Contacts molecular dynamics

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

Despite their simplicity, certainly compared to the all-atom potentials used in molecular dynamics studies, these contact energy functions enable the exploration of different interaction scenarios. This diversity is achieved by changing the heterogeneity of the sequence, by altering the number N of different types of residues that are being used. The most elementary lattice model involves only two types of monomers hydrophobic... 

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]. 

Molecular dynamics (MD) permits the nature of contact formation, indentation, and adhesion to be examined on the nanometer scale. These are computer experiments in which the equations of motion of each constituent particle are considered. The evolution of the system of interacting particles can thus be tracked with high spatial and temporal resolution. As computer speeds increase, so do the number of constituent particles that can be considered within realistic time frames. To enable experimental comparison, many MD simulations take the form of a tip-substrate geometry correspoudiug to scauniug probe methods of iuvestigatiug siugle-asperity coutacts (see Sectiou III.A). 

Several recent molecular dynamics simulations (e.g. [10] and references therein) have focussed on the wetting of interfaces (Section 6.1) and, for example, the behaviour of very small droplets at the nanoscale. Such simulations are able to relate the atomistic behaviour directly to relevant macroscopic parameters such as the contact angle and are able to show the dramatic effects at this length scale of addition of surfactant molecules or roughening of the surface. 

Here ji(qa) is the spherical Bessel function of order l,g(a) is the radial distribution function at contact, and f = /fSmn/Anpo2g a) is the Enskog mean free time between collisions. The transport coefficients in the above expressions are given only by their Enskog values that is, only collisional contributions are retained. Since it is only in dense fluids that the Enskog values represents the important contributions to transport coefficient, the above expressions are reasonable only for dense hard-sphere fluids. Earlier Alley, Alder, and Yip [32] have done molecular dynamics simulations to determine the wavenumber-dependent transport coefficients that should be used in hard-sphere generalized hydrodynamic equations. They have shown that for intermediate values of q, the wavenumber-dependent transport coefficients are well-approximated by their collisional contributions. This implies that Eqs. (20)-(23) are even more realistic as q and z are increased. 

In addition, one of the most relevant interactions resulting from the molecular dynamics calculations was found to be an aromatic contact between the 2,5-dichlorophenyl substituent and a Phe residue of the a -AR model. It is described in our pharmacophore as a more generic hydrophobic interaction involving the substituted phenyl ring attached to the piperazine nucleus. All these considerations prompted us to retrace the steps performed to build the pharmacophore model for a -AR inhibitors and check for any possibility of improving it. 

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