title: Implicit Time Integration for Multiscale Molecular Dynamics Using Transcendental Padé Approximants.
abstract: Molecular dynamics systems evolve through the interplay of collective and localized disturbances. As a practical consequence, there is a restriction on the time step imposed by the broad spectrum of time scales involved. To resolve this restriction, multiscale factorization was introduced for molecular dynamics as a method that exploits the separation of time scales by coevolving the coarse-grained and atom-resolved states via Trotter factorization. Developing a stable time-marching scheme for this coevolution, however, is challenging because the coarse-grained dynamical equations depend on the microstate; therefore, these equations cannot be expressed in closed form. The objective of this paper is to develop an implicit time integration scheme for multiscale simulation of large systems over long periods of time and with high accuracy. The scheme uses Padé approximants to account for both the stochastic and deterministic features of the coarse-grained dynamics. The method is demonstrated for a protein either undergoing a conformational change or migrating under the influence of an external force. The method shows promise in accelerating multiscale molecular dynamics without a loss of atomic precision or the need to conjecture the form of coarse-grained governing equations.
authors: Department of Chemistry and Center for Theoretical and Computational Nanoscience, Indiana University , Bloomington, Indiana 47405, United States.
authors: Andrew
authors: A
authors: Abi Mansour
authors: Department of Chemistry and Center for Theoretical and Computational Nanoscience, Indiana University , Bloomington, Indiana 47405, United States.
authors: Peter J
authors: PJ
authors: Ortoleva
mesh_terms: D001886:Bordetella pertussis / Q000737:chemistry*; D036022:Capsid Proteins / Q000737:chemistry*; D052162:Human papillomavirus 16 / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D009038:Motion; D009856:Oncogene Proteins, Viral / Q000737:chemistry*; D030361:Papillomavirus Infections / Q000821:virology; D037342:Pertussis Toxin / Q000737:chemistry*; D011487:Protein Conformation; D013269:Stochastic Processes; D013816:Thermodynamics; D014917:Whooping Cough / Q000382:microbiology
chemical_list: D036022:Capsid Proteins; C114580:HPV L1 protein, Human papillomavirus; D009856:Oncogene Proteins, Viral; D037342:Pertussis Toxin