Molecular dynamics, local density

MD Molecular dynamics TBMD Tight bonding molecular dynamics DFT Density functional theory LDA Local density approximation FEM Finite element method TEM Transmission electron microscope AFM Atomic force microscope. 

The concentration of salt in physiological systems is on the order of 150 mM, which corresponds to approximately 350 water molecules for each cation-anion pair. Eor this reason, investigations of salt effects in biological systems using detailed atomic models and molecular dynamic simulations become rapidly prohibitive, and mean-field treatments based on continuum electrostatics are advantageous. Such approximations, which were pioneered by Debye and Huckel [11], are valid at moderately low ionic concentration when core-core interactions between the mobile ions can be neglected. Briefly, the spatial density throughout the solvent is assumed to depend only on the local electrostatic poten-... 

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. 

Schnitker et al. s (1986) finding, based on classical molecular dynamics simulation, of a large density (4.4 ml-1 at 10°C) of local potential minima qualifying as trapping sites. 

This approach yields spectral densities. Although it does not require assumptions about the correlation function and therefore is not subjected to the limitations intrinsic to the model-free approach, obtaining information about protein dynamics by this method is no more straightforward, because it involves a similar problem of the physical (protein-relevant) interpretation of the information encoded in the form of SD, and is complicated by the lack of separation of overall and local motions. To characterize protein dynamics in terms of more palpable parameters, the spectral densities will then have to be analyzed in terms of model-free parameters or specific motional models derived e.g. from molecular dynamics simulations. The SD method can be extremely helpful in situations when no assumption about correlation function of the overall motion can be made (e.g. protein interaction and association, anisotropic overall motion, etc. see e.g. Ref. [39] or, for the determination of the 15N CSA tensor from relaxation data, Ref. [27]). 

Some of the major areas of activity in this field have been the application of the method to more complex materials, molecular dynamics, [28] and the treatment of excited states. [29] We will deal with some of the new materials in the next section. Two major goals of the molecular dynamics calculations are to determine crystal structures from first principles and to include finite temperature effects. By combining molecular dynamics techniques and ah initio pseudopotentials within the local density approximation, it becomes possible to consider complex, large, and disordered solids. 

Recent Monte Carlo- and Molecular Dynamics-simulations [8,9,11] seem to suggest a slight local decrease of the density directly at the center of the mole-... 

The local density augmentation caused by the large isothermal compressibility of the fluid may conceivably influence k i or ka. We assume that the lifetime of the clusters is extremely short and thus there is no effect on kd, based on the molecular dynamics study of Petsche and Debenedetti (29) and experimental measurements of binary diffusion coefficients near the critical point. It seems more likely that a higher local density would affect k i due to an increase in the number of... 

Substantial evidence suggests that in highly asymmetric supercritical mixtures the local and bulk environment of a solute molecule differ appreciably. The concept of a local density enhancement around a solute molecule is supported by spectroscopic, theoretical, and computational investigations of intermolecular interactions in supercritical solutions. Here we make for the first time direct comparison between local density enhancements determined for the system pyrene in CO2 by two very different methods-fluorescence spectroscopy and molecular dynamics simulation. The qualitative agreement is quite satisfactory, and the results show great promise for an improved understanding at a molecular level of supercritical fluid solutions. 

Figure 3 Relationship between local and bulk densities at two supercritical temperatures (T7TC = 1.02, 1.145) for an infinitely dilute mixture of Lennard-Jones atoms with potential parameters chosen so as to simulate pyrene in carbon dioxide (see Table II). Molecular dynamics simulation.

Figure 4 Location of the solvation shells within which local densities were calculated in the molecular dynamics simulations.

Figure 5 Relationship between local density augmentation (local/bulk density) and bulk density. Same system and conditions as in Figure 3. Molecular dynamics simulation.

Figure 6 Comparison between local density augmentation deduced from fluorescence spectroscopy ( ), and the corresponding molecular dynamics simulations at R = 1.94 (Q). Both curves are for a reduced temperature of 1.02. The arrow denotes the critical density of carbon dioxide.

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