Molecular-level modeling methods

Classical molecular simulation methods such as MC and MD represent atomistic/molecular-level modeling, which discards the electronic degrees of freedom while utilizing parameters transferred from quantum level simulation as force field information. A molecule in the simulation is composed of beads representing atoms, where the interactions are described by classical potential functions. Each bead has a dispersive pair-wise interaction as described by the Lennard-Jones (LJ) potential, ULj(Ly) ... 

Essential progress has been made recently in the area of molecular level modeling of capillary condensation. The methods of grand canonical Monte Carlo (GCMC) simulations [4], molecular dynamics (MD) [5], and density functional theory (DFT) [6] are capable of generating hysteresis loops for sorption of simple fluids in model pores. In our previous publications (see [7] and references therein), we have shown that the non-local density functional theory (NLDFT) with properly chosen parameters of fluid-fluid and fluid-solid intermolecular interactions quantitatively predicts desorption branches of hysteretic isotherms of nitrogen and argon on reference MCM-41 samples with pore channels narrower than 5 nm. 

The antiviral activities of natural products, including ingredients, fractions and extracts, need to be evaluated by various anti-viral models, including in vitro and in vivo models. Besides, the analysis of assay results of natural products is also very important. In the present section, the models to evaluate the in vitro anti-viral activities of potential natural products have been summarized, and the evaluation methods of several representative models have been introduced. The antiviral models include molecular level models and cellular level models (Table 3.2 Chattopadhyay et al. 2009). 

Molecular level computer simulations based on molecular dynamics and Monte Carlo methods have become widely used techniques in the study and modeling of aqueous systems. These simulations of water involve a few hundred to a few thousand water molecules at liquid density. Because one can form statistical mechanical averages with arbitrary precision from the generated coordinates, it is possible to calculate an exact answer. The value of a given simulation depends on the potential functions contained in the Hamiltonian for the model. The potential describing the interaction between water molecules is thus an essential component of all molecular level models of aqueous systems. 

Knowing the compositions and structures of gas hydrates are prerequisites for molecular-level modelling. Although gas hydrates were known in the early 1800s, the structure of these materials remained unknown until the advent of X-ray diffraction methods in the early twentieth century. Stackelberg" was the first to study the structure of gas hydrate with powder X-ray diffraction. He found that clathrate hydrates exist in two distinct cubic crystalline forms. However, the proposed structures were found to be incorrect. Remarkably, from the building of molecular models, Claussen was the first to arrive at the correct structures, which were later confirmed. Since then many hydrate structures have been studied. Under atmospheric pressure and low temperature, a majority can be classified in one of the two cubic structures termed structure I (S-I) and structure II (S-II). 

With the improvement in hardware and software tools, the ab initio electronic structure calculations will gain importance because they can deal with increasingly complex systems and yield higher precision in the result. Along with this trend, the hybrid techniques will grow in relevance. It is expected that the hybrid methods will play an important role in the molecular-level modelling of SOFCs in the near future. 

The traditional, essentially phenomenological modeling of boundary lubrication should retain its value. It seems clear, however, that newer results such as those discussed here will lead to spectacular modification of explanations at the molecular level. Note, incidentally, that the tenor of recent results was anticipated in much earlier work using the blow-off method for estimating the viscosity of thin films [68]. 

It is important to realize that many important processes, such as retention times in a given chromatographic column, are not just a simple aspect of a molecule. These are actually statistical averages of all possible interactions of that molecule and another. These sorts of processes can only be modeled on a molecular level by obtaining many results and then using a statistical distribution of those results. In some cases, group additivities or QSPR methods may be substituted. 

Moreover, molecular modeling is one key method of a wide range of computer-assisted methods to analyze and predict relationships between protein sequence, 3D-molecular structure, and biological function (sequence-structure-function relationships). In molecular pharmacology these methods focus predominantly on analysis of interactions between different proteins, and between ligands (hormones, drugs) and proteins as well gaining information at the amino acid and even to atomic level. 

The significance of the development of photoelectron spectroscopy over the last decade for a better understanding of solid surfaces, adsorption, surface reactivity, and heterogeneous catalysis has been discussed. The review is illustrative rather than exhaustive, but nevertheless it is clear that during this period XPS and UPS have matured into well-accepted experimental methods capable of providing chemical information at the molecular level down to 10% or less of a monolayer. The information in its most rudimentary state provides a qualitative model of the surface at a more sophisticated level quantitative estimates are possible of the concentration of surface species by making use of escape depth and photoionization cross-section data obtained either empirically or by calculation. 

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