Non-Markovian quantum state diffusion for absorption spectra of molecular aggregates

In many molecular systems one encounters the situation where electronic excitations couple to a quasi-continuum of phonon modes. That continuum may be highly structured e.g. due to some weakly damped high frequency modes. To handle such a situation, an approach combining the non-Markovian quantum state diffusion (NMQSD) description of open quantum systems with an efficient but abstract approximation was recently applied to calculate energy transfer and absorption spectra of molecular aggregates [Roden, Eisfeld, Wolff, Strunz, PRL 103 (2009) 058301]. To explore the validity of the used approximation for such complicated systems, in the present work we compare the calculated (approximative) absorption spectra with exact results. These are obtained from the method of pseudomodes, which we show to be capable of determining the exact spectra for small aggregates and a few pseudomodes. It turns out that in the cases considered, the results of the two approaches mostly agree quite well. The advantages and disadvantages of the two approaches are discussed

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators

Isosbestic points in the spectral function of correlated electrons

We investigate the properties of the spectral function A(omega,U) of correlated electrons within the Hubbard model and dynamical mean-field theory. Curves of A(omega,U) vs. omega for different values of the interaction U are found to intersect near the band-edges of the non-interacting system. For a wide range of U the crossing points are located within a sharply confined region. The precise location of these 'isosbestic points' depends on details of the non-interacting band structure. Isosbestic points of dynamic quantities therefore provide valuable insights into microscopic energy scales of correlated systems.Comment: 16 pages, 5 figure

Regulation-Structured Dynamic Metabolic Model Provides a Potential Mechanism for Delayed Enzyme Response in Denitrification Process

In a recent study of denitrification dynamics in hyporheic zone sediments, we observed a significant time lag (up to several days) in enzymatic response to the changes in substrate concentration. To explore an underlying mechanism and understand the interactive dynamics between enzymes and nutrients, we developed a trait-based model that associates a community’s traits with functional enzymes, instead of typically used species guilds (or functional guilds). This enzyme-based formulation allows to collectively describe biogeochemical functions of microbial communities without directly parameterizing the dynamics of species guilds, therefore being scalable to complex communities. As a key component of modeling, we accounted for microbial regulation occurring through transcriptional and translational processes, the dynamics of which was parameterized based on the temporal profiles of enzyme concentrations measured using a new signature peptide-based method. The simulation results using the resulting model showed several days of a time lag in enzymatic responses as observed in experiments. Further, the model showed that the delayed enzymatic reactions could be primarily controlled by transcriptional responses and that the dynamics of transcripts and enzymes are closely correlated. The developed model can serve as a useful tool for predicting biogeochemical processes in natural environments, either independently or through integration with hydrologic flow simulators

The transformative potential of reflective diaries for elite English cricketers

The sport of cricket has a history of its players suffering from mental health issues. The psychological study of cricket and, in particular, the attendant demands of participating at an elite level has not previously received rigorous academic attention. This study explored ten elite male cricketers’ experiences of keeping a daily reflective diary for one month during the competitive season. The aim was to assess how valuable qualitative diaries are in this field. Participants were interviewed regarding their appraisal of the methodology as a self‐help tool that could assist coping with performance pressures and wider life challenges. Three outcomes were revealed: first, that diary keeping was an effective opportunity to reflect upon the past and enhance one’s self (both as an individual and a performer); second, that diary keeping acted as a form of release that allowed participants to progress; and third, that diary keeping allowed participants to discover personal patterns of success that increased the likeliness of optimum performance

Nonlinear resonance reflection from and transmission through a dense glassy system built up of oriented linear Frenkel chains: two-level models

A theoretical study of the resonance optical response of assemblies of oriented short (as compared to an optical wavelength) linear Frenkel chains is carried out using a two-level model. We show that both transmittivity and reflectivity of the film may behave in a bistable fashion and analyze how the effects found depend on the film thickness and on the inhomogeneous width of the exciton optical transition.Comment: 26 pages, 9 figure

Linear optical properties of one-dimensional Frenkel exciton systems with intersite energy correlations

We analyze the effects of intersite energy correlations on the linear optical properties of one-dimensional disordered Frenkel exciton systems. The absorption line width and the factor of radiative rate enhancement are studied as a function of the correlation length of the disorder. The absorption line width monotonously approaches the seeding degree of disorder on increasing the correlation length. On the contrary, the factor of radiative rate enhancement shows a non-monotonous trend, indicating a complicated scenario of the exciton localization in correlated systems. The concept of coherently bound molecules is exploited to explain the numerical results, showing good agreement with theory. Some recent experiments are discussed in the light of the present theory.Comment: 18 pages, 3 figues, REVTeX, to appear in Physical Review

Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer

The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O6-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA directed assembly of homo- and hetero-dimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template directed assembly of PNA modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels which may find use in the study of assembly processes in cells