Molecular dynamics research applications

Chemically excited infrared lasers were the first major "application that derived from the early days of molecular dynamics research [1,2]. The significant research investment in the area of infrared chemiluminescence paralleled a substantially larger investment in coupling this chemical physics imderstanding to fluid mechanics and optical physics, as well as device teclmology. The results have been both large scale laser devices and a better fundamental understanding of the role of vibrational excitation as a product of reactioa... 

For nonequilibrium statistical mechanics, the present development of a phase space probability distribution that properly accounts for exchange with a reservoir, thermal or otherwise, is a significant advance. In the linear limit the probability distribution yielded the Green-Kubo theory. From the computational point of view, the nonequilibrium phase space probability distribution provided the basis for the first nonequilibrium Monte Carlo algorithm, and this proved to be not just feasible but actually efficient. Monte Carlo procedures are inherently more mathematically flexible than molecular dynamics, and the development of such a nonequilibrium algorithm opens up many, previously intractable, systems for study. The transition probabilities that form part of the theory likewise include the influence of the reservoir, and they should provide a fecund basis for future theoretical research. The application of the theory to molecular-level problems answers one of the two questions posed in the first paragraph of this conclusion the nonequilibrium Second Law does indeed provide a quantitative basis for the detailed analysis of nonequilibrium problems. 

The underlying physical principles of NMR have been established and are well understood.8 Applications of both solid- and solution-state NMR spectroscopy can be found in many different disciplines. It is routinely used in structural elucidation of organic and inorganic compounds, polymers, and biomolecules (e.g., proteins, nucleic acids, and carbohydrates). Additionally, NMR can be used to study molecular interactions (e.g., protein-protein and protein-ligand), molecular dynamics, and chemical reactions. It has also been used extensively in medical research and imaging (magnetic resonance imaging). 

In addition to the development of new methods, new applications of molecular dynamics computer simulation are also needed in order to make comparisons with experimental results. In particular, more complicated chemical reactions, beyond the relatively simple electron transfer reaction, could be studied. Examples include the study of chemical adsorption, hydrogen evolution reactions, and chemical modification of the electrode surface. All of the above directions and opportunities promise to keep this area of research very active ... 

A proposal for the comprehensive study of chemical processes in a variety of important condensed-phase systems using modern theoretical methodology has been presented. The primary goals of the research are to provide microscopic information on the mechanisms and structural and dynamical properties of the chemical systems proposed for investigation, to test the applicability of modern ab initio molecular dynamics (MD) by comparison with experiment, and to develop and apply novel ab initio MD techniques in simulating complex chemical systems. The proposed research will contribute to the forefront of modern theoretical chemistry and address a number of important technological issues. The PI has carefully attempted to demonstrate his knowledge, ability, and resources to carry out the proposed research projects. 

Molecular dynamics, Monte Carlo simulations (Haile, 1992), and very recently applications of cellular automata to drug research (Kier and Cheng,... 

For quasirigid molecules a symmetry concept has been used very early in some branches of molecular research, e.g. stereochemistry2,3 This symmetry concept was based on the concept of isometric mappings4) and formed the basis of extended applications to molecular dynamics since 1930, developed first by Wigner5). 

A description of the method of molecular dynamics simulations and its applications to energetic materials research is provided. We present an overview of the development of both reactive and non-reactive interaction potentials used to describe the energetic materials in different phases. Limitations as well as performances of the current models are indicated, including recent advances in reactive model development. Applications of the method to both gas and condensed phases of energetic materials are given to illustrate current capabilities. 

K. Boehncke, H. Heller, H. Grubmiiller, and K. Schulten, in Transputer Research and Applications 3, A. S. Wagner, Ed., Proceedings of the Third Conference of the North American Transputer Users Group, April 26—27, 1990, Sunnyvale, CA, lOS Press, Amsterdam, 1990, pp. 83-94. Molecular Dynamics Simulations on a Systolic Ring of Transputers. 

Although FCS has now been invoked in about 3,000 scientific publications, now at 400 per year, its use before about 1990 was limited by severe technological barriers involving instability of laser light sources, poor sensitivity of photon detectors, noisy electronics, and insufficient computer capacities for the correlation computations. These problems inhibited application of FCS, until suddenly about 1990 the electro-optical and computational technologies advanced so that it became feasible. These advances occurred in synchrony with our creation of Multiphoton Laser Scanning Microscopy, which has enabled effective research on the molecular dynamics of life in living tissues and animals [14]. 

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