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Methods for the analysis of the supercomputer efficiency, novel parallel algorithms for molecular dynamics calculations and modeling of transport processes in liquids and biomembranes

Priority areas of development: IT and mathematics
2020

Publications:


Belonoshko A. B., Gavryushkin P., Sagatov N., Banaev M., Litasov K. Disordered Aragonite: The New High-Pressure, High-Temperature Phase of CaCO3 // Journal of Physical Chemistry C. 2020. Vol. 124. No. 48. P. 26467-26473. doi
Gaydukov R. Numerical algorithm for solving Prandtl equations with induced pressure in the periodic case // Mathematics and Computers in Simulation. 2020. 
Dubovskii P. V., Ignatova A. A., Feofanov A. V., Utkin Y. N., Efremov R. Antibacterial activity of cardiotoxin-like basic polypeptide from cobra venom // Bioorganic and Medicinal Chemistry Letters. 2020. Vol. 30. No. 3. P. 126890-. doi
Kraevsky S. V., Tournassat C., Vayer M., Warmont F., Grangeon S., Ngouana-Wakou B. F., Kalinichev A. G. Identification of montmorillonite particle edge orientations by atomic-force microscopy // Applied Clay Science. 2020. Vol. 186. P. 105442-. doi
Ay A N, Zumreoglu-Karan, B., Kalinichev A. G., Rives V., Trujillano R., Temel A. Layered double hydroxide - borate composites supported on magnetic nanoparticles: preparation, characterization and molecular dynamics simulations // Journal of Porous Materials. 2020. Vol. 27. P. 735-743. doi
Kondratyuk N., Pisarev V., Ewen J. P. Probing the high-pressure viscosity of hydrocarbon mixtures using molecular dynamics simulations // Journal of Chemical Physics. 2020. Vol. 153. No. 15. P. 154502-. doi
Kondratyuk N., Orekhov M. Shear viscosity of n-pentane from diffusivity based molecular dynamics methods // Journal of Physics: Conference Series. 2020. Vol. 1556. P. 012048-. doi
Kondratyuk N., Lenev D. Y., Pisarev V. Transport coefficients of model lubricants up to 400 MPa from molecular dynamics // Journal of Chemical Physics. 2020. Vol. 152. No. 19. P. 191104-. doi
Alekseeva A. S., Volynsky P. E., Krylov N., Chernikov V. P., Vodovozova E. L., Boldyrev I. A. Phospholipase A2 way to hydrolysis: Dint formation, hydrophobic mismatch, and lipid exclusion // Biochimica et Biophysica Acta - Biomembranes. 2020. Vol. 1863. No. 1. P. 183481-183490. doi
Kuznetsov A., Zamaletdinov M., Bershatsky Y., Urban A., Bocharova O. V., Bennasroune A., Maurice P., Bocharov E. V., Efremov R. Dimeric states of transmembrane domains of insulin and IGF-1R receptors: Structures and possible role in activation // Biochimica et Biophysica Acta - Biomembranes. 2020. Vol. 1862. No. 11. P. 183417-. doi
Albrecht C., Kuznetsov A., Appert-Collin A., Dhaideh Z., Callewaert M., Bershatsky Y., Urban A., Bocharov E. V., Bagnard D., Baud S., Blaise S., Romier-Crouzet B., Efremov R., Dauchez M., Duca L., Maurice P., Bennasroune A. Transmembrane peptides as a new strategy to inhibit neuraminidase-1 activation // Frontiers in Cell and Developmental Biology. 2020. Vol. 8. P. 611121-. doi
Норман Г. Э., Флейта Д. Ю. Коллективные движения атомов в перегретом кристалле и переохлажденном расплаве простого металла // Письма в Журнал экспериментальной и теоретической физики. 2020. Т. 111. № 4. C. 251-256. doi
Priezjev N. A delayed yielding transition in mechanically annealed binary glasses at finite temperature // Journal of Non-Crystalline Solids. 2020. Vol. 548. P. 120324-. doi
