<span class=strong>Reception and Poster Session</span><br/><br/><br><b>Poster submissions welcome from all participants</b>

Monday, January 12, 2009 - 5:40pm - 7:00pm
Lind 400
  • Improved united-atom models for perfluorinated

    self-assembled monolayers

    Saulo Vázquez (University of Santiago de Compostela)
    Several united-atom (UA) force fields for perfluorinated self-assembled monolayer (FSAM) surfaces are proposed. These UA models of FSAM are based on a preceding force field, and the modifications done in this work involved the type of potential function and parameters used to represent the nonbonded interactions among the united atoms of the FSAM chains, which have been shown to play a key role in the energy transfer that takes place in collisions of gases with self-assembled monolayers.
  • Coherent and optimal control of adiabatic motion of ions

    in a trap

    Dmitri Babikov (Marquette University)
    Vibrational motion of ions in a linear trap can be efficiently controlled by creating small anharmonicity of the trapping potential and using optimally shaped MHz pulses to induce the desired states-to-state transitions. In this work the motional quantum states of ions in an anharmonic trap were calculated numerically using expansion over the basis set of Hermit polynomials. The Optimal Control Theory is employed in order to optimize shaped pulses for the major quantum gates, such as NOT, CNOT, Pi-rotation and the Hadamard transform.
  • Memory, hysteresis and oscillation induced by multiple

    covalent modifications and its

    application to circadian rhythm of Cyanobacteria

    Isamu Ohnishi (Hiroshima University)
    No transcription-translation feedback system of circadian clock by
    KaiC protein's
    phosphorylation is very interesting and also significant as a kind of
    core cycle of the
    circadian rhythm in Cyanobacteria. In order to understand the
    oscillation phenomena,
    we pay attention to a function of memory in a cell level. A standard
    structure of such a
    binary digit of memory is presented by use of multiple covalent
    modifications in this
    presentation. A key idea is bistability of covalent modification
    states which creates
    hysterecally and digitally switching mechanism between them. By use of
    this kind of
    memory, we see the circadian oscillation be realized. In fact, by deterministic
    simulations as well as by stochastic simulation, it is shown that the
    system obtains
    stable circadian oscillations, and shown that multiplicity of
    modification sites reinforces
    the stability of memory in several senses. Moreover, it is reported
    that this model
    explains well several molecular biologically experimental facts about
    period's change by
    use of mutants of Kai proteins in the circadian rhythm of Cyanobacteria.
  • A self-consistent, polarizable, electron-water potential for use in hydrated-electron simulations
    Leif Jacobson (The Ohio State University)
    Previously Turi and Borgis have parameterized an electron-water interaction potential in the static exchange approximation to yield a one-electron pseudopotential that has been applied to the study of anionic water clusters and the bulk hydrated electron. This potential has been used solely in conjunction with the Simple Point Charge (SPC) water model which is known to yield poor results for neutral water clusters. We re-parameterize the pseudopotential to be used with the polarizable AMOEBA water model to yield a potential in which the one-electron density polarizes the water molecules and vice versa in a fully self-consistent manner. The resulting model Hamiltonian is considerably more accurate for reproducing vertical electron binding energies (VEBEs), cluster geometries, and relative isomer energies when compared to ab initio results. The role of self-consistent polarization is particularly pronounced in clusters where the excess electron is bound in the interior of the cluster.
  • Infrared spectroscopy and dynamics of the Zundel cation
    Oriol Vendrell-Romagosa (Ruprecht-Karls-Universität Heidelberg)
    Results are presented on the dynamics and IR spectroscopy of the Zundel
    (H5O2+) cation. The full-dimensional (15D) quantum simulations are
    performed with the multiconfiguration time-dependent Hartree (MCTDH)

    We investigate the IR spectroscopy of H5O2+ and various of its
    isotopomers, namely D5O2+, HD4O2+ and DH4O2+ isotopomers, and provide a
    comparison to recent experiments on these systems. Dramatic changes in the
    dynamics and spectroscopy of the clusters are observed upon isotopic

