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We report on a molecular dynamics simulation based study of the thermal and mechanical properties of the elastin mimetic peptide [LGGVG]n (n = 3, 7). Our findings indicate that this peptide undergoes an inverse temperature transition as the temperature is raised from ∼20 °C to 42 °C. The thermal behavior is similar to what has been observed in other well studied short mimetic peptides of elastin. Both [LGGVG]n (n = 3, 7) peptides exhibit an increase in the number of side chain contacts and peptide-peptide hydrogen bonds when the temperature is raised from ∼20 °C to 42 °C. These observations are accompanied by a decrease in the number of proximal water molecules and number of peptide-water hydrogen bonds. This work also reports on a comparison of the thermal and mechanical properties of [LGGVG]3 and [VPGVG]3 and quantifies the interaction with surrounding waters of hydration under mechanically strained conditions. It is demonstrated, via a quasi-harmonic approach, that both model peptides exhibit a reduction in the population of low-frequency modes and an increase in population of high-frequency modes upon elongation. The shift in population of frequency modes causes the peptide entropy to decrease upon elongation and is responsible for the development of an entropic force that gives rise to elasticity. These observations are in disagreement with a previously published notion that model elastin peptides, such as [VPGVG]18, increase in entropy upon elongation. [ABSTRACT FROM AUTHOR]

Thermal electron attachment to C60 has been studied by relative rate measurements in a flowing afterglow Langmuir probe apparatus. The rate coefficients of the attachment k1 are shown to be close to 10-6 cm3 s-1 with a small negative temperature coefficient. These results supersede measurements from the 1990s which led to much smaller values of k1 with a large positive temperature coefficient suggesting an activation barrier. Theoretical modeling of k1 in terms of generalized Vogt–Wannier capture theory shows that k1 now looks more consistent with measurements of absolute attachment cross sections σat than before. The comparison of capture theory and experimental rate or cross section data leads to empirical correction factors, accounting for “intramolecular vibrational relaxation” or “electron-phonon coupling,” which reduce k1 below the capture results and which, on a partial wave-selected level, decrease with increasing electron energy. [ABSTRACT FROM AUTHOR]

A class II atomistic force field with Lennard-Jones 6–9 nonbond interactions is used to investigate equations of state (EOS) for important high explosive detonation products N2 and H2O in the temperature range of 700–2500 K and pressure range of 0.1–10 GPa. A standard sixth order parameter-mixing scheme is then employed to study a 2:1 (molar) H2O:N2 mixture, to investigate, in particular, the possibility of phase separation under detonation conditions. The simulations demonstrate several important results, including (i) the accuracy of computed EOS for both N2 and H2O over the entire range of temperature and pressure considered, (ii) accurate mixing-demixing phase boundary as compared to experimental data, and (iii) the departure of mixing free energy from that predicted by ideal mixing law. The results provide comparison and guidance to state-of-the-art chemical kinetic models. [ABSTRACT FROM AUTHOR]

The dynamics of a thin film of ice Ih deposited on MgO (001) is studied through molecular dynamics simulations performed with two new potential models of ice. This system is chosen because it is possible to compare the results of the simulations to incoherent neutron quasielastic scattering experiments performed few years ago and to previous molecular dynamics simulations using the TIP4P potential model. The present simulations are performed to determine the evolution of the translational and orientational order parameters of the ice film upon temperature increase in the 250–280 K range. They are also used to calculate the translational and orientational diffusion coefficients of the water molecules in the supported film as a function of the temperature. When using the TIP5P potential, the present results show a better agreement with experimental data than those calculated with the TIP4P potential, especially regarding the temperature above which significant changes are obtained in the dynamics of the water film. Similar conclusions are obtained when using the TIP4P/ice potential, although this latter potential clearly underestimates the translational diffusion coefficients. [ABSTRACT FROM AUTHOR]

We perform microscopic simulations of a reactive dilute gas and study the propagation of an exothermic chemical wave front in an infinite, one-dimensional medium. The simulation results concerning front propagation speed and concentrations, temperature and stream velocity profiles are compared with the results of the integration of the macroscopic continuity equations in the case of fast reactions. The discrepancies between the two approaches are related to a chemically induced departure from local equilibrium. [ABSTRACT FROM AUTHOR]

We numerically investigate the competition between phase separation and dynamical arrest in a colloidal system interacting via a short-ranged attractive potential. Equilibrium fluid configurations are quenched at two different temperatures below the critical temperature and followed during their time evolution. At the lowest studied T, the phase-separation process is interrupted by the formation of an attractive glass in the dense phase. At the higher T, no arrest is observed and the phase-separation process proceeds endlessly in the simulated time window. The final structure of the glass retains memory of the interrupted phase-separation process in the form of a frozen spinodal decomposition peak, whose location and amplitude is controlled by the average packing fraction. We also discuss the time evolution of the nonergodicity parameter, providing evidence of a progressively decreasing localization length on increasing the packing fraction. Finally, we confirm that the reported results are independent of the microscopic dynamics. [ABSTRACT FROM AUTHOR]

