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

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

Low Temperature Tunneling Dynamics in Condensed Media

There has been considerable interest recently in the low temperature dynamics of condensed phase tunneling phenomena. In this paper we consider the interplay between quasiparticle transport and vibrational relaxation; the former taking place via tunneling in a double well potential, and the latter occurring due to interactions of the tunneling system with a harmonic bath. Taking the system-bath interactions to be linear in the bath coordinates, and explicitly allowing for a vibrationally excited well, we present a unified treatment of the weak and strong coupling regimes and obtain reduced equations of motion for the tunneling particle position operator. Solutions are obtained for several important limiting cases. In particular, we find that at sufficiently low temperatures, the dynamical behavior strongly resembles that of multisite spin jump model

Correlated interaction fluctuations in photosynthetic complexes

The functioning and efficiency of natural photosynthetic complexes is strongly influenced by their embedding in a noisy protein environment, which can even serve to enhance the transport efficiency. Interactions with the environment induce fluctuations of the transition energies of and interactions between the chlorophyll molecules, and due to the fact that different fluctuations will partially be caused by the same environmental factors, correlations between the various fluctuations will occur. We argue that fluctuations of the interactions should in general not be neglected, as these have a considerable impact on population transfer rates, decoherence rates and the efficiency of photosynthetic complexes. Furthermore, while correlations between transition energy fluctuations have been studied, we provide the first quantitative study of the effect of correlations between interaction fluctuations and transition energy fluctuations, and of correlations between the various interaction fluctuations. It is shown that these additional correlations typically lead to changes in interchromophore transfer rates, population oscillations and can lead to a limited enhancement of the light harvesting efficiency

Electrodynamics of Amorphous Media at Low Temperatures

Amorphous solids exhibit intrinsic, local structural transitions, that give rise to the well known quantum-mechanical two-level systems at low temperatures. We explain the microscopic origin of the electric dipole moment of these two-level systems: The dipole emerges as a result of polarization fluctuations between near degenerate local configurations, which have nearly frozen in at the glass transition. An estimate of the dipole's magnitude, based on the random first order transition theory, is obtained and is found to be consistent with experiment. The interaction between the dipoles is estimated and is shown to contribute significantly to the Gr\"{u}neisen parameter anomaly in low $T$ glasses. In completely amorphous media, the dipole moments are expected to be modest in size despite their collective origin. In partially crystalline materials, however, very large dipoles may arise, possibly explaining the findings of Bauer and Kador, J. Chem. Phys. {\bf 118}, 9069 (2003).Comment: Submitted for publication; April 27, 2005 versio

Single-file dynamics with different diffusion constants

We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore interacting particles (the particles cannot pass each other) which are diffusing in a one-dimensional system where the particles have different diffusion constants. For the two particle case an exact result for the conditional probability density function (PDF) is obtained for arbitrary initial particle positions and all times. The two-particle PDF is used to obtain the tagged particle PDF. For the general N-particle case (N large) we perform stochastic simulations using our new computationally efficient stochastic simulation technique based on the Gillespie algorithm. We find that the mean square displacement for a tagged particle scales as the square root of time (as for identical particles) for long times, with a prefactor which depends on the diffusion constants for the particles; these results are in excellent agreement with very recent analytic predictions in the mathematics literature.Comment: 9 pages, 5 figures. Journal of Chemical Physics (in press