Molecular simulation techniques

Molecular simulation techniques can be used to predict how a compound will interact with a particular active site of a biological molecule. This is still not trivial because the molecular orientation must be considered along with whether the active site shifts geometry as it approaches. 

Molecular simulation techniques, namely Monte Carlo and molecular dynamics methods, in which the liquid is regarded as an assembly of interacting particles, are the most popular... 

Third, as the size and complexity of the biomolecular systems at hand further expand, there are more uncertainties in the molecular model itself. For example, the resolution of the X-ray structure may not be sufficiently high for identifying the locations of critical water molecules, ions and other components in the system the oxidation states and/or titration states of key reactive groups might be unclear. In those cases, it is important to couple QM/MM to other molecular simulation techniques to establish and to validate the microscopic models before elaborate calculations on the reactive mechanisms are investigated. In this context, pKa and various spectroscopic calculations [113,114] can be very relevant. 

A complete review of spectroscopic methods applied to the analysis of alkyl-modified surfaces with a comprehensive list of spectroscopic indicators of alkyl chain conformational order is provided elsewhere [9] this review will focus on the application of spectroscopic and other relevant experimental techniques for the characterization of shape-selective chromatographic materials. On the whole, it has been observed experimentally that any increase in alkyl stationary-phase conformational order promotes an increase in selectivity for shape-constrained solutes in RPLC separations [9], As a complement to the wealth of spectroscopic and chromatographic data, the use of molecular simulation techniques to visualize and characterize alkyl-modified surfaces may also provide new insights into molecular-level features that control shape selectivity. A review of progress in the field of chromatographic material simulations will also be discussed. 

A powerfull tool to provide an explanation of the molecular origin of the observed secondary relaxation is molecular simulation technique, to elucidate the... 

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)). 

The theory of simple liquids achieved a mature state in the era 1965-1975 (Barker and Henderson, 1976 Hansen and McDonald, 1976). As this mature theory was extended towards molecular liquids, simple molecular cases such as liquid N2 or liquid CCI4 were treated first. But the molecular liquids that were brought within the perimeter of the successful theory were remote extremities compared with the liquids synthesized, poured from bottles or pipes, and used. In addition, the results traditionally sought from molecular theories (Rowlinson and Swinton, 1982) often appear to have shifted to accommodate the limitations of the available theories. Overlooking molecular simulation techniques... 

As far as convective heat transfer is concerned, liquid and gaseous flows musf be considered separately. Liquid flow has been investigated experimentally, whereas analytical, numerical and molecular simulation techniques have been applied to understand the characteristics of gaseous flow and heat transfer. While the Navier-Stokes equations can still be applied, due to the small size of microchannels, some deviations from the conventionally sized applications have been observed. Flow regime boundaries are significantly different, as well as flow and heat transfer characteristics. 

In contrast to the experimental methods, the molecular simulation techniques, such as molecular dynamics and Monte Carlo methods, allowed one to obtain some details about the molecular arrangements on the nanometer scale. However, the... 

Freezing phenomena in nanoscale pores were investigated with the aid of various molecular simulation techniques. The benefit of employing molecular simulation would be that we were able to observe individual contribution of important factors that may affect the phenomena, while experimental measurements may suffer from complication by simultaneous affection of some factors. In the following summarized conclusions are shown referring to Fig. 8. 

Molecular simulation methods start from a description of the intermolecular forces of a system. For all but the simplest molecules, quantitative information on intermolecular potentials is not available. For this reason one has to resort to approximate, analytically convenient intermolecular potential functions and obtain the parameters by fitting experimental results. Although the need for fitting seems at least partly to negate some of the advantages of molecular simulation techniques over phenomenological approaches, the hope is that the fitted intermolecular potential parameters would be transferrable from system to system, and be applicable for a wide range of process conditions. 

The calculations reported in this paper and a related series of publications indicate that it is now quite feasible to obtain reasonably accurate results for phase equilibria in simple fluid mixtures directly from molecular simulation. What is the possible value of such results Clearly, because of the lack of accurate intermolecular potentials optimized for phase equilibrium calculations for most systems of practical interest, the immediate application of molecular simulation techniques as a replacement of the established modelling methods is not possible (or even desirable). For obtaining accurate results, the intermolecular potential parameters must be fitted to experimental results, in much the same way as parameters for equation-of-state or activity coefficient models. This conclusion is supported by other molecular-simulation based predictions of phase equilibria in similar systems (6). However, there is an important difference between the potential parameters in molecular simulation methods and fitted parameters of thermodynamic models. Molecular simulation calculations, such as the ones reported here, involve no approximations beyond those inherent in the potential models. The calculated behavior of a system with assumed intermolecular potentials is exact for any conditions of pressure, temperature or composition. Thus, if a good potential model for a component can be developed, it can be reliably used for predictions in the absence of experimental information. 

The study of highly confined fluids by molecular simulation techniques continues to grow in popularity. While there are many individual and widely... 

Molecular Simulations Molecular simulations are useful for predicting properties of bulk fluids and solids. Molecular dynamics (MD) simulations solve Newton s equations of motion for a small number (on the order of 10 ) of molecules to obtain the time evolution of the system. MD methods can be used for equilibrium and transport properties. Monte Carlo (MC) simulations use a model for the potential energy between molecules to simulate configurations of the molecules in proportion to their probability of occurrence. Statistical averages of MC configurations are useful for equilibrium properties, particularly for saturated densities, vapor pressures, etc. Property estimations using molecular simulation techniques are not illustrated in the remainder of this section as commercial software implementations are not generally available at this time. 

Most molecular simulation techniques can be categorized as being among three main types (1) quantum mechanics, (2) molecular dynamics (MD) and (3) kinetic Monte Carlo (KMC) simulation. Quantum mechanics methods, which include ah initio, semi-empirical and density functional techniques, are useful for understanding chemical mechanisms and estimating chemical kinetic parameters for gas-phase... 

Tools for Ab Initio Molecular Dynamics and Simulation Analysis This is a joint effort of researchers at the University of Illinois and Iowa State University. Their goal is to combine state-of-the-art molecular simulation techniques in a publicly available computer code, for use both by experts and nonexperts. Outcomes of this project include publicly available software tools, along with a workshop for dissemination. 

It is expected that entirely new options for thermodynamic modeling of simultaneous chemical and phase equilibrium will become available from molecular simulations techniques. Such methods are beginning to become available [12, 13], but can not be covered in the scope of the present chapter. 

Molecular dynamics (MD) and Monte Carlo (MC) simulations are popular molecular simulation techniques. These methods are well suited for modeling supercapacitor because EDLs in supercapacitors are essentially molecular phenomena, e.g., the thickness of EDLs in supercapacitors is typically less than a few nanometers. The uni(]ue advantage of these methods is that they provide direct information on both the microstructure (e.g., ion density distribution across EDL, which is difficult to measure experimentally) and the macroscopic properties (e.g., its capacitance) of EDLs. This allows one to establish the microscopic origins of the capacitance of supercapacitors and thus helps guide the design and selection of electrode/electrolyte materials for supercapacitors. MD simulation, as... 

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