Результаты поиска по 'molecular dynamics method':
Найдено статей: 23
  1. Lihachev I.V., Galzitskaya O.V., Balabaev N.K.
    Investigation of C-Cadherin mechanical properties by Molecular Dynamics
    Computer Research and Modeling, 2013, v. 5, no. 4, pp. 727-735

    The mechanical stability of cell adhesion protein Cadherin with explicit model of water is studied by the method of molecular dynamics. The protein in apo-form and with the ions of different types (Ca2+, Mg2+, Na+, K+) was unfolding with a constant speed by applying the force to the ends. Eight independent experiments were done for each form of the protein. It was shown that univalent ions stabilize the structure less than bivalent one under mechanical unfolding of the protein. A model system composed of two amino acids and the metal ion between them demonstrates properties similar to that of the cadherin in the stretching experiments. The systems with potassium and sodium ions have less mechanical stability then the systems with calcium and magnesium ions.

    Keywords: C-Cadherin, molecular dynamics, bivalent and univalent ions.
    Views (last year): 5.
  2. Podryga V.O., Polyakov S.V.
    3D molecular dynamic simulation of thermodynamic equilibrium problem for heated nickel
    Computer Research and Modeling, 2015, v. 7, no. 3, pp. 573-579

    This work is devoted to molecular dynamic modeling of the thermal impact processes on the metal sample consisting of nickel atoms. For the solution of this problem, a continuous mathematical model on the basis of the classical Newton mechanics equations has been used; a numerical method based on the Verlet scheme has been chosen; a parallel algorithm has been offered, and its realization within the MPI and OpenMP technologies has been executed. By means of the developed parallel program, the investigation of thermodynamic equilibrium of nickel atoms’ system under the conditions of heating a sample to desired temperature has been executed. In numerical experiments both optimum parameters of calculation procedure and physical parameters of analyzed process have been defined. The obtained numerical results are well corresponding to known theoretical and experimental data.

    Keywords: molecular dynamic simulation, nickel, EAM, temperature, thermostat, Newton mechanics equations, parallel algorithm and program, MPI and OpenMP technologies.
    Views (last year): 2.
  3. Shefov K.S., Stepanova M.M.
    An implementation of a parallel global minimum search algorithm with an application to the ReaxFF molecular dynamic force field parameters optimization
    Computer Research and Modeling, 2015, v. 7, no. 3, pp. 745-752

    Molecular dynamic methods that use ReaxFF force field allow one to obtain sufficiently good results in simulating large multicomponent chemically reactive systems. Here is represented an algorithm of searching optimal parameters of molecular-dynamic force field ReaxFF for arbitrary chemical systems and its implementation. The method is based on the multidimensional technique of global minimum search suggested by R.G. Strongin. It has good scalability useful for running on distributed parallel computers.

    Keywords: numerical simulation, molecular dynamics, reactive force field, chemically reactive systems, parameter optimization, parallel algorithm, absolute extremum search.
    Views (last year): 1. Citations: 1 (RSCI).
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