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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 3062-3073 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this article we describe a straightforward and general method for studying chemical reaction kinetics in equilibrium systems using molecular dynamics computer simulation. We have applied it to the problem of determining the rate constants for the trans–gauche isomerization processes in liquid n-butane. The method relies upon the fact that if a dynamic equilibrium exists in the system then it must apply to any chosen subset of the system. The power of the method is demonstrated by its high precision and in the discovery that a mechanism for direct gauche to gauche interconversions through the trans well is required to explain the data. The connection between the method applied here and other approaches to the determination of rate constants is discussed. The correlation function for isomerization dynamics is usually formulated as a collective property of the system. Its use leads to poor statistics when applied to simulation data. It is shown that the relaxation functions are equivalent to single particle correlation functions which fully define the isomerization kinetics. An additional observation from our 1.8 ns simulation is that the trans–gauche equilibrium in model liquid n-butane is shifted by ∼1% to excess gauche in comparison to the ideal gas at the same temperature. This is a smaller solvent effect than has been reported in the past.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 5465-5471 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Miller and co-workers [J. Chem. Phys. 61, 1823 (1974); ibid., 79, 4889 (1983)] have derived an exact quantum mechanical expression for reactive thermal rate constants in terms of the time integral of a flux autocorrelation function. The evaluation of this integral in a finite basis poses the problem that spurious oscillations in the correlation function due to recurrences can occur at long times, corrupting the result. To obviate this difficulty, we add to the Hamiltonian an optical potential in the asymptotic region, and evaluate eigenvalues and eigenvectors using the technique of successive truncation. These operations allow a diagonal (although nonorthogonal) representation of the propagator in which the eigenvalues are exponentially decaying functions of time, which damp the components of the propagated vectors before the spurious reflection back into the interaction region. In this manner, the infinite time limit of the integral may be evaluated properly. Furthermore, the results of a single diagonalization may be used to compute the thermal rate constant over a range of temperatures.
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 4684-4684 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 4117-4122 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this article we consider the calculation of rate constants from equilibrium molecular dynamics simulations using the conformational isomerization in liquid butane as an example. In particular we discuss the method by which transition state theory estmates of the rate constant may be calculated from simulation data. Care has to be taken when calculating the average velocity along the reaction coordinate at the barrier. If this is computed just from actual barrier crossings we show that there is a systematic overestimation by a factor of exactly π/2. Further analysis has allowed the connection between the barrier crossing rate and the transition state theory value for the rate constant to be established. We compare rate constants determined by the "reactive flux'' method with values obtained using alternative approaches applied to liquid n-butane [D. Brown and J. H. R. Clarke, J. Chem. Phys. 92, 3062 (1990)]. The results of this comparison have implications regarding the identification of the plateau value when using the reactive flux method. A straightforward procedure is described which can establish confidence limits for rate constants calculated in this way.
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  • 5
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Physics of Fluids 10 (1998), S. 2569-2586 
    ISSN: 1089-7666
    Source: AIP Digital Archive
    Topics: Physics
    Notes: This study is concerned with a fully nonlinear theoretical treatment of internal solitary waves in continuously stratified, incompressible, inviscid, shear-free Boussinesq fluids. Results are presented for wave propagation in both deep and shallow fluids with four different ambient stability profiles. Only the dominant mode with the greatest wave speed is considered. The morphology of finite-amplitude internal solitary waves in Boussinesq fluids is shown to be very sensitive to the precise form of the stability profile. The calculations indicate that a wave of maximum amplitude, which is less than the total fluid depth, exists for all internal solitary waves in continuously stratified Boussinesq fluids of finite depth. There is apparently no upper limit on the amplitude of internal solitary waves in many physically realistic unbounded fluids. Large amplitude waves of this type are mutually similar in form and the morphology of these waves appears to be independent of the ambient stability profile in the waveguide layer. It is shown that the properties of highly nonlinear waves with recirculating flow depend on the density distribution and vorticity of the trapped fluid inside the closed circulation cell. Fluid velocity components associated with the wave motion are evaluated and used to calculate the surface perturbation pressure. The surface perturbation pressure signature for internal solitary waves is found to change with the onset of recirculation from a single-crested profile at small wave amplitudes to a bimodal profile at large wave amplitudes. Results for solitary waves in finite-depth fluids differ from those found for deep fluids in that the surface perturbation pressure at the center of the wave eventually changes sign as wave amplitude increases. © 1998 American Institute of Physics.
