Simulations of structure and nonequilibrium dynamics of soft materials

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Macroscopic material behavior is often intimately controlled by mechanisms on the molecular level. Computer simulations are uniquely positioned to illuminate such mechanisms and have the capability to address the complexity of real materials.  We propose to use molecular simulations to study two important phenomena that occur in soft materials. One of our goals will be to understand the atomistic origin of the strength of disordered materials such as amorphous polymer or metallic glasses, which are used in many everyday load-bearing applications.  Simulations can identify microscopic mechanisms of plasticity on the nanoscale and relate them to the macroscopic material response. The toughness or fracture energy is determined by a range of nonlinear processes that include yielding, cavitation and the formation of shear bands. Molecular level results will enable us to construct new models that bridge the multiple length and time scales from an atomistic description to the macroscopic continuum and that can quantitatively predict material behavior. We will also develop new computational methods to calculate the structure and function of charged macromolecules. Virtually all biomolecular systems such as proteins,  membranes and DNA contain side groups that separate in water into a charged macromolecule and many small "counterions". Computing the resulting long ranged electrostatic forces between these molecules currently poses a major bottleneck to numerical simulations. It is even more difficult to efficiently take into account the large dielectric contrast between the molecules and the surrounding solvent, which has a strong effect on many biological functions such as protein folding or the binding of ligands onto receptors.  Our new algorithms will be capable of treating such local polarization effects and examine their consequences for typical biophysical situations such as molecules near charged surfaces.  The technique will finally lead to more accurate models for the transport of ions through small molecular pores or channels, which is a dynamical regulatory process of great importance for the function of living cells.