Formation of planetary systemsCall: 13th Open Access Grant Competition
Researcher: Ondřej Chrenko
Can life be created on planets discovered outside our solar system (on exoplanets)? One of the key steps to find the answer to this question is understanding how exoplanets and their systems are formed. Possible scenarios for planetary system formation will be researched by Dr Ondřej Chrenko from Charles University in Prague.
In this research project, he collaborates with other Czech astronomers Doc. Miroslav Brož and Dr David Nesvorný (working in the USA) as well as with Lund Observatory in Sweden. Using computer simulations generated by the IT4Innovations supercomputers, this project aims at researching formation of planetary embryos and their dynamic development in protoplanetary disks of dense gas and dust rotating around young newly formed stars.
Accuracy and precision for molecular solids - IICall: 13th Open Access Grant Competition
Researcher: Jiří Klimeš
Dr Jiří Klimeš and his research team were awarded almost 2 million core hours for their development of materials simulation methods. His “Accuracy and precision for molecular solids – II project” applies quantum chemistry knowledge and approaches used for the description of solids, and received the prestigious start-up grant by European Research Council.
In nature as well as industry molecular solids (molecular crystals) play an important role, for example, methane hydrate, also called Burning Ice, a potentially very important source of energy, carbon dioxide ice caps on Mars, and pharmaceuticals in pills. Some molecular crystals have peculiar yet important properties. An interesting example is polymorphism, which is the ability of a molecule of the same compound to exist in different structures under same conditions, and as such it may be crucial for effectiveness of drugs in the body.
The objective of Dr Klimeš‘ project is to develop methods for reliable calculations of lattice energies in materials such as molecular crystals, which will help understand their properties. In this project, the Salomon supercomputer will be used for extracting the lattice energies of 13 selected molecular crystals.
Reaction Mechanisms of Dinuclear Open-Shell MetalloenzymesCall: 13th Open Access Grant Competition
Researcher: Lubomír Rulíšek
Metalloproteins play an important role in nature as catalysts of biochemical reactions which would not occur in the absence of metal ions. These reactions include nearly all oxidation-reduction processes, spin-forbidden processes, or processes, during which fission of very stable chemical bonds (C-H bonds, triple or double bonds in N2 or O2 molecules) occur. These fundamental biological processes include, for example, photosynthesis and cellular respiration.
To understand the function and structure of metalloproteins, not only experiments (e.g. x-ray crystallography, spectroscopy, and electro-chemical measurements) but also computational methods of theoretical chemistry, which can provide insights into the structure and energetic properties of metalloproteins, are important.
The project led by Dr Lubomír Rulíšek from the Czech Academy of Sciences focuses on the research of three selected metalloproteins with polynuclear cores (hence more metal ions at enzyme active sites), which play an important role not only in nature but also as potential industrial catalysts. His project was awarded over 3 million core hours. The allocated computational resources will be used for comparing experimental results with results obtained from quantum-mechanical modelling (using the Turbomole, MOLCAS, Amber, ComQum, and ORZ programs) with the objective to obtain a description of the catalytic cycles of the studied metalloenzymes. The research results have the potential to be used for biomimetic (inspired by nature) designs for catalytic cycles finding their potential area of application in the chemical industry.
Parallelized reaction-transport model of contamination spread in groundwaterCall: 13th Open Access Grant Competition
Researcher: Michal Podhorányi
Radioactive waste (RAW) emits hazardous radiation even for tens of thousands of years. Therefore, it must be isolated from the environment for a long time until it turns into stable substances. In the Czech Republic, RAW is safely stored in three radioactive waste repositories. However, the globally most efficient and safest way for the disposal of these substances is considered to be a deep repository in a stable geological environment with the absence of natural disaster hazards, such as earthquakes and floods. In the Czech Republic, the Czech Radioactive Waste Repository Authority is responsible for the deep repository project, which is to be commenced in 2065. The Authority is currently identifying potentially suitable locations, and the final location is supposed to be selected in 2025.
Our colleagues Michal Podhorányi and Lukáš Vojáček have been cooperating with Masaryk University in Brno and the DHI company in the project titled Parallelized reaction-transport model of contamination spread in groundwater (PaReTran) supported by the Technology Agency of the Czech Republic (TH02030840). The objective of the PaReTran project is to improve methods of analyses of the potential risk of environmental contamination due to long-term spread of radioactive substances from the deep radioactive waste repository through the surrounding rock formation. Since simulations generated using reaction-transport models (FEFLOW) are computationally intensive, their parallelization for deployment on HPC systems will allow their speed-up.
The computational resources awarded in our 13th Open Access Grant Competition will be used by the researchers for the TRM program development. They will focus on testing and evaluating the scalability of the program parallelization using the open-source PhreeqcRM library for simulations of geochemical processes.
PredictSNP-Onco: Structural Bioinformatics Analysis for Personalized Pediatric OncologyCall: 13th Open Access Grant Competition
Researcher: Gaspar Pinto a Jan Štourač
The research teams of Prof. Jiří Damborský and David Bednář from Masaryk University in Brno, Prof. Jaroslav Štěrba from University Hospital Brno - Children‘s Hospital, and Doc. Ondřej Slabý from CEITEC are involved in development of the new PredictSNP-Onco computational tool designated for personalized pediatric oncology. The new tool aims at making it faster for doctors to design the most suitable treatment for each individual patient, whose treatment so far based on standard methods has failed, or where the probability a of successful cure by standard methods is very low.
Cancer cell formation may be caused by one single mutation. Therefore, it is vitally important to assess such mutations as fast as possible, and consider treatment by all available drugs (inhibitors) which have been certified by the European Medicine Agency (EMA), the State Institute for Drug Control (SIDC), or by the U.S. Food and Drug Administration (FDA).
