Molecular dynamics current research

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

The modeling of carbohydrates is undergoing rapid development. For example, the first comprehensive conformational mappings of disaccharides with flexible residues and the first molecular dynamics studies of carbohydrates have only recently been published. At the same time, interest in carbohydrates has been increasing dramatically, and there is a need for a publication that gently introduces the uninitiated and provides an overview of current research in the area. We feel that Computer Modeling ( Carbohydrate Molecules meets these needs. 

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. 

Theoretical approaches to structural biophysics, like the theories of transport and reaction kinetics explored in other chapters of this book, are grounded in physical chemistry concepts. Here we explore a few problems in molecular structural dynamics using those concepts. The first two systems presented, helix-coil transitions and actin polymerization, introduce classic theories. The material in the remainder of the chapter arises from the study of macromolecular interactions and is motivated by current research aimed at uncovering and understanding how large numbers of proteins (hundreds to thousands) interact in cells [7],... 

Understanding the structure and function of biomolecules requires insight into both thermodynamic and kinetic properties. Unfortunately, many of the dynamical processes of interest occur too slowly for standard molecular dynamics (MD) simulations to gather meaningful statistics. This problem is not confined to biomolecular systems, and the development of methods to treat such rare events is currently an active field of research. - If the kinetic system can be represented in terms of linear rate equations between a set of M states, then the complete spectrum of M relaxation timescales can be obtained in principle by solving a memoryless master equation. This approach was used in the last century for a number of studies involving atomic... 

We have noticed that most current LBM applications to microfluidics utilize LBM as a differential equation solver, and the true merit of this method - a good representation of the underlying microscopic interactions - has not been well exploited. Solid-fluid interfacial phenomena in microsystems could be particularly suitable for LBM, since it couples the fluid and interface dynamics in a natural way. Future directions for research may include utilizing nonuniform or unstructured lattice meshes for complex microstmctures (e.g., surface roughness), combining LBM with molecular dynamics and CFD (hybrid algorithms), and applying LBM to bio-microfluidic systems. 

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