding of laser absorption and hot electron flux generation. The results are expected to compare with the experimental data.
Primary Investigator: Filip Kostka
Project: Dynamic source inversion and Bayesian analysis of physical parameters controlling the source process of the 2017 Lesbos earthquake
Allocation: 200000 core hours
Abstract: Tectonic earthquakes are complex phenomena in both time and space due to the geometric and frictional heterogeneity of faults and the non-linearity of the physical laws governing the rupture process. Their detailed physical account is still missing. One of the ways of putting constraints on the rupture process is to invert the information obtained from seismograms, this is called a finite-extent source inversion. The inversion can be either kinematic or dynamic. In the kinematic approach, slip history along the fault is obtained directly, without assuming anything about the physical processes driving the rupture. In the dynamic approach, certain physical laws are assumed and physical parameters such as stress or frictional properties are obtained. These can be used to calculate the slip history but also permit interpretation of the earthquake properties in terms of earthquake physics. In this study we aim to investigate the source processes of an earthquake that occurred near the island of Lesbos, Greece, in June 2017, which had a magnitude of 6.3, resulted in one fatality and caused extensive damage on the southern part of the Island. To that end, we utilize a dynamic inversion technique formulated in a Bayesian framework, efficiently combining finite-difference forward dynamic solver and Parallel Tempering Monte Carlo algorithm, which samples the posterior probability density function. This way we not only retrieve the model parameters that provide the best fit with the observed seismograms, but also gain information about the uncertainty of the inverse solution and correlations between model parameters.
Primary Investigator: Ivan Kolos
Project: Numerical modeling of load of structures in quasi-static effect of wind
Allocation: 100000 core hours
Abstract: The project is focused on numerical modeling of flow around objects in the atmospheric boundary layer. This issue is complicated mainly due to the atmospheric turbulence, which require using advanced modelling techniques. The models based on a direct simulation of large vortices impose strict rules on the shape and density of the mesh, which leads to requirement of the high computational power.
Primary Investigator: Roman Diviš
Project: Innovative method for determining railway infrastructure capacity using nested simulations
Allocation: 350000 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: Jiri Brabec
Project: Deep learning for strongly correlated systems in quantum chemistry
Allocation: 778000 core hours
Abstract: It is known that the electronic structure problems quickly become unbearably difficult, as the electronic correlation effects play an important role. These strongly correlated (also called multireference) systems are almost everywhere as the essence of nature has multireference character (e.g. intermediates of chemical reactions, many electronic excited states, bond breaking, transition metal complexes, etc.). In this project, we develop machine learning algorithms mapping a structure to properties at the state-of-the-art level – multireference coupled cluster method and tailored coupled cluster (TCC) method corrected by density matrix renormalization group (DMRG). Simultaneously, we develop a machine learning algorithm predicting the most entangled pairs of orbitals, based on precomputed set of one-electron, mono and bicentric integrals. It could be seen as an automatic selection of the active space. We believe that the algorithm trained on small and medium-size systems could exploit learned information also for larger systems, for which is the selection of active space for CAS methods (like DMRG) difficult. Without a significant additional effort, we will also develop the algorithm mapping integrals to a property at DMRG level (energy, singlet-triplet gap energy).
Primary Investigator: Diego Lopez
Project: Interaction between nanodiamonds and organic molecules for the application in photovoltaics (INDOMAP)
Allocation: 400000 core hours
Abstract: The transformation of sunlight into electricity represents one of the major tasks that faces the scientists and engineers of the 21st century. This technology promises to provide clean, cheap and ubiquitous energy for powering our electronic devices. Nowadays, due to the dominance of crystalline silicon in the solar panel market, coupled with the fact that silicon was the first semiconductor material widely investigated for application in photovoltaics, most researchers have not broadened their focus beyond Si-based solar cells. However, this material is not without some disadvantages. One of them is the high energy required to fabricate the solar panel, which actually equates to a high percentage of the total energy that would be generated by the panel itself. Additionally, the performance of silicon solar cells drops in low-light conditions, which might be a big handicap in certain regions far from the equator. In order to overcome these drawbacks, organic photovoltaic (OPV) devices have been proposed, and many materials have been tested in order to achieve greater efficiencies. These devices are formed by an acceptor material placed close to a donor material, leading to the formation of hole/electron pairs. Nanodiamonds (ND), which can be described as fragments of diamonds, represent an unexplored kind of material in the field of photovoltaics that offer great promise. Compared with other materials (e.g. Si, TiO2), NDs provide great advantages for energy conversion, mainly because they are stable,8 non-toxic9,10, easy to dispose of, readily available and cheap.
Primary Investigator: Jiri Jaros
Project: Photoacoustic tomography of the breast executed on Nvidia DGX-2 and fat GPU nodes
Allocation: 400000 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 project 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 main goal is to adapt the PAT software to fat GPU nodes and an NVIDIA DGX-2 machine being deployed as a part of the small cluster by the IT4Innovations.
Primary Investigator: Marek Lampart
Project: Non-autonomous bouncing ball model with randomness
Allocation: 50000 core hours
Abstract: The main aim of the project is to analyze the dynamic properties of a mechanical system, with some type of randomness, consisting of a ball jumping between a movable baseplate and a fixed upper stop. The model movement is generated by the gravity force and oscillations of the baseplate I the vertical direction. As the main result, it is shown that the system exhibits a regular, irregular and chaotic pattern for a suitable choice of parameters.