The computational resources of almost 800 thousand core hours will be used by the researchers to assess all possible protein mutations which lead to cancer development, and for analyses of inhibitors using the computational molecular docking method. Using information from four world-wide databases of mutations along with the computed results, the researchers will help design new possibilities for personalized/precise treatment for various types of cancer. Doctors thus obtain information in a shorter time, which enables them to speed up the design of appropriate an treatment for each individual patient in good time.
Interactions of drug molecules with mimics of human tear filmCall: 13th Open Access Grant Competition
Researcher: Lukasz Cwiklik
The tear film protects the cornea of the human eye against water evaporation. It nourishes the cornea surface, and it serves as the first line of protection against eye surface infection. It is produced by spreading tears all over the eye surface by a blink of an eye. Its thickness changes during eye blinking. Essentially, it consists of a lipid and a water layer. Disorders in the lipid layer lead to dry eye syndrome, which is treated with eye drops.
The researchers from the J. Heyrovský Institute of Physical Chemistry CAS are the only ones worldwide to study the effectiveness of eye drops at the molecular level. They are seeking ways to transport the required substances through the lipid layer and cooperate with pharmaceutical companies in tear film research.
Microscopic research of the lipid layer will be supplemented with computer simulations using the Salomon supercomputer by Lukasz Cwiklik. His project was awarded more than 1.5 million core hours in our 13th Open Access Grant Competition. The allocated computational resources will be used for research of selected lipophilic drugs, in particular the way the drugs permeate through the lipid layer to the water layer. Experimental (use of biomimetic chip, the construction of which was awarded the prestigious Neuron Impulse grant) and computational results of the research will enhance our knowledge of the interaction of drugs with the human tear film, and eventually the design of a new generation of eye drops.
Research centre for low-carbon energy technologiesCall: 13th Open Access Grant Competition
Researcher: Jan Boháček
The supercomputing project of Jan Boháček from Brno University of Technology (BUT), who is involved in the fiveyear long project Research centre for low-carbon energy technologies (CVNET, CZ.02.1.01/0.0/0.0/16_019/0000753) supported by the Research, Development and Education Operational Programme, was awarded almost 1 million core hours.
The Heat Transfer and Fluid Flow Laboratory at BUT has been involved in the development of modern polymeric heat exchangers with hollow fibres for 10 years so far. The advantage of using polymeric hollow fibres in heat exchangers is their flexibility, low costs, and chemical resistance. Polymeric heat exchangers are ideal, for example, for heating, air-conditioning, and low-potential residual heat applications.
The allocated computational resources will be used by the group of BUT researchers for development of polymeric heat exchangers, in particular for detailed heat transfer simulations. They will analyse different factors, which affect heat transfer in polymeric hollow microfibers (diameter, lengths, and fibre spacing).
Structural studies of human and animal virusesCall: 12th Open Access Grant Competition
Researcher: Pavel Plevka
The project of Dr. Pavel Plevka from CEITEC at Masaryk University was awarded 2,213,000 core hours for his research of picornaviruses, flaviviruses, and bacteriophages. Our supercomputers and the allocated computational resources will be used for processing and analysis of micro images created by state-of-the-art electron microscopes.
Picornaviruses cause not only common cold but also serious diseases such as encephalitis and respiratory inflammation. Scientists determine the structure of virus particles (virions), by means of which the virus spreads from one cell to another, and describe viral replication in infected cells. Flaviviruses, including Zika and encephalitis viruses, cause potentially fatal neurological diseases. Scientists will focus on an encephalitis virus causing hundreds of potentially fatal infections in the Czech Republic every year. The results of the project shall provide scientists with a detailed description of the viral replication mechanism.
Optimization design of functional materials in a new type of lithium based batteryCall: 12th Open Access Grant Competition
Researcher: Dominik Legut
NOur colleague Dr. Dominik Legut is involved in the research of lithium-based metal batteries. Unlike lithium-ion batteries, these batteries have higher energy density and are capable of storing ten times more energy. However, lithium anodes face many of the challenges associated with their lower charging efficiency, change of volume while charging/ discharging, and especially with dendritic growth.
In 2017, Dr. Legut, together with his colleagues from the USA, China, and Singapore, published an article about protective films for lithium-based metal batteries in the Advanced Energy Materials journal with an impact factor of 16. Special protective two-dimensional films with a thickness of a few atoms are capable of preventing electrodes connecting (and the subsequent dangerous short-circuit), which can potentially occur as a result of dendritic growth on lithium-based anodes.
This time, Dr. Legut was awarded 8 million core hours for his research of the optimal structure of lithium-based anodes. Together with other colleagues, he will aim at designing optimal materials for lithium-based anodes using prediction algorithms, chemical stability and mechanical properties calculations.
Structural characterization of intrinsically disordered proteinsCall: 12th Open Access Grant Competition
Researcher: Lukáš Žídek
Intrinsically disordered proteins (IDPs) are macromolecules lacking a stable and well defined tertiary structure. They have no stable structure and hence no thermodynamic minimum determining their function. During the course of the last decade, they have attracted wide attention due to their important role in a vast number of cellular processes. They include, for example, transcription of genetic information as well as their potential connection with neurodegenerative diseases. Recent research findings have shown that the main role in the protein function is not in their structure but their dynamic behaviour.
The project of prof. Lukáš Žídek from Masaryk University, which was awarded 1,480,000 core hours, is aimed at a more detailed study of the conformational behaviour of selected IDPs using a combination of state-of-the-art extensive computer simulations with their own prediction codes and advanced experimental methods (e.g., nuclear magnetic resonance spectroscopy, or small angle X-ray scattering.
