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  • ­­­Atomistic multiscale modeling of properties and processes in materials and living systems; analysis of efficiency of new supercomputer technologies

­­­Atomistic multiscale modeling of properties and processes in materials and living systems; analysis of efficiency of new supercomputer technologies

Priority areas of development: engineering science
2018
The project has been carried out as part of the HSE Program of Fundamental Studies.

Goal of research: development of new mathematical methods and algorithms for multiscale model in material science and molecular biology of biomembranes based on atomistic approaches, implementations of these methods using modern supercomputer technologies and application to selected scientific problems. Analysis of supercomputer algorithms and technology efficiency.

Methodology: methods of classical molecular dynamics and statistical physics; Einstein-Smoluchowski and Green-Kubo methods for calculating diffusion coefficients and viscosity; for biological systems: homology modeling of proteins, molecular dynamics with parameters optimized for proteins and membranes, de novo protein structure prediction using the molecular hydrophobic potential approach.

Empirical base of research: open source software (LAMMPS, Gromacs, VASP, etc.) was used for calculations on high-performance computing equipment, including the latest generation of graphics accelerators.

Results of research: Using the method of molecular dynamics and Green-Kubo calculations, dependences of the density and shear viscosity were obtained for 2,2,4-trimethylhexane in the range of 1-10 kilobar pressure. The results were presented on 10th competition on modeling the properties of industrial liquids. The resulting model can be recommended for reliable calculations of the viscosity of hydrocarbons at pressures up to 5-6 thousand atmospheres.

Molecular aspects of protein-protein recognition and protein-lipid interactions are described for a number of critical cell receptors: the ErbB family, glycophorin A, neuraminidase-1, and model peptides. It has been shown that membrane properties can significantly affect the behavior of proteins, in particular, modulate the stability of active and inactive states of receptors. This provides the basis for the future creation of membrane-active compounds with given functions.

The configuration of a “trap” is proposed as a prototype of promising antimicrobial compounds targeting the “Achilles heel” of bacterial cells - lipid II molecule. We underlined the key role of hydrogen bonding in the formation of a stable configuration of a “trap” with pyrophosphate.

We performed tests of modern molecular dynamics codes using graphics accelerators and possible ways for further optimization are proposed. Also, the efficiency of calculations on the Russian Elbrus-9C processors is evaluated, and the possibility of achieving high performance is demonstrated on test problems.

Level of implementation,  recommendations on implementation or outcomes of the implementation of the results: computational performance estimates and energy efficiency of software code on different processor architectures are proposed to be used in development of new supercomputer systems in NRU HSE.

Publications:


