1,720,988 research outputs found
Mechanical Constraints in Molecular Dynamics Simulation
No full textAdvances in computational power and algorithm development have stimulated molecular dynamics research on diverse large and complicated physical systems. Part of this progress relies on algorithms that are able to account for widely separated time scales or activated processes that would otherwise degrade computational efficiency. This chapter describes how holonomic constraints can be used to overcome such difficulties. The constrained dynamical equations, the statistical mechanics that follows from these equations, and the algorithms needed to simulate the dynamics are presented. Examples related to rare event sampling and adiabatic dynamics are given to illustrate the methods
Sequential short-time propagation of quantum-classical dynamics
No full textAn algorithm for the simulation of quantum-classical dynamics is presented. Quantum-classical evolution is effected by a propagator exp(i (L) over capt) involving the quantum classical Liouville operator (L) over cap that describes the evolution of a quantum subsystem coupled to a classical bath. Such a mixed description provides a means to study the dynamics of complex many-body systems where certain degrees of freedom are treated quantum mechanically. The algorithm is constructed by decomposing the time interval Deltat into small segments of length At and successively applying the propagator in the short time segments to obtain the evolution for long times. The algorithm is shown to be a discretization of the iterated Dyson form of the propagator whose direct solution is vexatious. The sequential short-time propagation algorithm is applied to the spin-boson model for a range of values of the Kondo parameter and shown to be effective
Trotter-based simulation of quantum-classical dynamics
No full textQuantum rate processes in condensed phase systems are often computed by combining quantum and classical descriptions of the dynamics. An algorithm for simulating the quantum-classical Liouville equation, which describes the dynamics of a quantum subsystem coupled to a classical bath, is presented in this paper. The algorithm is based on a Trotter decomposition of the quantum-classical propagator, in conjunction with Monte Carlo sampling of quantum transitions, to yield a surface-hopping representation of the dynamics. An expression for the nonadiabatic propagator that is responsible for quantum transitions and associated bath momentum changes is derived in a form that is convenient for Monte Carlo sampling and exactly conserves the total energy of the system in individual trajectories. The expectation values of operators or quantum correlation functions can be evaluated by initial sampling of quantum states and use of quantum-classical Liouville dynamics for the time evolution. The algorithm is tested by calculations on the spin-boson model, for which exact quantum results are available, and is shown to reproduce the exact results for stronger nonadiabatic coupling and much longer times using fewer trajectories than other schemes for simulating quantum-classical Liouville dynamics
QUANTUM EFFECTS ON THE SOLVENT CONTRIBUTION TO THE ACTIVATION FREE-ENERGY
No full textQuantum effects on the activation free energy for the transfer of a quantum particle between two ions immersed in a classical dipolar solvent are investigated. The bare potential for the quantum particle-ion complex has an intrinsic barrier that is negligible compared to k(B)T and corresponds to a strongly hydrogen bonded system if the quantum particle is a proton. In this circumstance the activation free energy is dominated by solvent contributions. We compare the solvent free energies along the reaction coordinate for a classical particle with charge +1, a proton and a muon. The quantum calculations are carried out using Feynman's path integral methods. The smaller mass of the muon gives rise to enhanced quantum effects and allows one to probe the effects of the dispersion of the charge density of the particle undergoing transfer on the solvent contribution to the free energy
ACTIVATION FREE-ENERGY FOR PROTON-TRANSFER IN SOLUTION
No full textPath integral molecular dynamics methods are employed to compute the free energy for proton transfer reactions for strongly hydrogen bonded systems in a polar solvent. The free energy profile is calculated using several different techniques, including: integration of the mean force acting on the proton path with its centroid constrained at different values, the integral form of the free energy calculation in the constrained-reaction-coordinate-dynamics ensemble and direct simulation of the unconstrained dynamics. The results show that estimates of the free energy barrier obtained by harmonic extrapolation are likely to be in error. Both quantum and classical results for the free energy are obtained and compared with simulations using adiabatic quantum dynamics. Comparison of the quantum and classical results show that there are quantum corrections to the solvent contributions to the free energy
Activation energies by molecular dynamics with constraints
No full textRecently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the probability density P(≈r) = < δ(r - ≈r) &>; associated with rate values≈r of a spatial coordinate r. In this Letter we extend their approach to the case of a general reaction coordinate ξ(r), an arbitrary function of the configuration-space coordinates. The generalized version is shown to be the integral form of the free energy calculation in the constrained-reaction-coordinate ensemble where the mean force is computed as an average in a ξ-constrained ensemble. The two approaches are shown to be of equal computational efficiency for a very simple Lennard-Jones test case. © 1991
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
- …