Development of Relativistic Spectroscopy (ReSpect) computational code for study of heavy metal anticancer complexesCall: 12th Open Access Grant Competition
Researcher: Jan Vícha
One of the cancer medical treatment methods is chemotherapy. The most frequently used chemotherapeutics are platinum-based drugs. The key step for their further development is a more detailed study of their structure, properties, dynamics, and reaction mechanisms. The project of Dr. Jan Vícha from Tomáš Baťa University in Zlín carries on his previous research project, as well as the results of his project, which was awarded computational resources within our 9th Open Access Grant Competition. The objective of the new project, which has now been awarded 1,134,000 core hours, is to enhance prediction ability and the accuracy of computation of complex platinum-based alloys spectroscopic properties using the ReSpect program developed by the project partner organization - Arctic University of Norway. The newly modified code of the program will first be tested using magnetic resonance parameter computations of simple platinum chemotherapeutics, such as cisplatin and oxaliplatin in solution. The scope of the research activities will then be extended to simulations of new advanced carriers of platinum drugs, which is also the main topic of the Advanced Carriers for Platinum Drugs project supported by the Grant Agency of the Czech Republic, also implemented by Dr. Vícha.
The allocated computational resources will be used in testing the modified code and for relativistic quantum chemical computations performed by the ReSpect program for prediction and analysis of magnetic resonance parameters for heavy metal complex compounds.
Experimental comparison of word embedding methodsCall: 12th Open Access Grant Competition
Researcher: Martin Fajčík
Numeric representation of words used in natural language processing is referred to as word embedding. It consists in creating a vector for each word. Advanced word embedding methods have applications in various areas associated with, for example, speech recognition and translation.
The objective of the project by Ing. Martin Fajčík from Brno University of Technology, which was awarded 850,000 core hours, is to experiment with state-of-the-art word embedding methods (count-based and prediction methods) by training them on large data sets. The team of scientists aim to identify the drawbacks of different methods, and find ways for their further improvement. The project activities also include developing deeper understanding of the relation between the vectors of words and their real meaning. Other interesting research topics will be processing of homonyms, synonyms, antonyms, and hyponyms.
The models allow not only the relation between words they “learned” to be predicted but also the dimension of these relations to be represented. Moreover, they enable lexical arithmetic (e.g., the similarity between words).
Fiji Bioimage Informatics on HPC – "Path to Exascale"Call: 12th Open Access Grant Competition
Researcher: Michal Krumnikl
The IT4Innovations National Supercomputing Center – path to exascale project, which supports the research in the area of biological image analysis using HPC, allows IT4Innovations to participate in the research of large bioimage dataset processing using high performance computing (HPC) systems. This research is focused on parallelization of key steps in, for example, light sheet microscopy data processing. Light sheet microscopy has become popular for scanning living cells and organisms for its speed and low photo toxicity, which allows complex living systems such as embryos to be microscopically scanned three-dimensionally with high resolution and for their entire development period.
The main objective of the project is to extend the options of the Fiji platform, which is used by tens of thousands of users worldwide for the processing of large image datasets. The development team led by Dr. Krumnikl in collaboration with Dr. Pavel Tomančák from Max Planck Institute in Dresden (Germany) will modify each data analysis method for seamless running on HPC systems. Development and deployment of the Fiji platform on HPC systems shall allow its users to fully exploit its potential on large bioimage datasets.
Proton acceleration via laser interaction with plasma micro-bunches produced by cryogenic hydrogen ribbonCall: 12th Open Access Grant Competition
Researcher: Martin Matys
Being also involved as researchers in the ELI Beamlines project, Ing. Martin Matys and Dr. Jan Pšikal from the Czech Technical University in Prague were awarded 800,000 core hours for their project focusing on ion accelerator development. In particular, they are involved in research of proton acceleration induced by high power laser impulse interaction with a cryogenic hydrogen ribbon. Laser based ion accelerators have the potential to replace the extremely expensive conventional accelerators in the future, thereby, for example, lowering the costs of proton therapy for treatment of oncological diseases as well as the production costs of medical isotopes for positron emission tomography.
Scientists are particularly interested in the interaction when a laser pulse burns through the target and then interacts with the remaining plasma micro-bunches of much lower density than the initial target. Such a mechanism is capable of accelerating protons to energy ranges of hundreds of millions of electron volts. The project objective is deeper study of this mechanism using numerical three-dimensional simulations, which is significantly cheaper in comparison to real experiments.
Deep Learning for Novel Drug DiscoveryCall: 11th Open Access Grant Competition
Researcher: Vojtěch Cima
The Deep learning for Novel Drug Discovery project of Ing. Vojtěch Cima has been awarded 400,000 core hours. The allocated computational resources will be used for deep learning in predicting the effects of potential drugs and their possible toxic side effects. Using prediction algorithms, novel drug discovery and the related costs can simultaneously be accelerated and reduced respectively. This research is carried out as part of the ExCAPE project, the objective of which is to develop algorithms for solving complex pharmacological problems.
IntACall: 11th Open Access Grant Competition
Researcher: Petr Vrchota
Design of new regional aircraft and airlines is mainly influenced by economic and environmental factors. Individual parts of airplanes are optimized, for example, with respect to aerodynamic efficiency, fuel consumption, and emissions. Another option for reducing the aerodynamic drag and saving fuel are optimized integrated communication antennas. The antennas usually protrude and contribute to the total drag of the airplane.
The IntA project of Dr. Petr Vrchota from the Czech Aerospace Research Centre has been awarded 200,000 core hours. This project focuses on designing a new winglet with an integrated antenna to improve the flight performance and aerodynamic efficiency of the entire aeroplane and reduce fuel consumption as well as negative environmental impacts. The objective of the research project is to reduce the aerodynamic drag of the aeroplane by up to 2 % using the integrated antenna.
Molecular simulations of tin based materials for EUV lithographyCall: 11th Open Access Grant Competition
Researcher: Petr Slavíček
How can focused high-energy radiation change a material? What particular changes will occur at a molecular level? The chemical changes of materials under the influence of high-energy photons are studied by the team led by Prof. Petr Slavíček from the Laboratory of the Theoretical Photodynamics Research Group at the University of Chemistry and Technology in Prague. Their project titled Molecular simulations of tin based materials for EUV lithography has been awarded 1,082,000 core hours.
