title: Replica exchange methods in biomineral simulations.
abstract: Replica exchange methods are widely used for the purposes of accelerating the conformational sampling of small organic molecules and biopolymers and, to a lesser extent, to explore structural transformations in small Lennard-Jones clusters. Though the general ability of such approaches to enhance the sampling efficiency of both inorganic and organic systems makes replica exchange methods ideal candidates for simulations of biominerals and biomineralization, inherent limitations have largely restricted their applicability to small system sizes and/or short timescales, and their potential in this area has not yet been thoroughly explored. This chapter provides an introduction to the standard replica exchange molecular dynamics method and presents more advanced algorithmic variants, which are designed to improve the efficiency of the replica exchange procedure in large solvent-dominated systems.
authors.affiliation: Department of Geological Sciences, University of Delaware, Newark, Delaware, USA. Electronic address: afw@udel.edu.
authors.forename: Adam F
authors.initials: AF
authors.lastname: Wallace
mesh_terms: D000465:Algorithms; D002119:Calcium Carbonate / Q000737:chemistry*; D003460:Crystallization; D059625:Liquid-Liquid Extraction; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D044367:Phase Transition; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D012997:Solvents; D002119:Calcium Carbonate
keywords: Biomineralization; Calcium carbonate; Liquid–liquid separation; Molecular dynamics; Nucleation; Phase separation; Prenucleation clusters; Replica exchange; Simulation; Spinodal decomposition