Paper Info
Title
A Mathematical Model for Intracellular HIV-1 Gag Protein Transport and its Parallel Numerical Simulations.
Abstract
In this paper, we develop a mathematical model for intracellular HIV-1 gag protein tracking based on the hypotheses that gag proteins employ kinesins for active transport on microtubules and they can also diffuse in cytoplasm. This results in a time-dependent convection-diffusion equation in polar coordinates along with appropriate boundary and initial conditions. A finite element method based on tracking characteristics is established for accurately solving this type of transport problems. The numerical method has been implemented in C++. To validate the mathematical model, we perform numerical simulations on the virion timing, i.e., the time needed for HIV-1 virions (puncta) to first appear on the cell plasma membrane. Numerical simulation results and biological experimental data agree principally. For in silico analysis of gag protein tracking, the numerical simulation code needs to be executed repeatedly on a large collection of sets of model parameters. We further investigate code parallelization strategies using MPI and OpenMP.
Year
DOI
Venue
2012
10.1016/j.procs.2012.04.073
Procedia Computer Science
Keywords
Field
DocType
Active transport,cytoplasm,diffusion,finite element methods,gag proteins,HIV-1,microtubules,MPI,OpenMP
Mathematical optimization,Biological system,Computer simulation,Computer science,Kinesin,Intracellular,Polar coordinate system,Theoretical computer science,Finite element method,Numerical analysis,Group-specific antigen,In silico
Journal
Volume
ISSN
Citations 
9
1877-0509
1
PageRank 
References 
Authors
0.39
4
5
Name
Order
Citations
PageRank
Jiangguo Liu19011.37
Roberto Muñoz-Alicea210.39
Tingwen Huang35684310.24
Simon Tavener46811.86
Chao-Ping Chen55812.24