Exciton transport in thin-film cyanine dye J-aggregates

We present a theoretical model for the study of exciton dynamics in J-aggregated monolayers of fluorescent dyes. The excitonic evolution is described by a Monte-Carlo wave function approach which allows for a unified description of the quantum (ballistic) and classical (diffusive) propagation of an exciton on a lattice in different parameter regimes. The transition between the ballistic and diffusive regime is controlled by static and dynamic disorder. As an example, the model is applied to three cyanine dye J-aggregates: TC, TDBC, and U3. Each of the molecule-specific structure and excitation parameters are estimated using time-dependent density functional theory. The exciton diffusion coefficients are calculated and analyzed for different degrees of film disorder and are correlated to the physical properties and the structural arrangement of molecules in the aggregates. Further, exciton transport is anisotropic and dependent on the initial exciton energy. The upper-bound estimation of the exciton diffusion length in the TDBC thin-film J-aggregate is of the order of hundreds of nanometers, which is in good qualitative agreement with the diffusion length estimated from experiments.Comment: 16 pages, 14 figure

First Principles Semiclassical Calculations of Vibrational Eigenfunctions

Vibrational eigenfunctions are calculated on-the-fly using semiclassical methods in conjunction with ab initio density functional theory classical trajectories. Various semiclassical approximations based on the time-dependent representation of the eigenfunctions are tested on an analytical potential describing the chemisorption of CO on Cu(100). Then, first principles semiclassical vibrational eigenfunctions are calculated for the $CO_2$ molecule and its accuracy evaluated. The multiple coherent states initial value representations semiclassical method recently developed by us has shown with only six ab initio trajectories to evaluate eigenvalues and eigenfunctions at the accuracy level of thousands trajectory semiclassical initial value representation simulations.Chemistry and Chemical Biolog

On the alternatives for bath correlators and spectral densities from mixed quantum-classical simulations

We investigate on the procedure of extracting a "spectral density" from mixed QM/MM calculations and employing it in open quantum systems models. In particular, we study the connection between the energy gap correlation function extracted from ground state QM/MM and the bath spectral density used as input in open quantum system approaches. We introduce a simple model which can give intuition on when the ground state QM/MM propagation will give the correct energy gap. We also discuss the role of higher order correlators of the energy-gap fluctuations which can provide useful information on the bath. Further, various semiclassical corrections to the spectral density, are applied and investigated. Finally, we apply our considerations to the photosynthetic Fenna-Matthews-Olson complex. For this system, our results suggest the use of the Harmonic prefactor for the spectral density rather than the Standard one, which was employed in the simulations of the system carried out to date.Comment: 21 pages, 16 figure

Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex

A remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed long-lived quantum coherence in the electronic energy transfer process in biological photosynthetic systems. Although successful in many respects, several widely used descriptions only include an effective treatment of the protein-chromophore interactions. In this work, by combining an all-atom molecular dynamics simulation, time-dependent density functional theory, and open quantum system approaches, we successfully simulate the dynamics of the electronic energy transfer of the Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic beating of populations and quantum coherences is in good agreement with the experimental results and the hierarchy equation of motion approach. The experimental absorption, linear and circular dichroism spectra and dephasing rates are recovered at two different temperatures. In addition, we provide an extension of our method to include zero-point fluctuations of the vibrational environment. This work thus presents one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description.Comment: 24 pages, 6 figure

Absence of Selection for Quantum Coherence in the Fenna–Matthews–Olson Complex: A Combined Evolutionary and Excitonic Study

We present a study on the evolution of the Fenna–Matthews–Olson bacterial photosynthetic pigment–protein complex. This protein complex functions as an antenna. It transports absorbed photons—excitons—to a reaction center where photosynthetic reactions initiate. The efficiency of exciton transport is therefore fundamental for the photosynthetic bacterium’s survival. We have reconstructed an ancestor of the complex to establish whether coherence in the exciton transport was selected for or optimized over time. We have also investigated the role of optimizing free energy variation upon folding in evolution. We studied whether mutations which connect the ancestor to current day species were stabilizing or destabilizing from a thermodynamic viewpoint. From this study, we established that most of these mutations were thermodynamically neutral. Furthermore, we did not see a large change in exciton transport efficiency or coherence, and thus our results predict that exciton coherence was not specifically selected for

Estimation of the Temporal Dynamics of Posed and Spontaneous Facial Expression Formation Using LLE

When analysing facial expressions, it is not only the final expression itself, but also its formation that plays an important role when attempting to decipher its meaning. Currently in research there are two techniques for describing the dynamics of facial expression; quantitative and temporal based analysis. Quantitative-based techniques attempt to determine the amplitude of the expression in terms of intensity levels, where the levels correspond to some measure of the extent to which the expression is present on the face. Temporal-based techniques split the expression into three temporal phases (onset-apex-offset). In this paper we focus on the temporal aspects of facial expression formation, describing our research into applying a non-linear manifold extraction technique for modelling these temporal phases. We present initial results of our technique for modelling the temporal aspects of both posed and spontaneous facial expressions