Primary Investigator: Petr Kočí
Project: Development of new boundary conditions for multi-scale modeling of automotive exhaust gas aftertreatment
Allocation: 240000 core hours
Abstract: Current automotive exhaust gas aftertreatment systems consist of catalytic converters for abatement of gaseous pollutants and a filter trapping soot particles. So far only cars with Diesel engines have been equipped with the filter but the new emission regulations enforce the use of particulate filters also for gasoline engines. Both the catalyst and filter are cylindrical monoliths with a large number of parallel channels in a honeycomb arrangement. However, filter channels are alternately plugged at the inlet or outlet, forcing gas to flow through the porous wall to the adjacent channels so that soot is trapped. To make the exhaust system cheaper and more compact, the catalyst and the filter may be combined in a single device, a catalytic filter. Its end-use properties (pressure drop, conversion and filtration efficiency) are sensitive to distribution and structure of the catalytic coating on and/or in the filter wall. To accelerate the design of catalytic filters, it is necessary to understand the relation between the micro-structure and the whole device performance. This project is a part of the development of a reliable multi-scale CFD model for catalytic filters. In particular, we focus on information transfer between the macro-scale (channel) and micro-scale (porous wall with catalytic coating) models. Using a new boundary condition mapping the flow data from macro- to micro-scale simulation, we improve predictions of the flow patterns and filtration efficiency.
Primary Investigator: Libor Šachl
Project: Global ocean circulation model for a seamless coupling with other environmental models
Allocation: 200000 core hours
Abstract: The spherical coordinates are probably the most natural choice to represent dynamic processes on the sphere. Unfortunatelly, they suffer from the so-called pole problem. The meridians converge towards poles which affects the numerical stability and accuracy of numerical simulations. The ocean models solve the problem by using computational grids in which the North Pole is relocated to a continent(s). However, the other environmental models that operate over the continents such as atmospheric models can not use grids with relocated poles. Consequently, since our intension is to study oceans in a broader perspective, a more general framework in which all models are discretized on the same computational grid would be useful. Within this project, we would like to establish this framework in our ocean general circulation model LSOMG.
Primary Investigator: Petr Slavicek
Project: Benchmarking of new approaches for photodynamics in liquid phase
Allocation: 730000 core hours
Abstract: The project aims at quantitative simulations of hydrogen peroxide photodissociation and following geminate recombination of hydroxyl radicals in water. Hydrogen peroxide photodissociation is an important process from industrial perspective (wastewater treatment), in atmospheric chemistry (as a source of OH radicals) or in an astrochemical context (formation of new molecules). The main goal of the proposed project is testing and further improvement of computational techniques for photodynamical simulations in liquid phase recently developed in the Laboratory of theoretical photodynamics. In particular, we apply the methods recently developed for controlling photochemical reactivity by excitation wavelength in the liquid phase. Furthermore, we will extend the timespan of photodynamical simulations by connecting the non-adiabatic molecular dynamics with diffusion modelling.
Primary Investigator: Sergiu Arapan
Project: Calculations of magnetic exchange interactions and estimation of the Curie temperature of materials suitable for permanent magnets
Allocation: 1443000 core hours
Abstract: Permanent magnets (PMs) are an indispensable part of the modern technology. They are used as data and energy convertors in a wide range of applications: from electronic components and loudspeakers to electrical motors and generators. There is an increasing demand for efficient PMs in the automobile and energy production industries due to the current environmental crisis. Current high-performance PMs are totally dependent on scarce and expensive Rare-Earth (RE) materials like Nd, Sm and Dy, which have now become critical raw materials. This worrying situation makes the development of RE-free PMs an urgent priority, but also a great scientific and technological challenge. Our study aims to design a RE-free PM starting from a genetic algorithm search for new magnetic materials, selecting the phases with appropriate intrinsic magnetic properties (saturation magnetization, magneto-crystalline anisotropy and Curie temperature), and micromagnetic simulations of realistic systems. In the current study the objective is to estimate the Curie temperature of various predicted magnetic materials.
Primary Investigator: Martin Mrovec
Project: Optimization methods for solving the Kohn-Sham Equation
Allocation: 100000 core hours
Abstract: The Density Functional Theory (DFT) is one of approaches of solving problems of the Quantum Chemistry, more precisely the Electronic Structure Calculations. The problem is usually represented by the Kohn-Sham (KS) Equation which can be understood as a Non-linear Eigenvalue Problem (NEVP). In practice, the solution is searched within a finite dimensional space spanned by suitable basis functions. The NEVP has to be solved by an iteration of a Self-Consistent Field until the convergence is reached. The iterative process is usually stabilized using sophisticated iteration mixing methods such as the Direct Inverse of the Iterative Subspace (DIIS). However, as experiments shown, there exist situations where the DIIS approach fails, especially for nearly dissociated molecular systems. Although the DIIS methodology is still developing, it is reasonable to think about alternative approaches. One of those approaches is a direct constrained optimization of the energy of the system within the given basis. The optimization approach has been successfully tested within the Hartree-Fock (HF) Theory. We have already performed first experiments within DFT on simple molecular systems and low level approximations of the DFT energy functional and the results are promising. The main aim of the project is to perform a series of more accurate electronic structure calculations where the convergence of the optimization method will be tested on higher level DFT energy approximations.
