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Regular version of the site

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:


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., Makeev M. The influence of periodic shear on structural relaxation and pore redistribution in binary glasses // Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 2018
Priezjev N. The potential energy states and mechanical properties of thermally cycled binary glasses // Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 2018
Priezjev N., Makeev M. Structural transformations during periodic deformation of low-porosity amorphous materials // Modelling and Simulation in Materials Science and Engineering. 2018 doi
Priezjev N. The yielding transition in periodically sheared binary glasses at finite temperature // Computational Materials Science. 2018. Vol. 150. P. 162. 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
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., Liu Q. The influence of complex thermal treatment on mechanical properties of amorphous materials // Computational Materials Science. 2018
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.
Stegailov V., Dlinnova E., Ismagilov T., Khalilov M., Kondratyuk N., Makagon D., Semenov A., Simonov A., Smirnov G., Timofeev A. Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular-dynamics calculations // International Journal of High Performance Computing Applications. 2019
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
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
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.
Polyansky A. A., Bocharov E. V., Velghe A. I., Kuznetsov Andrey S., Bocharova O. V., Urban A. S., Arseniev A. S., Zagrovic B., Demoulin J., Efremov Roman G. Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain // Biochimica et Biophysica Acta - General Subjects. 2019. Vol. 1863. No. 1. P. 82-95. 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