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 98 (1993), S. 5999-5999 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 98 (1993), S. 1524-1530 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The coupling between internal molecular motions and transport properties is investigated with particular reference to the influence of torsional motions on the coefficients of self-diffusion and shear viscosity in n-butane. A novel technique, frozen distribution sampling (FDS), is designed to allow comparison of the dynamic properties of two fluids, one in which torsional motions are controlled by a well defined torsional potential, the other in which an equilibrium distribution of torsion angles are held completely rigid. It is shown that, as expected, the two fluids have exactly the same static equilibrium properties. The importance of satisfying the former criteria is illustrated by well chosen counter examples where related models of n-butane were studied in which the intramolecular potential was changed. In these cases interpretation of the relative values of transport properties is ambiguous since alterations of the potential cause significant changes in the equilibrium state. Our results show that there are no significant coupling effects between torsional motion and self-diffusion or shear viscosity at the state point considered.
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  • 8
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Rate equations for the densities of free excitons and excitons bound to two different neutral acceptors in silicon are solved for steady state in the absence of saturation. These rate equations explicitly include terms for forward and reverse tunneling of bound excitons from one type of neutral impurity to another. Both tunneling rates are calculated using a simple model of an exciton in a one-dimensional semi-infinite double potential well. The steady-state solutions of the rate equations yield an expression for the ratio of the bound exciton luminescence intensity as a function of the impurity concentrations. The relative photoluminescence intensities for the systems Si: (B, In), Si: (Al, In), Si: (Ga, In), Si: (B, Al), Si: (B, Ga), and Si: (Al, Ga) are calculated for the relevant free-exciton capture cross-section ratios. This model predicts no exciton tunneling for any of the above systems for the low-impurity concentration range of 1012–1013 cm−3. For those systems with large differences in the bound exciton energy levels such as Si: (B, In), Si: (Al, In), and Si: (Ga, In), and having indium concentrations exceeding 1015 cm−3, it predicts quenching of shallow impurity bound exciton luminescence because the forward exciton tunneling rate from the shallow level to the deep level of indium dominates and the reverse exciton tunneling rate from indium to the shallow impurities is negligible. For the systems with small differences in the bound exciton energy levels such as Si: (B, Al) and Si: (B, Ga), the theory predicts enhancement of shallow impurity bound exciton luminescence beyond certain concentrations depending upon the free-exciton capture cross-section ratios because in these cases the reverse exciton tunneling rate dominates. For the system Si: (Al, Ga) in which the difference in the bound exciton energy levels is very small, gallium bound exciton luminescence dominates when the gallium concentration exceeds 1016 cm−3.
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 2078-2082 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We describe simulations of a polymer melt sample containing 640 chains, each chain being composed of 100 methylene groups. Using these large scale simulations radii of gyration have been calculated with a statistical error of ∼2%. At this level of precision it is shown that even for this modest chain length configurational equilibrium is not achieved in less than 4 ns at 500 K. Values of the square radii of gyration, square end-to-end distances and proportion of conformers at equilibrium show good agreement with predictions of the Flory model of alkane chains in which all long range interactions along the chains are ignored. These simulations were performed using a Fujitsu AP1000 massively parallel processing machine with 1024 processors in conjunction with a recently described domain decomposition molecular dynamics algorithm [D. Brown, J. H. R. Clarke, M. Okuda, and T. Yamazaki, Comput. Phys. Commun. 83, 1 (1994)] capable of handling systems containing rigid bond constraints and threea are made with previous accurate data obtained for smaller samples containing just 10 n=100-site chains using the alternative cloning method of parallel processing [D. Brown, J. H. R. Clarke, M. Okuda, and T. Yamazaki, J. Chem. Phys. 100, 1684 (1994)]. © 1996 American Institute of Physics.
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  • 10
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 58 (1987), S. 1523-1529 
    ISSN: 1089-7623
    Source: AIP Digital Archive
    Topics: Physics , Electrical Engineering, Measurement and Control Technology
    Notes: We developed a pulse generator that uses high-voltage step recovery diodes to produce 400- to 500-V pulses with rise and fall times of 0.8 ns. The output pulse width is continuously adjustable. For a pulse width of 0.8-ns FWHM, the amplitude into 50 Ω is 400 V. With the pulse-width control set at maximum, the output pulse amplitude is about 500 V and the width is 3.5-ns FWHM. The delay of the output pulse with respect to the input trigger is 38 ns with a jitter of about ±30 ps. An unusual feature of the pulse generator is that the 38-ns delay time to the centroid of the output pulse is approximately constant and independent of the pulse width.
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