Primary Investigator: Ricky Nencini
Project: Accurate binding of metalic ions to lipid membranes in CHARMM36 based force-field
Allocation: 1528000 core hours
Abstract: Biological systems are often studied using molecular dynamics simulations. The accuracy of these simulations depends on the quality of the models which are used to describe interactions between atoms and molecules in the system. However in classical empirical models, the description quantum effects, including electronic polarization, is missing, which leads to inaccurate description of systems with charged particles, such as ions, proteins, nucleic acids and lipid bilayers. We address this insufficiency by applying the ‘Electronic Continuum Correction’ (ECC) which accounts for the missing polarization effects by scaling of the partial atomic charges. Our goal is to implement the ECC approach for the phosphatidylcholine (PC) CHARMM36 lipid model to improve the ion-membrane interactions. CHARMM36 is one of the most widely used computer models for biological systems. We will modify the atomic partial charges according to the ECC approach so that the membrane behavior and interaction with ions agree with NMR and Raman spectroscopy experimental data. In particular, we will focus on calcium ions-membrane interaction which plays a crucial role in a variety of signaling pathways.
Primary Investigator: Martin Kuna
Project: Total visibility of landscape in the Czech Republic
Allocation: 400000 core hours
Abstract: In many fields of scientific research, landscape belongs among the key concepts. It is usually understood as an environment providing people with food, shelter and other products. In the humanities, however, other levels of landscape are emphasized, including its use in social interactions and/or symbolic communication. Archaeologists are convinced that properties of landscape were crucial for the development of the past societies and the relation between the landscape characteristics and the distribution of archaeological sites may explain some of the processes and events which the past societies went through. Visibility of the landscape relief has always had a significant impact on human activities. It is an important factor in the acquisition of raw materials, agriculture, movement, settlement location, social power, territorial claims and communication. The project seeks to evaluate the terrain relief of the CR by its visual properties. For each part of the territory (each cell of its digital elevation model) a value will be calculated corresponding to the percentage of the visible area within the given radius. For archaeology, this will help to understand the function of sites and settlement structures, e.g. prehistoric hillforts, burial monuments, medieval castles, etc. Both the methodology and the resulting model itself may be influential for other disciplines connected to landscape research.
Primary Investigator: Michael Owen
Project: Alzheimer’s Lipids II
Allocation: 1501000 core hours
Abstract: Neuronal membranes can enhance or prevent the formation of oligomers of the amyloid-β (Aβ) peptide, the neurotoxic species implicated in Alzheimer’s disease. Membrane gangliosides have an important role in brain development, regeneration, and in the progression of Alzheimer’s disease, however, the specific role of gangliosides in Ab oligomerisation remains unclear. We previously tested (in the 12th Open Access Call) the validity of various computational models, also known as force fields, in their ability to accurately represent the structural behaviour of gangliosides and the Ab peptide using all-atom molecular dynamics (MD) simulations. In addition to further investigating GM1, the interactions between Ab and GM2, GM3, GD1a, GD1b, GT1b must also be investigated. These simulations will characterise the interactions between Ab and the various gangliosides and determine how these interactions affect the structure of the Ab and mediate the conversion to the more oligomerisation prone, b-sheet conformation in Ab. This innovative research project has great potential for the development of new treatment strategies targeting Aβ toxicity and is supported by the South Moravian Project (SoMoPro) and Marie Skłodowska-Curie Actions.
Primary Investigator: Florian Belviso
Allocation: 1584000 core hours
Abstract: The energy dissipation due to friction in mechanical systems is estimated to reach a considerable rate of 20%. As such, most surfaces sliding on top of another experience friction-induced wear; this automatically calls for high performance lubricants. When classic liquid lubricants cannot be used, due to high pressure/temperature conditions or open geometries, the solution is found in the form of solid lubricants. Some have been known and used for decades, such as graphite pulverized inside moving machine parts, or Boron Nitrides used as additives in oils. They have been particularly successful in several demanding applications, such as aerospace or nuclear industries .The discovery of the low-friction behavior of graphene marked the beginning of a new chapter of research of novel solid lubricants. Yet, industrial implementation has still notbeen achieved. Transition metal dichalcogenides (TMDs), a family of lamellar materials, are currently the most extensively studied in this field. They have shown a wide range of applicability in the last decade. TMDs consist of hexagonally-ordered planes of M cations, inserted between two hexagonally-ordered planes of X anions (chalcogens). This X-M-X “sandwiches” are held together by weak van der Waals forces and yielding a lamellar structure.
Primary Investigator: Michal Kolar
Project: Nascent proteins under external mechanical force
Allocation: 738000 core hours
Abstract: Proteins are key biomolecules that play a role in almost all processes in cells. In all living organisms, proteins are synthesized by large biomolecular complexes called ribosomes, which makes the ribosomes one of the most essential cellular machines. The ribosome helps connecting amino acids one by one to form a protein. The chemical reaction happens deep inside the ribosome, so the newly created protein, i.e. nascent protein, leaves the ribosome through a tunnel. Proteins spend considerable time in the exit tunnel attached to the ribosomes. During that time, nascent proteins are subject of many events such as folding or chemical modification. We propose computer simulations which will study what happens with the protein in the tunnel before it exits the ribosome. Namely, we will pull the nascent protein out of the tunnel by a mechanical force and investigate how it interacts with the walls during its journey. Overall, the knowledge will help us understand how the ribosome works at atomic level.
