39 research outputs found
Modelling excitonic-energy transfer in light-harvesting complexes
The theoretical and experimental study of energy transfer in photosynthesis
has revealed an interesting transport regime, which lies at the borderline
between classical transport dynamics and quantum-mechanical interference
effects. Dissipation is caused by the coupling of electronic degrees of freedom
to vibrational modes and leads to a directional energy transfer from the
antenna complex to the target reaction-center. The dissipative driving is
robust and does not rely on fine-tuning of specific vibrational modes. For the
parameter regime encountered in the biological systems new theoretical tools
are required to directly compare theoretical results with experimental
spectroscopy data. The calculations require to utilize massively parallel
graphics processor units (GPUs) for efficient and exact computations.Comment: 20 pages, submitted to the AIP conference proceedings of the Latin
American School of Physics Marcos Moshinsky (ELAF 2013
Efficiency of energy funneling in the photosystem II supercomplex of higher plants
The investigation of energy transfer properties in photosynthetic
multi-protein networks gives insight into their underlying design
principles.Here, we discuss excitonic energy transfer mechanisms of the
photosystem II (PS-II) CSM supercomplex, which is the largest
isolated functional unit of the photosynthetic apparatus of higher
plants.Despite the lack of a decisive energy gradient in CSM, we
show that the energy transfer is directed by relaxation to low energy states.
CSM is not organized to form pathways with strict energetic
downhill transfer, which has direct consequences on the transfer efficiency,
transfer pathways and transfer limiting steps. The exciton dynamics is
sensitive to small structural changes, which, for instance, are induced by the
reorganization of vibrational coordinates. In order to incorporate the
reorganization process in our numerical simulations, we go beyond rate
equations and use the hierarchically coupled equation of motion approach
(HEOM). While transfer from the peripherical antenna to the proteins in
proximity to the reaction center occurs on a faster time scale, the final step
of the energy transfer to the RC core is rather slow, and thus the limiting
step in the transfer chain. Our findings suggest that the structure of the
PS-II supercomplex guarantees photoprotection rather than optimized efficiency.Comment: 23 pages, 6 figure
Exact Stochastic Unraveling of an Optical Coherence Dynamics by Cumulant Expansion
A numerically exact Monte Carlo scheme for calculation of open quantum system
dynamics is proposed and implemented. The method consists of a Monte-Carlo
summation of a perturbation expansion in terms of trajectories in Liouville
phase-space with respect to the coupling between the excited states of the
molecule. The trajectories are weighted by a complex decoherence factor based
on the second-order cumulant expansion of the environmental evolution. The
method can be used with an arbitrary environment characterized by a general
correlation function and arbitrary coupling strength. It is formally exact for
harmonic environments, and it can be used with arbitrary temperature. Time
evolution of an optically excited Frenkel exciton dimer representing a
molecular exciton interacting with a charge transfer state is calculated by the
proposed method. We calculate the evolution of the optical coherence elements
of the density matrix and linear absorption spectrum, and compare them with the
predictions of standard simulation methods.Comment: 11 pages, 6 figure
High-performance solution of hierarchical equations of motions for studying energy-transfer in light-harvesting complexes
Excitonic models of light-harvesting complexes, where the vibrational degrees
of freedom are treated as a bath, are commonly used to describe the motion of
the electronic excitation through a molecule. Recent experiments point toward
the possibility of memory effects in this process and require to consider time
non-local propagation techniques. The hierarchical equations of motion (HEOM)
were proposed by Ishizaki and Fleming to describe the site-dependent
reorganization dynamics of protein environments (J. Chem. Phys., 130, p.
234111, 2009), which plays a significant role in photosynthetic electronic
energy transfer. HEOM are often used as a reference for other approximate
methods, but have been implemented only for small systems due to their adverse
computational scaling with the system size. Here, we show that HEOM are also
solvable for larger systems, since the underlying algorithm is ideally suited
for the usage of graphics processing units (GPU). The tremendous reduction in
computational time due to the GPU allows us to perform a systematic study of
the energy-transfer efficiency in the Fenna-Matthews-Olson (FMO)
light-harvesting complex at physiological temperature under full consideration
of memory-effects. We find that approximative methods differ qualitatively and
quantitatively from the HEOM results and discuss the importance of finite
temperature to achieve high energy-transfer efficiencies.Comment: 14 pages; Journal of Chemical Theory and Computation (2011
Disentangling Electronic and Vibronic Coherences in Two-Dimensional Echo Spectra
The prevalence of long-lasting oscillatory signals in two-dimensional (2D) echo spectroscopy of light-harvesting complexes has led to a search for possible mechanisms. We investigate how two causes of oscillatory signals are intertwined: (i) electronic coherences supporting delocalized wavelike motion and (ii) narrow bands in the vibronic spectral density. To disentangle the vibronic and electronic contributions, we introduce a time-windowed Fourier transform of the signal amplitude. We find that 2D spectra can be dominated by excitations of pathways which are absent in excitonic energy transport. This leads to an underestimation of the lifetime of electronic coherences by 2D spectra.Chemistry and Chemical BiologyPhysic
Mechanistic Regimes of Vibronic Transport in a Heterodimer and the Design Principle of Incoherent Vibronic Transport in Phycobiliproteins
Following the observation of coherent oscillations in non-linear spectra of
photosynthetic pigment protein complexes, particularly phycobilliprotein such
as PC645, coherent vibronic transport has been suggested as a design principle
for novel light harvesting materials operating at room temperature. Vibronic
transport between energetically remote pigments is coherent when the presence
of a resonant vibration supports transient delocalization between the pair of
electronic excited states. Here, we establish the mechanism of vibronic
transport for a model heterodimer across a wide range of molecular parameter
values. The resulting mechanistic map demonstrates that the molecular
parameters of phycobiliproteins in fact support incoherent vibronic transport.
This result points to an important design principle: incoherent vibronic
transport is more efficient than a coherent mechanism when energetic disorder
exceeds the coupling between the donor and vibrationally excited acceptor
states. Finally, our results suggest that the role of coherent vibronic
transport in pigment protein complexes should be reevaluated
Modelling of Oscillations in Two-Dimensional Echo-Spectra of the Fenna-Matthews-Olson Complex
Recent experimental observations of time-dependent beatings in the
two-dimensional echo-spectra of light-harvesting complexes at ambient
temperatures have opened up the question whether coherence and wave-like
behaviour plays a significant role in photosynthesis. We perform a numerical
study of the absorption and echo-spectra of the Fenna-Matthews-Olson (FMO)
complex in chlorobium tepidum and analyse the requirements in the theoretical
model needed to reproduce beatings in the calculated spectra. The energy
transfer in the FMO pigment-protein complex is theoretically described by an
exciton Hamiltonian coupled to a phonon bath which account for the pigments
electronic and vibrational excitations respectively. We use the hierarchical
equations of motions method to treat the strong couplings in a non-perturbative
way. We show that the oscillations in the two-dimensional echo-spectra persist
in the presence of thermal noise and static disorder.Comment: updated text and references, corrected figures 4-7, 20 pages, 7
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