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

Exciton-Exciton Annihilation Is Coherently Suppressed in H-Aggregates, but Not in J-Aggregates

We theoretically demonstrate a strong dependence of the annihilation rate between (singlet) excitons on the sign of dipole-dipole couplings between molecules. For molecular H-aggregates, where this sign is positive, the phase relation of the delocalized two-exciton wavefunctions causes a destructive interference in the annihilation probability. For J-aggregates, where this sign is negative, the interference is constructive instead, as a result of which no such coherent suppression of the annihilation rate occurs. As a consequence, room temperature annihilation rates of typical H- and J-aggregates differ by a factor of ~3, while an order of magnitude difference is found for low-temperature aggregates with a low degree of disorder. These findings, which explain experimental observations, reveal a fundamental principle underlying exciton-exciton annihilation, with major implications for technological devices and experimental studies involving high excitation densities

Electron-solid and electron-liquid phases in graphene

We investigate the competition between electron-solid and quantum-liquid phases in graphene, which arise in partially filled Landau levels. The differences in the wave function describing the electrons in the presence of a perpendicular magnetic field in graphene with respect to the conventional semiconductors, such as GaAs, can be captured in a form factor which carries the Landau-level index. This leads to a quantitative difference in the electron-solid and -liquid energies. For the lowest Landau level, there is no difference in the wave function of relativistic and nonrelativistic systems. We compute the cohesive energy of the solid phase analytically using a Hartree-Fock Hamiltonian. The liquid energies are computed analytically as well as numerically, using exact diagonalization. We find that the liquid phase dominates in the n=1 Landau level, whereas the Wigner crystal and electron-bubble phases become more prominent in the n=2 and 3 Landau level

Optical Signatures of the Coupling between Excitons and Charge Transfer States in Linear Molecular Aggregates

Charge Transfer (CT) has enjoyed continuous interest due to increasing experimental control over molecular structure leading to applications in, for example, photovoltaics and hydrogen production. In this paper, we investigate the effect of CT states on the absorption spectrum of linear molecular aggregates using a scattering matrix technique that allows us to deal with arbitrarily large systems. The presented theory performs well for both strong and weak mixing of exciton and CT states, bridging the gap between previously employed methods which are applicable in only one of these limits. In experimental spectra the homogeneous linewidth is often too large to resolve all optically allowed transitions individually, resulting in a characteristic two-peak absorption spectrum in both the weak- and strong-coupling regime. Using the scattering matrix technique we examine the contributions of free and bound states in detail. We conclude that the skewness of the high-frequency peak may be used as a new way to identify the exciton-CT-state coupling strength.Comment: 12 pages, 9 figure

Exciton localization in tubular molecular aggregates:Size effects and optical response

We study the exciton localization and resulting optical response for disordered tubular aggregates of optically active molecules. It has been shown previously that such tubular structures allow for excitons delocalized over more than a thousand molecules, owing to the combined effects of long-range dipole-dipole interactions and the higher-dimensional (not truly one-dimensional) nature of the aggregate. Such large delocalization sizes prompt the question to what extent in experimental systems the delocalization may still be determined by the aggregate size (diameter and length) and how this affects the aggregate's optical response and dynamics. We perform a systematic study of the size effects on the localization properties, using numerical simulations of the exciton states in a cylindrical model structure inspired by the previously derived geometry of a cylindrical aggregate of cyanine dye molecules (C8S3). To characterize the exciton localization, we calculate the participation ratio and the autocorrelation function of the exciton wave function. Also, we calculate the density of states and absorption spectrum. We find strong effects of the tube's radius on the localization and optical properties in the range of parameters relevant to experiment. In addition, surprisingly, we find that even for tubes as long as 750 nm, the localization size is limited by the tube's length for disorder values that are relevant to experimental circumstances, while observable effects of the tube's length in the absorption spectrum still occur for tube lengths up to about 150 nm. The latter may explain changes in the optical spectra observed during the aging process of bromine-substituted C8S3 aggregates. For weak disorder, the exciton wave functions exhibit a scattered, fractal-like nature, similar to the quasi-particles in two-dimensional disordered systems

Excitons in tubular molecular aggregates

Abstract We present a brief overview of recent work on the optical properties of molecular aggregates with a tubular (cylindrical) shape. The exciton states responsible for these properties can be distinguished with regard to a transverse wave number, which directly relates to optical selection rules and polarization direction of the associated absorption line. We discuss two types of analytical solutions for the exciton wave functions and the associated absorption and dichroism spectra.

Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Drastic effects of damping mechanisms on the third-order optical nonlinearity

We have investigated the optical response of superradiant atoms, which undergoes three different damping mechanisms: radiative dissipation ($\gamma_r$), dephasing ($\gamma_d$), and nonradiative dissipation ($\gamma_n$). Whereas the roles of $\gamma_d$ and $\gamma_n$ are equivalent in the linear susceptibility, the third-order nonlinear susceptibility drastically depends on the ratio of $\gamma_d$ and $\gamma_n$: When $\gamma_d \ll \gamma_n$, the third-order susceptibility is essentially that of a single atom. Contrarily, in the opposite case of $\gamma_d \gg \gamma_n$, the third-order susceptibility suffers the size-enhancement effect and becomes proportional to the system size.Comment: 5pages, 2figure