Primary Investigator: Dominika Mašlárová
Project: Stabilization of electron bunches generated by laser wakefield acceleration
Allocation: 792000 core hours
Abstract: Laser wakefield acceleration is currently considered as one of the most promising mechanisms to potentially reduce size and cost of future electron accelerators. In this technique, plasma electrons are injected into a plasma wave (wakefield) dragged by an ultra-short, ultra-intense laser pulse in underdense plasmas. Such electrons gain relativistic energy within few millimeters, which is three orders of magnitude lower than by the contemporary technology. Quality and reproducibility of generated electron bunches are crucial from the viewpoint of practical applications in industry, medicine, and fundamental research. Parameters of the bunch significantly depend on the electron injection mechanism into the wakefield. However, several methods proposed recently show that manipulation with wakefield dynamics in later acceleration phases may also vastly improve bunch properties. In order to address this issue, the main aim of this project is to study the temporal evolution of the wakefield. This research will be carried out by means of particle-in-cell simulations for standard parameters feasible with current sub-100 TW laser systems, which ensures a fast introduction of this technology to applications. This approach improves understanding of laser wakefield accelerators tremendously and enables to develop and optimize the design of laser wakefield accelerators without repetitive expensive and time demanding experiments.
Primary Investigator: Petr Valenta
Project: Relativistic Mirrors in Laser-Plasma Interaction II
Allocation: 400000 core hours
Abstract: High-intensity laser pulses have a capability to accelerate electrons from a target to relativistic velocities, forming accelerated electron or electron-ion sheaths. Concept of an interaction of the accelerated sheath with electromagnetic wave is called Relativistic Mirror (RM). Within the scope of this project, we plan to investigate RM in three different forms: 1) Plasma shutter, an ultra-thin overdense foil which increases spatio-temporal contrast of intense laser beam by filtering a prepulse that accompanies the main pulse. This is crucial for mitigation of some unwanted phenomena (e.g. excessive preheating of the target, creation of a low density preplasma before the main pulse arrives); 2) Relativistic flying mirror (RFM), realized using wake waves driven by intense laser pulse in underdense plasmas and a counter-propagating pulse reflecting from these waves, leading to an unique tool for both, fundamental research and practical applications (e.g. a method to generate ultrahigh intense electromagnetic fields, high-energy photon radiation for imaging of biological samples). 3) New regimes of coherent RFM. Making use of various kinds of electron density spikes produced in interaction of intense laser with underdense plasma can help to explore and further understand novel regimes of laser-plasma interaction.
Primary Investigator: Ondrej Gutten
Project: Improving the database of metal-ligand complexes as models for metal-protein interactions
Allocation: 753000 core hours
Abstract: Transition metals are the wizards of biochemistry and are ubiquitous across species and functions they can provide. Their interactions with proteins – machinery of life – are crucial not only for understanding the details of the roles they already play – in enzymes found throughout all biochemistry – but also for roles they could play – in tools and catalysts tweaked to perform desired functions. The project aims at improving our understanding of metal-peptide interactions by enlarging a database of metal-ligand complexes as models for these interactions and identifying factors responsible for observed variations in metal-ion selectivity trends.
Primary Investigator: Jozef Hritz
Project: Computational characterization of selected proteins association free energies II.
Allocation: 1627000 core hours
Abstract: A number of critically important functions for cellular machinery rely on protein−protein recognition and association. Perturbation and disruption of the network of interactions underlying the formation of protein−protein complexes may lead to a number of pathologies. Binding affinities, which reflect the natural inclination of molecular entities to associate, are key thermodynamic quantities for understanding recognition and association phenomena, and possible dysfunctions thereof. The static information about interacting proteins at the atomic level is usually provided by contemporary experimental techniques like X-ray crystallography. However, the more important dynamic picture determining their temporal behavior, interaction pattern dynamics, and mechanism of protein complexes formation in cellular environment is inherently missing and by far more complicated to obtain experimentally. The in-depth knowledge of the dynamical processes through which protein complexes interact with each other or with cellular bioactive molecules is essential to get insight into their biological functions. The intrinsic dynamics of protein complexes can be studied either experimentally, which is non-trivial and highly expensive, or theoretically using state-of-the-art computer simulations. The main aim of the proposed project is to apply various advanced simulation techniques to reveal the structural and free energy changes underlying the protein-protein complex formation. Our project concerns mainly the molecular complexes of human tyrosine hydroxylase, one of key enzymes operative in human brain.
Primary Investigator: Luigi Cigarini
Project: Thermal effects induced by electron-phonon interactions in 2D nanostructured materials
Allocation: 300000 core hours
Abstract: In this project we plan to study the effects of temperature on the electronic structure of a particular class of materials, named 2D materials, in which atoms are disposed on single plans, like microscopical foils. This atomic structure creates unique properties which is possible to exploit in order to obtain innovative applications like new generation solar cells with increased efficiency or chemical sensors useful for industrial or medical applications. It is very important to understand, from a very theoretical point of view, how the electronic structure of these materials is influenced by temperature in order to improve, in future, the efficiency of these devices.
