1,398 research outputs found
Instanton calculation of the density of states of disordered Peierls chains
We use the optimal fluctuation method to find the density of electron states
inside the pseudogap in disordered Peierls chains. The electrons are described
by the one-dimensional Dirac Hamiltonian with randomly varying mass (the
Fluctuating Gap Model). We establish a relation between the disorder average in
this model and the quantum-mechanical average for a certain double-well
problem. We show that the optimal disorder fluctuation, which has the form of a
soliton-antisoliton pair, corresponds to the instanton trajectory in the
double-well problem. We use the instanton method developed for the double-well
problem to find the contribution to the density of states from disorder
realizations close to the optimal fluctuation.Comment: 14 pages, revtex, epsf, 3 Postscript figure
Chiral exciton wave functions in cylindrical J aggregates
We study the exciton wave functions and the optical properties of cylindrical molecular aggregates. The cylindrical symmetry allows for a decomposition of the exciton Hamiltonian into a set of effective one-dimensional Hamiltonians, characterized by a transverse wave number k2 . These effective Hamiltonians have interactions that are complex if the cylinder exhibits chirality. We propose analytical Ansätze for the eigenfunctions of these one-dimensional problems that account for a finite cylinder length, and present a general study of their validity. A profound difference is found between the Hamiltonian for the transverse wave number k2=0 and those with k2≠0. The complex nature of the latter leads to chiral wave functions, which we characterize in detail. We apply our general formalism to the chlorosomes of green bacteria and compare the wave functions as well as linear optical spectra (absorption and dichroism) obtained through our Ansätze with those obtained by numerical diagonalization as well as those obtained by imposing periodic boundary conditions in the cylinder’s axis direction. It is found that our Ansätze, in particular, capture the finite-length effect in the circular dichroism spectrum much better than the solution with periodic boundary conditions. Our Ansätze also show that in finite-length cylinders seven superradiant states dominate the linear optical response.
First-principles simulations of the initial phase of self-aggregation of a cyanine dye: structure and optical spectra
Using first-principles simulations, we investigated the initial steps of the self-aggregation of the dye pseudoisocyanine (PIC) in water. First, we performed molecular dynamics (MD) simulations of the self-aggregation process, in which pile-of-coins oligomers ranging from dimers to stacks of about 20 molecules formed. The oligomer structures were found to be very flexible, with the dimers entering a weakly coupled state and then returning to a stable π-π stacked conformation on a nanosecond time scale. The structural information from the MD simulations was combined with quantum chemical calculations to generate a time-dependent Frenkel exciton Hamiltonian for monomers, dimers, and trimers, which included vibronic coupling. This Hamiltonian, in turn, was used to calculate the absorption spectra for these systems. The simulated dimer spectrum compared well to experiment, validating the face-to-face stacked dimer arrangement found in our MD simulations. Comparison of the simulated trimer spectrum to experiment suggested that oligomers larger than the dimer cannot be abundant at the onset of J-aggregation. Finally, the conformation of the PIC J-aggregate was investigated by testing the stability of several possible conformations in our MD simulations; none of the tested structures was found to be stable
Optical excitation of interacting electron-hole pairs in disordered one-dimensional semiconductors
We apply the optimal fluctuation method to the calculation of the optical
absorption in disordered one-dimensional semiconductors below the fundamental
optical gap. We find that a photon energy exists at which the shape of the
optimal fluctuation undergoes a dramatic change, resulting in a different
energy dependence of the absorption rate above and below this energy. In the
limit when the interaction of an electron and a hole with disorder is stronger
than their interaction with each other, we obtain an analytical expression for
the optical conductivity. We show that to calculate the absorption rate, it is,
in general, necessary to consider a manifold of optimal fluctuations, rather
than just a single fluctuation. For an arbitrary ratio of the Coulomb
interaction and disorder, the optimal fluctuation is found numerically.Comment: 19 pages, 6 figure
Disorder-induced solitons in conjugated polymers
We show that weak off-diagonal disorder in degenerate ground state conjugated
polymers results in a finite density of randomly positioned kinks (solitons and
antisolitons) in the lattice dimerization. For realistic values of the
disorder, these kinks should clearly show up in the optical and magnetic
properties.Comment: 5 pages, revtex, 2 Postscript figure
Signatures of β-sheet secondary structures in linear and two-dimensional infrared spectroscopy
Using idealized models for parallel and antiparallel β sheets, we calculate the linear and two-dimensional infrared spectra of the amide I vibration as a function of size and secondary structure. The model assumes transition–dipole coupling between the amide I oscillators in the sheet and accounts for the anharmonic nature of these oscillators. Using analytical and numerical methods, we show that the nature of the one-quantum vibrational eigenstates, which govern the linear spectrum, is, to a large extent, determined by the symmetry of the system and the relative magnitude of interstrand interactions. We also find that the eigenstates, in particular their trends with system size, depend sensitively on the secondary structure of the sheet. While in practice these differences may be difficult to distinguish in congested linear spectra, we demonstrate that they give rise to promising markers for secondary structure in the two-dimensional spectra. In particular, distinct differences occur between the spectra of parallel and antiparallel bsheets and between β hairpins and extended β sheets.
