Computer and Mathematical Modelling of Biological Systems Lab

Laboratory web-pagehttp://hpc.mipt.ru/zhmurov/lab/

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 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 Computer and mathematical modelling of biological systems Lab

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)
Contacts
Phone +7 926 793 0460
Email zhmurov@gmail.com

Philipp Orekhov

Deputy Head of the Laboratory,
Senior Researcher

Contacts
Phone +7 968 463 3964
Email ps.orekhov@gmail.com
Perelman School of Medicine

Address
  • Phystech-BIO building, office 518 Moscow Institute of Physics and Technology, 9 Institusky per, Dolgoprudny, Moscow Area, 141701, Russia