Primary Investigator: Marek Capek
Project: Simulation of clotting coupled with blood flow
Allocation: 400000 core hours
Abstract: The motivation for this work is the question whether mathematical modeling can be of direct help in medical decision when encountering certain situations in cardiovascular system. Among these situations of paramount importance are thrombus development because of atherosclerosis and unwanted coagulation on the surface of prosthetic devices such as artificial implants. Understanding of the blood coagulation process could therefore help either pharmaceutical industry with design of new anticoagulants or companies producing prosthetic devices with design of these devices. The proper design of the implants will hinder blood from coagulation on the artificial surfaces of these implants. Current anticoagulants seem namely to be effective mostly in the veins, not in areas of larger arteries. The profound insight into the process of blood coagulation could also help neurosurgeons to decide, whether the operation of an aneurysm is necessary and safe, as the blood coagulation process can set off even in the aneurysms, where specific blood flow conditions are present.
Primary Investigator: Zdeněk Grof
Project: Micro-scale simulation of pharmaceutical tablet disintegration
Allocation: 360000 core hours
Abstract: In pharmaceutical industry, the development of new products is a lengthy and costly process. Our aim is the development of mathematical modeling tools that will help to make this process more efficient by reducing the number of necessary experiments. We study the disintegration and dissolution of a directly compressed tablet that consists of an active pharmaceutical ingredient, filler and disintegrant components. The model enables to make “computational experiments” and predict the rate the active pharmaceutical ingredient is released from the tablet. The model will be validated by comparing its predictions with experiments in a dissolution cell. The effect of model and tablet formulation parameters on the dissolution rate will be also investigated. The positive impact of the proposed project will be a better understanding of the relation between material preparation parameters and the properties of resulting products such as their dissolution and disintegration behavior.
Primary Investigator: Tomas Brzobohaty
Project: ESPRESO FEM – module for structural mechanics
Allocation: 750000 core hours
Abstract: The latest technological advances in computing have brought a significant change in the concept of new product design, production control, or autonomous systems. In the last few years, we have been witnessing the considerable transition to virtual prototyping and gradual pressure on integrating large part of the industrial sector in the fourth industrial revolution, or Industry 4.0. The main objective of the ESPRESO library development is to create a robust open-source package applicable for a wide range of complex engineering simulations in areas such as mechanical engineering, civil engineering, biomechanics and energy industry. The free license for the developed package allows automatized simulation chains, based on HPC as a service, such as automatized systems for shape or topological optimization to be created on the top of the ESPRESO framework. For all the framework components, development of highly scalable methods allowing full utilization of the computational capacity of state-of-the-art supercomputers will be strictly enforced.
Primary Investigator: Dominik Legut
Project: High Speed Transfer Mechanism of Lithium Ions in Lithium Alloy for Lithium Batteries
Allocation: 10106000 core hours
Abstract: Nowadays the increasing demand for personal electronic devices and electric vehicles raises an urgent need for a development of high energy density batteries. Lithium metal-anode-based secondary batteries exhibit highest theoretical capacity (3860 mAh/g), low density (0.534g/cm) and the lowest electrochemical potential (-3.040 eV vs standard hydrogen electrode). Unfortunately, their commercialization still faces many challenges, the most critical issues is the lithium dendrite of the metal anode during the charging process, which not only consumes the electrolyte leading to the “dead Li”, but also face severe safety problems of short-circuit due to the cracks of a separator. Recently, lithium alloy materials (e.g. Sn-Li alloys) are used as the protective films and has been proved to achieve excellent electrochemical performance. However, as the lithium alloying with the Sn metal goes on, the composition of the Sn-Li alloy undergoes a change during batteries operation (e.g. LiSn, Li13Sn5, Li7Sn2 and so on). The mechanism of lithium alloy’s high transport properties may also undergo a big change due to the different diffuse behavior of lithium in the Sn-Li alloy with different composition. Here, we investigate the diffusion mechanism of lithium on the alloy through the climbing image-nudged elastic band methods. Through exploring lots of diffuse paths we obtain the optimal path for the different alloy phases. Then we try to establish a detail image on the diffusion mechanism in the alloy electrode which can be used to explore the new type alloy electrode with high-rate performance.
Primary Investigator: Miroslav Voznak
Project: Analysis of Causes and Prediction of PCRF events in 4G and 5G Networks
Allocation: 453000 core hours
Abstract: High reliability of telecommunication networks is ensured by sub-analyses performed for each technology or network unit. However, a number of technical problems in networks are caused by a combination of their various parts or technologies. Therefore, it is difficult to identify the causes of these problems using the existing approaches and methods. Moreover, identification of the root cause is also time-consuming. The objective of our research is to find the key data sources, gather information about technical problems in one place, and identify performance indicators, which can be used to increase reliability and prevent problems in the network.
