Atomistic structural functional models

An atomistic approach, which has relevance to the current work, is the previously discussed normal-mode method. In the normal-mode method the constituent monomer units in the cluster are assumed to interact with a reasonable model potential in a fixed structure. From the assumed structure and model potential a normal-mode analysis is jjerformed to determine a vibrational partition function. Rotational and translational partition functions are then included classically. The normal-mode method treats the cluster as a polyatomic molecule and is most appropriate at very low temperatures where anharmonic contributions to the intermolecular forces can be ignored. As we shall show by numerical example, as the temperature is increased, the... 

The atomistic approach to modelling the crystal structure and properties involves the definition of interatomic potential functions to simulate the forces acting between ions. As discussed in Chapter 1, interatomic pair potentials can be written as ... 

To see how the different mapping schemes proposed in the literatures for PS were able to reproduce the atomistic structure, we plotted the intermolecular radial distribution functions (RDFs) between the centers of mass of PS monomers, ethylbenzene (EB) molecules, or both, obtained from the CG model proposed by... 

Research needs will occur in the study of structural and functional properties, including very small structures, the modeling of tribological systems, scale-dependent properties, the tailoring of defect structures, the thermodynamics and kinetics of ceramic interfaces, and an atomistic simulation of crystal structures... 

Empirical energy functions can fulfill the demands required by computational studies of biochemical and biophysical systems. The mathematical equations in empirical energy functions include relatively simple terms to describe the physical interactions that dictate the structure and dynamic properties of biological molecules. In addition, empirical force fields use atomistic models, in which atoms are the smallest particles in the system rather than the electrons and nuclei used in quantum mechanics. These two simplifications allow for the computational speed required to perform the required number of energy calculations on biomolecules in their environments to be attained, and, more important, via the use of properly optimized parameters in the mathematical models the required chemical accuracy can be achieved. The use of empirical energy functions was initially applied to small organic molecules, where it was referred to as molecular mechanics [4], and more recently to biological systems [2,3]. 

Molecular simulation methods can be a complement to surface complexation modeling on metal-bacteria adsorption reactions, which provides a more detailed and atomistic information of how metal cations interact with specific functional groups within bacterial cell wall. Johnson et al., (2006) applied molecular dynamics (MD) simulations to analyze equilibrium structures, coordination bond distances of metal-ligand complexes. 

Two broad classes of technique are available for modeling matter at the atomic level. The first avoids the explicit solution of the Schrodinger equation by using interatomic potentials (IP), which express the energy of the system as a function of nuclear coordinates. Such methods are fast and effective within their domain of applicability and good interatomic potential functions are available for many materials. They are, however, limited as they cannot describe any properties and processes, which depend explicitly on the electronic structme of the material. In contrast, electronic structure calculations solve the Schrodinger equation at some level of approximation allowing direct simulation of, for example, spectroscopic properties and reaction mechanisms. We now present an introduction to interatomic potential-based methods (often referred to as atomistic simulations). 

There are immense challenges also to model protein function, which will rely on better theoretical models for secondary structure formation (a helices, p sheets). Models presently used are molecular force field approaches, which are rather phenomenological. Realistic atomistic modelling is a long-term goal. In the meantime, energy landscape approaches should help us elucidate the detailed folding mechanisms that lead to protein function. 

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