9,314 research outputs found
Influence of environment induced correlated fluctuations in electronic coupling on coherent excitation energy transfer dynamics in model photosynthetic systems
Two-dimensional photon-echo experiments indicate that excitation energy transfer between chromophores near the reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides occurs coherently with decoherence times of hundreds of femtoseconds, comparable to the energy transfer time scale in these systems. The original explanation of this observation suggested that correlated fluctuations in chromophore excitation energies, driven by large scale protein motions could result in long lived coherent energy transfer dynamics. However, no significant site energy correlation has been found in recent molecular dynamics simulations of several model light harvesting systems. Instead, there is evidence of correlated fluctuations in site energy-electronic coupling and electronic coupling-electronic coupling. The roles of these different types of correlations in excitation energy transfer dynamics are not yet thoroughly understood, though the effects of site energy correlations have been well studied. In this paper, we introduce several general models that can realistically describe the effects of various types of correlated fluctuations in chromophore properties and systematically study the behavior of these models using general methods for treating dissipative quantum dynamics in complex multi-chromophore systems. The effects of correlation between site energy and inter-site electronic couplings are explored in a two state model of excitation energy transfer between the accessory bacteriochlorophyll and bacteriopheophytin in a reaction center system and we find that these types of correlated fluctuations can enhance or suppress coherence and transfer rate simultaneously. In contrast, models for correlated fluctuations in chromophore excitation energies show enhanced coherent dynamics but necessarily show decrease in excitation energy transfer rate accompanying such coherence enhancement. Finally, for a three state model of the Fenna-Matthews-Olsen light harvesting complex, we explore the influence of including correlations in inter-chromophore couplings between different chromophore dimers that share a common chromophore. We find that the relative sign of the different correlations can have profound influence on decoherence time and energy transfer rate and can provide sensitive control of relaxation in these complex quantum dynamical open systems
Energy-scales convergence for optimal and robust quantum transport in photosynthetic complexes
Underlying physical principles for the high efficiency of excitation energy
transfer in light-harvesting complexes are not fully understood. Notably, the
degree of robustness of these systems for transporting energy is not known
considering their realistic interactions with vibrational and radiative
environments within the surrounding solvent and scaffold proteins. In this
work, we employ an efficient technique to estimate energy transfer efficiency
of such complex excitonic systems. We observe that the dynamics of the
Fenna-Matthews-Olson (FMO) complex leads to optimal and robust energy transport
due to a convergence of energy scales among all important internal and external
parameters. In particular, we show that the FMO energy transfer efficiency is
optimum and stable with respect to the relevant parameters of environmental
interactions and Frenkel-exciton Hamiltonian including reorganization energy
, bath frequency cutoff , temperature , bath spatial
correlations, initial excitations, dissipation rate, trapping rate, disorders,
and dipole moments orientations. We identify the ratio of \lambda T/\gamma\*g
as a single key parameter governing quantum transport efficiency, where g is
the average excitonic energy gap.Comment: minor revisions, removing some figures, 19 pages, 19 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
Numerical Evidence for Robustness of Environment-Assisted Quantum Transport
Recent theoretical studies show that decoherence process can enhance
transport efficiency in quantum systems. This effect is known as
environment-assisted quantum transport (ENAQT). The role of ENAQT in optimal
quantum transport is well investigated, however, it is less known how robust
ENAQT is with respect to variations in the system or its environment
characteristic. Toward answering this question, we simulated excitonic energy
transfer in Fenna-Matthews-Olson (FMO) photosynthetic complex. We found that
ENAQT is robust with respect to many relevant parameters of environmental
interactions and Frenkel-exciton Hamiltonian including reorganization energy,
bath frequency cutoff, temperature, and initial excitations, dissipation rate,
trapping rate, disorders, and dipole moments orientations. Our study suggests
that the ENAQT phenomenon can be exploited in robust design of highly efficient
quantum transport systems.Comment: arXiv admin note: substantial text overlap with arXiv:1104.481
Molecular Mechanics Simulations and Improved Tight-binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment
We present molecular mechanics {and spectroscopic} calculations on prototype
artificial light harvesting systems consisting of chromophores attached to a
tobacco mosaic virus (TMV) protein scaffold. These systems have been
synthesized and characterized spectroscopically, but information about the
microscopic configurations and geometry of these TMV-templated chromophore
assemblies is largely unknown. We use a Monte Carlo conformational search
algorithm to determine the preferred positions and orientations of two
chromophores, Coumarin 343 together with its linker, and Oregon Green 488, when
these are attached at two different sites (104 and 123) on the TMV protein. The
resulting geometric information shows that the extent of disorder and
aggregation properties, and therefore the optical properties of the
TMV-templated chromophore assembly, are highly dependent on the choice of
chromophores and protein site to which they are bound. We used the results of
the conformational search as geometric parameters together with an improved
tight-binding Hamiltonian to simulate the linear absorption spectra and compare
with experimental spectral measurements. The ideal dipole approximation to the
Hamiltonian is not valid since the distance between chromophores can be very
small. We found that using the geometries from the conformational search is
necessary to reproduce the features of the experimental spectral peaks
Transform-Limited-Pulse Representation of Excitation with Natural Incoherent Light
We study the natural excitation of molecular systems, applicable to, for
example, photosynthetic light-harvesting complexes, by natural incoherent
light. In contrast with the conventional classical models, we show that the
light need not have random character to properly represent the resultant linear
excitation. Rather, thermal excitation can be interpreted as a collection of
individual events resulting from the system's interaction with individual,
deterministic pulsed realizations that constitute the field. The derived
expressions for the individual field realizations and excitation events allow
for a wave function formalism, and therefore constitute a useful calculational
tool to study dynamics following thermal-light excitation. Further, they
provide a route to the experimental determination of natural incoherent
excitation using pulsed laser techniques.Comment: 5 pages, 3 figures, 1 page supplementary information. Comments
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Geometrical effects on energy transfer in disordered open quantum systems
We explore various design principles for efficient excitation energy
transport in complex quantum systems. We investigate energy transfer efficiency
in randomly disordered geometries consisting of up to 20 chromophores to
explore spatial and spectral properties of small natural/artificial
Light-Harvesting Complexes (LHC). We find significant statistical correlations
among highly efficient random structures with respect to ground state
properties, excitonic energy gaps, multichromophoric spatial connectivity, and
path strengths. These correlations can even exist beyond the optimal regime of
environment-assisted quantum transport. For random configurations embedded in
spatial dimensions of 30 A and 50 A, we observe that the transport efficiency
saturates to its maximum value if the systems contain 7 and 14 chromophores
respectively. Remarkably, these optimum values coincide with the number of
chlorophylls in (Fenna-Matthews-Olson) FMO protein complex and LHC II monomers,
respectively, suggesting a potential natural optimization with respect to
chromophoric density.Comment: 11 pages, 10 figures. Expanded from the former appendix to
arXiv:1104.481
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