We use the recently developed reactive force field ReaxFF with molecular dynamics to study thermal induced chemistry in RDX [cyclic-[CH2N(NO2)]3] at various temperatures and densities. We find that the time evolution of the potential energy can be described reasonably well with a single exponential function from which we obtain an overall characteristic time of decomposition that increases with decreasing density and shows an Arrhenius temperature dependence. These characteristic timescales are in reasonable quantitative agreement with experimental measurements in a similar energetic material, HMX [cyclic-[CH2N(NO2)]4]. Our simulations show that the equilibrium population of CO and CO2 (as well as their time evolution) depend strongly of density: at low density almost all carbon atoms form CO molecules; as the density increases larger aggregates of carbon appear leading to a C deficient gas phase and the appearance of CO2 molecules. The equilibrium populations of N2 and H2O are more insensitive with respect to density and form in the early stages of the decomposition process with similar timescales. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

An extended system molecular dynamics method for the isomolar semigrand ensemble (fixed number of particles, pressure, temperature, and fugacity fraction) is developed and applied to the calculation of liquid-liquid equilibria (LLE) for two Lennard-Jones mixtures. The method utilizes an extended system variable to dynamically control the fugacity fraction ξ of the mixture by gradually transforming the identity of particles in the system. Two approaches are used to compute coexistence points. The first approach uses multiple-histogram reweighting techniques to determine the coexistence ξ and compositions of each phase at temperatures near the upper critical solution temperature. The second approach, useful for cases in which there is no critical solution temperature, is based on principles of small system thermodynamics. In this case a coexistence point is found by running N-P-T-ξ simulations at a common temperature and pressure and varying the fugacity fraction to map out the difference in chemical potential between the two species A and B (μA-μB) as a function of composition. Once this curve is known the equal-distance/equal-area criterion is used to determine the coexistence point. Both approaches give results that are comparable to those of previous Monte Carlo (MC) simulations. By formulating this approach in a molecular dynamics framework, it should be easier to compute the LLE of complex molecules whose intramolecular degrees of freedom are often difficult to properly sample with MC techniques. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We describe a novel approach to synthesize two-dimensional nanocrystalline TiS2 islands on Au(111). Ti is deposited by physical vapor deposition at room temperature on AuS-covered Au(111) surfaces. Subsequent annealing to temperatures between 670 K and 800 K leads to the formation of single-layer, triangular TiS2 islands. These TiS2 nanocrystallites reflect the structure of bulk TiS2, and are composed of S–Ti–S stacking units with hexagonally close-packed layers of sulfur atoms and titanium occupying the octahedral sites in between. The lattice constant of the hexagonal unit cell is 3.45 Å. A superlattice with a repeat distance of 17.3 Å results from the coincidence of five TiS2 units with six Au atoms and is observed in scanning tunneling microscopy and low energy electron diffraction. The triangular shape of the islands indicates a preference for one of the two possible edge terminations. The observation of two island orientations rotated by 60° with respect to each other can be attributed to the formation of twin-related TiS2 domains. The population of the two different island orientations changes during annealing at 800 K indicating a thermodynamic preference for one of the possible stacking sequences. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Time-resolved fluorescence spectra of naphthalene in the S1 state have been measured in various gases below 102 kPa. The band shape of the fluorescence changed in an earlier time region after the photoexcitation when an excess energy (3300 cm-1) above the 0-0 transition energy was given. The excitation energy dependence of the fluorescence band shape of an isolated naphthalene molecule was measured separately, and the time dependence of the fluorescence band shape in gases was found to be due to the vibrational energy relaxation in the S1 state. We have succeeded in determining the transient excess vibrational energy by comparing the time-resolved fluorescence band shape with the excitation energy dependence of the fluorescence band shape. The excess vibrational energy decayed almost exponentially. From the slope of the decay rate against the buffer gas pressure, we have determined the collisional decay rate of the excess vibrational energy in various gases. The dependence of the vibrational energy relaxation rate on the buffer gas species was similar to the case of azulene. The comparisons with the results in the low temperature argon and the energy relaxation rate in the S0 state in nitrogen were also discussed. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The distribution of rotational and vibrational energy in HCO produced by the O(3P)+C2H4 reaction has been measured using laser-induced fluorescence detection via the B2A′-X2A′ transition. Over a detection wavelength range of 248–290 nm, our experiments have shown that HCO is formed in both the ground state and in at least six vibrationally excited states with up to two quanta of energy in the C-O stretch and the bending mode. Dispersed fluorescence experiments were conducted to positively assign all of the HCO vibrational bands. The experiments confirmed that many bands, including the B(000)-X(000) band, are affected by overlap with other HCO bands. Spectral modeling was used to separate the contributions of overlapping HCO B-X bands and to determine a nascent HCO rotational temperature of ∼600 K, corresponding to ∼6% of the total energy from the O(3P)+C2H4 reaction. HCO vibrational distributions were determined for two different average collision energies and were fit with vibrational temperatures of 1850±80 K and 2000±100 K, corresponding to ∼15% of the total energy. The observed Boltzmann distribution of vibrational energy in HCO indicates that HCO and CH3 are formed by the dissociation of an energized intermediate complex. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The reaction of CO and O over a catalytic surface is studied with a cellular automata (CA) model. We extend the CA model proposed by Mai and von Niessen [Phys. Rev. A 44 R6165 (1991)] taking into account the variation of the temperature of the catalyst with the aim of analyzing the existence of oscillations in this reaction. The rate constants for different processes which govern the reaction are chosen in the Arrhenius form. Quasiperiodic, aperiodic, O-poisoned, and CO-poisoned regimes are observed depending on the temperature relaxation parameter. The results from the CA model presented are in agreement with several oscillatory behaviors which the catalyzed oxidation of CO exhibits. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Direct current conductivity of p-sexiphenyl films with 0.2–2.5 μm thickness deposited on glass substrates was investigated at temperatures between 10 and 300 K. The molecular dynamics simulations and quantum chemical calculations of the experimentally observed conductivity have shown that there exist at least three different states of the films effectively contributing to the observed features of the dc conductivity: conductivity caused by proper crystalline states, conductivity originated from amorphous-like inter-grain region and caused by grain’s boundary. Comparison of the experimental data and theoretically calculated dependences shows that the main contribution to the observed dc conductivity gives grain boundaries between polycrystalline grains and amorphous-like background, though the latter possesses a relatively low part of the total volume.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Classical trajectory calculations using the MERCURY/VENUS code have been carried out on the H + O2 reactive system using the DMBE-IV potential energy surface. The vibrational quantum number and the temperature were selected over the ranges v = 0 to 15, and T = 300 to 10 000 K, respectively. All other variables were averaged. Rate constants were determined for the energy transfer process, H + O2(v)→H + O2(v″), for the bimolecular exchange process, H + O2(v) → OH(v′) + O, and for the dissociative process, H + O2(v)→H + O + O. The dissociative process appears to be a mere extension of the process of transferring large amounts of energy. State-to-state rate constants are given for the exchange reaction, and they are in reasonable agreement with previous results, while the energy transfer and dissociative rate constants have never been reported previously. The lifetime distributions of the HO2 complex, calculated as a function of v and temperature, were used as a basis for determining the relative contributions of various vibrational states of O2 to the thermal rate coefficients for recombination at various pressures. This novel approach, based on the complex's ability to survive until it collides in a secondary process with an inert gas, is used here for the first time. Complete falloff curves for the recombination of H + O2 are also calculated over a wide range of temperatures and pressures. The combination of the two separate studies results in pressure- and temperature-dependent rate constants for H + O2(v) (+ Ar) rlarr2; HO2(+ Ar). It is found that, unlike the exchange reaction, vibrational and rotational­translational energy are liabilities in promoting recombination. [ABSTRACT FROM AUTHOR]

