title: Molecular dynamics extended for fluctuating networks: application to water.
abstract: Molecular simulation models are increasingly important tools in efforts to understand the role that water plays in biochemical processes. However, existing models of water have limited capacity to deal with the characteristics of hydrogen bond networks. This article proposes a new fluctuating network (FN) algorithm as an extension of the standard molecular dynamics algorithm. The new algorithm allows for the simulation of a molecular system based on an underlying network, such as the hydrogen bond network in water. This algorithm distinguishes strong from weak network connections, applying a potential that best describes the specific connection behavior. We model liquid water with this new technique using a single-site, isotropic, short-range potential. We successfully reproduce liquid water's signature molecular spacing (as represented by the radial distribution function) and characterize its dynamic properties including the exponential hydrogen bond lifetime distribution, diffusion rate, and average hydrogen bonds per molecule. The FN algorithm allows exploration of the behavior of networked systems where explicit coordination limits are required. As such it could also be used to model covalent interactions, reaction dynamics, and applied to simulation of cellular networks.
authors.affiliation: Monash University, Faculty of Information Technology, Clayton Campus, Bldg. 63, Wellington Road, Clayton 3800, Australia. jenny.kashmirian@gmail.com
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Kashmirian
authors.forename: Alfred
authors.initials: A
authors.lastname: Uhlherr
authors.forename: Alan
authors.initials: A
authors.lastname: Dorin
authors.forename: David G
authors.initials: DG
authors.lastname: Green
mesh_terms: D000465:Algorithms; D004058:Diffusion; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water