A witness for coherent electronic oscillations in ultrafast spectroscopy

We report a conceptually straightforward witness that isolates coherent electronic oscillations from their vibronic counterparts in nonlinear optical spectra of molecular aggregates: Coherent oscillations as a function of waiting time in broadband pump/broadband probe spectra correspond to coherent electronic oscillations. Oscillations in individual peaks of 2D electronic spectra do not necessarily yield this conclusion. Our witness is simpler to implement than quantum process tomography and potentially resolves a long-standing controversy on the character of oscillations in ultrafast spectra of photosynthetic light harvesting systems.Comment: 4 pages, 2 figures, plus Supplementary Information. Work presented by the first author on March 1, 2012 at APS, Boston, Session W41, Focus Session on Quantum Coherence in Biological System

Application of compressed sensing to the simulation of atomic systems

Compressed sensing is a method that allows a significant reduction in the number of samples required for accurate measurements in many applications in experimental sciences and engineering. In this work, we show that compressed sensing can also be used to speed up numerical simulations. We apply compressed sensing to extract information from the real-time simulation of atomic and molecular systems, including electronic and nuclear dynamics. We find that for the calculation of vibrational and optical spectra the total propagation time, and hence the computational cost, can be reduced by approximately a factor of five.Comment: 7 pages, 5 figure

Anisotropy and controllable band structure in supra-wavelength polaritonic metasurfaces

In this letter we exploit the extended coherence length of mixed plasmon/exciton states to generate active metasurfaces. For this purpose, periodic stripes of organic dye are deposited on a continuous silver film. Typical metasurface effects, such as effective behavior and geometry sensitivity, are measured for periods exceeding the polaritonic wavelength by more than one order of magnitude. By adjusting the metasurface geometry, anisotropy, modified band structure and unidimensional polaritons are computationally simulated and experimentally observed in reflectometry as well as in emission.Comment: 4 figures, 1 Supplementary Material

PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs

Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets.published_or_final_versio

Molecular Emission near Metal Interfaces: The Polaritonic Regime

Copyright © 2018 American Chemical Society. The strong coupling of a dense layer of molecular excitons with surface-plasmon modes in a metal gives rise to polaritons (hybrid light-matter states) called plexcitons. Surface plasmons cannot directly emit into (or be excited by) free-space photons due to the fact that energy and momentum conservation cannot be simultaneously satisfied in photoluminescence. Most plexcitons are also formally nonemissive, even though they can radiate via molecules upon localization due to disorder and decoherence. However, a fraction of them are bright even in the presence of such deleterious processes. In this Letter, we theoretically discuss the superradiant emission properties of these bright plexcitons, which belong to the upper energy branch and reveal huge photoluminescence enhancements compared to bare excitons, due to near-divergences in the density of photonic modes available to them. Our study generalizes the well-known problem of molecular emission next to a metal interface to the polaritonic regime

Operational approach to open dynamics and quantifying initial correlations

A central aim of physics is to describe the dynamics of physical systems. Schrodinger's equation does this for isolated quantum systems. Describing the time evolution of a quantum system that interacts with its environment, in its most general form, has proved to be difficult because the dynamics is dependent on the state of the environment and the correlations with it. For discrete processes, such as quantum gates or chemical reactions, quantum process tomography provides the complete description of the dynamics, provided that the initial states of the system and the environment are independent of each other. However, many physical systems are correlated with the environment at the beginning of the experiment. Here, we give a prescription of quantum process tomography that yields the complete description of the dynamics of the system even when the initial correlations are present. Surprisingly, our method also gives quantitative expressions for the initial correlation.Comment: Completely re-written for clarity of presentation. 15 pages and 2 figure

Requirement of CRTC1 coactivator for hepatitis B virus transcription

Transcription of hepatitis B virus (HBV) from the covalently closed circular DNA (cccDNA) template is essential for its replication. Suppressing the level and transcriptional activity of cccDNA might have anti-HBV effect. Although cellular transcription factors, such as CREB, which mediate HBV transcription, have been well described, transcriptional coactivators that facilitate this process are incompletely understood. In this study we showed that CREB-regulated transcriptional coactivator 1 (CRTC1) is required for HBV transcription and replication. The steady-state levels of CRTC1 protein were elevated in HBV-positive hepatoma cells and liver tissues. Ectopic expression of CRTC1 or its homolog CRTC2 or CRTC3 in hepatoma cells stimulated the activity of the preS2/S promoter of HBV, whereas overexpression of a dominant inactive form of CRTC1 inhibited HBV transcription. CRTC1 interacts with CREB and they are mutually required for the recruitment to the preS2/S promoter on cccDNA and for the activation of HBV transcription. Accumulation of pregenomic RNA (pgRNA) and cccDNA was observed when CRTC1 or its homologs were overexpressed, whereas the levels of pgRNA, cccDNA and secreted HBsAg were diminished when CRTC1 was compromised. In addition, HBV transactivator protein HBx stabilized CRTC1 and promoted its activity on HBV transcription. Our work reveals an essential role of CRTC1 coactivator in facilitating and supporting HBV transcription and replication.published_or_final_versio