We mediate efficient utilization of our leading national supercomputing infrastructure in order to increase the competitiveness and innovation of Czech science and industry. IT4Innovations primarily provides computational resources to researchers and academics from the Czech Republic as part of the Open Access Grant Competition. Within this competition in the years 2013-2020, 902 projects with a total of 1,027 billion core hours have been supported so far with the overall demand for the computational resources exceeding 1,404 billion core hours in this period (a core hour = one processor core per hour).
Computational resources allocated within the Open Access Grant Competitions in 2020 by scientific disciplines [%]
Computational resources allocated within the Open Access Grant Competitions in 2020 by institutions [%]
selected projects from 19th open access grant competition
Search for new Anticancer Compounds and Investigation their Mechanism of Action
Call: 19th Open Access Grant Competition
Researcher: Dr Olena Mokshyna
Institution: Institute of Molecular and Translational Medicine, Palacky University in Olomouc
Field: Life Sciences
The development of novel anticancer agents is a long and complicated process, which involves an investigation of many potential targets for such therapies. In this project we are going to address several of such targets. Bystin is a compact protein promoting human cancer cell growth. Despite bystin being a promising target for anticancer drugs and drugs against Blackfan anemia, no site of binding was previously identified. Olena Mokshyna, who was awarded 510 000 core hours for her project, found that bystin has two primary shallow binding sites. Exploring the mechanisms of binding of promising drug-like compounds, she was able to establish stable binding poses for most of the ligands and distinguish two main groups of ligands with varying activity. Her project aims to further explore bystin dynamics using enhanced sampling methods and perform free energy calculations of ligand-protein systems. These methods are used with emphasis on metadynamics simulations, which would allow to explore the ligands’ mechanism of actions in silico. The second target protein is CYP2w1. The uniqueness of CYP2w1 consists in the fact that it is mostly expressed in tumor cells rather than in healthy tissues. This feature makes it a potential target for selective anticancer agents. There are currently a few compounds known, which not only selectively bind to the metabolic site of the protein but also turn to a cytotoxic compound, thus destroying a cancer cell, but not damaging the healthy tissues. Olena Mokshyna aims to perform virtual screening to select compounds with a similar mode of action for further experimental testing. The results of her project will facilitate development of anticancer drugs and medication to treat Diamond-Blackfan anemia
Deoxiribonucleic acid (DNA)double helix is composed of two complementary strands, which are held together by Watson-Crick base pairing. Base-pairing mismatches can result in the development of inherited genetic diseases, cancer, and aging. Therefore, organisms developed several ways how to detect and repair these base-pairing errors and thus keep the integrity of genetic information for next generations. One of them is the mismatch repair pathway (MMR), in which the MutS enzyme detects mismatches and once found, it triggers a cascade of processes leading towards their repair. Petr Kulhanek and his research team tried to decipher how MutS can effectively detect base-pairing mismatches. In order to do so, they applied molecular mechanics and dynamics methods based on simplified physical description. This, at the cost of lower accuracy, makes it possible to study large biomolecular systems. Petr Kulhánek will use the awarded 532 000 core hours for quantum-chemical calculations to validate accuracy of the results achieved in previous studies. In this way, he will not only obtain information on the quality of the simplified physical description but also more detailed information about individual interactions in non-complementary base pairing and their relevance to MutS enzyme recognition. The obtained data is important for future rational design of chemical substances suitable in anti-cancer therapy, which will target damaged DNA.
