The Work-Hamiltonian Connection and the Usefulness of the Jarzynski Equality for Free Energy Calculations

The connection between work and changes in the Hamiltonian for a system with a time-dependent Hamiltonian has recently been called into question, casting doubt on the usefulness of the Jarzynski equality for calculating free energy changes. In this paper, we discuss the relationship between two possible definitions of free energy and show how some recent disagreements regarding the applicability of the Jarzynski equality are the result of different authors using different definitions of free energy. Finally, in light of the recently raised doubts, we explicitly demonstrate that it is indeed possible to obtain physically relevant free energy profiles from molecular pulling experiments by using the Jarzynski equality and the results of Hummer and Szabo.Comment: 3 page

An application of Hirschfelder-Silbey perturbation theory to the H2 plus ion

Hirschfelder-Silbey perturbation theory applied to positive hydrogen io

Theory of Single File Diffusion in a Force Field

The dynamics of hard-core interacting Brownian particles in an external potential field is studied in one dimension. Using the Jepsen line we find a very general and simple formula relating the motion of the tagged center particle, with the classical, time dependent single particle reflection ${\cal R}$ and transmission ${\cal T}$ coefficients. Our formula describes rich physical behaviors both in equilibrium and the approach to equilibrium of this many body problem.Comment: 4 Phys. Rev. page

Efficient energy transfer in light-harvesting systems, I: optimal temperature, reorganization energy, and spatial-temporal correlations

Understanding the mechanisms of efficient and robust energy transfer in light-harvesting systems provides new insights for the optimal design of artificial systems. In this paper, we use the Fenna-Matthews-Olson (FMO) protein complex and phycocyanin 645 (PC 645) to explore the general dependence on physical parameters that help maximize the efficiency and maintain its stability. With the Haken-Strobl model, the maximal energy transfer efficiency (ETE) is achieved under an intermediate optimal value of dephasing rate. To avoid the infinite temperature assumption in the Haken-Strobl model and the failure of the Redfield equation in predicting the Forster rate behavior, we use the generalized Bloch-Redfield (GBR) equation approach to correctly describe dissipative exciton dynamics and find that maximal ETE can be achieved under various physical conditions, including temperature, reorganization energy, and spatial-temporal correlations in noise. We also identify regimes of reorganization energy where the ETE changes monotonically with temperature or spatial correlation and therefore cannot be optimized with respect to these two variables

Variational Treatment of a Harmonic Oscillator Coupled to a Dissipative Heat Bath

We consider the problem of a single quantum oscillator coupled linearly to a heat bath of independent harmonic modes. An exact solution is presented for the system-oscillator observables of interest. The exact results are then used to evaluate the utility of a variational approach to the problem that has proven useful recently in elucidating the dynamics of dissipatively coupled systems. We find that the variational approach does provide a good description for most, but not all, observables of interest. Both the exact and the variational treatment demonstrate the important role played by the low-frequency bath modes in determining qualitative features of the dynamical behavior