Kinetic Schemes in Open Interacting Systems

We discuss utilization of kinetic schemes for description of open interacting systems, focusing on vibrational energy relaxation for an oscillator coupled to a nonequilibirum electronic bath. Standard kinetic equations with constant rate coefficients are obtained under the assumption of timescale separation between system and bath, with the bath dynamics much faster than that of the system of interest. This assumption may break down in certain limits and we show that ignoring this may lead to qualitatively wrong predictions. Connection with more general, nonequilibrium Green's function (NEGF) analysis, is demonstrated. Our considerations are illustrated within generic molecular junction models with electron-vibration coupling.Comment: 22 pages, 4 figure

Nuclear dynamics at molecule-metal interfaces: A pseudoparticle perspective

We discuss nuclear dynamics at molecule-metal interfaces including non-equilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we introduce gradient expansion in order to reduce the adiabatic nuclear dynamics (that is, nuclear dynamics on a single molecular potential surface) into its semi-classical form while maintaining the effect of the non-adiabatic electronic transitions between different molecular charge states. This yields a set of equations for the nuclear dynamics in the presence of these non-adiabatic transitions, which reproduce surface hopping formulation in the limit of small metal-molecule coupling (where broadening of the molecular energy levels can be disregarded) and Ehrenfest dynamics (motion on the potential of mean force) when information on the different charging states is traced out, which is relevant when this coupling is strong.Comment: 9 page

A Thermal Gradient Approach for the Quasi-Harmonic Approximation and its Application to Improved Treatment of Anisotropic Expansion

We present a novel approach to efficiently implement thermal expansion in the quasi-harmonic approximation (QHA) for both isotropic and more importantly, anisotropic expansion. In this approach, we rapidly determine a crystal's equilibrium volume and shape at a given temperature by integrating along the gradient of expansion from zero Kelvin up to the desired temperature. We compare our approach to previous isotropic methods that rely on a brute-force grid search to determine the free energy minimum, which is infeasible to carry out for anisotropic expansion, as well as quasi-anisotropic approaches that take into account the contributions to anisotropic expansion from the lattice energy. We compare these methods for experimentally known polymorphs of piracetam and resorcinol and show that both isotropic methods agree to within error up to 300 K. Using the Gr\"{u}neisen parameter causes up to 0.04 kcal/mol deviation in the Gibbs free energy, but for polymorph free energy differences there is a cancellation in error with all isotropic methods within 0.025 kcal/mol at 300 K. Anisotropic expansion allows the crystals to relax into lattice geometries 0.01-0.23 kcal/mol lower in energy at 300 K relative to isotropic expansion. For polymorph free energy differences all QHA methods produced results within 0.02 kcal/mol of each other for resorcinol and 0.12 kcal/mol for piracetam, the two molecules tested here, demonstrating a cancellation of error for isotropic methods. We also find that when expanding in more than a single volume variable, there is a non-negligible rate of failure of the basic approximations of QHA. Specifically, while expanding into new harmonic modes as the box vectors are increased, the system often falls into alternate, structurally distinct harmonic modes unrelated by continuous deformation from the original harmonic mode.Comment: 38 pages, including 9 pages supporting informatio

On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions

Within a generic model we analyze the Stokes linewidth in surface enhanced Raman scattering (SERS) from molecules embedded as bridges in molecular junctions. We identify four main contributions to the off-resonant Stokes signal and show that under zero voltage bias (a situation pertaining also to standard SERS experiments) and at low bias junctions only one of these contributions is pronounced. The linewidth of this component is determined by the molecular vibrational relaxation rate, which is dominated by interactions with the essentially bosonic thermal environment when the relevant molecular electronic energy is far from the metal(s) Fermi energy(ies). It increases when the molecular electronic level is close to the metal Fermi level so that an additional vibrational relaxation channel due to electron-hole (eh) excition in the molecule opens. Other contributions to the Raman signal, of considerably broader linewidths, can become important at larger junction bias.Comment: 17 pages, 5 figure

Born Oppenheimer Dynamics Near Metal Surfaces

We discuss the usefulness of Born-Oppenheimer potential surfaces for nuclear dynamics for molecules strongly coupled to metal surfaces. A simple model demonstrating the construction of such surface for a molecular junction is discussed.Comment: 5 pages, 2 figure

Reply to Comment by Alexandrov and Bratkovsky [cond-mat/0603467, cond-mat/0606366]

The submitted Comment is based on using an isolated quantum dot approach to discuss the situation where the coupling to the leads is considerable (not negligible). This finite lead coupling is the situation in most molecular transport junctions. In such situations the population on the molecule is not static and dynamical effects (fluctuations) are crucial. While the discussion in [Phys. Rev. B 67, 235312 (2003)], and in the Comment may well apply for an isolated molecule, it is simply irrelevant for the very different transport situation analyzed in our original contribution.Comment: 3 pages, no figures; Original Comment [cond-mat/0603467] was submitted to Nano Letters and following our reply the editor has decided against publication; Later submission [cond-mat/0606366] is essentially a reproduction (with new title and abstract and equations rearranged) of the original Comment [cond-mat/0603467