Molecular dynamics three dimensional

Ivanov VI and Karpeisky MY (1969) Dynamic three-dimensional model for enzymic transamination. Advances in Enzymology and Related Areas of Molecular Biology 32, 21-53. 

Abstract. This paper presents results from quantum molecular dynamics Simula tions applied to catalytic reactions, focusing on ethylene polymerization by metallocene catalysts. The entire reaction path could be monitored, showing the full molecular dynamics of the reaction. Detailed information on, e.g., the importance of the so-called agostic interaction could be obtained. Also presented are results of static simulations of the Car-Parrinello type, applied to orthorhombic crystalline polyethylene. These simulations for the first time led to a first principles value for the ultimate Young s modulus of a synthetic polymer with demonstrated basis set convergence, taking into account the full three-dimensional structure of the crystal. 

The visualization of volumetric properties is more important in other scientific disciplines (e.g., computer tomography in medicine, or convection streams in geology). However, there are also some applications in chemistry (Figure 2-125d), among which only the distribution of water density in molecular dynamics simulations will be mentioned here. Computer visualization of this property is usually realized with two or three dimensional textures [203]. 

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... 

High-resolution observation of dynamics of bio-macromolecules in cells and bio-organisms atomic or molecular level, regional or focused observation, three-dimensional analysis ... 

How many atoms must be included in a three-dimensional molecular dynamics (MD) calculation for a simple cubic lattice (lattice spacing a = 3 x 10 ° m) such that ten edge dislocations emerge from one face of the cubic sample Assume a dislocation density of N = 10 m . ... 

Computational methods have played an exceedingly important role in understanding the fundamental aspects of shock compression and in solving complex shock-wave problems. Major advances in the numerical algorithms used for solving dynamic problems, coupled with the tremendous increase in computational capabilities, have made many problems tractable that only a few years ago could not have been solved. It is now possible to perform two-dimensional molecular dynamics simulations with a high degree of accuracy, and three-dimensional problems can also be solved with moderate accuracy. 

Selected art in the text is supported by dynamic media. Students can view motion, three-dimensional effects, and atomic and molecular interactions to learn to visualize as chemists do—at a molecular level. 

A review is given of the application of Molecular Dynamics (MD) computer simulation to complex molecular systems. Three topics are treated in particular the computation of free energy from simulations, applied to the prediction of the binding constant of an inhibitor to the enzyme dihydrofolate reductase the use of MD simulations in structural refinements based on two-dimensional high-resolution nuclear magnetic resonance data, applied to the lac repressor headpiece the simulation of a hydrated lipid bilayer in atomic detail. The latter shows a rather diffuse structure of the hydrophilic head group layer with considerable local compensation of charge density. 

Using molecular mechanics calculations to assess the three-dimensional shape of a molecule, various surface properties such as polarity and size can be calculated. The dynamic molecular surface properties can be determined from the (low energy) conformation(s) of the drug molecule obtained by molecular mechanics calculations of conformational preferences. The potential advantage of this method is that the calculated surface character-sitics determine numerous physicochemical properties of the molecules including lipophilicity, the energy of hydration and the hydrogen bond formation capacity [187-... 

Hoppe, A. D., Shorte, S. L., Swanson, J. A. and Heintzmann, R. (2008). Three-dimensional FRET reconstruction microscopy for analysis of dynamic molecular interactions in live cells. Biophys. J. 95, 400-18. 

Equation (9.3) has been derived for one-dimensional diffusion and supported by molecular dynamics simulation in the three-dimensional case (Powles, 1985 Tsurumi and Takayasu, 1986 Rappaport, 1984). For the partially diffusion-controlled recombination reaction we again refer to Figure 9.1, where the inner (Collins-Kimball) boundary condition is now given as... 

A vital activity of the chemical sciences is the determination of structure. Detailed molecular structure determinations require identifying the spatial locations of all of the atoms in molecules, that is, the atomic distances and bond angles of a species. It is important to realize that the three-dimensional architecture of molecules very much defines their reactivity and function. However, molecules are dynamic, a feature that is not reflected by static pictures. This last point requires further explanation. Because the atoms in all molecules move, even in the limit of the lowest temperatures obtainable, molecular structures really describe the average position about some equilibrium arrangement. In addition, rotations about certain bonds occur freely at common temperatures. Consequently, some molecules exist in more than one structure (conformation). Some molecules are so floppy that structural characterizations really refer to averages among several structures. Yet other molecules are sufficiently rigid that molecular structures can be quite precisely determined. 

The chemical world is often divided into measurers and makers of molecules. This division has deep historic roots, but it artificially impedes taking advantage of both aspects of the chemical sciences. Of key importance to all forms of chemistry are instruments and techniques that allow examination, in space and in time, of the composition and characterization of a chemical system under study. To achieve this end in a practical manner, these instruments will need to multiplex several analytical methods. They will need to meet one or more of the requirements for characterization of the products of combinatorial chemical synthesis, correlation of molecular structure with dynamic processes, high-resolution definition of three-dimensional structures and the dynamics of then-formation, and remote detection and telemetry. 

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