Выходит 6 номеров в год
ISSN Печать: 1543-1649
ISSN Онлайн: 1940-4352
Indexed in
Parallel Multiscale Modeling of Biopolymer Dynamics with Hydrodynamic Correlations
Краткое описание
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic molecular dynamics with a mesoscopic lattice Boltzmann method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. We describe an efficient parallel implementation of the method that exhibits excellent scalability on the Blue Gene platform. We investigate both dynamical and statistical aspects of the translocation process by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.
-
Bernaschi Massimo, Fatica Massimiliano, Melchionna Simone, Succi Sauro, Kaxiras Efthimios, A flexible high-performance Lattice Boltzmann GPU code for the simulations of fluid flows in complex geometries, Concurrency and Computation: Practice and Experience, 22, 1, 2010. Crossref
-
Bernaschi M., Melchionna S., Succi S., Fyta M., Kaxiras E., Sircar J.K., MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations, Computer Physics Communications, 180, 9, 2009. Crossref
-
Ilg Patrick, Mavrantzas Vlasis, öttinger Hans Christian, Multiscale Modeling and Coarse Graining of Polymer Dynamics: Simulations Guided by Statistical Beyond-Equilibrium Thermodynamics, in Modeling and Simulation in Polymers, 2010. Crossref
-
Bernaschi Massimo, Succi Sauro, Fyta Maria, Kaxiras Efthimios, Melchionna Simone, Sircar Jayanta K., MUPHY: A parallel high performance MUlti PHYsics/Scale code, 2008 IEEE International Symposium on Parallel and Distributed Processing, 2008. Crossref
-
Peng Zhangli, Chen Yeng-Long, Lu Huijie, Pan Zehao, Chang Hsueh-Chia, Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs, Computational Particle Mechanics, 2, 4, 2015. Crossref
-
Alapati Suresh, Che Woo, Suh Yong, Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study, Materials, 6, 9, 2013. Crossref
-
Afrasiabian Navid, Denniston Colin, The journey of a single polymer chain to a nanopore, Soft Matter, 16, 39, 2020. Crossref