Fundamental transport properties of liquid para-hydrogen (p-H2), i.e., diffusion coefficients, thermal conductivity, shear viscosity, and bulk viscosity, have been evaluated by means of the path integral centroid molecular dynamics (CMD) calculations. These transport properties have been obtained over the wide temperature range, 14–32 K. Calculated values of the diffusion coefficients and the shear viscosity are in good agreement with the experimental values at all the investigated temperatures. Although a relatively large deviation is found for the thermal conductivity, the calculated values are less than three times the amount of the experimental values at any temperature. On the other hand, the classical molecular dynamics has led all the transport properties to much larger deviation. For the bulk viscosity of liquid p-H2, which was never known from experiments, the present CMD has given a clear temperature dependence. In addition, from the comparison based on the principle of corresponding states, it has been shown that the marked deviation of the transport properties of liquid p-H2 from the feature which is expected from the molecular parameters is due to the quantum effect. [ABSTRACT FROM AUTHOR]

We investigate the nature of cooperative relaxation at the crossover temperature. The relaxation time for a cooperative rearranging region at the crossover temperature is related to the ratio of the entropy and the heat capacity of the supercooled liquid, and the ratio of the glass transition to the crossover temperatures. The lifetime of “elementary” excitations in supercooled liquid is determined by a variational technique. By imposing self-consistency between lifetime of elementary excitations and hopping relaxation time on the potential energy surface, the relaxation time at the crossover temperature is estimated. The predictions are in excellent agreement with available experimental data. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Thermal conductivity measurements show that ice continues to amorphize for several days when kept at a fixed pressure p in the 0.79–0.88 GPa range, and fixed temperature T in the 127–130 K range. Thermal conductivity κ decreases according to a stretched exponential in time, and its limiting long time value κ(∞) varies with p and T. At 0.8 GPa and 128 K, κ(∞) remains 2.5 times the value observed for high-density amorph. Consequences of these findings for our understanding of amorphization are discussed. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]