Excitation energy transfer between closely spaced multichromophoric systems: Effects of band mixing and intraband relaxation
We theoretically analyze the excitation energy transfer between two closely
spaced linear molecular J-aggregates, whose excited states are Frenkel
excitons. The aggregate with the higher (lower) exciton band edge energy is
considered as the donor (acceptor). The celebrated theory of F\"orster
resonance energy transfer (FRET), which relates the transfer rate to the
overlap integral of optical spectra, fails in this situation. We point out that
in addition to the well-known fact that the point-dipole approximation breaks
down (enabling energy transfer between optically forbidden states), also the
perturbative treatment of the electronic interactions between donor and
acceptor system, which underlies the F\"orster approach, in general loses its
validity due to overlap of the exciton bands. We therefore propose a
nonperturbative method, in which donor and acceptor bands are mixed and the
energy transfer is described in terms of a phonon-assisted energy relaxation
process between the two new (renormalized) bands. The validity of the
conventional perturbative approach is investigated by comparing to the
nonperturbative one; in general this validity improves for lower temperature
and larger distances (weaker interactions) between the aggregates. We also
demonstrate that the interference between intraband relaxation and energy
transfer renders the proper definition of the transfer rate and its evaluation
from experiment a complicated issue, which involves the initial excitation
condition.Comment: 13 pages, 6 PostScript figure
Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy
We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.
Low-temperature dynamics of weakly localized Frenkel excitons in disordered linar chains
We calculate the temperature dependence of the fluorescence Stokes shift and
the fluorescence decay time in linear Frenkel exciton systems resulting from
the thermal redistribution of exciton population over the band states. The
following factors, relevant to common experimental conditions, are accounted
for in our kinetic model: (weak) localization of the exciton states by static
disorder, coupling of the localized excitons to vibrations in the host medium,
a possible non-equilibrium of the subsystem of localized Frenkel excitons on
the time scale of the emission process, and different excitation conditions
(resonant or non resonant). A Pauli master equation, with microscopically
calculated transition rates, is used to describe the redistribution of the
exciton population over the manifold of localized exciton states. We find a
counterintuitive non-monotonic temperature dependence of the Stokes shift. In
addition, we show that depending on experimental conditions, the observed
fluorescence decay time may be determined by vibration-induced intra-band
relaxation, rather than radiative relaxation to the ground state. The model
considered has relevance to a wide variety of materials, such as linear
molecular aggregates, conjugated polymers, and polysilanes.Comment: 15 pages, 8 figure
Thermal effects in exciton harvesting in biased one-dimensional systems
The study of energy harvesting in chain-like structures is important due to
its relevance to a variety of interesting physical systems. Harvesting is
understood as the combination of exciton transport through intra-band exciton
relaxation (via scattering on phonon modes) and subsequent quenching by a trap.
Previously, we have shown that in the low temperature limit different
harvesting scenarios as a function of the applied bias strength (slope of the
energy gradient towards the trap) are possible \cite{Vlaming07}. This paper
generalizes the results for both homogeneous and disordered chains to nonzero
temperatures. We show that thermal effects are appreciable only for low bias
strengths, particularly so in disordered systems, and lead to faster
harvesting.Comment: 8 pages, 2 fugures, to appear in Journal of Luminescenc
- …