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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 89 (1985), S. 3994-3998 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 86 (1982), S. 2166-2177 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 88 (1984), S. 6720-6727 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    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 96 (1992), S. 8840-8852 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study a quenching reaction occurring at sinks within a spherical cavity and at the cavity surface. One may think of reactions at these two, distinct locations as two, coupled reactive channels. Reactions of the type D*+A→D+A are studied in the limit of nondilute A, present at both locations, and dilute D, present within the cavity. We use a Monte Carlo algorithm to compute mean rates, pseudo-first-order rates and branching ratios, and compare with results obtained by assuming that the two reactive channels operate in parallel. The ratio of activities of the two channels are varied; static and moving sinks are studied. We discuss an application to the determination of pore structure by NMR (nuclear magnetic resonance).
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 7566-7566 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 1287-1291 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A frequently encountered problem in molecular dynamics simulations is the long runs required to study condensed systems consisting of both high frequency and low frequency degrees of freedom. Standard integrators require the choice of time step sufficiently small to guarantee stable solution of the highest frequency motion with the consequence that simulations require a very large number of central processing unit (CPU) cycles. In this note we present a new integrator that allows one to use a time step appropriate for the low frequency degrees of freedom without making any approximations related to the separation of time scales. This method is based on a choice of an analytically solvable reference system for the high frequency motion. We show how the analytical solution can be incorporated into a numerical integrator. The method is applied to two cases which are paradigms for this problem and it is shown that this approach and suitable generalizations should be very useful for future simulations of quantum and classical condensed matter systems.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 6359-6366 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Two energy estimators, the Barker estimator and the Berne virial estimator, commonly used in path integral simulations of quantum systems are compared with respect to statistical accuracy. It is found that the accuracy of these estimators is strongly affected by the algorithm used. Four common algorithms are considered here: (1) the pure primitive algorithm, (2) the primitive algorithm augmented by whole chain moves, (3) the normal-mode algorithm, and (4) the staging algorithm. The error of the mean of the Barker energy estimator is found to grow as (P)1/2, where P is the number of discretization points of the quantum paths (or the number of chain particles in the isomorphic classical chain), for all of the algorithms above. The error of the mean of the Berne virial energy estimator is independent of P for algorithms 2, 3, and 4, and increases as (P)1/2 for algorithm 1. It is concluded that the virial estimator is far more accurate than the Barker estimator for algorithms 2, 3, and 4, and is at least as accurate for algorithm 1. Because the error analysis depends strongly on the temporal correlations in the sequence of values of the energy estimator generated during Monte Carlo or molecular-dynamics simulations, we review the general question of error analysis in simulations.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 5809-5826 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Rate constants evaluated from (1) the energy-loss turnover theory of Pollak, Grabert, and Hänggi (PGH), (2) the Grote–Hynes extension of Kramers theory (GH), and (3) the microcanonical variational transition state theory for dissipative systems of Tucker and Pollak (μVTST) are compared with rate constants determined from direct computer simulations of generalized Langevin dynamics. The comparisons are made for a cubic oscillator under the influence of a slow bath characterized by a Gaussian friction kernel. In the μVTST calculations, which are based on an effective two degree of freedom Hamiltonian, barrier crossing due to energy transfer from the bath to the effective Hamiltonian is neglected. This neglect is significant only at very strong coupling, where it causes the μVTST results to drop below the simulation results. Both GH and μVTST theories fail (as expected) in the energy diffusion regime, while PGH theory is only moderately successful. The μVTST results agree extremely well with the simulation results in the spatial diffusion regime, providing a significant improvement over the GH results at intermediate coupling strengths and over the PGH results at strong coupling strengths. This improvement is a result of nonlinear effects which are included in the μVTST approach but neglected in the PGH and GH theories.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 4389-4396 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The generalized Langevin equation (GLE) has been used to model a wide variety of systems in which a subset of the degrees of freedom move on a potential of mean force surface subject to fluctuating forces and dynamic friction. When there is a wide separation in the time scales for motion on the potential surface and for relaxation of the friction kernel, direct integration of the GLE is very costly in CPU time. In this paper we introduce an integrator based on our previous work using numerical analytical propagator algorithm (NAPA) and reference system propagator algorithm (RESPA) that greatly accelerates such simulations. We also discuss sampling methods for the random force. Accuracy of this algorithm is assessed by comparisons with an analytically solvable example. Introducing dynamic friction kernels determined from full molecular dynamics (MD) simulations allows us to compare the accuracy of the GLE simulations with full scale molecular dynamics simulations.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 8362-8364 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: When there are high and low frequency motions in systems with long and short range forces a judicious choice of reference system leads to very large accelerations in molecular dynamic (MD) simulations. Building on our previous work where we have developed reference system methods for systems with high frequency oscillators, disparate masses, or long range forces, we present a double reference system method which leads to acceleration of as much as 20 in systems consisting of 864 molecules with Lennard-Jones (12-6) forces. Much larger savings should be achieved when this method is applied to longer range forces and larger systems.
    Type of Medium: Electronic Resource
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