Relation of exact Gaussian basis methods to the dephasing representation: Theory and application to time-resolved electronic spectra

We recently showed that the Dephasing Representation (DR) provides an efficient tool for computing ultrafast electronic spectra and that further acceleration is possible with cellularization [M. \v{S}ulc and J. Van\'i\v{c}ek, Mol. Phys. 110, 945 (2012)]. Here we focus on increasing the accuracy of this approximation by first implementing an exact Gaussian basis method, which benefits from the accuracy of quantum dynamics and efficiency of classical dynamics. Starting from this exact method, the DR is derived together with ten other methods for computing time-resolved spectra with intermediate accuracy and efficiency. These methods include the Gaussian DR, an exact generalization of the DR, in which trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. The newly obtained methods are tested numerically on time correlation functions and time-resolved stimulated emission spectra in the harmonic potential, pyrazine S0/S1 model, and quartic oscillator. Numerical results confirm that both the Gaussian basis method and the Gaussian DR increase the accuracy of the DR. Surprisingly, in chaotic systems the Gaussian DR can outperform the presumably more accurate Gaussian basis method, in which the two bases are evolved separately.Comment: 15 pages, 7 figure

Excitace molekul studenými elektrony

Název práce: Excitace molekul studenými elektrony Autor: Miroslav Šulc Katedra / Ústav: Ústav teoretické fyziky, Univerzita Karlova v Praze Vedoucí disertační práce: prof. RNDr. Jiří Horáček, DrSc., Ústav teoretické fyziky, Univerzita Karlova v Praze Abstrakt: Pozornost je věnována vybraným metodám pro popis nízkoenergetických elektron-molekulových srážek. První část práce se zabývá aplikací metody R-matice v kombinaci se Schwinger-Lanczos variačním principem pro potenciálový rozptyl v pří- padě dalekodosahových interakcí. Další sekce se zaobírají aspekty konstrukce ko- relačně-polarizačního potenciálu v metodě Discrete Momentum Representation (DMR) s využitím prostředků aproximace lokální hustoty v kontextu teorie funkcionálu hus- toty (DFT). Získané poznatky jsou následně aplikovány pro body-frame výpočty na úrovni aproximace statické výměny se zahrnutou polarizací (SEP) v rámci analýzy ex- perimentálních dat pro e−-N2 srážky představující součást širšího projektu věnovaného studiu rotačních excitací malých molekul v plynné fázi iniciovaných srážkami s elek- trony. V případě N2 bylo pozorováno potlačení dozadního průřezu pro energie pod 95 meV zdůvodnitelné z teoretického hlediska destruktivní...Title: Excitation of molecules by cold electrons Author: Miroslav Šulc Department / Institute: Institute of Theoretical Physics, Charles University in Prague Supervisor of the doctoral thesis: prof. RNDr. Jiří Horáček, DrSc., Institute of Theoretical Physics, Charles University Abstract: Several methods for low energy collisional processes are investigated. In the first part, attention is especially devoted to examination of applicability of the R-matrix method combined with the Schwinger-Lanczos (SL) variational principle for potential scattering with long-range forces. Next sections deal with the development of the interaction correlation-polarization (CP) potential in the framework of the Dis- crete Momentum Representation (DMR) method on the grounds of the Local Density Approximation in the Density Functional Theory (DFT) context. Obtained results are then utilized in body-frame (BF), static exchange + polarization (SEP), calcula- tions within an analysis of experimental data for e−-N2 scattering comprising a part of a larger project addressing theoretical examination of rotational excitations of small molecules in the gas phase induced by electron impact. For N2, a new phenomenon consisting in suppression of backward cross-section below 95 meV is observed and con- sequently attributed to...Ústav teoretické fyzikyInstitute of Theoretical PhysicsFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Biotransformation of benzonitrile herbicides via the nitrile hydratase–amidase pathway in rhodococci

Abstract The aim of this work was to determine the ability of rhodococci to transform 3,5-dichloro-4-hydroxybenzonitrile (chloroxynil), 3,5-dibromo-4-hydroxybenzonitrile (bromoxynil), 3,5-diiodo-4-hydroxybenzonitrile (ioxynil) and 2,6-dichlorobenzonitrile (dichlobenil); to identify the products and determine their acute toxicities. Rhodococcus erythropolis A4 and Rhodococcus rhodochrous PA-34 converted benzonitrile herbicides into amides, but only the former strain was able to hydrolyze 2,6-dichlorobenzamide into 2,6-dichlorobenzoic acid, and produced also more of the carboxylic acids from the other herbicides compared to strain PA-34. Transformation of nitriles into amides decreased acute toxicities for chloroxynil and dichlobenil, but increased them for bromoxynil and ioxynil. The amides inhibited root growth in Lactuca sativa less than the nitriles but more than the acids. The conversion of the nitrile group may be the first step in the mineralization of benzonitrile herbicides but cannot be itself considered to be a detoxification

Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations

Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered “half-closed” intermediates. Detailed free-energy landscapes of the transitions were obtained by sophisticated enhanced sampling simulations. Because the force field overstabilizes the closed conformation of HJs, we developed a system-specific modification which for the first time allows the observation of spontaneous opening-closing HJ transitions in unbiased MD simulations and opens the possibilities for more accurate HJ computational studies of biological processes and nanomaterials

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3′ untranslated regions (3′ UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3′ UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA–mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA–mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats