Heavy atom quantum diffraction by scattering from surfaces

Typically one expects that when a heavy particle collides with a surface, the scattered angular distribution will follow classical mechanics. The heavy mass assures that the de Broglie wavelength of the incident particle in the direction of the propagation of the particle (the parallel direction) will be much shorter than the characteristic lattice length of the surface, thus leading to a classical description. Recent work on molecular interferometry has shown that by increasing the perpendicular coherence length, one may observe interference of very heavy species passing through a grating. Here we show, using quantum mechanical simulations, that the same effect will lead to quantum diffraction of heavy particles colliding with a surface. We find that the effect is robust with respect to the incident energy, the angle of incidence and the mass of the particle. It may also be used to verify the quantum nature of the surface and its fluctuations at very low temperatures.Comment: 9 pages, 3 figure

Dissipating the Langevin equation in the presence of an external stochastic potential

In the Langevin formalism, the delicate balance maintained between the fluctuations in the system and their corresponding dissipation may be upset by the presence of a secondary, space-dependent stochastic force, particularly in the low friction regime. In prior work, the latter was dissipated self-consistently through an additional uniform (mean-field) friction [Shepherd and Hernandez, J. Chem. Phys., 115, 2430-2438 (2001).] An alternative approach to ensure that equipartition is satisfied relies on the use of a space-dependent friction while ignoring nonlocal correlations. The approach is evaluated with respect to its ability to maintain constant temperature for two simple one-dimensional, stochastic potentials of mean force wherein the friction can be evaluated explicitly when there is no memory in the barriers. The use of a space-dependent friction is capable of providing qualitatively similar results to those obtained previously, but in extreme cases, deviations from equipartition may be observed due to the neglect of the memory effects present in the stochastic potentials.Comment: 9 pages, 5 figures, to appear in J. Chem. Phy

Forster resonance energy transfer, absorption and emission spectra in multichromophoric systems: III. Exact stochastic path integral evaluation

A numerically exact path integral treatment of the absorption and emission spectra of open quantum systems is presented that requires only the straightforward solution of a stochastic differential equation. The approach converges rapidly enabling the calculation of spectra of large excitonic systems across the complete range of system parameters and for arbitrary bath spectral densities. With the numerically exact absorption and emission operators one can also immediately compute energy transfer rates using the multi-chromophoric Forster resonant energy transfer formalism. Benchmark calculations on the emission spectra of two level systems are presented demonstrating the efficacy of the stochastic approach. This is followed by calculations of the energy transfer rates between two weakly coupled dimer systems as a function of temperature and system-bath coupling strength. It is shown that the recently developed hybrid cumulant expansion is the only perturbative method capable of generating uniformly reliable energy transfer rates and spectra across a broad range of system parameters.Comment: 20 pages, 4 figure

Coherent quantum transport in disordered systems I: The influence of dephasing on the transport properties and absorption spectra on one-dimensional systems

Excitonic transport in static disordered one dimensional systems is studied in the presence of thermal fluctuations that are described by the Haken-Strobl-Reineker model. For short times, non-diffusive behavior is observed that can be characterized as the free-particle dynamics in the Anderson localized system. Over longer time scales, the environment-induced dephasing is sufficient to overcome the Anderson localization caused by the disorder and allow for transport to occur which is always seen to be diffusive. In the limiting regimes of weak and strong dephasing quantum master equations are developed, and their respective scaling relations imply the existence of a maximum in the diffusion constant as a function of the dephasing rate that is confirmed numerically. In the weak dephasing regime, it is demonstrated that the diffusion constant is proportional to the square of the localization length which leads to a significant enhancement of the transport rate over the classical prediction. Finally, the influence of noise and disorder on the absorption spectrum is presented and its relationship to the transport properties is discussed.Comment: 23 pages, 7 figure

Coherent quantum transport in disordered systems: A unified polaron treatment of hopping and band-like transport

Quantum transport in disordered systems is studied using a polaron-based master equation. The polaron approach is capable of bridging the results from the coherent band-like transport regime governed by the Redfield equation to incoherent hopping transport in the classical regime. A non-monotonic dependence of the diffusion coefficient is observed both as a function of temperature and system-phonon coupling strength. In the band-like transport regime, the diffusion coefficient is shown to be linearly proportional to the system-phonon coupling strength, and vanishes at zero coupling due to Anderson localization. In the opposite classical hopping regime, we correctly recover that the dynamics are described by the Fermi's Golden Rule (FGR) and establish that the scaling of the diffusion coefficient depends on the phonon bath relaxation time. In both the hopping and band-like transport regimes, it is demonstrated that at low temperature the zero-point fluctuations of the bath lead to non-zero transport rates, and hence a finite diffusion constant. Application to rubrene and other organic semiconductor materials shows a good agreement with experimental mobility data.Comment: 19 pages, 4 figure

