François G . Amar | University of Maine (original) (raw)

Papers by François G . Amar

She also provided leadership to establish the Master of Science in Teaching Program and serves as... more She also provided leadership to establish the Master of Science in Teaching Program and serves as its graduate coordinator. Dr. McKay's research interests include: condensed matter theory, phase transitions and critical phenomena, systems with quenched disorder, spin glasses, random-field ferromagnets, complex fluids, non-linear systems, and chaos. She managed and supervised all aspects of planning, implementing, and evaluating the project from its inception and continues to direct all project follow-up activities.

$Research paper thumbnail of Simulation of Xe$_{n}$Ar$_{m}$ Cluster Formation in a Molecular Beam: Comparison with Photoelectron Spectroscopy$

Bulletin of the American Physical Society, Mar 15, 2006

ME 04469-5706-We perform direct MD simulations of the formation of mixed Xe n Ar m clusters (500<... more ME 04469-5706-We perform direct MD simulations of the formation of mixed Xe n Ar m clusters (500<n+m<3000) in a supersonic beam as a function of initial beam conditions. We then model the 4d 5/2 (Xe) and 2p 3/2 (Ar) core hole photoelectron spectra of these clusters and compare them to the experimental spectra of Tchaplyguine et al [1]. The predicted spectra are calculated as the sum of final state energy shifts of the ionized atoms (within the cluster) relative to the isolated gas phase ion using a self-consistent polarization formalism. We use the results of our earlier calculations on pure argon and xenon clusters [2] to determine the appropriate inelastic mean free path value for the signal electrons leaving the mixed clusters. These results allow us to gain a refined understanding of the size, stoichiometry, and core/shell structure of these mixed clusters. [1] M. Tchaplyguine, et al,

Springer eBooks, 1987

The dynamics of photexcited dihalide species such as I2 has been extensively studied (1) in small... more The dynamics of photexcited dihalide species such as I2 has been extensively studied (1) in small van der Waals molecules with emphasis placed on the role of intramolecular energy transfer (2). In fluids, the geminate recombination dynamics of I2 excited to several electronic states has been studied both experimentally by picosecond spectroscopy and theoretically by molecular dynamics (MD) and other techniques (3), In order to bridge the gap between van der Waals molecules and condensed phases it is necessary to study small clusters of between 5 and 100 molecules in molecular beams. Our previous MD simulation study of photoexcitation dynamics of Br2ArN neutrals under beam condition demonstrated a gradual transition between the small molecule limit and the condensed phase limit as the numberof argon atoms was increased from 6 to 70 (4). For clusters of less than about 20 atoms, the Br2 caging dynamics is extremely sensitive to cluster geometry and loss of argon atoms occurs by impulsive energy transfer from Br2. For two shell cluster (70 atoms), loss of argon occurs by evaporation after the whole cluster is heated.

Springer eBooks, 1991

We discuss simulation studies of cluster evaporation dynamics for several systems which can be co... more We discuss simulation studies of cluster evaporation dynamics for several systems which can be considered typical of two limiting regimes: a statistical regime and a mode-specific regime. At the statistical limit, we compare the results of molecular dynamics (MD) simulations of the evaporation of small neutral argon clusters with both approximate statistical theories and exact classical phase space theory. In the limit of mode-specific excitation we discuss the photoexcitation and caging of diatomic molecules and ions in rare-gas and molecular clusters. Special attention is given to the I2(CO2)1 system. We compare simulation results with existing experimental data and discuss the transition from non-statistical to statistical evaporation as a function of cluster size.

2013 Annual Conference, Nov 9, 2013

Journal of Chemical Physics, Feb 15, 1979

Correlation diagrams are constructed to connect the rotation–vibration energy levels of idealized... more Correlation diagrams are constructed to connect the rotation–vibration energy levels of idealized limiting models for the tetratomic molecule. One limit is the completely nonrigid homonuclear four-atom cluster. Several choices are taken for the other limit: the nearly rigid regular tetrahedron and square, the dimer of two identical homonuclear diatomics, and the ammonialike inverter. A dimensionless parameter, the ratio of two energies, is proposed to characterize the degree of nonrigidity for molecules of arbitrary size or complexity. The parameter is evaluated for several examples.