Primary Investigator: Michal Novotný
Project: Structural and vibrational properties of boron nitride
Allocation: 300000 core hours
Abstract: Hexagonal boron nitride is an interesting material proposed as a candidate for new generation solar cells, chemical sensors and a wide range of very promising applications. In order to reach commercial applications it is still necessary to study this chemical system from a very theoretical point of view by performing computational simulations of the microscopical structure of it at an atomic level. Here we propose a quantum mechanical study to asses the accuracy of available methods and to provide accurate vibrational properties and geometrical structure data of this interesting material.
Primary Investigator: Aleš Slíva
Project: VECTOR 05-New Aeropacket
Allocation: 200000 core hours
Abstract: Formula Student VSB-TU Ostrava project, by which students of university of jointed together and develops student formula cars. Main aim of the project to get theoretical knowledge and use them in practice during designing of caring car. The competition is guaranteed maximum creativity in the building new monopost. Team have to show up new generation of vehicle every year which is competitive with cars of other universities around the world. To build the competitive car, is necessary to know airflow of formula student aeropacket (bodywork, rear and front wings, etc.) to be able to design a better aerodynamic car using new usually used aeropacket elements (Drag Reduction System etc.), to develop totally new car aeropacket.
Primary Investigator: Matus Dubecky
Project: Accuracy limits of quantum Monte Carlo in weak-interaction limit II.
Allocation: 3299000 core hours
Abstract: Stochastic methods like fixed-node diffusion Monte Carlo (FNDMC) play prominent role in electronic structure computations of complex quantum many-fermion systems for their native massive parallelism to thousands of cores, low-order polynomial CPU cost scaling, and, accurate description of quantum many-body effects. Electronic structure FNDMC has recently become a promising choice for benchmark treatment of large noncovalent systems (e.g., host-guest complexes with 100+ carbon atoms), overcoming the limits of more traditional approaches like coupled-cluster, if combined with 1-determinant trial wave functions. Such an approximation has nevertheless its limits, that are still poorly understood. The primary goal of this project is to contribute to our understanding of 1-determinant FNDMC limits in complex low-dimensional noncovalent systems. We plan extensive tests of our recently invented FNDMC approach for noncovalent systems that is expected to significantly lower bias in noncovalent energy differences by about an order of magnitude vs. its predecessors. Successful accomplishment of this project will contribute to deeper understanding of FNDMC limitations, development of 1-determinant FNDMC accuracy map, and, design of a new generation of “protocols” for reference FNDMC computations in large (noncovalent) systems.
Primary Investigator: Ekaterina Grakova
Project: Testing and Adaptation of Optimization Algorithms for Vehicle Routing Problem
Allocation: 200000 core hours
Abstract: One of the basic principles of operational research is search for optimal solution of the problem with the use of the mathematical modeling. For example, the optimization problems are to be find in transportation, economy, business, machinery, and in industry in general. Optimization problems are being solved by large number of optimization methods and algorithms which are mathematically complex and represent NP-hard problem. The complexity of the tasks is viewed from the point of computational sources. The domain of transportation tasks is complex. It is based on the theory of graphs, and theory of decision. General transportation tasks called Vehicle Routing Problem (VRP) are optimization tasks. These problems are solved by an optimization algorithm. The quality of results from the algorithms depends on the adjustment of the configuration parameters of the algorithm. In this project, we will use the HyperLoom platform for optimal parameters setting for the optimization of the VRP algorithms.
Primary Investigator: Jan Brandejs
Project: Relativistic externally corrected coupled clusters
Allocation: 400000 core hours
Abstract: Od svého představení ve fyzice pevné fáze se metoda DMRG ukázala jako účinná pro popis silně korelovaných systémů. V posledních letech byla také úspěšně aplikována v kvantové chemii, kde se stala jednou z nejlepších metod pro silně multikonfigurační systémy. Byla též implementována v rámci relativistického čtyřkomponentního formalismu pro molekuly obsahující těžké atomy. Nedostatečný popis dynamické korelace v této metodě však zůstává vážnou překážkou pro dosažení “chemické přesnosti”. Navrhujeme využít informace získané z relativistické DMRG metody k externí korekci relativistické jedno- a multireferenční metody spřažených klastrů za účelem popisu zbývající dynamické korelace. Naše nedávná práce ukázala, že toto schéma dává slibné výsledky v nerelativistickém režimu a chtěli bychom rozšířit jeho aplikovatelnost na těžké atomy vyvinutím jeho relativistické verze.
Primary Investigator: Ales Vitek
Project: Methane adsorption on graphene
Allocation: 426000 core hours
Abstract: This project is focused on computer study of adsorption of methane on graphene. Methane capture has gained a lot of interest because of two main reasons. First of all there is an increasing urgency to reduce greenhouse gas emissions, as was highlighted by the recently signed Paris agreement.1 While less methane is emitted than carbon dioxide, its higher energy-uptake makes it a big contributor to the greenhouse effect,2 and thus materials capable of filtering methane from exhaust gas mixtures are highly welcomed. On the other hand, methane is often suggested as a transition fuel until alternative energy sources become feasible for large-scale use. In our computations, we will use classical isobaric-isothermal Monte Carlo simulation to predict possibilities of adsorption of methane on graphene surface under different thermodynamics condition.