The objective of this project is to describe molecular changes occurring in extreme ultraviolet (EUV) ionization of tin based organic compounds (particularly so-called Sn-O cages). These compounds may potentially be used as photoresist materials for EUV lithography, a new generation of lithography for nanometric dimensions applicable in effective production of new computer chips. The method is based on the changes of physical and chemical properties of photoresists (e.g. their solubility) after EUV radiation. By exposing specific areas of a material to the radiation, the dimension of the resulting structure can be up to 10 nm, which is the threshold limit dimension of today's commercial chips.
Considerable computational intensity of molecular simulations of ionized Sn-O compounds is generated by the rich electron structure of tin. Simulation of a single trajectory taking half a picosecond requires almost a week to be computed using common processors. With its 76,896 cores (Intel Haswell processors and Intel Xeon Phi accelerators), our Salomon supercomputer will allow the researchers to perform extensive simulation, which would not be practically executable otherwise.
Relative Stabilities of Mismatches in Nucleic AcidsCall: 11th Open Access Grant Competition
Researcher: Petr Kulhánek
The research team led by Dr. Kamila Réblová and Dr. Petr Kulhánek from the Central European Institute of Technology - Masaryk University (CEITEC MU) has been awarded 634,000 core hours for their research into the relative stability of base pairing in deoxyribonucleic acids (DNA).
Chains of the double helix structure of DNA carry genetic information, the integration of which is secured by Watson-Crick complementary pairing. During the process of DNA replication, which occurs when cells divide, this complementarity is used in creating two identical copies of DNA. However, during the replication process, errors such as mismatched base pairs can occur. This is then recognized by various reparation mechanisms. One of them is mismatch repair (MMR), with the MutS enzyme being the active component in mismatch recognition. When such mismatch is detected, this enzyme activates a cascade of processes leading to its repair.
The allocated computational resources of IT4Innovations supercomputers will allow scientists to perform molecular simulations of short molecules of DNA and focus on describing the stability of all possible combinations of bases containing both the correct Watson-Crick pair and all other combinations. It is believed that this stability can be one of the many factors affecting the effectivity of the MMR mechanism in detecting errors. The information obtained may thus be important for understanding the development of genetically determined diseases or the formation of cancerous growths.
In silico drug designCall: 10th Open Access Grant Competition
Researcher: Pavel Hobza
Prof. Pavel Hobza from the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences conducts research on computer-aided drug design. His project “In silico drug design” has been awarded 7,425,000 core hours within the 10th Open Access Competition. The allocated computational resources will be used for developing virtual screening methods for drugs. Used by the pharmaceutical industry, this approach is based on molecular modelling (docking and scoring) in order to identify suitable substances for designing new drugs. Due to high computing performance requirements, the reliability of these methods has been low so far. Using the IT4Innovations supercomputers and employing exact quantum chemistry computations, the researchers from Prof. Hobza’s team are able to predict both the drug structure at the active site of proteins and their ability to bind, which determines their therapeutic effects. The recently published approach is currently used in collaboration with leading pharmaceutical companies.
Simulation and planning of ultrasound surgeriesCall: 10th Open Access Grant Competition
Researcher: Jiří Jaroš
The research team of Dr. Jiří Jaroš has been awarded 2,678,000 core hours for their research in the field of computer simulations of ultrasound propagation in biological tissues. The researchers focus on targeted ultrasound, which is applied in the non-invasive treatment of cancer and other diseases. Targeted ultrasound is based on the principle of focusing high-power ultrasound beams through biological tissues. Surgeons are thus able to remove a tumour from the body of their patients using a non-invasive procedure. However, the results of the ultrasound surgery are influenced by many factors, such as presence of bones, large blood vessels, and fat surrounding organs. These factors lead to attenuation, scattering, and reflection of the ultrasound wave, which then do not have enough energy in the required area. Therefore, the awarded allocation will be used by the research team from Brno University of Technology for evaluating the accuracy and optimization of the models of ultrasound propagation in biological tissues.
ESPRESO FEM - Heat Transfer ModuleCall: 10th Open Access Grant Competition
Researcher: Tomáš Brzobohatý
The project by Dr. Tomáš Brzobohatý “ESPRESO FEM – Heat Transfer Module“ has been awarded 2,425,000 core hours. The research team will focus on developing and testing the finite element method-based complex and massively parallel library for performing simulations of heat transfer problems, and their optimization. This library includes the massively parallel iterative ESPRESO solver continually developed at IT4Innovations.
Particle-in-cell simulations of heat flux distribution at plasma-facing components in support with experiments at WEST tokamakCall: 10th Open Access Grant Competition
Researcher: Michael Komm
Researchers from the Institute of Plasma Physics of the Czech Academy of Sciences are involved in the research associated with a long-term international effort to tame thermonuclear fusion. The project of Dr. Michael Komm has been awarded 300,000 core hours, and focuses on modelling the deposition of heat transferred by plasma particles on plasma-facing components. The research focuses on the experiments in the WEST tokamak, located in Cadarache in Southern France, where the prototypes of the components designated for the currently built ITER tokamak will be tested. As the first fusion device, ITER is supposed to generate more energy than it consumes. However, this is linked with extreme heat fluxes that reach the material limits of the plasma-facing components. The objective of the Czech Academy of Sciences project is to find out whether the understanding of the interaction of plasma and the plasma-facing components is accurate enough for successful operation of the thermonuclear reactor.