Zeitschrift für Physik, Jun 1, 1992

We present resonant two-photon two-color photoionization (R2P2CI) spectra of a series of Aniline-... more We present resonant two-photon two-color photoionization (R2P2CI) spectra of a series of Aniline-Ar n complexes ( n=1-6). An apparently anomalous blue shifted spectra for An-Ar3 is explained by a modified spectral shift additivity rule which assigns different shifts to different relative positions of the Ar with respect to aniline. Evidence is presented for the existence of several isomers of clusters

Springer eBooks, 1992

Molecular dynamics simulations of Aniline-(Ar)n Van der Waals clusters have been performed. Isome... more Molecular dynamics simulations of Aniline-(Ar)n Van der Waals clusters have been performed. Isomerisatinn studies for An-(Ar)3 are described. Statistical evaporation rates for Ao-(Ar)3 are given and the results discussed in relation to isomerisation. Simulated spectra of An-(Ar)n with n=l−3 obtained with the spectral density method are also presented.

Metallomics, 2015

QM/MM studies were performed to explore the energetics of exchange reactions of glutathione disul... more QM/MM studies were performed to explore the energetics of exchange reactions of glutathione disulfide (GSSG) and the active site of thioredoxin [Cys32-Gly33-Pro34-Cys35] with and without zinc(II), in vacuum and solvated models. The activation energy for exchange, in the absence of zinc, is 29.7 kcal mol À1 for the solvated model. This is 3.3 kcal mol À1 higher than the activation energy for exchange in the gas phase, due to ground state stabilization of the active site Cys-32 thiolate in a polar environment. In the presence of zinc, the activation energy for exchange is 4.9 kcal mol À1 lower than in the absence of zinc (solvated models). The decrease in activation energy is attributed to stabilization of the charge-separated transition state, which has a 4-centered, cyclic arrangement of Zn-S-S-S with an estimated dipole moment of 4.2 D. A difference of 4.9 kcal mol À1 in activation energy would translate to an increase in rate by a factor of about 4000 for zinc-assisted thiol-disulfide exchange. The calculations are consistent with previously reported experimental results, which indicate that metal-thiolate, disulfide exchange rates increase as a function of solvent dielectric. This trend is opposite to that observed for the influence of the dielectric environment on the rate of thiol-disulfide exchange in the absence of metal. The results suggest a dynamic role for zinc in thiol-disulfide exchange reactions, involving accessible cysteine sites on proteins, which may contribute to redox regulation and mechanistic pathways during oxidative stress.

Zeitschrift für Physik, Mar 1, 1993

ABSTRACT We present results of semiclassical simulations of the electronic spectra and dynamics o... more ABSTRACT We present results of semiclassical simulations of the electronic spectra and dynamics of aniline-Arn (1=n=3) clusters. The spectral density formalism of Mukamel [3] is used to generate the spectra from the time dependent energy difference of the S0 and S1 states of aniline solvated by the argon atoms. A repulsive Ar-N interaction is incorporated in the Hamiltonian of the S1 state; this term permits a quantitative prediction of the origin shifts of the S10 transition (both red and blue shifts) for all the clusters studied. The temperature dependence of the spectrum of aniline-Ar2 is correlated with the underlying dynamics of this cluster.

Chemical Physics Letters, Nov 1, 1988

Molecular dynamics simulations for SF,-(Ar), clusters at effective temperatures in the range 5-45... more Molecular dynamics simulations for SF,-(Ar), clusters at effective temperatures in the range 5-45 K show that the system undergoes two different "melting" transitions, one at Tz I5 K marking the onset of Ar atom mobility wilhin a unimolecular layer around the SF6, and a second at Tz 35 K marking the onset of facile Ar atom motion out of and back into this layer. Moreover, on a narrow interval midway between these two points, the nine Ar atoms show a propensity for spontaneously isomerizing into and out of a long-lived near-rigid two-layer structure.

The Journal of Physical Chemistry, Dec 1, 1984

We present the results of a molecular dynamics trajectory study of the photodissociation/recombin... more We present the results of a molecular dynamics trajectory study of the photodissociation/recombination reaction of Br2 in argon clusters. Initial conditions of the clusters correspond to the cold, collision-free regime obtainable in a supersonic molecular beam. We compare our results to gas-and liquid-phase studies.

Journal of Chemical Physics, Jan 15, 1996

This paper reports the results of molecular dynamics (MD) simulations of isomerization and evapor... more This paper reports the results of molecular dynamics (MD) simulations of isomerization and evaporation processes of the aniline–Ar2 cluster. The trajectory results are analyzed in terms of a simple unimolecular kinetics scheme in order to extract isomer-specific evaporation rate constants. The less stable isomer, denoted (2/0) is found to have an evaporation rate constant that is about 25% smaller than that for the more stable isomer, (1/1). This result is explained in terms of the densities of states associated with each isomer. We present preliminary results on the aniline–Ar3 cluster and connect this latter system to possible experiments.

