Field dependent collision frequency of the two-dimensional driven random Lorentz gas

In the field-driven, thermostatted Lorentz gas the collision frequency increases with the magnitude of the applied field due to long-time correlations. We study this effect with computer simulations and confirm the presence of non-analytic terms in the field dependence of the collision frequency as predicted by kinetic theory.Comment: 6 pages, 2 figures. Submitted to Phys. Rev.

Precision shooting: Sampling long transition pathways

The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest simulated trajectories that exemplify such processes is typically made difficult by a very low acceptance rate for newly generated trajectories. We address this problem by introducing a new generation algorithm based on the linear short-time behavior of small disturbances in phase space. Using this ``precision shooting'' technique, arbitrarily small disturbances can be propagated in time, and any desired acceptance ratio of shooting moves can be obtained. We demonstrate the method for a simple but computationally problematic isomerization process in a dense liquid of soft spheres. We also discuss its applicability to barrier crossing events involving metastable intermediate states.Comment: 9 pages, 12 figures, submitted to J. Chem. Phy

The Kolmogorov-Sinai Entropy for Dilute Gases in Equilibrium

We use the kinetic theory of gases to compute the Kolmogorov-Sinai entropy per particle for a dilute gas in equilibrium. For an equilibrium system, the KS entropy, h_KS is the sum of all of the positive Lyapunov exponents characterizing the chaotic behavior of the gas. We compute h_KS/N, where N is the number of particles in the gas. This quantity has a density expansion of the form h_KS/N = a\nu[-\ln{\tilde{n}} + b + O(\tilde{n})], where \nu is the single-particle collision frequency and \tilde{n} is the reduced number density of the gas. The theoretical values for the coefficients a and b are compared with the results of computer simulations, with excellent agreement for a, and less than satisfactory agreement for b. Possible reasons for this difference in b are discussed.Comment: 15 pages, 2 figures, submitted to Phys. Rev.

Kinetics and mechanism of proton transport across membrane nanopores

We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across the membrane diffusively in single-file chains of hydrogen-bonded water molecules. Proton passage through the membrane is opposed by a high barrier along the effective potential, reflecting the large electrostatic penalty for desolvation and reminiscent of charge exclusion in biological water channels. At neutral pH, we estimate a translocation rate of about 1 proton per hour and tube.Comment: 4 pages, 4 figure

A proof of Jarzynski's non-equilibrium work theorem for dynamical systems that conserve the canonical distribution

We present a derivation of the Jarzynski identity and the Crooks fluctuation theorem for systems governed by deterministic dynamics that conserves the canonical distribution such as Hamiltonian dynamics, Nose-Hoover dynamics, Nose-Hoover chains and Gaussian isokinetic dynamics. The proof is based on a relation between the heat absorbed by the system during the non-equilibrium process and the Jacobian of the phase flow generated by the dynamics.Comment: 12 page

Rate constants for diffusive processes by partial path sampling

We introduce a path sampling method for the computation of rate constants for systems with a highly diffusive character. Based on the recently developed algorithm of transition interface sampling (TIS) this procedure increases the efficiency by sampling only parts of complete transition trajectories confined within a certain region. The algorithm assumes the loss of memory for highly diffusive progression along the reaction coordinate. We compare the new technique to the TIS method for a simple diatomic system and show that the computation time of the new method scales linearly, instead of quadraticaly, with the length of the diffusive barrier. The validity of the memory loss assumption is also discussed.Comment: 12 pages, including 8 figures, RevTeX

A Novel Path Sampling Method for the Calculation of Rate Constants

We derive a novel efficient scheme to measure the rate constant of transitions between stable states separated by high free energy barriers in a complex environment within the framework of transition path sampling. The method is based on directly and simultaneously measuring the fluxes through many phase space interfaces and increases the efficiency with at least a factor of two with respect to existing transition path sampling rate constant algorithms. The new algorithm is illustrated on the isomerization of a diatomic molecule immersed in a simple fluid.Comment: 14 pages, including 13 figures, RevTeX