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  • 1
    Electronic Resource
    Electronic Resource
    On the determination of rate constants from equilibrium molecular dynamics simulations (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 4117-4122 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458744
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  • 2
    Electronic Resource
    Electronic Resource
    A direct method of studying reaction rates by equilibrium molecular dynamics: Application to the kinetics of isomerization in liquid n-butane (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 3062-3073 
    Details
    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
    URL: http://dx.doi.org/10.1063/1.457904
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  • 3
    Electronic Resource
    Electronic Resource
    Polaron formation in the acoustic chain (1987)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 87 (1987), S. 6700-6705 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Exact calculations are presented which detail the process of polaron formation in the one-dimensional acoustic chain. Exact solution is possible because the limit considered is the transportless limit in which the Hamiltonian matrix elements responsible for the motion of an excitation among site states have been set to zero. The polaron formation process is found to be decomposable into two subprocesses having distinct time scales. A disparity of time scales is possible in the case of long wavelength excitations. The consistency of our conclusions is demonstrated through the consensus of results obtained for the discrete acoustic chain, the Debye model, and the elastic continuum.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.453731
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  • 4
    Electronic Resource
    Electronic Resource
    Erratum: On the determination of rate constants from equilibrium molecular dynamics simulations [J. Chem. Phys. 93, 4117 (1990)] (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 4684-4684 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.460747
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  • 5
    Electronic Resource
    Electronic Resource
    Preparation of bulk melt chain configurations of polycyclic polymers (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 708-717 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The configurations of oligomers of polyimide and polyetherketone polycyclic polymers in the melt are predicted by a new hybrid pivot Monte Carlo (PMC)/molecular dynamics (MD) single-chain sampling technique restricted to a limited number of near-neighbor interactions. These are then compared to configurations obtained for the same models by running MD simulations on the corresponding multichain systems in the bulk melt. A new phantom-atom technique is introduced which avoids interlocking rings during construction of the bulk melt samples. Similar to earlier work carried out on polyethylene, polyvinylchloride and uncharged polyethylene oxide, both theoretical and bulk melt sampled conformational and configurational properties are found to be in very good agreement. This confirms that the new hybrid PMC/MD sampling is a promising and cost-effective technique for preparing polymer samples prior to subsequent MD simulations of the bulk amorphous phase. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1379073
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  • 6
    Electronic Resource
    Electronic Resource
    A molecular dynamics study of chain configurations in n-alkane-like liquids (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 1684-1692 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present precise measurements of the configurational properties of n-alkane-like liquids with 4, 5, 8, 20, 50, and 100 methylene groups. Quantities measured include the distributions of square radii of gyration, square end-to-end distances and proportion of conformers. To achieve high precision for n=50 and 100 a Fujitsu AP 1000 massively parallel processing machine with up to 512 processors is used. The results are compared with those obtained for the Flory model of alkane chains in which only correlation between nearest-neighbor torsion angles are considered; the latter were obtained by Monte Carlo sampling of isolated chains using the pivot algorithm. Discrepancies between the two sets of data are discussed in terms of solvent and end effects. For n=100 full configurational relaxation was not observed within 2 ns.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466596
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  • 7
    Electronic Resource
    Electronic Resource
    A molecular dynamics study of the coupling of torsional motions to self-diffusion in liquid n-hexane (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 2174-2180 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Dynamic coupling of molecular flexibility with self-diffusion has been studied for a model of liquid n-hexane using the technique of frozen distribution sampling (FDS) [Travis et al., J. Chem. Phys. 98, 1524 (1993)]. FDS facilitates comparison of transport properties between a liquid of flexible molecules and a liquid in which the molecular shape fluctuations are frozen in an equilibrium distribution; thus the two liquids have identical equilibrium configurational properties. The diffusion coefficient of model hexane was found to increase by a factor of ∼20 on raising the temperature from 200 and 1000 K; coupling with torsional motions enhances the diffusion coefficient by about 20% over the whole of this range. At each temperature a quantitative measure of the coupling was obtained by making comparisons with self-diffusion in a liquid for which the potential restricting torsional motion is removed—called flexane [D. Brown and J. H. R. Clarke, J. Chem. Phys. 86, 1542 (1987)]. Using FDS it was confirmed that the enhancement of the diffusion coefficient in flexane as compared to hexane arises from differences in the short time dynamics and not from differences in the static structure of the two liquids. For hexane a coupling parameter is defined which shows that the extent of dynamic coupling increases from ∼10% at 200 K and appears to have reached a maximum by 1000 K. The coupling mechanism is discussed using power spectra obtained from the relative velocities of the methylene (and methyl) groups relative to the molecular centers of mass. It is concluded that torsional oscillations mainly involving the outer dihedral angles provide the probable mechanism for the coupling. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468739
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  • 8
    Electronic Resource
    Electronic Resource
    Kohn variational principle for a general finite-range scattering functional (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 3723-3728 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The Kohn variational principle (KVP) has been used to compute both the R and the log-derivative matrices, which are formally inverses of one another. We show that the KVP for these matrices are special cases of a KVP for a more general functional which can be derived by imposing more general boundary conditions on the trial function space. This more general matrix, which we denote Z, can then be used to compute the S-matrix in a procedure analogous to that for R and Y. This approach is demonstrated for the Eckart barrier problem. Our studies suggest that within the framework presented, the log derivative case presents some computational advantage.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.467556
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  • 9
    Electronic Resource
    Electronic Resource
    On the Munn–Silbey approach to nonlocal exciton–phonon coupling (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 2335-2345 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A canonical transformation method originally proposed by Munn and Silbey is used to partially diagonalize a model Hamiltonian which incorporates both local and nonlocal exciton–phonon coupling. At the heart of the method is a secular elimination principle which poses a difficult self-consistency problem. A limited form of this self-consistency problem was solved in an approximate fashion by primarily analytical methods in the original work of Munn and Silbey. We take a numerical approach, solving the general self-consistency problem to desired accuracy. Among the differences between our findings and those of the original work are polaron binding energies much larger and Debye–Waller factors much smaller than originally anticipated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466480
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  • 10
    Electronic Resource
    Electronic Resource
    Subnanosecond high-voltage pulse generator (1987)
    [S.l.] : American Institute of Physics (AIP)
    Review of Scientific Instruments 58 (1987), S. 1523-1529 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1139392
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