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.
Publications:
Nikolskiy V., Stegailov V. Graphics-processing-unit-accelerated finite-difference time-domain simulation of the interaction between ultrashort laser pulses and metal nanoparticles // Journal of Physics: Conference Series. 2018. Vol. 946. No. 012011. P. 1-4. 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
Тимофеев А. В., Николаев В. С. Влияние параметров тлеющего разряда на среднее межчастичное расстояние в плазменно-пылевых структурах в диапазоне температур от криогенных до комнатной // Журнал экспериментальной и теоретической физики. 2019. Т. 155. № 2. С. 356-370. doi
Кирова Е. М., Норман Г. Э., Писарев В. В. Изменение вязкости алюминия в процессе стеклования по данным молекулярной динамики // Журнал физической химии. 2018. Т. 92. № 10. С. 1525-1530. 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
Dubovskii P. V., Efremov R. The role of hydrophobic /hydrophilic balance in the activity of structurally flexible vs rigid cytolytic polypeptides and analogues developed on their basis // Expert Review of Proteomics. 2018. Vol. 15. No. 11. P. 873-886. 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
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
Priezjev N. Slow relaxation dynamics in binary glasses during stress-controlled, tension-compression cyclic loading // Computational Materials Science. 2018. Vol. 153. P. 235-240. doi
Priezjev N. Molecular dynamics simulations of the mechanical annealing process in metallic glasses: Effects of strain amplitude and temperature // Journal of Non-Crystalline Solids. 2018. Vol. 479. P. 42-48. doi
Priezjev N. The effect of cryogenic thermal cycling on aging, rejuvenation, and mechanical properties of metallic glasses // Journal of Non-Crystalline Solids. 2019. Vol. 503-504. P. 131-138. 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. Structural transformations and mechanical properties of porous glasses under compressive loading // Journal of Non-Crystalline Solids. 2018. Vol. 500. P. 1-10. 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
Kirova E. M., Pisarev V. The behavior of stress correlations and glass transition temperature in liquid aluminum at cooling and heating process // Journal of Physics: Conference Series. 2018. Vol. 946. P. 012115-1-012115-7. 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.
Efremov R., Pyrkova D. V., Krylov N. Fine Tuning of Microscopic Properties in Two-Component Zwitterionic- Anionic Lipid Bilayers: Determinant Role of H-Bonding // Biophysical Journal. 2018. Vol. 114. No. 3. P. 601А-601А.
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
Gaydukov R. Double-deck structure in the problem of a compressible flow along a plate with small localized irregularities on the surface // European Journal of Mechanics - B/Fluids. 2018. Vol. 71. P. 59-65. 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
Семенов В. П., Тимофеев А. В. Параметрический резонанс и перенос энергии в пылевой плазме // Математическое моделирование. 2018. Т. 30. № 2. С. 3-17.
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.