    Accurate measurements of IR spectra of protonated water clusters prepared
    in the gas phase has become possible in recent years. The aim of our
    theoretical studies is to sheed light on interpretation of these complex
    spectra, provide useful physical insight in the dynamics of the hydrated
    proton, and last but not least, to advance in the description of complex
    molecular systems and clusters by full quantum methods.
  • A model for the photo-orientation of a molecular sample irradiated with

    polarized light

    Maurizio Persico
    Molecules irradiated by polarized light have a maximum excitation
    probability when their transition dipole vector is parallel to the light
    polarization. An excited molecule, because of its internal motions and
    of the interactions with the chemical environment, will change its
    orientation. As a consequence, a molecular sample gets oriented when
    irradiated, but the spontaneous rotational diffusion tends to restore the
    isotropic conditions. We have set up a stochastic model to represent
    the photo-induced anisotropy and its development in time. The
    calculation uses as input the results of single chromophore surface
    hopping simulations. The method is tested on azobenzene and shows the
    interplay of photo-orientation, rotational diffusion, and
  • Solvation dynamics in supercritical fluoroform
    Francesca Ingrosso (Université de Nancy I (Henri Poincaré))
    We present a molecular dynamics simulation study of solvation and collective polarizability dynamics supercritical fluoroform at a series of densities at constant temperature, slightly above the critical temperature, T_c. Our solvation dynamics studies were designed to represent the time-dependent frourescence Stokes shift for the chromophore coumarin 153. The equilibrium and nonequilibrium solvation responses were calculated. We found strong density dependence of solvation time correlations, with slower decay at lower densities and more pronounced for the excited-state than for the ground-state response. As for the nonequilibrium response, we showed that the inclusion of the interaction between the solute charge density and solvent induced dipoles improves the agreement with available experimental data. Preliminary results of an investigation of collective polarizability anisotropy relaxation in pure supercritical fluoroform are also presented. We focus on the nuclear response observable in optical Kerr effect and show that the results at higher densities are sensitive to the model used for the interaction-induced polarizability.
  • Mechanistic simulation of the autocatalytic isopeptide bond

    formation in pili with QM/MM minimum free energy path method

    Xiangqian Hu (Duke University)
    We studied the detailed reaction mechanism of autocatalytic intramolecular isopeptide bond formations in pili of Gram-negative bacteria with the recently developed QM/MM minimum free-energy path (QM/MM-MFEP) method. The scrutinized reaction mechanism consists of at least three steps in which proton transfers occur prior to and after the formation of the intramolecular isopeptide bond. Preliminary results revealed crucial roles of an active-site Glu residue in both the proton transfer reactions and the formation of the intramolecular isopeptide bond. Our results will provide important information for identifying and designing new vaccine candidates that can be applied to the bacterial
  • Analysis of structured populations in aquaculture
    József Farkas (University of Stirling)
    Farmed and wild salmonid fish are subject to parasitism from a number of
    copepod parasites of the family Caligidae. These sea lice are damaging,
    causing reduced growth and appetite, wounding and susceptability to
    secondary infections. Economic losses due to this type of parasites are
    high, with a value in excess of US $100 million globally. The life history
    of the parasite involves a succession of ten distinct developmental stages
    from egg to adult. In the present talk I will focus on the mathematical
    analysis of a nonlinear partial differential equation model with
    distributed states-at-birth, which type of model is intended to desribe
    the dynamics at the first chalimus stage of the parasite.