Priezjev N. Accelerated relaxation in disordered solids under cyclic loading with alternating shear orientation // Journal of Non-Crystalline Solids. 2019
Priezjev N. The effect of thermal history on the atomic structure and mechanical properties of amorphous alloys // Computational Materials Science. 2019
Priezjev N., Makeev M. Structural transformations and mechanical properties of porous glasses under compressive loading // Journal of Non-Crystalline Solids. 2018. Vol. 500. P. 1-10. doi
Priezjev N. The yielding transition in periodically sheared binary glasses at finite temperature // Computational Materials Science. 2018. Vol. 150. P. 162-168. doi
Priezjev N., Makeev M. Strain-induced deformation of the porous structure in binary glasses under tensile loading // Computational Materials Science. 2018. Vol. 150. P. 134-143. doi
Kondratyuk N., Smirnov G., Dlinnova E., Stegailov V., Biryukov S. Hybrid Supercomputer Desmos with Torus Angara Interconnect: Efficiency Analysis and Optimization, in: Communications in Computer and Information Science Vol. 910: Parallel Computational Technologies. Springer, 2018. doi P. 77-91. doi
Stegailov V., Дергунов Д. О., Timofeev A. Performance of Elbrus Processors for Computational Materials Science Codes and Fast Fourier Transform, in: Communications in Computer and Information Science Vol. 910: Parallel Computational Technologies. Springer, 2018. doi P. 92-103. doi
Stegailov V., Timofeev A. Deploying Elbrus VLIW CPU Ecosystem for Materials Science Calculations: Performance and Problems., in: Supercomputing. RuSCDays 2018. Communications in Computer and Information Science, vol 965. Springer, Cham. Springer, 2019. P. 543-553. doi
Khalilov M., Timofeev A. Optimization of MPI-Process Mapping for Clusters with Angara Interconnect // Lobachevskii Journal of Mathematics. 2018. Vol. 39. No. 9. P. 1188-1198. doi
Панина И. С., Chugunov A., Efremov R. Lipid II as a Target for Novel Antibiotics:Structural and Molecular Dynamics Studies. / Пер. с рус. // Russian Journal of Bioorganic Chemistry. 2018. Vol. 44. No. 6. P. 653-664. doi
Алексеева А. С., Волынский П. Е., Chugunov A., Онищенко Н. Р., Молотковский Ю. Г., Efremov R., Болдырев И. А., Водовозова Е. Л. Behavior of Doxorubicin Lipophilic Conjugates in Liposomal Lipid Bilayers. / Пер. с рус. // Russian Journal of Bioorganic Chemistry. 2018. Vol. 44. No. 6. P. 732-739. doi
Bragin P., Kuznetsov A.S., Bocharova O., Volynsky P., Arseniev A., Efremov R.G., Mineev K. Probing the effect of membrane contents on transmembrane protein-protein interaction using solution NMR and computer simulations // Biochimica et Biophysica Acta - Biomembranes. 2018. Vol. 1860. No. 12. P. 2486-2498. doi
Efremov R., Osmakov D., Koshelev S., Andreev Y., Dubinnyi M., Kublitski V., Sobolevsky A., Kozlov S. Proton-independent activation of acid-sensing ion channel ASIC3 by alkaloid lindoldhamine from Laurus nobilis // British Journal of Pharmacology. 2018. Vol. 175. No. 6. P. 924-937. doi
Darvishzadeh T., Bhattarai B., Priezjev N. The critical pressure for microfiltration of oil-in-water emulsions using slotted-pore membranes // Journal of Membrane Science. 2018. Vol. 563. P. 610-616. doi
Fleita D. Y., Norman Genri E., Pisarev Vasily V. Study of phase transition in the pure metal melt during ultrafast cooling by method of higher-order correlation functions // Journal of Physics: Conference Series. 2018. Vol. 946. No. 1. P. 012102-1-012102-7. doi
Semyonov V., Timofeev A. Resonant Energy Transfer Between Degrees of Freedom in a Dusty Plasma System // IEEE Transactions on Plasma Science. 2018. Vol. 46. No. 5. P. 1855-1858. doi
Kuznetsov A., Efremov R. Glycophorin A transmembrane helices dimerization: the role of the lipid environment, in: Biomembranes 2018. International Conference. 1-5 October 2018. Book of Abstracts.. Dolgoprudni : MIPT, 2018. P. 256-257.
Polyansky A. A., Kuznetsov A., Volynsky P. E., Efremov R. Proteins and membranes: born to be together. A computational view, in: Biomembranes 2018. International Conference. 1-5 October 2018. Book of Abstracts.. Dolgoprudni : MIPT, 2018. P. 89-90.
Кузнецов А. С., Ефремов Р. Г. Роль липидного окружения в формировании димера гликофорина А // В кн.: Математика. Компьютер. Образование. Тезисы. Вып. 25: Двадцать пятая международная конференция "Математика. Компьютер. Образование." Симпозиум с международным участием "Биофизика сложных систем, вычислительная и системная биология, молекулярное моделирование, медицинская биофизика". Ижевск : Ижевский институт компьютерных исследований, 2018. С. 70-71.
Kuzmenkov A., Nekrasova⁠ O., Peigneur⁠ S., Tabakmakher⁠ V., Gigolaev⁠ A., Fradkov⁠ A., Kudryashova⁠ K., Chugunov A., Efremov R., Tytgat⁠ J., Feofanov⁠ A., Vassilevski A. K⁠V1.2 channel-specific blocker from Mesobuthus eupeus scorpion venom: Structural basis of selectivity. // Neuropharmacology. 2018. Vol. 143. P. 228-238. doi
Bocharov E., Lesovoy D., Bocharova O., Urban A., Pavlov K., Volynsky P., Efremov R., Arseniev A. Structural basis of the signal transduction via transmembrane domain of the human growth hormone receptor // Biochimica et Biophysica Acta - General Subjects. 2018. Vol. 1862. No. 6. P. 1410-1420. doi
Norman G., Saitov I., Sartan R. A. Metastable states of warm dense hydrogen // Interfacial Phenomena and Heat Transfer. 2017. Vol. 5. No. 3. P. 165-171. doi
Kalinichev A. G. Universality of hydrogen bond distributions in liquid and supercritical water // Journal of Molecular Liquids. 2017. Vol. 241. P. 1038-1043. doi
Kondratyuk N., Norman G., Stegailov V. Quantum nuclear effects in water using centroid molecular dynamics // Journal of Physics: Conference Series. 2018. Vol. 946. No. 012109. P. 1-7. doi
Mishra R. K., Kunhi Mohamed A., Geissbühler D., Manzano H., Jamil T., Shahsavari R., Kalinichev Andrey G, Galmarini S., Tao L., Heinz H., Pellenq R., van Duin A. C., Parker S. C., Flatt R. J., Bowen P. cemff: A force field database for cementitious materials including validations, applications and opportunities // Cement and Concrete Research. 2017. Vol. 102. P. 68-89. doi
Amirov R. K., Lankin A. V., Norman G. Solvation suppression of ion recombination in gas discharge afterglow // Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 2018. Vol. 97. No. 3. P. 1-7. doi
Reinholz H., Röpke G., Broda I., Morozov I., Bystryi R., Lavrinenko Y. Relaxation and collective excitations of cluster nano-plasmas // Journal of Physics B: Atomic, Molecular and Optical Physics. 2018. Vol. 51. No. 01-4001. P. 1-9. doi
Norman G., Saitov I. Molecules ionization at phase transition in warm dense hydrogen // Journal of Physics: Conference Series. 2018. Vol. 946. No. 012121 doi
Valeev B., Pisarev V. The equation of state of n-pentane in the atomistic model TraPPE–EH // Journal of Physics: Conference Series. 2018. Vol. 946. P. 1-6. doi
Norman G., Saitov I. Plasma phase transition in warm dense hydrogen // Contributions to Plasma Physics. 2018. Vol. 58. No. 2-3. P. 122-127. doi
Pisarev V., Zakharov S. A. Comparison of forcefields for molecular dynamics simulations of hydrocarbon phase diagrams // Journal of Physics: Conference Series. 2018. Vol. 946. P. 012100-1-012100-6. doi
Chugunov A., Panina I. S., Nolde D. E., Efremov R. "Achilles Heel" of the Bacterial Membranes: Computational Modeling of Lipid II - Target for Novel Antibiotics, in: Biomembranes 2018. International Conference. 1-5 October 2018. Book of Abstracts.. Dolgoprudni : MIPT, 2018. P. 105-106.