title: A Multi-Scale Method for Dynamics Simulation in Continuum Solvent Models I: Finite-Difference Algorithm for Navier-Stokes Equation.
abstract: A multi-scale framework is proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent. This article reports our initial efforts to formulate the physical concepts necessary for coupling the two mechanics and develop a 3D numerical algorithm to simulate the solvent fluid via the Navier-Stokes equation. The numerical algorithm was validated with multiple test cases. The validation shows that the algorithm is effective and stable, with observed accuracy consistent with our design.
authors.affiliation: Department of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
authors.forename: Li
authors.initials: L
authors.lastname: Xiao
authors.affiliation: Department of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
authors.forename: Qin
authors.initials: Q
authors.lastname: Cai
authors.affiliation: Department of Mathematics, North Carolina State University, Raleigh, NC 27695.
authors.forename: Zhilin
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Mathematics, University of California, Irvine, CA 92697.
authors.forename: Hongkai
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Department of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 ; Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697.
authors.forename: Ray
authors.initials: R
authors.lastname: Luo