Molecular Dynamics and Stochastic Simulations of Surface Diffusion

Despite numerous advances in experimental methodologies capable of addressing the various phenomenon occurring on metal surfaces, atomic scale resolution of the microscopic dynamics remains elusive for most systems. Computational models of the processes may serve as an alternative tool to fill this void. To this end, parallel molecular dynamics simulations of self-diffusion on metal surfaces have been developed and employed to address microscopic details of the system. However these simulations are not without their limitations and prove to be computationally impractical for a variety of chemically relevant systems, particularly for diffusive events occurring in the low temperature regime. To circumvent this difficulty, a corresponding coarse-grained representation of the surface is also developed resulting in a reduction of the required computational effort by several orders of magnitude, and this description becomes all the more advantageous with increasing system size and complexity. This representation provides a convenient framework to address fundamental aspects of diffusion in nonequilibrium environments and an interesting mechanism for directing diffusive motion along the surface is explored. In the ensuing discussion, additional topics including transition state theory in noisy systems and the construction of a checking function for protein structure validation are outlined. For decades the former has served as a cornerstone for estimates of chemical reaction rates. However, in complex environments transition state theory most always provides only an upper bound for the true rate. An alternative approach is described that may alleviate some of the difficulties associated with this problem. Finally, one of the grand challenges facing the computational sciences is to develop methods capable of reconstructing protein structure based solely on readily-available sequence information. Herein a checking function is developed that may prove useful for addressing whether a particular proposed structure is a viable possibility.Ph.D.Committee Chair: Hernandez, Rigoberto; Committee Member: Bredas, Jean-Luc; Committee Member: Ludovice, Peter; Committee Member: Orlando, Thomas; Committee Member: Sherrill, C. Davi

A hybrid stochastic hierarchy equations of motion approach to treat the low temperature dynamics of non-Markovian open quantum systems

The hierarchical equations of motion technique has found widespread success as a tool to generate the numerically exact dynamics of non-Markovian open quantum systems. However, its application to low temperature environments remains a serious challenge due to the need for a deep hierarchy that arises from the Matsubara expansion of the bath correlation function. Here we present a hybrid stochastic hierarchical equation of motion (sHEOM) approach that alleviates this bottleneck and leads to a numerical cost that is nearly independent of temperature. Additionally, the sHEOM method generally converges with fewer hierarchy tiers allowing for the treatment of larger systems. Benchmark calculations are presented on the dynamics of two level systems at both high and low temperatures to demonstrate the efficacy of the approach. Then the hybrid method is used to generate the exact dynamics of systems that are nearly impossible to treat by the standard hierarchy. First, exact energy transfer rates are calculated across a broad range of temperatures revealing the deviations from the Forster rates. This is followed by computations of the entanglement dynamics in a system of two qubits at low temperature spanning the weak to strong system-bath coupling regimes.Comment: 20 pages, 6 figure

Quantum Diffusion on Molecular Tubes: Universal Scaling of the 1D to 2D Transition

The transport properties of disordered systems are known to depend critically on dimensionality. We study the diffusion coefficient of a quantum particle confined to a lattice on the surface of a tube, where it scales between the 1D and 2D limits. It is found that the scaling relation is universal and independent of the disorder and noise parameters, and the essential order parameter is the ratio between the localization length in 2D and the circumference of the tube. Phenomenological and quantitative expressions for transport properties as functions of disorder and noise are obtained and applied to real systems: In the natural chlorosomes found in light-harvesting bacteria the exciton transfer dynamics is predicted to be in the 2D limit, whereas a family of synthetic molecular aggregates is found to be in the homogeneous limit and is independent of dimensionality.Comment: 10 pages, 6 figure

An exact equilibrium reduced density matrix formulation I: The influence of noise, disorder, and temperature on localization in excitonic systems

An exact method to compute the entire equilibrium reduced density matrix for systems characterized by a system-bath Hamiltonian is presented. The approach is based upon a stochastic unraveling of the influence functional that appears in the imaginary time path integral formalism of quantum statistical mechanics. This method is then applied to study the effects of thermal noise, static disorder, and temperature on the coherence length in excitonic systems. As representative examples of biased and unbiased systems, attention is focused on the well-characterized light harvesting complexes of FMO and LH2, respectively. Due to the bias, FMO is completely localized in the site basis at low temperatures, whereas LH2 is completely delocalized. In the latter, the presence of static disorder leads to a plateau in the coherence length at low temperature that becomes increasingly pronounced with increasing strength of the disorder. The introduction of noise, however, precludes this effect. In biased systems, it is shown that the environment may increase the coherence length, but only decrease that of unbiased systems. Finally it is emphasized that for typical values of the environmental parameters in light harvesting systems, the system and bath are entangled at equilibrium in the single excitation manifold. That is, the density matrix cannot be described as a product state as is often assumed, even at room temperature. The reduced density matrix of LH2 is shown to be in precise agreement with the steady state limit of previous exact quantum dynamics calculations.Comment: 37 pages, 12 figures. To appear in Phys. Rev.