DOI: https://doi.org/10.26089/NumMet.v25r434

Using parallel computing in the transition interface sampling method implementation

Authors

  • Sergey V. Poluyan
  • Nikolay M. Ershov

Keywords:

transition interface sampling
protein-protein interaction
reaction rate constant
MPI
Intel oneTBB

Abstract

Numerical estimation of the reaction rate constant is an important task in the field of bioinformatics. This constant provides information on the binding kinetics of the protein complex components. One approach to perform this estimation is to apply the transition interface sampling method, which is based on the simulation of transitions between different states of the modeled system along several trajectories. Each state and transition is characterized by the estimated energy of the interaction between the components of a protein complex. In this paper, we provide a way to apply parallel computing to multiple trajectory construction. We present the principles of using MPI technology and Intel oneTBB library, along with the demonstration of various experimental results. The purpose of the study is to determine the most effective parallel programming tool for constructing multiple trajectories in the transition interface sampling method within the given computational systems.

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Published

2024-11-20

Issue

Vol. 25 (2024): Issue 4.

Section

Methods and algorithms of computational mathematics and their applications

Author Biographies

Sergey V. Poluyan

Dubna State University,
Institute of System Analysis and Management
• Senior Teacher

Nikolay M. Ershov

Lomonosov Moscow State University,
Faculty of Computational Mathematics and Cybernetics
• Senior Researcher

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Copyright (c) 2024 С. В. Полуян, Н. М. Ершов

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