Molecular simulation types

In principle, mesoscale methods can provide a means for connecting one type of simulation to another. For example, a molecular simulation can be used to describe a lipid. One can then derive the parameters for a lipid-lipid potential. These parameters can then be used in a simulation that combines lipids to form a membrane, which, in turn, can be used to compute parameters describing a membrane as a flexible sheet. Such parameters could be used for a simulation with many cells in order to obtain parameters that describe an organ, which could be used for a whole-body biological simulation. Each step, in theory, could be modeled in a different way using parameters derived not from experiment but from a more low-level form of simulation. This situation has not yet been realized, but it is representative of one trend in computational technique development. 

However, in other types of molecular simulation, any sampled configuration may be correlated with configurations not sequential in the ultimate "trajectory7 produced. That is, the final result of some simulation algorithms is really a list of configurations, with unknown correlations, and not a true trajectory in the sense of a time series. 

One of the most important new areas of theory of charge transfer reactions is direct molecular simulations, which allows for an unprecedented, molecular level view of solvent motion during reactions in this class. One of the important themes for research of this type is to ascertain the validity at a molecular level of the linear response theory estimates of solvent interactions that are inherent in Marcus theory and related approaches. In addition, the importance of dynamic solvent effects on charge transfer kinetics is being examined. Recent papers on this subject have been published by Warshel [71], Hynes [141] and Bader and Chandler [137, 138],... 

In MD calculations, the molecular system is following along a time course (trajectory). In the second type of molecular simulations, MC, the system follows a random walk through configuration space (85). A huge... 

As expected, the total interaction energies depend strongly on the van der Waals radii (of both sorbate and sorbent atoms) and the surface densities. This is true for both HK type models (Saito and Foley, 1991 Cheng and Yang, 1994) and more detailed statistical thermodynamics (or molecular simulation) approaches (such as Monte Carlo and density functional theory). Knowing the interaction potential, molecular simulation techniques enable the calculation of adsorption isotherms (see, for example, Razmus and Hall, (1991) and Cracknell etal. (1995)). 

Although experimental and theoretical works have been successful for studying phenomena of this type, however, for example the experimental methods cannot reveal the detailed solvation structures to describe the interaction between solvent and polymer. Theoretical methods are also either not completely atomistic or they assume a certain molecular behavior. Molecular simulation methods, on the other hand, can produce most atomistic information about the solvation process. 

Molecular simulation, on the other hand, can provide the most detailed molecular view for the process. However, a let-it-do type simulation does not work for the problem at all, because the MR process is usually a slow... 

Special cases of charge-transfer spectra are the so-called charge-transfer-to-solvent (CTTS) spectra [17, 68]. In this type of CT transitions, solute anions may act as electron-donors and the surrounding solvent shell plays the role of the electron-acceptor. A classical example of this kind of CTTS excitation is the UV/Vis absorption of the iodide ion in solution, which shows an extreme solvent sensitivity [68, 316]. Solvent-dependent CTTS absorptions have also been obtained for solutions of alkali metal anions in ether or amine solvents [317]. Quantum-mechanical molecular simulations of the CTTS spectra of halide ions in water are given in reference [468]. 

In this study, equilibria and isosteric heat of adsorption for the system of chlorinated hydrocarbons and Y-type zeolite were obtained with gravimetric method and chromatographic method. By comparing an experiment result with a molecular simulation result, the validity of forcefield parameters and zeohte model was exartuned... 

Willetts and Rice attempted to develop a continuum model (type II) to calculate the EFISH response of liquid acetonitrile. Their results were compared with accurate calculations and measurements of the hyperpolarizability of the isolated molecule and measured solution for two different cavity radii. One natural choice of cavity radius is based on the van der Waals radius of the compound and with this value of a the discrepancy between the gas and solution measurements is not resolved. A rather smaller value of a can be selected to give much better agreement. The arbitrariness of the choice of cavity radius places a serious limitation on the usefulness of the continuum theories and, in recent years, there has been a considerable effort to develop hyperpolarizability calculations based on discrete molecular simulations of liquid and solution structure. 

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