Simulations of biomolecular assembly processes at interfaces

Although biomolecular folding, binding, and assembly are usually conceived of as occurring in a bulk aqueous solution, there are numerous instances of such processes occurring near interfaces within cells. Examples of these interfaces include very large macromolecules, membranes bounding intracellular compartments and the cell membrane itself. Interfacial behavior of biomolecules is also important in several technological applications such as DNA-based nanomaterials, biosensors, and microarrays. In this talk, I will discuss several ongoing research problems in my group that illustrate rich behavior exhibited by biomolecules (protein, DNA) at interfaces

Structure, thermodynamics and dynamics of confined and supercooled liquids

textStatic measures such as density and entropy, which are intimately connected to structure, have featured prominently in modern thinking about the dynamics of the liquid state. In this dissertation, we explore the connections between self-diffusivity, density, available space, and excess entropy in two non-trivial problems in liquid state theory, confined and supercooled liquids. We present exact simulation data for the relationship between self-diffusivity and excess entropy for a wide range of simple of simple fluids (i.e. hard-sphere, Lennard-Jones and square-well) confined to pores with a variety of different sizes and fluid-wall interations. Our main finding is that, at a given temperature, self-diffusivity of the confined fluids collapses onto the bulk behavior when plotted versus excess entropy. In other words, the only information required to "predict" the implications of confinement for the single-particle dynamics is the bulk fluid behavior at a given temperature and the excess entropy of the confined fluid. This should prove practically useful given that the bulk behavior is well known for these fluid systems, and the excess entropy of the confined fluids can be readily estimated from classical density functional theory. We also show that the self-diffusivity of the confined fluids approximately collapses onto the data for the corresponding bulk fluid when plotted versus the average packing fraction (which is based on total, rather than center accessible volume). For continuous interaction potentials such as Lennard-Jones, calculation of effective packing fraction requires knowledge of both the number density of the fluid and a temperature-dependent Boltzmann diameter associated with the repulsive part of the interparticle interactions. We suggest a way to calculate this effective diameter, which to a very good approximation, collapse the temperature- and density-dependent data for the self-diffusivity of the bulk Lennard-Jones fluid onto hard-sphere fluid data plotted versus the fluid's effective packing fraction. Finally, we found that the self-diffusivities of several model systems in their supercooled state also scale exponentially not only with the excess entropy, but also with the two-body contribution to the excess entropy obtained from the pair correlation function of the fluid. The latter observation is particularly interesting because it provides direct evidence of a quantitative link between the dynamics and the average structural order of supercooled liquids. Whether such a connection could indeed be discovered is part of a long-standing question in the study of liquids.Chemical Engineerin

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids

We calculate the pair diffusion coefficient D(r) as a function of the distance r between two hard-sphere particles in a dense monodisperse suspension. The distance-dependent pair diffusion coefficient describes the hydrodynamic interactions between particles in a fluid that are central to theories of polymer and colloid dynamics. We determine D(r) from the propagators (Green's functions) of particle pairs obtained from discontinuous molecular dynamics simulations. At distances exceeding 3 molecular diameters, the calculated pair diffusion coefficients are in excellent agreement with predictions from exact macroscopic hydrodynamic theory for large Brownian particles suspended in a solvent bath, as well as the Oseen approximation. However, the asymptotic 1/r distance dependence of D(r) associated with hydrodynamic effects emerges only after the pair distance dynamics has been followed for relatively long times, indicating non-negligible memory effects in the pair diffusion at short times. Deviations of the calculated D(r) from the hydrodynamic models at short distances r reflect the underlying many-body fluid structure, and are found to be correlated to differences in the local available volume. The procedure used here to determine the pair diffusion coefficients can also be used for single-particle diffusion in confinement with spherical symmetry.Comment: 6 pages, 5 figure

Relationship between thermodynamics and dynamics of supercooled liquids

Diffusivity, a measure for how rapidly a fluid self-mixes, shows an intimate, but seemingly fragmented, connection to thermodynamics. On one hand, the "configurational" contribution to entropy (related to the number of mechanically-stable configurations that fluid molecules can adopt) has long been considered key for predicting supercooled liquid dynamics near the glass transition. On the other hand, the excess entropy (relative to ideal gas) provides a robust scaling for the diffusivity of fluids above the freezing point. Here we provide, to our knowledge, the first evidence that excess entropy also captures how supercooling a fluid modifies its diffusivity, suggesting that dynamics, from ideal gas to glass, is related to a single, standard thermodynamic quantity.Comment: to appear in Journal of Chemical Physic