Design of a new Smart Material with Magnetic Shape Memory Effect
Call: 19th Open Access Grant Competition
Researcher: Dr Martin Zeleny
Institution: Faculty of Mathematics and Physics, Charles University in Prague
Field: Material Sciences
Magnetic shape memory (MSM) alloys have a large application potential in actuators, sensors, energy harvesters, and magnetic refrigeration systems thanks to the extraordinary properties of their multiferroic martensite structure. The macroscopic deformation of such materials in an external magnetic field is caused by the motion of highly mobile twin boundaries in combination with high magnetic anisotropy. However, operating temperatures of currently used materials are too low for engineering applications, which is caused by their low transformation temperatures between austenite and martensite. Within the OP RDE MATFUN project, which was awarded more than 4.1 million core hours in the first period, Martin Zeleny will search for new materials with a high application potential that combine the stability of martensitic phase up to high temperature with its high magnetic anisotropy and low twining stress necessary for motion of twin boundaries, which are also necessary prerequisites of a successful MSM alloy development. Such alloys will in turn enable the miniaturisation and development of new devices in robotics, automotive, aerospace, and biomedical industries. In addition to finding new candidates for experimental preparation, Martin Zeleny will also investigate in depth the basic aspects of the multiferroic behaviour of alloys with magnetic shape memory, such as the physical origin of the martensitic transformation or the mobility of twin boundaries.
Nuclear fusion technology might enable us to generate energy without releasing large amounts of greenhouse gases into the atmosphere or leaving behind us long lived radioactive waste. Among the approaches to fusion, tokamak seems to be the most promising one. The concept involves the use of magnetic fields to confine plasma hot enough to sustain fusion within itself. Within the international ITER project, a new tokamak is being built in Southern France. 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 issues related to the operation of the future ITER. Fabien Jaulmes and his team was awarded more than 1.7 million core hours for his project focused on the study and modelling of narrow band imaging-born particle (NBI) behaviour, which might have impact on the future design of the system and its integration in COMPASS as wel as in the planned upgrade of the machine in 2022. The project aims at achieving better scientific understanding of tokamak nuclear power stations as well as cheaper and more sustainable power generation on larger scale. Having high potential impact on future reactor maintenance costs, this study aims to optimise heating systems.
Thermodynamics of Actinium Metal
Call: 19th Open Access Grant Competition
Researcher: Lukas Kyvala
Institution: IT4Innovations, VSB-TUO
Field: Material Sciences
The half-life of the most stable actinium isotope is only 21.77 years. Therefore, its concentration in nature is significantly low. Were it not for one of the products of the decay of thorium and uranium, it would have long since disappeared from Earth. Due to its high radioactivity, only a few experiments on metal actinium were done and actinium remains as one of the least explored naturally occurring elements. Even the basic property as lattice constant has been subject of discussion for many years and its unusually small value has not been fully elucidated. Lukas Kyvala will use the awarded computational resources (272 000 core hours) to analyse physical properties of actinium, its stability under different temperatures, and the relativistic effects as actinium, due to its high radioactivity (150 times higher than in the case of radium) has become a preferred element in radiotherapy. Study of actinium might not only help understand the physics of actinoids but also enable the obtained knowledge to be utilized in its applications such as the source of neutrons and geochemical indicator for deep circulation of sea water. Moreover, its ability to deliver stable amounts of heat is suitable for generating electricity in space where solar power is not available (i.e., for missions on the dark side of the moon).
Within the project awarded 481 000 core hours, the seismology team from the Department of Geophysics at the Faculty of Mathematics and Physics of Charles University in Prague will focus on the study of earthquake source model parameters that control the rupture propagation process on a fault. Based on the random sampling method, they will generate a large number of rupture propagation simulations (up to several ten thousand). However, not all such synthetic earthquakes correspond to real phenomena. Therefore, statistically, only those simulations that generate strong ground motions agreeing with observations from a large number of real earthquakes, i.e. an empirical model, are accepted into the database. The result will take the form of a large database of earthquake scenarios (several thousand) with varying magnitudes and varying complexities of rupture propagation. These phenomena arise from the determined laws of physics for processes at the fault, while at the same time arousing realistic ground movements. Due to the complexity of this synthetic database and lack of observation errors, characteristics such as rupture duration, size of the ruptured area, stress drop, and energy budget are compared with their real counterparts determined from actual phenomena in further analysis. The key focus in this project includes the study of obtained parameters acting in the friction law (their variance and potential correlations), which are not generally accessible for real events and which have significant impact on the resulting ground motions. Thus, studying a seismic source using numerical simulations may also be useful for assessing the effects of earthquakes and seismic hazards.