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.

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

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

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