Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations

Common algorithms for computationally simulating Langevin dynamics must discretize the stochastic differential equations of motion. These resulting finite time step integrators necessarily have several practical issues in common: Microscopic reversibility is violated, the sampled stationary distribution differs from the desired equilibrium distribution, and the work accumulated in nonequilibrium simulations is not directly usable in estimators based on nonequilibrium work theorems. Here, we show that even with a time-independent Hamiltonian, finite time step Langevin integrators can be thought of as a driven, nonequilibrium physical process. Once an appropriate work-like quantity is defined -- here called the shadow work -- recently developed nonequilibrium fluctuation theorems can be used to measure or correct for the errors introduced by the use of finite time steps. In particular, we demonstrate that amending estimators based on nonequilibrium work theorems to include this shadow work removes the time step dependent error from estimates of free energies. We also quantify, for the first time, the magnitude of deviations between the sampled stationary distribution and the desired equilibrium distribution for equilibrium Langevin simulations of solvated systems of varying size. While these deviations can be large, they can be eliminated altogether by Metropolization or greatly diminished by small reductions in the time step. Through this connection with driven processes, further developments in nonequilibrium fluctuation theorems can provide additional analytical tools for dealing with errors in finite time step integrators.Comment: 11 pages, 4 figure

Space-time thermodynamics and subsystem observables in a kinetically constrained model of glassy systems

In a recent article [M. Merolle et al., Proc. Natl. Acad. Sci. USA 102, 10837 (2005)] it was argued that dynamic heterogeneity in $d$-dimensional glass formers is a manifestation of an order-disorder phenomenon in the $d+1$ dimensions of spacetime. By considering a dynamical analogue of the free energy, evidence was found for phase coexistence between active and inactive regions of spacetime, and it was suggested that this phenomenon underlies the glass transition. Here we develop these ideas further by investigating in detail the one-dimensional Fredrickson-Andersen (FA) model in which the active and inactive phases originate in the reducibility of the dynamics. We illustrate the phase coexistence by considering the distributions of mesoscopic spacetime observables. We show how the analogy with phase coexistence can be strengthened by breaking microscopic reversibility in the FA model, leading to a non-equilibrium theory in the directed percolation universality class.Comment: 12 pages, 11 figures, final version with minor change

Effect of transient pinning on stability of drops sitting on an inclined plane

We report on new instabilities of the quasi-static equilibrium of water drops pinned by a hydrophobic inclined substrate. The contact line of a statically pinned drop exhibits three transitions of partial depinning: depinning of the advancing and receding parts of the contact line and depinning of the entire contact line leading to the drop's translational motion. We find a region of parameters where the classical Macdougall-Ockrent-Frenkel approach fails to estimate the critical volume of the statically pinned inclined drop

Strain Hardening of Polymer Glasses: Entanglements, Energetics, and Plasticity

Simulations are used to examine the microscopic origins of strain hardening in polymer glasses. While stress-strain curves for a wide range of temperature can be fit to the functional form predicted by entropic network models, many other results are fundamentally inconsistent with the physical picture underlying these models. Stresses are too large to be entropic and have the wrong trend with temperature. The most dramatic hardening at large strains reflects increases in energy as chains are pulled taut between entanglements rather than a change in entropy. A weak entropic stress is only observed in shape recovery of deformed samples when heated above the glass transition. While short chains do not form an entangled network, they exhibit partial shape recovery, orientation, and strain hardening. Stresses for all chain lengths collapse when plotted against a microscopic measure of chain stretching rather than the macroscopic stretch. The thermal contribution to the stress is directly proportional to the rate of plasticity as measured by breaking and reforming of interchain bonds. These observations suggest that the correct microscopic theory of strain hardening should be based on glassy state physics rather than rubber elasticity.Comment: 15 pages, 12 figures: significant revision

Restoration of the Salmon River salt marshes : retrospect and prospect

"Final report to the U.S. Environmental Protection Agency. Funds supporting this study have been provided by Region 10 of the U.S. Environmental Protection Agency, Seattle, WA."We assessed restoration of a 21 ha diked pasture in the Salmon River estuary to a naturally functioning estuarine salt marsh in 1988, eleven years after partial dike removal in 1978. Diane Mitchell (1981) collected base line data, established an intensive sampling system of permanent plots in the diked pasture and flanking "intact" control marshes, and analyzed restoration progress from 1978 to 1980. our report continues Mitchell's earlier research by evaluating the composition, structure, function, and long term prospects for the restored wetland