Computer modelling of martensitic transformations in Ni-Mn-Ga systemCall: 10th Open Access Grant Competition
Researcher: Martin Zelený
Have you ever heard of magnetic memory alloys? At Charles University, scientists are exploring these metal alloys, which can restore their original shape and dimensions in a magnetic field. Shape memory alloys are made to meet the needs of humans and are called intelligent materials. They have the ability to regain their original shape due to heat, stress, or magnetism. The shape memory effect is caused by the transition of the metal from one crystalline structure to a different one, which is most energy-efficient under certain conditions. For shape memory effects, the necessary condition is martensitic phase transformation. This change can be triggered by temperature change, pressure, or magnetic fields. The main goal of the project of Dr. Martin Zelený from Charles University is modeling martensite transformations of alloys based on Ni-Mn-Ga, which can exhibit (reversible) deformation up to 12 % in an external magnetic field. The project received 1,468,000 core hours and its results will be used to design new intelligent materials, which have a large application potential in actuators, sensors, energy harvesters, and magnetic refrigeration systems.
The role of hybridization in triggering asexual reproduction in fishCall: 9th Open Access Grant Competition
Researcher: Karel Janko
Researchers from the University of Ostrava will deal with a very interesting topic – asexual reproduction in ﬁsh. They will focus on the ﬁsh family Cobitidae, which are widespread throughout Europe. You may know some species of this family occurring throughout the Czech Republic: Danubian spined loach (Cobitis elongatoides) and Spined Loach (Cobitis taenia). The reproductive abilities of this ﬁsh can be repeatedly disrupted by interspecies breeding. Interspecies breeding can lead to emergence of asexual ﬁsh individuals: both infertile males and fertile females that do not reproduce sexually, but reproduce clonally. The asexual females need only the presence of the sperm cell (male reproductive cell) to stimulate egg cell development, without the fertilization process itself. The offspring are all females, clones of their mother. Why are clonally reproducing individuals produced during interspecies breeding only? Does the emergence of such asexual ﬁsh individuals represent a natural evolutionary step in the formation of new species? Using the IT4Innovations supercomputers, the answers to these questions will hopefully be answered by the research team led by Dr. Karel Janko within this project.
Protein-protein interactions important in neurodegenerative diseasesCall: 9th Open Access Grant Competition
Researcher: Jozef Hritz
The research team led by Dr. Jozef Hritz will use the allocation of 3 300 000 core hours, for the research of the 14-3-3 protein complexes, which are associated with oncological and neurodegenerative diseases, such as Alzheimer's and Parkinson's disease. On the atomic level, the static molecular structure of these proteins has already been studied using experimental techniques such as X-ray crystallography and nuclear magnetic resonance. However, their dynamics have not been thoroughly studied yet. Study of the dynamical properties is essential for understanding the origin of these protein complexes because this knowledge allows target action to be taken in order to prevent the processes causing the development and progression of Alzheimer’s and Parkinson’s disease. The researchers from Masaryk University would like to describe these changes and thus contribute to the understanding of both neurodegenerative diseases.
Detection and evaluation of orbital floor fractures using HPC resourcesCall: 9th Open Access Grant Competition
Researcher: Petr Strakoš
The research team at IT4Innovations implements state-of-the-art approaches to information technologies in medical diagnostic methods. They focus on precise detection and measurement of orbital ﬂoor fractures from computer tomography (CT) scans in cooperation with the doctors from the University Hospital Ostrava. The objective of the project, with the allocation of 200 000 core hours, is to develop new and improve existing methods for CT scan analysis using image ﬁltering and segmentation, and developing parallel algorithms for 3D model reconstruction. The algorithms will be applied to analysis of post-traumatic treatments of patients with eye injuries.
BEM4I – Development of the parallel boundary element library IICall: 9th Open Access Grant Competition
Researcher: Michal Merta
Researchers from IT4Innovations will continue to develop the BEM4I library based on the boundary element method. In previous projects, the BEM4I library was accelerated using the Intel Xeon Phi processors (Knights Corner, KNC), which complemented the already existing and operating parallelization using Open MPI. The current project, with the allocation of 350 000 core hours, aims at further optimization of the code and its testing on the new generation of the Intel Xeon Phi processors. BEM4I can be used for solving real engineering problems in the ﬁeld of sound propagation and shape optimization.
Conformational transitions and membrane binding of the neuronal calcium sensor recoverinCall: 7th Open Access Grant Competition
Researcher: Pavel Jungwirth
Do you know about the protein called recoverin? It regulates the sensitivity of the photoreceptor cells in the eye and allows us to adapt our vision to changing light conditions, and is sensitive to calcium. Scientists from the Czech Academy of Sciences used our supercomputers to simulate the molecular dynamics of structural changes of recoverin. Furthermore, they used molecular dynamics simulations to look at how calcium-activated recoverin binds to photoreceptor cell membranes, where it interacts with other proteins. The acquired computer image of the recoverin dynamics helps to better understand the important molecular details associated with the vision process.
Climate-chemistry-landsurface interactions on the regional scaleCall: 7th Open Access Grant Competition
Researcher: Peter Huszár
It is generally assumed that cities overheat mainly because of their lack of greenery. Most areas in cities are covered with buildings, pavements, and roads. Properties of concrete and asphalt are very different from natural surfaces (e.g. soil, vegetation). Artificial surfaces absorb sunlight, accumulate heat, and are unable to bind and release water (unlike vegetation). In summer, the climate in big cities can be unbearably hot, and its inhabitants inhabitants find respite in swimming pools and lakes. With the help of supercomputers, scientists from Charles University, under the leadership of Dr. Peter Huszár, have been simulating the impact of cities, and urban surfaces generally, on surface temperature using the latest climate models. During modeling, they took into account, for example, the phenomenon of the urban heat island, including the effects of turbulence in urban areas, heat flows, and radiation between the air in the street canal and surrounding buildings. Scientists also predicted (up to 2099) the probable future climatic conditions in cities including, with the help of our supercomputers, their impact on the regional climate.
Low-level vision and image enhancement with convolutional networksCall: 7th Open Access Grant Competition
Researcher: Michal Hradiš
Researchers from the Brno University of Technology are working on image reconstruction with convolutional neural networks, the most successful method of machine learning today. Convolutional neural networks are, for example, used for image enhancement, replenishment of damaged parts, and photo focusing. The team of Dr. Michal Hradiš focuses on two basic types of image degradation and their recovery: JPEG compression and motion blur. Significant successes have been achieved, for example, in focusing blurred photos of text from mobile phones and recognizing licence plate numbers from traffic cameras. And because the training of convolutional networks for computational reconstruction is computationally challenging (large networks are trained on the latest GPUs for a month), the research team used our supercomputers.
