- Structure and nanomechanics of fibrin polymers
- Nanomechanics of viral capsids
- Nanomechanics of supersecondary structures
- Molecular dynamics simulations of the bacterial/eukaryotic cell walls and cell membranes and their interactions with antibacterial drugs and drug-like molecules
- Molecular mechanisms of Signaling and Adaptation in Prokaryotic Receptors
- Computational models for coarse-grained modeling on GPU
- Agent-based modeling of biological systems
Laboratory of Computer and Mathematical Modeling of Biological Systems
Laboratory of Computer and Mathematical Modeling of Biological Systems was founded in Moscow Institute of Physics and Technology in 2016. It is lead by Artem Zhmurov, Philipp Orekhov and Valeri Barsegov, a visiting professor from University of Massachusetts at Lowell
Laboratory web-page: http://hpc.mipt.ru/zhmurov/lab/
Artem Zhmurov

Head of laboratory
Education
Professional experience
Contacts
Phone | +7 926 793 0460 |
zhmurov@gmail.com |
Philipp Orekhov

Deputy head of laboratory, senior researcher
Education
Contacts
Phone | +7 968 463 3964 |
ps.orekhov@gmail.com |
Valeri Barsegov

Visiting scientist, senior researcher
Education
Olga Kononova

Visiting scientist
Education
Nikolay Shuvalov

Education
Kirill Minin

Education
Evgeny Klyuchnikov

Education
Ilya Rozhok

Education
Ilya Kirillov

Education
Nikita Berezyuk

Education
Ksenia Yagafarova
Education
Anna Goncharova

Education
Tatyana Selezneva

Education
2017
Journal of the American Chemical Society
Dynamic Transition from α-Helices to β-Sheets in Polypeptide Coiled-Coil Motifs
A. Zhmurov, K.A. Minin, K.A. Marx, P.K. Purohit, V. Barsegov
16168–16177 page
Moscow Institute of Physics and Technology
Photochemistry and Photobiology
P. Orekhov, A. Bothe, H.‐J. Steinhoff, K.V. Shaitan, S. Raunser, D. Fotiadis, R. Schlesinger, J.P. Klare, M. Engelhard
796-804 page
Moscow Institute of Physics and Technology
Journal of Physics: Condensed Matter
Dynamics of microtubules: highlights of recent computational and experimental investigations
V. Barsegov, J. Ross, R. Dima
Moscow Institute of Physics and Technology
Journal of Physical Chemistry
Conformational Flexibility and Self-Association of Fibrinogen in Concentrated Solutions
Y.F. Zuev, R.I. Litvinov, A.E. Sitnitsky, B.Z. Idiyatullin, D.R. Bakirova, D.K. Galanakis, A. Zhmurov, V. Barsegov, J.W. Weisel
7833–7843 page
Moscow Institute of Physics and Technology
Biochemistry
Mechanistic Basis for the Binding of RGD- and AGDV-Peptides to the Platelet Integrin αIIbβ3
O. Kononova, R.I. Litvinov, D.S. Blokhin, V.V. Klochkov, J.W. Weisel, J.S. Bennett, V. Barsegov
1932–1942 page
Moscow Institute of Physics and Technology
Applied Nanoindentation in Advanced Materials
Nanoindentation in silico of Biological Particles
O. Kononova, K.A. Marx, V. Barsegov
Moscow Institute of Physics and Technology
Series of Computational Biophysics: Coarse-grained Modeling of Biomolecules
Mechanics of Viruses
O. Kononova, A. Zhmurov, K.A. Marx, V. Barsegov
Moscow Institute of Physics and Technology
Journal of Biomolecular Structure and Dynamics
An anti-DNA antibody prefers damaged dsDNA over native
N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, R.I. Litvinov
219-232 page
Moscow Institute of Physics and Technology
2013
Computational Research and Modelling
Force-induced phase transition from α-Helices to β-Sheets in fibrous proteins
A. Zhmurov, O. Kononova, Y. Kholodov, V. Barsegov
Moscow Institute of Physics and Technology
2012
