Molecular dynamics simulations Subject

The strong point of molecular dynamic simulations is that, for the particular model, the results are (nearly) exact. In particular, the simulations take all necessary excluded-volume correlations into account. However, still it is not advisable to have blind confidence in the predictions of MD. The simulations typically treat the system classically, many parameters that together define the force field are subject to fine-tuning, and one always should be cautious about the statistical certainty. In passing, we will touch upon some more limitations when we discuss more details of MD simulation of lipid systems. We will not go into all the details here, because the use of MD simulation to study the lipid bilayer has recently been reviewed by other authors already [31,32]. Our idea is to present sufficient information to allow a critical evaluation of the method, and to set the stage for comparison with alternative approaches. 

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]). 

The most striking feature of AIMD and the novelty over traditional molecular dynamics simulations is the fact that the electronic structure is available all the time. Therefore, the analysis of the wavefunction in the course of the simulation or along the trajectory is one of the major subjects that can contribute to the understanding on the molecular and on the electronic level. The importance of analyzing the wavefunction in bioinorganic systems has been shown in many applications, see also Section... 

Subject areas for the Series include solutions of electrolytes, liquid mixtures, chemical equilibria in solution, acid-base equilibria, vapour-liquid equilibria, liquid-liquid equilibria, solid-liquid equilibria, equilibria in analytical chemistry, dissolution of gases in liquids, dissolution and precipitation, solubility in cryogenic solvents, molten salt systems, solubility measurement techniques, solid solutions, reactions within the solid phase, ion transport reactions away from the interface (i.e. in homogeneous, bulk systems), liquid crystalline systems, solutions of macrocyclic compounds (including macrocyclic electrolytes), polymer systems, molecular dynamic simulations, structural chemistry of liquids and solutions, predictive techniques for properties of solutions, complex and multi-component solutions applications, of solution chemistry to materials and metallurgy (oxide solutions, alloys, mattes etc.), medical aspects of solubility, and environmental issues involving solution phenomena and homogeneous component phenomena. 

The DNA-carbon nanotube interaction is a complicated and dynamic process. Many studies on this subject have been pursued through a series of techniques, including molecular dynamic simulation, microscopy, circular dichroism, and optical spectroscopy.57,58 Although the detailed mechanism is not fully understood at present, several physical factors have been proposed to be driving DNA-carbon nanotube interactions,46,59-61 such as entropy loss due to confinement of the DNA backbone, van der Waals and hydrophobic (rr-stacking) interactions, electronic interactions between DNA and carbon nanotubes, and nanotube deformation. A recent UV optical spectroscopy study of the ssDNA-SWNT system demonstrated experimentally that... 

The general method of molecular dynamics simulations is based on evaluation of the time history of positions and linear momenta for the ensemble of particles (atoms or molecules) subject to investigation. For classical systems it is assumed that the Bom-Oppenheimer approximation for separation of the electronic and nuclear degrees of freedom is valid and the evolution of the system takes place without changes in the electronic... 

At the liquid-liquid interface, completely different properties of water and organic phases can be met in the two-dimensional boundary with a thickness of only 1 nm. In practical two-phase systems with highly miscible components, however, the formation of nano- and micro-droplets at the interfacial nano-region is suggested. The structural and dynamic properties of molecules at the interface are the most important subject in the study of physics and chemistry at the interface. The solution theory of the liquid-liquid interface has not been established yet, though the molecular dynamics simulations have been developed as a useful tool for depicting the molecular picture of the solvent and solute molecules in the interfacial region. 

Finally, dynamic structure-based pharmacophore models can be derived through a method first described by Carlson et al that uses multiple conformations of the target protein, which are obtained either by molecular dynamics simulation or by the use of multiple experimentally determined conformations. The binding sites of the respective snapshots are flooded with small molecular probes (e.g., methanol for hydrogen-bond interactions and benzene for aromatic hydrophobic interactions) and while the protein structure is held rigid the probe molecules are subjected to a low-temperature Monte Carlo minimization where they undergo multiple, simultaneous gas-phase... 

The general principle of BD is based on Brownian motion, which is the random movement of solute molecules in dilute solution that result from repeated collisions of the solute with solvent molecules. In BD, solute molecules diffuse under the influence of systematic intermolecular and intramolecular forces, which are subject to frictional damping by the solvent, and the stochastic effects of the solvent, which is modeled as a continuum. The BD technique allows the generation of trajectories on much longer temporal and spatial scales than is feasible with molecular dynamics simulations, which are currently limited to a time of about 10 ns for medium-sized proteins. 

Fig. 3.16. Variation with time t (in number of iterations) of the molecular dynamic simulation data for the number nt of broken bonds in a given configuration of site dilute Lennard-Jones system (of linear size L = 21), for different initial concentraions of dilution, when subjected to a stress just greater than the corresponding fracture stress af (Chakrabarti et al 1986).

CILS spectroscopy is concerned with the frequency, density, polarization, and temperature dependences of supermolecular light scattering. Pure and mixed gases are considered, that is, complexes of like and of dissimilar molecules are of interest. In Section 1.3, we consider ordinary collision-induced Raman scattering nonlinear and electronic collision-induced Raman processes are the subject of the Appendix CILS of liquid and solid samples are considered in Part II, together with molecular dynamics simulations. 

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