Dynamics, computational aspects

S. Gupta, Computing aspects of molecular dynamics simulation , Comp. Phys. Comm., Vol 70, no 2, 243-70, 1992. 

We have reviewed above the GH approach to reaction rate constants in solution, together with simple models that give a deeper perspective on the reaction dynamics and various aspects of the generalized frictional influence on the rates. The fact that the theory has always been found to agree with Molecular Dynamics computer simulation results for realistic models of many and varied reaction types gives confidence that it may be used to analyze real experimental results. 

An important aspect of the study of water under electrochemical conditions is that one is able to continuously modify the charge on the metal surface and thus apply a well-defined external electric field, which can have a dramatic effect on adsorption and on chemical reactions. Here we briefly discuss the effect of the external electric field on the properties of water at the solution/metal interface obtained from molecular dynamics computer simulations. A general discussion of the theoretical and experi-... 

Central to the understanding of surface-related phenomena has been the study of gas-surface reactions. A comprehensive understanding of these reactions has proven challenging because of the intrinsic many-body nature of surface dynamics. In terms of theoretical methods, this complexity often forces us either to treat complex realistic systems using approximate approaches, or to treat simple systems with realistic approaches. When one is interested in studying processes of technological importance, the latter route is often the most fruitful. One theoretical technique which embodies the many-body aspect of the dynamics of surface chemistry (albeit in a very approximate manner) is molecular dynamics computer simulation. 

D. A. Micha. Density matrix theory and computational aspects of quantum dynamics in an active medium. Intern. J. Quantum Chem., 80 394, 2000. 

In this chapter, we have reviewed some of our own work on solvation properties in supercritical fluids using molecular dynamics computer simulations. We have presented the main aspects associated with the solvation structures of purine alkaloids in CO2 under different supercritical conditions and in the presence of ethanol as co-solvent, highlighting the phenomena of solvent density augmentation in the immediate neighborhood of the solute and the effects from the strong preferential solvation by the polar co-solvent. We have also presented a summary of our results for the structure and dynamics of supercritical water and ammonia, focusing on the dielectric behavior of supercritical water as functions of density and temperature and the behavior of excess solvated electrons in aqueous and non-aqueous associative environments. 

S. Gupta, Comput. Phys. Commun., 70, 243 (1992). Computing Aspects of Molecular Dynamics Simulations. 

In an exposition which aims to encompass general systems and ensembles, it is appropriate to make use of the Hamiltonian version of dynamics. In this view forces do not appear explicitly and the dynamics of the system evolve so as to keep the Hamiltonian function constant. In Newtonian dynamics forces appear explicitly and molecules move as a response to the forces they experience. For our purposes, the Newtonian view is sufficient since we will illustrate the large scale computational aspects with simplest possible particles, atoms with spherical, central force fields. The same principles hold for molecules with internal degrees of freedom as well. 

Another excellent book we should mention here is that of Griebel et al. [155], which explores the computational aspects of molecular dynamics in the setting of high performance computing. This would provide an excellent complementary book for a course focussed more on the issues relevant to software, large scale simulation, and parallel computing. 

Recent reviews from this Laboratory provide an overview of the literature of MD simulations on DNA oligomers through 1993 (27) and theoretical and computational aspects of DNA hydration (28) and counterion atmosphere (29). References to the most recent literature can be found in (30). Experimental data for comparison with MD results are available for crystal structures in the Nucleic acids Data Bank (NDB) (31), and for NMR structure in a review by Ulyanov and James (52). The research described in this article is directed towards understanding the dynamical structure of the various right-handed helical forms of DNA, their deformations and interconversions. The canonical A and B structures of DNA are shown for reference in Figure 1. The A and B forms are distinguishable in three major ways the displacement of nucleotide base pairs from the helix axis, the inclination of base pairs with respect to the helix axis, and sugar puckers. Details on these and other structural features of DNA relevant to MD analysis is readily available (33). 

Heethaar RM, Pao YC, Ritman EL (1977) Computer aspects of three dimensional finite element analysis of stresses and strains in the intact heart. Comp Biomed Res 10 271-285 Heethaar RM, Mol CR, Elshuraydeh K, Heethaar J, Van Dort JMT, Batianen GW, Sneek JHJ, Borst C, Meijler FL (1982) Cardiac function fibre shortening and dynamic geometry. Mayo Clinic Proc suppl, 57 104-113... 

In Section II we look more closely at the computational aspects of DPD, before focusing attention on the specific application to polymer systems. Section III describes the matching of simulation parameters to the properties of real polymer systems, with an emphasis on the relation between the conservative force field and the common Flory-Huggins / parameter for mixtures. The dynamics of individual polymer chains in a solvent and in a melt are discussed in Section IV, and the ordering dynamics of quenched block copolymer systems is described in Section V. A summary and conclusions are given in Section VI. 

We do not view the terms theoretical chemistry and computational chemistry as synonymous. Computational chemistry sometimes involves application of computerized algorithms from quantum theory, but computational chemistry is certainly more than quantum chemistry. In fact, in an industrial setting, the latter is a very small part of it. Molecular mechanics, molecular dynamics, computer graphics, molecular modeling, and computer-assisted molecular design are other important aspects of computational chemistry. In industry, a... 

In addition to the presentation of some basic formulations and methodologies in dynamics of multibody systems, including computational aspects, major applications of developments to date are presented herein. The scope of applications is extended to vehicle dynamics, aerospace technology, robotics, mechanisms design, intermittent motion and crashworthiness analysis. 

In this chapter we focus on methodological and computational aspects that are key to accurately modeling the spectroscopic and thermodynamic properties of molecular systems containing actinides within the density functional theory (DFT) framework. Our focus is on properties that require either an accurate relativistic all-electron description or an accurate description of the dynamical behavior of actinide species in an environment at finite temperature, or both. The implementation of the methods and the calculations discussed in this chapter were carried out with the NWChem software suite [1]. In the first two sections we discuss two methods that account for relativistic effects, the ZORA and the X2C Hamiltonian. Section 12.2.1 discusses the implementation of the approximate relativistic ZORA Hamiltonian and its extension to magnetic properties. Section 12.3 focuses on the exact X2C Hamiltonian and the application of this methodology to obtain accurate molecular properties. In Section 12.4 we examine the role of a dynamical environment at finite temperature as well as the presence of other ions on the thermodynamics of hydrolysis and exchange reaction mechanisms. Finally, Section 12.5 discusses the modeling of XAS... 

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