Journal of the American Chemical Society
Mechanical transition from α-Helical coiled-coils to β-Sheets in Fibrin(ogen)
A. Zhmurov, O. Kononova, R.I. Litvinov, R.I. Dima, V. Barsegov, J.W. Weisel
20396-20402 page
Moscow Institute of Physics and Technology
2014
PloS ONE
M.E. Bozdaganyan, P.S. Orekhov, A.K. Shaytan, K.V. Shaitan
Moscow Institute of Physics and Technology
2015
PloS Computational Biology
P.S. Orekhov, D. Klose, A.Y. Mulkidjanian, K.V. Shaitan, M. Engelhard, J.P. Klare, H.-J. Steinhoff
Moscow Institute of Physics and Technology
2016
Journal of Computational Chemistry
A. Alekseenko, O. Kononova, Y. Kholodov, K.A. Marx, V. Barsegov
1537-1551 page
Moscow Institute of Physics and Technology
Structure
Structural Basis of Interfacial Flexibility in Fibrin Oligomers
A. Zhmurov, A.D. Protopopova, R.I. Litvinov, P. Zhukov, A.R. Mukhitov, J.W. Weisel, V. Barsegov
1907-1917 page
Moscow Institute of Physics and Technology
Biomacromolecules
J. Snijder, O. Kononova, I.M. Barbu, C. Uetrecht, W. F. Rurup, R.J. Burnley, M.S.T. Koay, J.J.L.M. Cornelissen, W.H. Roos, V. Barsegov, G.J.L. Wuite, A.J.R. Heck
2522–2529 page
Moscow Institute of Physics and Technology
PloS Computational Biology
Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles
O. Kononova, J. Snijder, Y. Kholodov, K.A. Marx, G.J.L. Wuite, W.H. Roos, V. Barsegov
Moscow Institute of Physics and Technology
BioNanoScience
Essential Dynamics of DNA-Antibody Complexes
N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, R.I. Litvinov
543–549 page
Moscow Institute of Physics and Technology
Molecular Biology
Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment
N.I. Akberova, A.A. Zhmurov, T.A. Nevzorova, R.I. Litvinov
442-451 page
Moscow Institute of Physics and Technology
2011
Journal of Physical Chemistry
A. Zhmurov, K. Rybnikov, Y. Kholodov, V. Barsegov
5278-5288 page
Moscow Institute of Physics and Technology
Computational Research and Modelling
Efficient generators of pseudorandom numbers for molecular modeling on Graphics Processors
A.A. Zhmurov, I.I. Morozov, Y.A. Kholodov, V.A. Barsegov, A.S. Kholodov
296-311 page
Moscow Institute of Physics and Technology
Mathematical Modeling
Modeling micromechanics on Graphics Processors using Langevin Dynamics
A.A. Zhmurov, V.A. Barsegov, S.V. Trifonov, Y.A. Kholodov, A.S. Kholodov
133-156 page
Moscow Institute of Physics and Technology
2010
Proteins
A. Zhmurov, R.I. Dima, Y. Kholodov, V. Barsegov
2984-2999 page
Moscow Institute of Physics and Technology
Perelman School of Medicine, University of Pennsylvania, USA
Pennsylvania
John Weisel and Rustem Litvinov
Lomonosov Moscow State University
Moscow
Ilya Kovalenko (Dept. of Biophysics, School of Biology), Konstantin Shaitan (Dept. of Bioengineering, School of Biology), Fazli Ataullakhanov and Nikita Gudimchuk (School of Physics)
University of Osnabrück, Germany
Osnabruck
Heinz-Jürgen Steinhoff (Experimental Physics/Macromolecular Structure group)
Russian Foundation for Basic Research
Grant #17-00-00479: "A multi-scale molecular modeling study of tubulin and its complex with Ndc80"
Grant #15-37-21027: "A molecular modeling study of the protein fibers nanomechanics"
Grant #15-01-06721: "Multi-scale molecular modeling study of fibrin oligomers, protofibrils, fibrin fibers and fibrin gel"
Russian Science Foundation
Grant #17-71-10202: "Describing intra- and inter-protein interactions using co-evolution analysis"

5-100 Competitive Growth program, Moscow Institute of Physics and Technology
Laboratory startup grant