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/

Laboratory employs 9 MIPT students, including 3 undergraduate, 5 graduate and 1 PhD student. The key research objectives of the laboratory is (1) to develop novel GPU-based computational approaches for biomolecular modeling and (2) to use widely avalible and in-house software to investigate biochemical, biomechanical and biological properties of various biomolecules. We use wide variety of molecular modeling techniques, including explicit solvent Molecular Dynamics (in NAMD, Gromacs, ACEMD), implicit solvent Langevin Dynamics simulations (using our own software), coarse-grained molecular modeling (SOP-GPU software package, MARTINI force-field in Gromacs and our own codes), Monte-Carlo simulations. We work with various biological molecules, including fibrinogen, fibrin oligomers, protofibrils, fibrin fibers and fibrin gel; viral capsids, both containing DNA and not; α-helical coiled coils and β-helical structures; bacterial receptors and biomembranes.

Research areas:
  • 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

Artem Zhmurov

Head of laboratory

Education
2014 — PhD in Chemistry, Biochemistry Option, University of Massachusetts at Lowell (advisers: Valeri Barsegov and Kenneth Marx) [Thesis] 2012 — PhD in Mathematics and Physics (к.ф.-м.н.), Moscow Institute of Physics and Technolody (advisers: Yaroslav Kholodov and Valeri Barsegov) [In Russian: Диссертация, Автореферат] 2006 — M.S. in Applied Mathematics and Physics, Moscow Institute of Physics and Technolody (adviser: Alexey Evdokimov) 2004 — B.S. in Applied Mathematics and Physics, Moscow Institute of Physics and Technolody (adviser: Andrey Galkin)
Professional experience
Teaching/Research Assotiate, Division of Computational Mathematics Post-Doctoral Fellow, Laboratory of Human Physiology Moscow Institute of Physics and Technology
Academic Interests
Contacts
Phone +7 926 793 0460
Email zhmurov@gmail.com

Philipp Orekhov

Deputy head of laboratory, senior researcher

Education
PhD in physics and mathematics
Contacts
Phone +7 968 463 3964
Email ps.orekhov@gmail.com

Valeri Barsegov

Visiting scientist, senior researcher

Education
PhD in chemistry

Olga Kononova

Visiting scientist

Education
Master of Science

Nikolay Shuvalov

Education
Doctoral student

Kirill Minin

Education
Doctoral student

Evgeny Klyuchnikov

Education
Graduate student

Ilya Rozhok

Education
Graduate student

Ilya Kirillov

Education
Graduate student

Nikita Berezyuk

Education
Graduate student

Ksenia Yagafarova

Education
Graduate student

Anna Goncharova

Education
Graduate student

Tatyana Selezneva

Education
Graduate student

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

Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers

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

2015

PloS Computational Biology

Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

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

SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies

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

Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin

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

Generation of Random Numbers on Graphics Processors: Forced Indentation In Silico of the Bacteriophage HK97

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

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

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

John Weisel and Rustem Litvinov

University of Massachusetts at Lowell, USA
Lomonosov Moscow State University

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

Heinz-Jürgen Steinhoff (Experimental Physics/Macromolecular Structure group)

Kazan Federal University, Russia
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