Primary Investigator: Ondřej Vlček
Project: Validation of the model PALM-4U against observation campaign in Prague-Dejvice
Allocation: 1026000 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 heat island and air quality. The new significantly enhanced version 6.0 of the model has been released recently and our team has strongly contributed to its development. The goal of the proposed project is to perform detailed validation of the model against the observation campaign done in Praha-Dejvice area. The campaign was accomplished within the project UrbiPragensi and took two fourteen-day episodes, one in summer and the other in winter of 2018 year. The measurements were conducted by CHMI specialists with three fully equipped stationary observation vehicles, one mobile vehicle, drone, infrared camera and other equipments. This allows to compare a wide range of the modelled and observed values. Being long-term PALM/PALM-4U developers and users, our team was invited to contribute to the special issue of GMD paper dedicated to the new version 6.0 of PALM-4U. The final goal of the proposed project is to publish results of our validation study in this GMD issue. We tightly collaborate on this work with our partners in the Germany project MOSAIK.
Primary Investigator: Jiří Kolář
Project: Investigation of fluidization regimes in Wurster fluid bed coater
Allocation: 2979000 core hours
Abstract: Wurster fluid bed device is widely used in pharmacy for coating of small pellets. Coating is used to apply layers onto the pellets with various functions. Some layers can consist of active pharmaceutical ingredient (API), or others can be used to protect the API from decomposing or prolong the drug effect. However, it is difficult to set the process operating parameters optimally to obtain product in pharmaceutical quality. One of the necessary conditions is to ensure optimal fluidization, which, in Wurster, means, that air flow drives enough pellets through the central part of the device, in a fountain-like manner. The number of particles lifted per second depends on many parameters (fluidization air flow rate, batch size or geometry of the device). Measurement of particle flow rate involves a modification of the device with detector and usage of special trackable particles, which is often not possible in pharmacy. But, these experiments can be used for validation of computer model, and validated model can be used for predictions of the optimal parameters. Problem is, that the model has to capture the fluid and particle dynamic. Thus, it is computationally expensive. In this project we would like to investigate possible solution. First conduct a full, large scale, computationally expensive simulation of Wurster device, validate this simulation and finally find a simplification of the model that can accurately estimate the results from the large scale model.
Primary Investigator: Pavel Jungwirth
Project: An ab initio molecular dynamic study of solvated electron in liquid ammonia
Allocation: 698000 core hours
Abstract: Adding alkali metals into liquid ammonia gives deep blue solution, which is caused by dissolving electrons from metal atoms to the ammonia. Such solution is for example used by organic chemists in Birch reduction. Hydrated electron has been already studied in detail theoretically and experimentally, however in liquid ammonia the electron is much more chemically stable and therefore ideal for studying of concentrated solutions. Ab initio molecular dynamics have been successfully used for studying similar systems in water1,2,3. In our study we use ab initio molecular dynamics to simulate behavior of single solvated electron in liquid ammonia to study its structure, dynamics and vertical detachment energy which should be directly comparable to experiment done by our colleagues. This should be first step for future studying of dielectrons and more concentrated solutions containing also counterions.
Primary Investigator: Jan Geletic
Project: Assessing the sensitivities of urban climate model PALM-4U
Allocation: 1616000 core hours
Abstract: UrbiPragensi is an EU funded project focused on urban meteorological and air quality modelling. Our team is engaged in the street level modelling in very fine resolution of 1-2 m. We utilize the model PALM-4U (www.palm4u.org), a newly developed urban climate model. 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 are interested in results of this modelling. In the proposed project we plan to perform sensitivities test in two phases. Firstly, the sensitivity of PALM-4U model itself to input data precision shall be done. These tests should answer the basic question “How precise data do we actually need to get proper results?” which can optimize the efforts at collecting of highly detailed input data. Secondly, the sensitivity of urban climate measures shall be assessed. This assessment will answer the “What difference does it make if we replace all asphalt surfaces by cobblestones?” kind of questions. This part helps the local authorities to focus on design and implementation of effective urban climate adaptation measures. As the significant contributors of the PALM-4U model, we were invited to publish in the special issue of GDM paper dedicated to the new version 6.0 of PALM-4U model. The results of this cooperative work with our colleagues from Germany and Finland are supposed to be published in a common paper.
Primary Investigator: Martin Matys
Project: Laser-driven acceleration of charged particles
Allocation: 764000 core hours
Abstract: Laser-plasma particle 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, radio isotope source or high-energy electron radiography and radiotherapy. Currently, laser-driven particle acceleration still needs to face several drawbacks, like further improvement of produced particle beam quality and properties. Therefore, two novel schemes for ion and electron acceleration are proposed in this project. 1.) Interaction of high-intensity laser pulse with thin overdense double layer targets with initial corrugation on the interface, resulting into controlled rupturing of the foil and acceleration of remaining clumps as whole well-collimated structures, exhibiting mono-energetic behavior. 2.) Interaction of high-intensity laser pulse with nitrogen gas targets for controlled production of ring-shaped electron beams, which is of great interest for ,e.g., compact collimator for proton bunches. 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.
