The effect of salt on the dynamics of water molecules follows the Hofmeister series. For some "structure-making" salts, the self-diffusion coefficient of the water molecules, D, decreases with increasing salt concentration. For other "structure-breaking" salts, D increases with increasing salt concentration. In this work, the concentration and temperature dependence of the self-diffusion of water in electrolyte solutions is studied using molecular dynamics simulations and pulsed-field-gradient NMR experiments; temperature-dependent viscosities are also independently measured. Simulations of rigid, nonpolarizable models at room temperature show that none of the many models tested can reproduce the experimentally observed trend for the concentration dependence of D; that is, the models predict that D decreases with increasing salt concentration for both structure-breaking and structure-making salts. Predictions of polarizable models are not in agreement with experiment either. These results suggest that many popular water models do not accurately describe the dynamic nature of the hydrogen bond network of water at room temperature. The simulations are in qualitative agreement, however, with experimental results for the temperature dependence of water dynamics; simulations and experiment show an Arrhenius dependence of D with temperature, T, with added salt, that is, ln D ∼ 1/T, over a range of temperatures above the freezing point of water.

The effect of macromolecular crowding on the rates of association reactions are investigated using theory and computer simulations. Reactants and crowding agents are both hard spheres, and when two reactants collide they form product with a reaction probability, p(rxn). A value of p(rxn) < 1 crudely mimics the fact that proteins must be oriented properly for an association reaction to occur. The simulations show that the dependence of the reaction rate on the volume fraction of crowding agents varies with the reaction probability. For reaction probabilities close to unity where most of encounters between reactants lead to a reaction, the reaction rate always decreases as the volume fraction of crowding agents is increased due to the reduced diffusion coefficient of reactants. On the other hand, for very small reaction probabilities where, in most of encounters, the reaction does not occur, the reaction rate increases with the volume fraction of crowding agents--in this case, due to the increase probability of a recollision. The Smoluchowski theory refined with the radiation boundary condition and the radial distribution function at contact is in quantitative agreement with simulations for the reaction rate constant and allows the quantitative analysis of both effects separately.

We present molecular dynamics (MD) simulations of a single poly(N-isopropylacrylamide) (PNIPAM) chain in explicit water at temperatures between 270 and 320 K near the lower critical solution temperature (LCST). The force-fields of OPLS-AA and TIP4P/2005 are used for a PNIPAM chain and water molecules, respectively. Three independent simulations with durations of 1 μs are performed at each temperature for a 30-mer PNIPAM chain starting with three distinct conformations: extended, loosely collapsed, and tightly collapsed states. The simulation trajectories exhibit reversible conformational transitions between swollen- and collapsed-chain conformations, which has rarely been reported in previous simulation studies, with the overall transition occurring at different temperatures depending on the initial conformation. The inconsistency of the transition temperatures depending on the initial conformation implies that, in spite of the simulation duration of 1 μs distinctly longer than that in previous simulation studies, the conformational sampling from the MD simulations is not enough to draw conclusions on equilibrium properties. Instead of evaluating average properties, therefore, the focus is on dynamic changes in the chain conformation during reversible collapse-swelling transitions at each temperature. The simulation trajectories are analyzed in terms of the radius of gyration, intrachain distances, hydrophobic contacts, and chain-water and intrachain hydrogen bonding. In particular, the formation of stable intrachain hydrogen bonds is a signature of the tightly collapsed-chain conformations that persist, once formed, for the entire simulation duration.

We investigate structural alterations of random-loop polymers due to changes in the crowding condition, as a model to study environmental effects on the structure of chromosome subcompartments. The polymer structure is changed in a nonmonotonic fashion with an increasing density of crowders: condensed at small volume fractions; decondensed at high crowding volume fractions. The nonmonotonic behavior is a manifestation of the nontrivial distance dependence of the depletion interactions. We also show that crowding-induced structural alterations affect the access of binding proteins to the surface of polymer segments and are distinguished from structural changes due to the increased number of specific polymer loops.