title: Prospective on multiscale simulation of virus-like particles: Application to computer-aided vaccine design.
abstract: Simulations of virus-like particles needed for computer-aided vaccine design highlight the need for new algorithms that accelerate molecular dynamics. Such simulations via conventional molecular dynamics present a practical challenge due to the millions of atoms involved and the long timescales of the phenomena of interest. These phenomena include structural transitions, self-assembly, and interaction with a cell surface. A promising approach for addressing this challenge is multiscale factorization. The approach is distinct from coarse-graining techniques in that it (1) avoids the need for conjecturing phenomenological governing equations for coarse-grained variables, (2) provides simulations with atomic resolution, (3) captures the cross-talk between disturbances at the atomic and the whole virus-like particle scale, and (4) achieves significant speedup over molecular dynamics. A brief review of multiscale factorization method is provided, as is a prospective on its development.
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, United States.
authors.forename: Andrew
authors.initials: A
authors.lastname: Abi Mansour
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, United States.
authors.forename: Yuriy V
authors.initials: YV
authors.lastname: Sereda
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, United States.
authors.forename: Jing
authors.initials: J
authors.lastname: Yang
authors.affiliation: Center for Theoretical and Computational Nanoscience, Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN, United States. Electronic address: ortoleva@indiana.edu.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Ortoleva
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D055808:Drug Discovery / Q000379:methods*; D006801:Humans; D056004:Molecular Dynamics Simulation; D058425:Vaccines, Virus-Like Particle / Q000737:chemistry / Q000235:genetics / Q000276:immunology* / Q000302:isolation & purification
chemical_list: D058425:Vaccines, Virus-Like Particle
keywords: Computer-aided vaccine design; Molecular dynamics; Multiscale factorization; Virus-like particle