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.

Exciton superradiance in molecular crystal slabs

We investigate the spontaneous emission rate γ of dipolar excitons in molecular crystal slabs of variable thickness, L, ranging from monolayers to bulk crystals. We find a smooth transition between superradiant excitons (γ ∝ L) at thickness small compared to an optical wavelength (λ) and radiatively stable polaritons for thick crystals (γ ∝ 1/L). The maximum cooperativity volume of the molecules in the slab is found to be of the order λ^3

THE TRANSIENT GRATING AS A PROBE FOR POLARITON DYNAMICS

A theory is presented that microscopically accounts for the role of polariton propagation in the transient grating experiment. The basis of our theory is formed by coupled equations of motion for polariton amplitudes and coherences, in which we account for polariton-phonon scattering. It is demonstrated that at low temperature the transient grating experiment probes polariton dynamics. Explicit results for the transient grating signal are obtained within two specific (strong-collision) models for polariton scattering

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.

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.

Peierls transition with acoustic phonons and twist deformation in carbon nanotubes

We consider the Peierls instability due to the interaction of electrons with both acoustic and optical phonons. We suggest that such a transition takes place in carbon nanotubes with small radius. The topological excitations and the temperature dependence of the conductivity resulting from the electron-lattice interactions are considered.Comment: 5 pages, 3 PostScript figures included; submitted to Phys. Rev. Let