Using molecular dynamics simulations we examine the effective interactions between two like-charged rods as a function of angle and separation. In particular, we determine how the competing electrostatic repulsions and multivalent-ion-induced attractions depend upon concentrations of simple and multivalent salts. We find that with increasing multivalent salt, the stable configuration of two rods evolves from isolated rods to aggregated perpendicular rods to aggregated parallel rods; at sufficiently high concentration, additional multivalent salt reduces the attraction. Monovalent salt enhances the attraction near the onset of aggregation and reduces it at a higher concentration of multivalent salt.

We present the first numerical simulation of actin-driven propulsion by elastic filaments. Specifically, we use a Brownian dynamics formulation of the dendritic nucleation model of actin-driven propulsion. We show that the model leads to a self-assembled network that exerts forces on a disk and pushes it with an average speed. This simulation approach is the first to observe a speed that varies nonmonotonically with the concentration of branching proteins (Arp2/3), capping protein, and depolymerization rate, in accord with experimental observations. Our results suggest a new interpretation of the origin of motility. When we estimate the speed that this mechanism would produce in a system with realistic rate constants and concentrations as well as fluid flow, we obtain a value that is within an order-of-magnitude of the polymerization speed deduced from experiments.

We report numerical simulation results for the force-velocity relation for actin-polymerization-driven motility. We use Brownian dynamics to solve a physically consistent formulation of the dendritic nucleation model with semiflexible filaments that self-assemble and push a disk. We find that at small loads, the disk speed is independent of load, whereas at high loads, the speed decreases and vanishes at a characteristic stall pressure. Our results demonstrate that at small loads, the velocity is controlled by the reaction rates, whereas at high loads the stall pressure is determined by the mechanical properties of the branched actin network. The behavior is consistent with experiments and with our recently proposed self-diffusiophoretic mechanism for actin-polymerization-driven motility. New in vitro experiments to measure the force-velocity relation are proposed.

The aggregation of two highly charged semiflexible polyelectrolytes in the presence of generalized linkers is studied theoretically. This model provides insight into biological processes such as DNA condensation and F-actin self-assembly induced by either multivalent counterions or bundling proteins. The interplay between the bending rigidity of the chains and their electrostatic interactions leads to an effective interlinker interaction that is repulsive at large distances and attractive at short ones. We find a rounded phase transition from a dilute linker gas where the chains form large loops to a dense disordered linker fluid where the chains are almost parallel. The onset of chain pairing occurs as soon as the free energy of a pair of chains becomes lower than that of two isolated chains and is located well within the crossover regime between the two linker phases. Our main findings are confirmed by molecular dynamics simulations of two semiflexible charged chains in a mixture of monovalent and polyvalent counterions. This simple model allows us to recover qualitative features of experimental aggregation diagrams of DNA and F-actin and can also be used to study DNA denaturation.

We report the effects of added acid in the reaction of singlet oxygen with trans-4-propenylanisole (1). We provide evidence that solvent acidity modifies the behavior of the transient intermediates. Relative to reactions in aprotic solvent, enhanced dioxetane concentrations are observed in MeOH and in nonprotic solvents with acid. We suggest a new mechanism that invokes a proton transfer from MeOH and benzoic acid to perepoxide (2) and zwitterion (3) intermediates.