  • Born-Oppenheimer corrections near a Renner-Teller intersection
    Mark Herman (University of Minnesota, Twin Cities)
    We perform a rigorous mathematical analysis of the bending modes of
    a linear triatomic molecule that exhibits the Renner-Teller effect.
    Assuming the potentials are smooth, we prove that the wave functions
    and energy levels have asymptotic expansions in powers of epsilon,
    where the fourth power of epsilon is the ratio of an electron mass to the mass of a
    nucleus. To prove the validity of the expansion, we must prove
    various properties of the leading order equations and their
    solutions. The leading order eigenvalue problem is analyzed in
    terms of a parameter b, which is equivalent to the parameter
    originally used by Renner. Perturbation theory and finite
    difference calculations suggest that there is a crossing involving the ground bending vibrational
    state near b=0.925. The crossing involves two states with
    different degeneracy.
  • Quantum transition state theory applied to collinear reactions
    Arseni Goussev (University of Bristol)Roman Schubert (University of Bristol)
    We apply a recently developed quantum version of Transition State Theory based on Quantum Normal Forms (QNF) to simple collinear reactions. We find that the normal form converges quickly for molecules which are not too light.
  • Many-body theory of surface-enhanced Raman scattering
    David Masiello (Northwestern University)
    Joint work with George C. Schatz.

    A many-body Green's function approach to the microscopic theory
    of surface-enhanced Raman
    scattering is presented. Interaction ects between a general
    molecular system and a spatially
    anisotropic metal particle supporting plasmon excitations in
    the presence of an external radiation
    field are systematically included through many-body
    perturbation theory. Reduction of the
    exact ects of molecular-electronic correlation to the level of
    Hartree-Fock mean-field theory is
    made for practical initial implementation, while description of
    collective oscillations of conduction
    electrons in the metal is reduced to that of a classical plasma
    density; extension of the former to
    a Kohn-Sham density-functional or second-order Møller-Plesset
    perturbation theory is discussed;
    further specialization of the latter to the random-phase
    approximation allows for several salient
    features of the formalism to be highlighted without need for
    numerical computation. Scattering and
    linear-response properties of the coupled system subjected to
    an external perturbing electric field
    in the electric-dipole interaction approximation are
    investigated. Both damping and finite-lifetime
    ects of molecular-electronic excitations as well as the
    characteristic fourth-power enhancement
    of the molecular Raman scattering intensity are elucidated from
    first principles. It is demonstrated
    that the presented theory reduces to previous models of
    surface-enhanced Raman scattering and
    leads naturally to a semiclassical picture of the response of a
    quantum-mechanical molecular system
    interacting with a spatially anisotropic classical metal
    particle with electronic polarization
    approximated by a discretized collection of electric dipoles.
  • A quantum chemist’s view of molecular conduction via

    the reduced density matrix

    Joseph Subotnik (Tel Aviv University)
    We present a very simple model for numerically describing the steady state dynamics of a system interacting with continua of states representing a bath. Our model can be applied to equilibrium and non-equilibrium problems. For a one-state system coupled to two free electron reservoirs, our results match the Landauer formula for current traveling through a molecule. More significantly, we can also predict the non- equilibrium steady state population on a molecule between two out-of-equilibrium contacts. While the method presented here is for one-electron Hamiltonians, we outline how this model may be extended to include electron-electron interactions and correlations, an approach which suggests a connection between the conduction problem and the electronic structure problem.
  • Calculating solution redox free energies with Ab initio QM/MM

    minimum free energy path method

    Xiancheng Zeng (Duke University)
    A quantum mechanical/molecularmechanical minimum free energy path
    (QM/MM-MFEP) method was developed to calculate the redox free energies
    of large systems in solution with greatly enhanced efficiency for
    conformation sampling. The QM/MM-MFEP method describes the
    thermodynamics of a system on the potential of mean force (PMF)
    surface of the solute degrees of freedom. The MD sampling is only
    carried out with the QM subsystem fixed. It thus avoids on-the-fly
    QM calculations and overcomes the high computational cost of the
    direct ab initio QM/MM molecular dynamics (MD) needed for sampling.
    The enhanced efficiency and uncompromised accuracy of this approach
    are especially significant for biochemical systems. The QM/MM-MFEP
    method thus provides an efficient approach to free energy simulation
    of complex electron transfer reactions.
  • Non–adiabatic scattering wave functions in a simple

    Born–Oppenheimer model

    George Hagedorn (VPI and SU)
    No Abstract
  • Symmetry-broken independent-particle models in Born-Oppenheimer

    molecular dynamics of chemical bond dissociation

    Igor Schweigert (Naval Research Laboratory)
    Joint work with Brett I. Dunlap.

