Molecular modeling nonequilibrium approaches

The convective diffusion equations presented above have been used to model tablet dissolution in flowing fluids and the penetration of targeted macro-molecular drugs into solid tumors [5], In comparison with the nonequilibrium thermodynamics approach described below, the convective diffusion equations have the advantage of theoretical rigor. However, their mathematical complexity dictates a numerical solution in all but the simplest cases. 

Peter Kusalik took up an appointment at Dalhousie University in 1989 and developed a research program focused on computer simulation studies of molecular liquids, solids, and solutions. As well as standard simulation approaches, he has explored nonequilibrium molecular dynamics techniques and applied field simulations, the development of new models and methodologies being one aim of his research. A common focus throughout his work has been the examination of the interplay between microscopic structure and dynamics in condensed matter and their relationship to bulk properties. 

Abstract The computational study of excited states of molecular systems in the condensed phase implies additional complications with respect to analogous studies on isolated molecules. Some of them can be faced by a computational modeling based on a continuum (i.e., implicit) description of the solvent. Among this class of methods, the polarizable continuum model (PCM) has widely been used in its basic formulation to study ground state properties of molecular solutes. The consideration of molecular properties of excited states has led to the elaboration of numerous additional features not present in the PCM basic version. Nonequilibrium effects, state-specific versus linear response quantum mechanical description, analytical gradients, and electronic coupling between solvated chromophores are reviewed in the present contribution. The presentation of some selected computational results shows the potentialities of the approach. 

The unique features of our system enable us to use three different theoretical tools — a molecular dynamics simulation, models which focus on the repulsion between atoms and a statistical approach, based on an information theory analysis. What enables us to use a thermodynamic-like language under the seemingly extreme nonequilibrium conditions are the high density, very high energy density and the hard sphere character of the atom-atom collisions, that contribute to an unusually rapid thermalization. These conditions lead to short-range repulsive interactions and therefore enable us to use the kinematic point of view in a useful way. 

In a series of papers, Stock and coworkers have combined the quasiclassi-cal techniques used in the description of gas phase reactions with biomolecular force fields used in molecular dynamics (MD) simulations. This leads to nonequilibrium MD simulations, which mimic the laser excitation of the molecules by nonequilibrium phase-space initial condition for the solute and the solvent atoms. This approach is based on the following assumptions. Firstly, it is assumed that an empirical force field at least provides a qualitative modeling of the process. This is because the initial relaxation appears to be an ultrafast and generic process and because it can be expected that the strong interaction with the polar solvent smoothes out many details of the intramolecular force field. Secondly, quantum-mechanical effects are only included via the nonequilibrium initial conditions of the classical simulations. This means that the method represents a short-time approximation of quantum mechanics. 

As one would expect, developments in the theory of such phenomena have employed chemical models chosen more for analytical simplicity than for any connection to actual chemical reactions. Due to the mechanistic complexity of even the simplest laboratory systems of interest in this study, moreover, application of even approximate methods to more realistic situations is a formidable task. At the same time a detailed microscopic approach to any of the simple chemical models, in terms of nonequilibrium statistical mechanics, for example, is also not feasible. As is well known, the method of molecular dynamics discussed in detail already had its origin in a similar situation in the study of classical fluids. Quite recently, the basic MD computer model has been modified to include inelastic or reactive scattering as well as the elastic processes of interest at equilibrium phase transitions (18), and several applications of this "reactive" molecular dynamicriRMD) method to simple chemical models involving chemical instabilities have been reported (L8j , 22J. A variation of the RMD method will be discussed here in an application to a first-order chemical phase transition with many features analogous to those of the vapor-liquid transition treated earlier. 

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