REIMAGINING OF OPTICAL KERR EFFECT SPECTROSCOPY: DEVELOPMENT OF A NEW SPECTROSCOPIC TECHNIQUE

Multidimensional nonlinear spectroscopic methods are powerful tools to investigate ultrafast vibrational dynamics and coherences. Several techniques that have recently been applied to excited electronic states require three or more ultrashort pulses to measure the nonlinear optical response. The additional beamsplitters, mirrors and optical delay stages in these techniques complicates their application in the extreme ultraviolet and X-ray regime, where reflectance is low except at grazing incidence. Optical Kerr effect spectroscopy is a traditional two-pulse technique to measure the 3$^{rd}$-order nonlinear optical susceptibility of molecules in their ground electronic state. Ultrafast transient polarization spectroscopy (UTPS) is an extension of this technique to excited electronic states, enabling coupled electronic and nuclear dynamics to be investigated by the 3$^{rd}$-order nonlinear optical susceptibility. In UTPS, a pump pulse excites a population, then a Kerr gate and probe pulse monitor the 3$^{rd}$-order nonlinear response of excited-state molecules, as a function of delay between each of the three pulses. Two-photon absorption of femtosecond pump pulses populate the S$_{1}$ excited-state of nitrobenzene. We were able to extract a dephasing time that oscillates as function of the time delay after excitation. This dephasing time and supporting theoretical calculation allows for distinguishing between an intersystem crossing conical intersection and an internal conversion conical intersection on the same excited-state potential energy surface

ULTRAFAST DYNAMICS IN DNA AND RNA DERIVATIVES MONITORED BY BROADBAND TRANSIENT ABSORPTION SPECTRSCOPY

The ultrafast dynamics of nucleic acids have been under scrutiny for the past couple of decades because of the role that the high-energy electronic states play in mutagenesis and carcinogenesis. Kinetic models have been proposed, based on both experimental and theoretical discoveries. Direct experimental evidence of the intersystem crossing rate and population of the triplet state for most nucleic acid bases has yet to be reported, even though the triplet state is thought to be the most reactive species. Utilizing broadband femtosecond transient absorption spectroscopy, we reveal the time scale at which singlet-to-triplet population transfer occurs in several nucleic acid derivatives in the condensed phase. The implication of these results to the current understanding of the DNA and RNA photochemistry will be discussed. The authors acknowledge the CAREER program of the National Science Foundation (Grant No. CHE-1255084) for financial support

Time-Resolved Ultrafast Transient Polarization Spectroscopy to Investigate Nonlinear Processes and Dynamics in Electronically Excited Molecules on the Femtosecond Time Scale

We report a novel experimental technique to investigate ultrafast dynamics in photoexcited molecules by probing the third-order nonlinear optical susceptibility. A non-colinear 3-pulse scheme is developed to probe the ultrafast dynamics of excited electronic states using the optical Kerr effect by time-resolved polarization spectroscopy. Optical heterodyne and optical homodyne detection are demonstrated to measure the third-order nonlinear optical response for the S1 excited state of liquid nitrobenzene, which is populated by 2-photon absorption of a 780 nm 35 fs excitation pulse.Comment: 12 pages, 4 figures. Changes from previous version: added panel labels to figures 3-

Ultrafast Dynamics of Excited Electronic States in Nitrobenzene Measured by Ultrafast Transient Polarization Spectroscopy.

We investigate ultrafast dynamics of the lowest singlet excited electronic state in liquid nitrobenzene using ultrafast transient polarization spectroscopy, extending the well-known technique of optical Kerr effect spectroscopy to excited electronic states. The third-order nonlinear response of the excited molecular ensemble is measured using a pair of femtosecond pulses following a third femtosecond pulse that populates the S1 excited state. By measuring this response, which is highly sensitive to details of the excited state character and structure, as a function of time delays between the three pulses involved, we extract the dephasing time of the wave packet on the excited state. The dephasing time, measured as a function of time delay after pump excitation, shows oscillations indicating oscillatory wave packet dynamics on the excited state. From the experimental measurements and supporting theoretical calculations, we deduce that the wave packet completely leaves the S1 state potential energy surface after three traversals of the intersystem crossing between the singlet S1 and triplet T2 states

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc. Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification

Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.Peer reviewe

Taxonomy of prokaryotic viruses : 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Peer reviewe

Taxonomy of prokaryotic viruses : 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.Peer reviewe