Modeling of elementary processes in cold rare-gas plasmasCall: 7th and 9th Internal Grant Competition
Researcher: René Kalus
Researchers at VŠB - Technical University of Ostrava and Université Toulouse III Paul Sabatier are interested in cold rare-gas plasmas (helium, neon, argon, krypton, xenon), which are used in many areas of medicine, e.g. surface sterilization, wound healing, inactivation of cancer cells and for blood coagulation processes. To understand the processes leading to the healing properties of cold plasma, it is necessary to understand what is happening within the plasma and what happens to it after entering the external environment (in contact with the air). Researchers simulate particle collisions in carrier gases, and in the near future they want to simulate collisions of primary carrier gas ions with air molecules. And since these simulations are computationally challenging, especially in the case of molecular ions, the scientists use our supercomputers.
Molecular docking and high performance computersCall: 5th Open Access Grant Competition
Researcher: Rafael Doležal
Molecular docking is one of the methods commonly used in rational drug development. This method is able to find the optimal arrangement for small molecule drugs and thier related receptors, so that they can interact with each other. Molecules are considered flexible structures that can change their shape, which greatly increases the complexity of the calculations. Scientists from Hradec Králové University use supercomputers for molecular docking as they focus on finding potential drugs in databases with millions of chemical structures. Using computer methods, they attempted to design the most powerful algorithm for simulating interactions between the enzyme acetylcholinesterase and the selected potential drug for Alzheimer's disease.
Structural analysis of the human mitochondrial Lon protease and its mutant formsCall: 5th Open Access Grant Competition
Researcher: Lubomír Kováčik
The eukaryotic cells of our body are complicated biochemical systems that uses energy in the form of adenosine triphosphate (ATP) to fuel activity. The sources of ATP are mitochondria, cellular organelles which require more than a thousand proteins to function properly. One of these is Lon protease, which is particularly involved in decomposing proteins toxic for cells and maintaining the balance of the internal environment in the mitochondria. Changing amounts of Lon protease produced by the cell is an indicator of imbalance and is associated with a number of serious illnesses such as epilepsy, myopathy, paraplegia, and cancer. Lon protease could be also used to treat cancer. Therefore, it is important to find out as much as possible about Lon protease. So far, for example, information about its entire structure and changes during its life cycle is missing. Scientists from Charles University, with the help of supercomputers, managed to determine the whole 3D structure of human mitochondrial Lon protease. They are one step closer to understaing the studied protein and possible treatment of the aforementioned diseases.
Computational studies of reaction profiles including excited states of small organic ions relevant for the modeling of Titan´s atmosphereCall: 5th Open Access Grant Competition
Researcher: Jan Hrušák
Titan, the moon of Saturn, is a remarkable object of the Solar System. Scientists have been interested in Titan for a long time because it is similar to Earth. The Cassini spacecraft has made many passes to find out more about this moon. It has been found that Titan has a stone surface, a dense atmosphere, and even rain and methane lakes can be found there. The atmosphere of Titan consists mainly of oxygen, nitrogen and methane. Scientists from the Czech Academy of Sciences simulated methane reaction with oxygen, and used our supercomputers to make quantum chemistry calucations. Thanks to the presence of excited oxygen atoms in Titan's atmosphere, they can recreate the molecules necessary for life. They simulated similar conditions that prevailed on the surface of our young Earth.
Ensemble modeling of ocean flows, and their magnetic signatures in satellite dataCall: 5th Open Access Grant Competition
Researcher: Jakub Velímský
The computational resources of IT4Innovations have enabled researchers from Charles University to explore the magnetic trace of the oceanic flow, which is driven by tidal phenomena (the consequence of which is also tide and outflow) and interactions with the atmosphere. Water in the oceans contains high concentrations of dissolved salts and therefore efficiently carry electrical current. The main magnetic field induces an electric current in the flowing water, and then a secondary magnetic field is formed. Research by Charles University could open the way for satellite tracking of the oceanic flow and contribute to the study of global climate change.
Origin of the Second Stellar Generation in Globular ClustersCall: 5th Open Access Grant Competition
Researcher: Richard Wünsch
Scientists from the Czech Academy of Sciences study globular clusters; compact groups of hundreds of thousands of stars. In our Milky Way Galaxy, there are about 150 globular clusters. Their age is comparable to the age of the universe, and the way they originate is one of the greatest mysteries of astrophysics. Modern instruments, such as the Hubble Space Telescope, have revealed the surprising and difficult to explain chemical composition of the stars forming these clusters. It has shown, for example, that in a given globular cluster the stars have the same iron content. This strongly supports the idea that the whole cluster of stars originated from a single cloud of gas. On the other hand, star cluster stars differ in the content of some light elements, such as helium or oxygen, and this suggests that the stars have been created in more generations, and the younger generations contain elements created by older generations. Using our supercomputers, scientists led by Dr. Richard Wünsch simulated the creation of the second generation stars. They have developed a model according to which the second generation originated from the material of the star winds - the particle stream that escapes from the atmosphere of the first generation stars.
Scalable Solvers for Subsurface Flow SimulationsCall: 4th Open Access Grant Competition
Researcher: Jakub Šístek
Scientists led by Dr. Jakub Šístek from the Mathematical Institute of the Czech Academy of Sciences further developed and optimized their programs for solving large systems of equations. These were used in conjunction with the underground water simulator developed at the Technical University of Liberec. As two places of interest, they have chosen one of the possible locations for building a safe underground nuclear waste repository near the Bedřichov tunnel in the Jizera Mountains. Using supercomputers, they've been able to optimize the solver and solve major problems with up to 15 million unknowns while maintaining parallel scalability.