Priezjev N. Alternating shear orientation during cyclic loading facilitates yielding in amorphous materials // Journal of Materials Engineering and Performance. 2020. Vol. 29. P. 7328-7335. doi
Priezjev N. Spatiotemporal analysis of nonaffine displacements in disordered solids sheared across the yielding point // Metallurgical and Materials Transactions A: Physical Metallurgy and Materials Science. 2020. Vol. 51. doi
Priezjev N., Jana P. Structural relaxation in amorphous materials under cyclic tension-compression loading // Journal of Non-Crystalline Solids. 2020. Vol. 540. P. 120098-. doi
Priezjev N., Bao Luyao, Hu Haibao The local slip length and flow fields over nanostructured superhydrophobic surfaces // International Journal of Multiphase Flow. 2020. Vol. 126. P. 103258-. doi
Smirnov G. Non-Arrhenius diffusion in bcc titanium: vacancy-interstitialcy model // Physical Review B. 2020. Vol. 102. P. 184110-1-184110-8. doi
Fleita D., Norman G., Pisarev V. Collective behaviour of a glass-forming film of pure aluminium // Journal of Physics Condensed Matter. 2020. Vol. 32. No. 21. P. 214009-. doi
Пахомов А., Фролова А., Табакмахер В., Chugunov A., Efremov R., Мартынов В. Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies // Journal of Photochemistry and Photobiology B: Biology. 2020. Vol. 206. P. 111853 -. doi
Лубова К., Chugunov A., Волынский П., Trofimov Y., Королькова Ю., Мошарова И., Козлов С., Андреев Я., Efremov R. Probing temperature and capsaicin-induced activation of TRPV1 channel via computationally guided point mutations in its pore and TRP domains // International Journal of Biological Macromolecules. 2020. Vol. 158. P. 1175-1183. doi
Belozerova O., Osmakov D., Vladimirov A., Koshelev S., Chugunov A., Andreev Y., Palikov V., Palikova Y., Shaykhutdinova E., Gvozd A., Dyachenko I., Efremov R., Kublitski V., Kozlov S. Sevanol and Its Analogues: Chemical Synthesis, Biological Effects and Molecular Docking // Pharmaceuticals. 2020. Vol. 13. No. 8. P. 1-20. doi
Gigolaev A., Kuzmenkov A., Peigneur S., Tabakmakher V., Pinheiro-Junior E., Chugunov A., Efremov R., Tytgat J., Vassilevski A. Tuning Scorpion Toxin Selectivity: Switching From KV1.1 to KV1.3 // Frontiers in Pharmacology. 2020. Vol. 11. P. 1010-. doi
Dlinnova E., Biryukov S., Stegailov V. Energy Consumption of MD Calculations on Hybrid and CPU-Only Supercomputers with Air and Immersion Cooling, in: Parallel Computing: Technology Trends.: IOS Press, 2020. С. 574-582. 
Kuznetsov E., Kondratyuk N., Logunov M., Nikolskiy V., Stegailov V. Performance and portability of state-of-art molecular dynamics software on modern GPUs, in: PPAM 2019: Parallel Processing and Applied Mathematics. Lecture Notes in Computer Science.: Springer, 2020. С. 324-334. 
Nikolskiy V., Stegailov V. GPU Acceleration of Four-Site Water Models in LAMMPS, in: Parallel Computing: Technology Trends.: IOS Press, 2020. С. 565-573. 
Choi Y. R., Nikolskiy V., Stegailov V. Matrix-Matrix Multiplication Using Multiple GPUs Connected by Nvlink, in: Proceedings of IEEE: 2020 Global Smart Industry Conference (GloSIC), Chelyabinsk, Russia, 2020.: IEEE, 2020. С. 354-361. 
Kirova E. M., Pisarev V. Morphological aspect of crystal nucleation in wall-confined supercooled metallic film // Journal of Physics Condensed Matter. 2021. Vol. 33. No. 3. P. 034003-1-034003-12. doi