    Simulating chemical bond dissociation dynamics requires
    structure methods to seamlessly describe the transition
    from the initial closed-shell configuration to an open-shell
    Direct-dynamic simulations of the RO-NO2 bond dissociation
    in nitric
    esters are presented to demonstrate the importance of using
    unrestricted single-determinant methods and
    spin-symmetry-broken orbitals. Challenges in locating the symmetry-broken
    electronic potential energy surface in the course of a reactive
    trajectory are discussed. The second derivative of the unrestricted energy
    with respect to nuclear displacement is shown to be
    discontinuous at the onset of symmetry breaking, in analogy with the
    discontinuous specific heat in the Landau theory of second-order phase
  • Tunneling dynamics in a double well within the approximate

    quantum trajectories framework

    Sophya Garashchuk (University of South Carolina)
    Quantum-mechanical (QM) effects in molecular dynamics –
    zero-point energy, tunneling and nonadiabatic dynamics –
    essential for accurate description and understanding of
    reactions in complex molecular systems.
    Since the exact solution of the Schrödinger equation for such
    systems in full dimension is neither feasible nor necessary,
    the trajectory-based approaches have special appeal: classical
    description is often appropriate for dynamics of heavy
    particles such as nuclei, and cheap – methods of molecular
    mechanics are routinely applied to high-dimensional systems of
    hundreds of atoms. The challenge is to include quantum effects
    on dynamics of the trajectories.

    We use the de Broglie-Bohm formulation of the Schrodinger
    equation to formulate a semiclassical trajectory method. QM
    effects are included through the quantum force due to
    localization of the trajectory ensemble, acting on the
    trajectories in addition to the classical forces. A cheap
    approximation to the quantum potential makes the method
    practical in many dimensions and captures dominant quantum
    effects in semiclassical systems.
    The latest development is a description of the double well
    dynamics – a prototype of the proton transfer
    reactions – which exhibits hard quantum effect of tunneling. This is
    achieved by combining the approximate quantum trajectory
    dynamics with the population amplitudes in the reactant and
    product wells. The trajectories are driven by the asymptotic
    classical potentials, while the population amplitudes are
    described in a small basis. The method is exact if these
    reactant/product potentials are harmonic and the basis size is
    sufficiently large. In the semiclassical regime trajectory
    dynamics is approximate, and the basis size can be as small as
    two functions. The approach is fully compatible with the
    trajectory description of multidimensional systems capturing
    quantum tunneling along the reactive coordinate and ZPE flow
    among all degrees of freedom.
  • Azobenzene in solution: excited state dynamics simulation
    Maurizio Persico
    We present a set of surface hopping simulations of the excited state
    decay and photoisomerization of azobenzene, in vacuo and in two solvents
    of different viscosity, methanol and ethylene glycol. We are able to
    reproduce the experimental quantum yields and the fluorescence
    transients (both intensity and anisotropy). We bring out the effects of
    solvation on the photodynamics and propose a new interpretation of
    recent experiments.
  • Partial differential equations in chemical dynamics

    with finite elements

    Craig Michoski (The University of Texas at Austin)
    We introduce some mathematical analysis in the form of existence and uniqueness results for chemically miscible compressible classical systems of equations. Then we show some extensions to chemical reactor systems, where chemical kinetics and intermolecular diffusion is taken into consideration, and applied to atmospheric chemistry. Finally we show an extension to quantum hydrodynamic systems of equations, used to model chemical reactions.