Time changes of Enceladus water eruption and its internal structureCall: 3rd and 4th Open Access Grant Competition
Researcher: Marie Běhounková
Enceladus, the moon of the planet Saturn, is one of the most active bodies of the solar system. It has a very young surface, and spills of material from geysers are observed from breaks in the southern pole. Exploring the composition and activity of these geysers can help answer the question of whether there can be life on Enceladus. The study of Enceladus is also conducted by researchers from Charles University. Dr. Marie Běhounková attempted to determine a model of the inner structure that best explains the timing of the geyser activity during Enceladus' orbit around Saturn. She helped to optimize the computational code so that hundreds of calculations can be performed for a different internal structure. Our supercomputers processed numerical calculations, and simulation results contributed to understanding the response of the Enceladus ice shell to tidal forces for various possible internal structures.
Calculation of absolute binding affinities of phosphopeptides to 14‐3‐3 proteinCall: 2nd External Access Competition
Researcher: Jozef Hritz
14-3-3 proteins, found in all eukaryotic cells, are known to be important in cell-cycle regulation, apoptosis, and regulation of gene expression. They are also associated with oncogenic and neuro-degenerative amyloid diseases. The main aim of the project is to calculate the binding affinity between the 14-3‐3 protein and its selected target phospho-peptides. Experimental production of many phosphorylated proteins binding to 14-3‐3 in sufficient amounts for experimental binding affinity measurements is almost impossible. Once the approach is validated for PKCe and C-RAF kinase peptides by their comparison with the experimental data, the approach can be used almost for any of 850 known binding partners important particularly in neurobiochemistry and neurodegenerative diseases.
Air quality modelling in fine resolutionCall: 2nd External Access Competition
Researcher: Jaroslav Resler
Air quality is an important factor affecting health and life quality of a large part of the population. It is well known that transportation is an important source of air pollution, especially in large cities. Model simulations are an essential tool for the quantification of the impact of transportation on air quality; they serve as an aid for policy making and planning of transportation solutions. The main objective is to perform a pilot simulation of the air quality in very high resolution using Eulerian chemical transport model. Chemical transport model CMAQ (US EPA, USA) will be configured on matching domains and the main focus will be on the fine resolution domain and on the influence of the urban model. We expect to obtain new insights to dependence of air quality on emission sources and to a role of transportation and its impact on pollutant concentrations.
Blood flow simulation in a patient specific geometryCall: 2nd External Access Competition
Researcher: Jaroslav Hron
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, specifically an aneurysm. Aneurysm is a specific local expansion of the blood vessel wall and its rupture can lead to a fatal situation. With increasing popularity of computer tomography and magnetic resonance imaging an aneurysm is often diagnosed as byproduct and raises a question if one can identify some indicators suggesting a chance of its rupture. The geometry for each case is unique and demands accurate computation. Proper understanding of blood rheology and connected chemical reactions, like coagulation process, and interactions with the vessel walls can be factors with significant importance. Identifying which of these parts plays important role in such decision will require great amount of computations which are considerably demanding on computational resources.
Modeling and shape optimization of periodic nanostructuresCall: 3rd Internal Access Competition
Researcher: Lukáš Halagačka
This project is focused on modelling and optimization of novel plasmonic and photonic periodic structures. Light propagation in the complex structures is hardly described using simple models and, therefore, advanced numerical modeling is needed. The main goal of the project is to use our own parallel code based on Rigorous Coupled Wave Analysis (RCWA) to model optical and magneto-optical properties of nanostructures, optimize geometric parameters to increase the figure-of-merit function in experimental data fitting procedure. Design of 1D periodic magnetoplasmonic devices founds possible application as a unidirectional optical filter. Such a type of device can be useful in further increasing of speed of optical telecommunications, for holographic applications and the solar cell structures.
Support for Exa2ct projectCall: 3rd Internal Access Competition
Researcher: David Horák
Today, only around one percent of codes support 10k+ cores, whereas machines with more than 200k cores are already available. EXA2CT Project aims to development of new algorithms and optimization of the existing ones to reach the scalability on future exascale supercomputers. As the communication among computational cores is the bottleneck in this time, an attention will be paid to rearrangement of known scalable algorithms based on avoiding or hiding the communication in the first phase of the project.
BEM4ICall: 3rd Internal Access Competition
Researcher: Michal Merta
Boundary element methods (BEM) are used for modelling physical phenomena by partial differential equations. Compared to volume discretization methods, such as finite element methods, BEM introduces unknowns only on the boundary, which is advantageous in case of unbounded computational domains, e.g. in electromagnetic scattering problems, or shape optimization. However if we want to use BEM to solve large real life problems, it is necessary to parallelize the computation on a supercomputer ANSELM.
Pure and doped water clusters - non zero pressure Monte Carlo simulationsCall: 3rd Internal Access Competition
Researcher: Aleš Vítek
This project is focused on the modeling of thermodynamics and structural properties of finite molecular systems – pure and doped water clusters under non-zero temperatures and pressures. Main attention will be focused on selected system sizes up to 50 molecules. The goal of this project is theoretical prediction of properties of this water - admixture complexes under different thermodynamic condition (broad interval of pressures and temperatures) and study of local structure in the admixture molecule vicinity. Our attention will be focused on these sizes of clusters, which create cage structures and may wrap the admixture atom or molecule. Results of this basic research may by interesting for understanding of behavior, stability and properties of very important crystalline hydrates, where bulk limit of water molecules at non-zero pressure can create a crystal structure with cages occupied by (usually hydrophobic) admixture particles, rare gases, CO2 and methane molecules. Methane and carbon dioxide hydrates are of general interest of many physical and chemical scientists now because of storage of this greenhouse gases or in the case of methane, as a possible source of energy for the future.
