Geodesic
Using parallel computing in the transition interface sampling method implementation
Numerical methods and programming, Tome 25 (2024) no. 4, pp. 453-463

Voir la notice de l'article provenant de la source Math-Net.Ru

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.
Keywords: transition interface sampling, protein-protein interaction, MPI, Intel oneTBB.
Mots-clés : reaction rate constant 
@article{VMP_2024_25_4_a5,
     author = {S. V. Poluyan and N. M. Ershov},
     title = {Using parallel computing in the transition interface sampling method implementation},
     journal = {Numerical methods and programming},
     pages = {453--463},
     publisher = {mathdoc},
     volume = {25},
     number = {4},
     year = {2024},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/VMP_2024_25_4_a5/}
}
TY  - JOUR
AU  - S. V. Poluyan
AU  - N. M. Ershov
TI  - Using parallel computing in the transition interface sampling method implementation
JO  - Numerical methods and programming
PY  - 2024
SP  - 453
EP  - 463
VL  - 25
IS  - 4
PB  - mathdoc
UR  - http://geodesic.mathdoc.fr/item/VMP_2024_25_4_a5/
LA  - ru
ID  - VMP_2024_25_4_a5
ER  - 
%0 Journal Article
%A S. V. Poluyan
%A N. M. Ershov
%T Using parallel computing in the transition interface sampling method implementation
%J Numerical methods and programming
%D 2024
%P 453-463
%V 25
%N 4
%I mathdoc
%U http://geodesic.mathdoc.fr/item/VMP_2024_25_4_a5/
%G ru
%F VMP_2024_25_4_a5
S. V. Poluyan; N. M. Ershov. Using parallel computing in the transition interface sampling method implementation. Numerical methods and programming, Tome 25 (2024) no. 4, pp. 453-463. http://geodesic.mathdoc.fr/item/VMP_2024_25_4_a5/