Attosecond electronic and nuclear quantum photodynamics of ozone: time-dependent Dyson orbitals and dipole

A nonadiabatic scheme for the description of the coupled electron and nuclear motions in the ozone molecule was proposed recently. An initial coherent nonstationary state was prepared as a superposition of the ground state and the excited Hartley band. In this situation neither the electrons nor the nuclei are in a stationary state. The multiconfiguration time dependent Hartree method was used to solve the coupled nuclear quantum dynamics in the framework of the adiabatic separation of the time-dependent Schr\"odinger equation. The resulting wave packet shows an oscillation of the electron density between the two chemical bonds. As a first step for probing the electronic motion we computed the time-dependent molecular dipole and the Dyson orbitals. The latter play an important role in the explanation of the photoelectron angular distribution. Calculations of the Dyson orbitals are presented both for the time-independent as well as the time-dependent situations. We limited our description of the electronic motion to the Franck-Condon region only due to the localization of the nuclear wave packets around this point during the first 5-6 fs

The role of quantum fluctuations in the optomechanical properties of a Bose-Einstein condensate in a ring cavity

We analyze a detailed model of a Bose-Einstein condensate trapped in a ring optical resonator and contrast its classical and quantum properties to those of a Fabry-P{\'e}rot geometry. The inclusion of two counter-propagating light fields and three matter field modes leads to important differences between the two situations. Specifically, we identify an experimentally realizable region where the system's behavior differs strongly from that of a BEC in a Fabry-P\'{e}rot cavity, and also where quantum corrections become significant. The classical dynamics are rich, and near bifurcation points in the mean-field classical system, the quantum fluctuations have a major impact on the system's dynamics.Comment: 11 pages, 11 figures, submitted to PR

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)

The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium’s spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic. © 2019 National Academy of Sciences. All rights reserved

Residues within the transmembrane domain of the glucagon-like peptide-1 receptor involved in ligand binding and receptor activation: modelling the ligand-bound receptor

The C-terminal regions of glucagon-like peptide-1 (GLP-1) bind to the N terminus of the GLP-1 receptor (GLP-1R), facilitating interaction of the ligand N terminus with the receptor transmembrane domain. In contrast, the agonist exendin-4 relies less on the transmembrane domain, and truncated antagonist analogs (e.g. exendin 9–39) may interact solely with the receptor N terminus. Here we used mutagenesis to explore the role of residues highly conserved in the predicted transmembrane helices of mammalian GLP-1Rs and conserved in family B G protein coupled receptors in ligand binding and GLP-1R activation. By iteration using information from the mutagenesis, along with the available crystal structure of the receptor N terminus and a model of the active opsin transmembrane domain, we developed a structural receptor model with GLP-1 bound and used this to better understand consequences of mutations. Mutation at Y152 [transmembrane helix (TM) 1], R190 (TM2), Y235 (TM3), H363 (TM6), and E364 (TM6) produced similar reductions in affinity for GLP-1 and exendin 9–39. In contrast, other mutations either preferentially [K197 (TM2), Q234 (TM3), and W284 (extracellular loop 2)] or solely [D198 (TM2) and R310 (TM5)] reduced GLP-1 affinity. Reduced agonist affinity was always associated with reduced potency. However, reductions in potency exceeded reductions in agonist affinity for K197A, W284A, and R310A, while H363A was uncoupled from cAMP generation, highlighting critical roles of these residues in translating binding to activation. Data show important roles in ligand binding and receptor activation of conserved residues within the transmembrane domain of the GLP-1R. The receptor structural model provides insight into the roles of these residues

Computation of conical intersections by using perturbation techniques

Multiconfigurational second-order perturbation theory, both in its single-state multiconfigurational second-order perturbation theory (CASPT2) and multistate (MS-CASPT2) formulations, is used to search for minima on the crossing seams between different potential energy hypersurfaces of electronic states in several molecular systems. The performance of the procedures is tested and discussed, focusing on the problem of the nonorthogonality of the single-state perturbative solutions. In different cases the obtained structures and energy differences are compared with available complete active space self-consistent field and multireference configuration interaction solutions. Calculations on different state crossings in LiF, formaldehyde, the ethene dimer, and the penta-2,4-dieniminium cation illustrate the discussions. Practical procedures to validate the CASPT2 solutions in polyatomic systems are explored, while it is shown that the application of the MS-CASPT2 procedure is not straightforward and requires a careful analysis of the stability of the results with the quality of the reference wave functions, that is, the size of the active [email protected] [email protected] [email protected]

Algebraic description of spacetime foam

A mathematical formalism for treating spacetime topology as a quantum observable is provided. We describe spacetime foam entirely in algebraic terms. To implement the correspondence principle we express the classical spacetime manifold of general relativity and the commutative coordinates of its events by means of appropriate limit constructions.Comment: 34 pages, LaTeX2e, the section concerning classical spacetimes in the limit essentially correcte

Structure of Colloid-Polymer Suspensions

We discuss structural correlations in mixtures of free polymer and colloidal particles based on a microscopic, 2-component liquid state integral equation theory. Whereas in the case of polymers much smaller than the spherical particles the relevant polymer degree of freedom is the center of mass, for polymers larger than the (nano-) particles conformational rearrangements need to be considered. They have the important consequence that the polymer depletion layer exhibits two widely different length scales, one of the order of the particle radius, the other of the order of the polymer radius or the polymer density screening length in dilute or semidilute concentrations, respectively. Their consequences on phase stability and structural correlations are discussed extensively.Comment: 37 pages, 17 figures; topical feature articl