Soft matter systems simulated by molecular methods

Molecular simulations are increasingly being used to interpret experiments and to test possible design variations. Experimental work on complex condensed matter spans a broad range of temporal and spatial scales, from femtosecond dynamics and atomistic detail to real-time macroscopic phenomena. A toolbox of computational techniques has been developed over the years that can be used to model a system depending on its relevant time and length scales. Atomistic level molecular dynamics (AMD) simulations have provided considerable insight into specific interactions that depend sensitively on the chemical nature of the functional groups involved. We employ AMD in the modeling of the unfolding of spectrin family proteins to get a better understanding of the role of protein-water hydrogen bonding interactions in the folding/unfolding pathways. Results demonstrate the role played by the α-helical linker connecting sequential repeats in the unfolding pathways and the overall stability of the tandem constructs, as well as the relative stability of individual repeats under force. Coarse grain (CG) models, which retain close connections to the underlying atomistic representation, have enjoyed a revival and are currently being developed to faithfully replicate atomistic interactions. CG models involve representing a group of atoms by a single sphere with the aim of studying events which occur on timescales of hundreds of nanoseconds to milliseconds and spatial scales of microns. This makes CG modeling the method of choice for the description of polymeric systems. In our research, we use CG models and also simpler dissipative particle dynamics (DPD) methods to simulate aqueous block copolymer systems at molecular weights relevant to the experimental conditions. We present measurements on the mechanical properties of block copolymers assemblies that are comparable to experimental values and provide insight into the structural properties and mechanisms of phase transformations