Lowdimensional magnetic systemsCall: 2nd Internal Access Competition
Researcher: Dominik Legut
One- and two-dimensional magnetically frustrated systems are suitable candidates for advancement of the current technology based on giant magnetic resistance (GMR) or tunnelling magnetic resistance (TMR). Both these methods are commercialized for read/write heads of the hard-drives, as, sensors for acceleration and for bearings detecting small magnetic fields. This research lies in mimic of the multilayered systems by using compounds that exhibit one- or two-dimensional magnetic ordering. These materials show high magnetic frustration, i.e. magnetic moment orientation. Using firstprinciples (ab initio) calculations, we are able to determine the level of frustration and the strength of magnetic interactions, which enables us to precisely determine the magnetic structure in these low-dimensional systems.
MatSol library - development, testing and support libraries developmentCall: 2nd Internal Access Competition
Researcher: Oldřich Vlach
The MatSol library, developed by IT4I researchers for computing problems from the field of mechanics, is written in MatLab, which enables quick code development. Implementation and debugging is more time consuming in C or FORTRAN. The MatSol library will therefore be used to test new algorithms so that it can be determined whether the given algorithm is suitable for implementation in a more difficult language, or whether it has to be modified.
Modeling of elementary processes in cold rare-gas plasmasCall: 2nd Internal Access Competition
Researcher: René Kalus
Low-temperature plasma with a rare-gas carrier medium seem to be a promising tool for medical applications. For example, it has been shown recently that low-temperature plasmas are very effective in surface sterilization, wounds healing, or even malignant cell inactivation. The main aim of this project is elementary collision processes modelling, particularly collisions of plasma particles and and their interaction with electromagnetic radiation. The results of this microscopic modelling will provide input for subsequent studies of plasma at the macroscopic level and optimization of its generators (it will be carried on in cooperation with Paul Sabatier University in Toulouse, France). Improvement of our knowledge can be thus expected not only in the field of basic research but also in the development of new technologies based on that research.
Axially and radially cooled GCS brake discs
Brake discs with internal cooling (or vented discs) are currently the most efficient braking system and are widely used in the automotive industry. Compared to drum brakes, they are much lighter and their cooling system is more efficient. On the other hand, they are more expensive and prone to malfunctions caused by dirt. The research focuses on optimizing air flow in the brake disc and the diffuser while taking account of the disc’s strength and material fatigue. Mathematical simulations on the supercomputer will significantly help in designing the geometry of the disc and the diffuser, as they will provide improved visualization of airflow, heat radiation, convection and conduction in the prototype. This will allow for minimizing disk deformations resulting from high temperatures and pressure. The GCS brake system may mark the same progress in braking technology as did the change from unvented to vented discs, because the authors assume that GCS reinforces the benefits of vented discs while minimising their drawbacks.
Testing codes for computational fluid dynamics
The main objective of this project is to test the scalability of freely available and commercial codes focusing on Computational Fluid Dynamics (CFD). Given the substantial demands of this type of calculation on computing time, the use of supercomputers in CFD is very important. Understanding the behaviour of the algorithms used within available libraries is crucial to the future efficient use of the small cluster in CFD calculations. The results will be processed into a freely accessible database covering typical fluid dynamics tasks and will be used for future collaboration with IT4Innovations’ external partners.
Thermal expansion of materials for Generation IV reactors
Generation IV fast nuclear reactors rely on melted alkali salts for cooling, which are also used for distributing nuclear fuel e.g. in the form of uranium carbide particles. This method provides much better heat transfer and allows for higher operating temperatures and, in turn, improves primary cycle efficiency. Possible materials for this use include the aforementioned uranium carbide compounds that have high melting points of about 2500 K. However, some of these compounds exhibit very unusual dimensional changes as temperatures increase. The main objective of this research is to understand this behaviour and to map the phase transformations of these compounds using first-principle (ab initio) calculations, i.e. procedures based on quantum mechanics.
Performance and scalability test of a hydrological model with remote execution
As a service, HPC (High Performance Computing) is a new area of hydrological modelling, which is of great benefit to end users such as flood warning committees and fire departments, but also the general public. These users need to get the results of hydrological simulations in real time so that they can use them to make informed decisions in emergency situations. The tests of this architecture will help assess and improve its scalability, identify possible shortcomings and improve its overall efficiency, thereby ensuring quick responses to the requirements of its users.
Enzymatic reaction mechanisms investigated by Car-Parinello ab initio dynamics
Carbohydrates play a critical role in many biological processes. On cell surfaces, they often take the form of highly branched glycoconjugates. The synthesis of such glycoconjugates involves many enzymes. Disruption of these enzyme activities can lead to life-threatening pathological conditions such as diabetes, Alzheimer’s disease and cancer. The study aims to investigate the reaction mechanisms of these enzymes at the atomic level, which may aid e.g. in drug development.
Simulations of particle acceleration by short ultra-intense laser pulses
The spatial and financial requirements of current particle accelerators considerably complicate their use in medicine, for example in cancer treatment. The main objective of this research is to understand how particle acceleration by high-intensity lasers operates. This research may contribute significantly to the development of future high-quality and less expensive sources of protons and X-rays from accelerated electron beams. These can be used for imaging very small structures on the order of nanometres (e.g. biological samples) and also for researching matter in astrophysics.
In silico drug design
Computer aided drug development has garnered a lot of attention due to its advantages, which include speed, low costs and the ability to select appropriate components for synthesis and subsequent biological screening. The aim of this project is to identify novel ligands that bind with therapeutically relevant proteins. Over the long term, the team has been researching components that are active in the treatment of cancer and acquired immunodeficiency syndrome (AIDS).
FLOCON – A Project by the Aerospace Research and Test Establishment
The FloCon project is aimed at affecting the boundary layer on the wings of modern commercial aircraft through blowing. The objective is to improve aerodynamic performance and reduce environmental impacts. CFD models for simulating modern 3D active flow control technologies will be prepared, tested and validated and subsequently implemented into the aerodynamic optimization loop.