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- A. S. Lemak, N. K. Balabaev
- Journal of Computational Chemistry
- 1996

This article describes the collisional dynamics (CD) method adapted for molecules with geometrical constraints within a description using Cartesian coordinates for the atoms. In the CD method, stochastic collisions with virtual particles are included in usual molecular dynamics simulations to couple the considered polymer molecule to a solvent. The actual… (More)

- A L Rabinovich, N K Balabaev, M G Alinchenko, V P Voloshin, N N Medvedev, P Jedlovszky
- The Journal of chemical physics
- 2005

Computer simulation of the liquid crystalline phase of five different hydrated unsaturated phosphadidylcholine (PC) lipid bilayers, i.e., membranes built up by 18:0/18:1omega9cis PC, 18:0/18:2omega6cis PC, 18:0/18:3omega3cis PC, 18:0/20:4omega6cis PC, and 18:0/22:6omega3cis PC molecules have been performed on the isothermal-isobaric ensemble at 1 atm and… (More)

- Anna V Glyakina, Nikolay K Balabaev, Oxana V Galzitskaya
- Protein and peptide letters
- 2010

Mechanical properties of (protein L)(5) have been recently investigated by single-molecule force spectroscopy. It has been demonstrated that the unfolding of individual domains proceeds through a two-state mechanism. Here, we study mechanical properties of protein L at the atomic level under stretching at constant velocity using molecular dynamics… (More)

- A V Glyakina, N K Balabaev, O V Galzitskaya
- The Journal of chemical physics
- 2009

Mechanical unfolding of proteins L and G, which have similar structures, is considered in this work, and the question arises what changes happen in the unfolding pathways under the action of mechanical force. Molecular dynamics simulations with explicit water (134 trajectories) demonstrate that the mechanical unfolding with constant force occurs through at… (More)

- A. L. Rabinovich, V. V. Kornilov, N. K. Balabaev, F. A. M. Leermakers, A. V. Filippov
- Biochemistry (Moscow) Supplement Series A…
- 2007

Properties of hydrated unsaturated phosphatidylcholine (PC) lipid bilayers containing 40 mol % cholesterol and of pure PC bilayers have been studied. Various methods were applied, including molecular dynamics simulations, self-consistent field calculations, and the pulsed field gradient nuclear magnetic resonance technique. Lipid bilayers were composed of… (More)

- F A M Leermakers, A L Rabinovich, N K Balabaev
- Physical review. E, Statistical, nonlinear, and…
- 2003

A molecular-level self-consistent-field (SCF) theory is applied to model the lipid bilayer structures composed of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (18:0/18:1 omega 9cis PC) and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (18:0/22:6 omega 3cis PC). As compared to earlier attempts to model (saturated) PC membranes several… (More)

- A L Rabinovich, P O Ripatti, N K Balabaev, F A M Leermakers
- Physical review. E, Statistical, nonlinear, and…
- 2003

Molecular dynamics simulations, using the collision dynamics method, were carried out for hydrated bilayers of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (18:0/18:1 omega 9cis PC, SOPC) and 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (18:0/22:6 omega 3cis PC, SDPC). The simulation cells of the two bilayers consisted of 96 SOPC… (More)

- Anna V Glyakina, Ilya V Likhachev, Nikolay K Balabaev, Oxana V Galzitskaya
- Proteins
- 2014

Here, we study mechanical properties of eight 3-helix proteins (four right-handed and four left-handed ones), which are similar in size under stretching at a constant speed and at a constant force on the atomic level using molecular dynamics simulations. The analysis of 256 trajectories from molecular dynamics simulations with explicit water showed that the… (More)

- Mikhail A Mazo, Leonid I Manevitch, +4 authors Gregory C Rutledge
- The journal of physical chemistry. B
- 2008

We present the results of molecular dynamics (MD) simulation of the structure and thermomechanical behavior of Wyoming-type Na+-montmorillonite (MMT) with poly(ethylene oxide) (PEO) oligomer intercalates. Periodic boundary conditions in all three directions and simulation cells containing two MMT lamellae [Si248Al8][Al112Mg16]O640[OH]128 oriented parallel… (More)

- Mikhail A Mazo, Leonid I Manevitch, +4 authors Gregory C Rutledge
- The journal of physical chemistry. B
- 2008

The structure and mechanical properties of clay nanoparticles is a subject of growing interest because of their numerous applications in engineering. We present the results of molecular dynamics simulation for a single nanoplate of pyrophyllite - a 2:1 clay mineral consisting of two tetrahedral sheets of SiO4 and an intervening octahedral AlO6 sheet.… (More)