Journal of Chemical Physics, Jun 15, 1989

We present results of molecular dynamics calculations of the recombination dynamics of a model sy... more We present results of molecular dynamics calculations of the recombination dynamics of a model system intended to mimic the main features of Br−2 in clusters of argon and CO2. The calculation displays a number of novel features, most notably, a consistent treatment of the asymptotic localization of the ‘‘extra’’ negative charge on one of the bromine atoms at large rBr–Br. We simulate the photoexcitation of Br−2 to the 2Πg state and present a summary of results for the dissociation dynamics and caging behavior of minimum energy structures of Br−2Xn, 5<n<17 where X can be Ar or structureless CO2. The structural control of caging is most pronounced for these minimum energy configurations. We then present results of thermal averaging over an ensemble of trajectories for each cluster. These results are compared with recent experiments on Br−2(CO2)n.

Journal of Chemical Physics, Nov 15, 1986

We have carried out a molecular dynamics (MD) simulation study of melting of Ar7. By periodically... more We have carried out a molecular dynamics (MD) simulation study of melting of Ar7. By periodically quenching trajectories, we are also able to follow the path of the cluster through configuration space. This procedure yields information about isomerization rates, isomerization dynamics, and the connectivity of the phase space as a function of energy. New criteria for melting and the coexistence of phases in small clusters are compared with the traditional T(E) curves and rms bond fluctuations available from time averages in MD simulations.

European Physical Journal D, Jun 1, 2003

Using realistic pair potentials, we investigate the structures of mixed clusters of argon and nit... more Using realistic pair potentials, we investigate the structures of mixed clusters of argon and nitrogen in order to interpret the experimental electron diffraction patterns reported by the Torchet group. Simulations of small clusters indicate that argon tends to segregate at the center of the clusters. For larger clusters, in the range of 50 to 200 molecules, MC methods have been used to simulate structures that are likely to be generated in the molecular beam. By comparing predicted electron diffraction patterns with those recorded in the experiments, our models allow us to estimate the average size and composition of the mixed clusters for a given set of experimental conditions (nozzle stagnation pressure and Ar partial pressure).

Journal of Chemical Physics, Oct 17, 2003

The molecular dynamics (MD) simulation method is used to study Arm(N2)n clusters. Using realistic... more The molecular dynamics (MD) simulation method is used to study Arm(N2)n clusters. Using realistic pair potentials for the argon–argon, nitrogen–nitrogen, and argon–nitrogen interactions, the structures and thermodynamics of these clusters are investigated. The initial focus of the study is the series of thirteen particle clusters of Arm(N2)13−m (0⩽m⩽13). These icosahedral argon–nitrogen clusters display systematic changes in energetics when argon is substituted by nitrogen in the central position. The relative stability of argon-centered clusters over nitrogen-centered clusters is further investigated by defining and calculating a “species-centric” order parameter which can be monitored during a MD simulation. These results are interpreted in terms of frustration effects due to anisotropy in the N2–N2 and N2–Ar potentials. The consequences of these observations for cluster stability and for dynamical behavior, such as melting and evaporation, are investigated. The dynamical studies of larger clusters reveal that the mixed clusters evolve towards a structure with an argon core coated by a nitrogen shell.

Journal of Physical Chemistry C, Jul 28, 2010

Journal of Chemical Physics, Mar 15, 1993

We have simulated the cluster dissociation reaction Arn→Arn−1+Ar (12≤n≤14) using molecular dynami... more We have simulated the cluster dissociation reaction Arn→Arn−1+Ar (12≤n≤14) using molecular dynamics (MD) with well defined internal energy and total angular momentum. Reaction rates and kinetic energy release distributions are compared to the predictions of several statistical theories: Rice, Ramsperger, and Kassel (RRK), Engelking, and phase space theory (PST). We employ the Nosé prescription for constant temperature dynamics coupled with the multiple histogram method of Labastie and Whetten to obtain highly accurate vibrational densities of states for the clusters. The absolute densities are determined by the adiabatic switching method of Reinhardt. Incorporation of these accurate anharmonic vibrational densities of states into classical PST allows us to make a direct comparison with the simulation results and eliminates any parameters from the theory. Then PST predictions for the kinetics of evaporation are given for the low energy (long time scale) regime where MD simulations are prohibitively expensive. A critical evaluation of the approximate statistical theories is presented.