Primary Investigator: Pavel Krc
Project: Validation and parallel benchmarking of the new Raditative Transfer Model version 3.0 for PALM-4U urban climate model
Allocation: 121680 core hours
Abstract: PALM  is an open-source large-eddy atmospheric model developed jointly by Leibniz University of Hanover and other European academic institutions. PALM-4U is a PALM-based urban climate model. The Institute of Computer Science (ICS) is the main author of the urban surface energy balance model (USM) and the multi-reflection radiative transfer model (RTM) for PALM-4U. The recently released PALM-4U version 6.0 contains an overall upgrade of the RTM (version 3.0), which increases the scope of modelled processes and enables modelling of larger areas by utilizing new algorithms with improved efficiency and scalability and reduced computational complexity. This new version will be described in an invited article in the upcoming special issue  of Geoscientific Model Development (GMD) dedicated solely to PALM and PALM-4U version 6.0. For this article, we need to run multiple simulations to both validate the model using different scenarios and to prove the enhanced scalability.
Primary Investigator: Antonio Portero
Project: ESPRESO FEM – Topology Optimization – Tests
Allocation: 2000 core hours
Abstract: The main goal of this project is development and testing of a complex and massively parallel finite element library for topological optimization problems from different engineering sectors such as mechanical engineering, civil engineering, and energetic. This library will be part of solver ESPRESO which contains several domain decomposition techniques and iterative solvers for the solution of large-scale problems. This allows users of the ESPRESO library to solve large problems with using topological optimization techniques, especially if user combine topological optimization techniques with large assembly discretized by billions of unknowns. Stable massively parallel solver with strong resistance to large coefficient jumps in the system matrices will be developed. Especially in the field of topological optimization methods, where coefficient jumps go to infinity, the efficient precondition techniques with a combination of stable iterative solvers is needed.
Primary Investigator: Jan Tinka
Project: Machine Learning in Biometrics and Biomedicine
Allocation: 934000 core hours
Abstract: The computational resources allocated to this project help the STRaDe research group of FIT VUTBR in research in the fields of biometrics, biomedicine and security, mainly the research of an automatic diabetic retinopathy detection system, and removal of influence of skin diseases on fingerprint recognition, both with the help of artificial neural networks. Retinopathy often refers to a retinal vascular disease, or a damage to the retina caused by abnormal blood flow. Diabetes patients have risk of different kinds of retinopathy. In 2002 diabetic retinopathy accounted for about 5% of world blindness (5 million blind) and is considered a priority eye disease by the World Health Organization. Hence, diabetic patients need to be under regular examination of eye specialists. However, the number of eye specialists in proportion to the number of patients is not satisfactory in either developing or developed countries. Using the cutting edge machine learning algorithms, we would like to develop an automatic detection system which would be easy to use for eye specialists as well as for patients. There is an ongoing research in computer-aided imaging tools in order to support the early detection and diagnosis of skin diseases. Our preliminary experimental results show that our work is a candidate to cope with typical use cases of medical doctors (dermatologists), criminal police (dactyloscopic experts) and biometrics (detection and computation of fingerprint image quality).
Primary Investigator: Zbyšek Posel
Project: NanO tools for small molecules SEnsing (NOSE)
Allocation: 100000 core hours
Abstract: Highly-sensitive, highly-selective chemical and biological sensors are desired in a broad range of applications in chemistry, biology, healthcare, medicine and environment protection. The development of efficient, cost-effective, versatile miniaturized sensors requires advanced technology coupled with fundamental knowledge in chemistry, biology, and material sciences. NOSE will provide a rational map to design sensitive and selective sensors based on gold nanoparticles specifically protected by self-assembled monolayers. Taking advantage of the versatility provided by the functionalization of the gold surface coupled with the ability of in-silico calculations to screen extensive libraries of functional ligands and target molecules, NOSE will make available to experimentalists in the field a virtual map to strategically support their design process, thanks to an enhanced molecular understanding of the principles driving the recognition and sensing phenomena involving these gold-based nanotools.
Primary Investigator: Judita Nagyová
Project: Dynamical properties of the Belousov-Zhabotinsky reaction models
Allocation: 50000 core hours
Abstract: The main aim of this project is to investigate the dynamics of different models of the Belousov – Zhabotinsky reaction and their comparison. This research is motivated by the complexity of this oscillating chemical system modeled by various systems of nonlinear ordinary differential equations, which can lead to different behavior. Simulations depending on the parameter are done resulting in phase portraits and bifurcations diagrams. Different dynamics are identified by the 0-1 test for chaos. As the main result, some models exhibit regular oscillatory behavior, while another exhibit regular, irregular and chaotic patterns for different choices of the parameter.
Primary Investigator: Pavel Janos
Project: Reaction mechanism of the FucT glycosyltransferase investigated by QM/MM dynamics.
Allocation: 660000 core hours
Abstract: Glycosylation, i.e., attachment of a glycan to a protein or peptide, is one of the most common post-translational modifications in living systems. This modification is involved in various biological processes, such as cell adhesion and recognition, immune response, stem cells migration and differentiation, or even cancer metastasis. Compared to protein biosynthesis, controlled by a DNA template, glycosylation is only determined by the cooperation of a diverse set of enzymes, glycosyltransferases, and glycoside hydrolases. These enzymes are therefore potential targets for directed drug development. Deep knowledge of the processes involved in glycosylation is a key prerequisite for the understanding of complex biological processes and medical applications. This project focuses on the study of the reaction mechanism of a glycosyltransferase with the use of state-of-the-art QM/MM molecular dynamics methods. Employing the quantum chemistry methods allows us to study the reaction mechanism and find the transition state with high precision.