Molecular dynamics using atomistic models

Using a molecular dynamics module, atomistic models for C6o, ethylene, naphthalene and benzene were developed accomplishing ground energy structures. Electrostatic potentials for C6o fullerene and radical species were calculated to know if an electrostatic attraction can be established between the fullerene and each one of the radical species. After this, UV-response up to 400 nm for the radical species was calculated and compared with the experimental spectra obtained from literature. 

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 dynamics simulations using atomistic models, and hence relatively detailed potentials of interatomic interactions, of surfactants and solvent molecules [9,10] have been attempted for studying surfactant assemblies. However, as mentioned earlier, detailed atomistic modeling approaches demand intensive computations and as a result require drastic simplifications that prevent examination of certain aspects of structural or temporal features of the system. One such example is an a priori selection of the structure of the micelle itself in the simulations this clearly precludes the potential use of the simulations to examine the self-assembly process. 

In most microfluidics and nanofluidics, the atomistic effects on electroosmotic flows are neghgible. But when the characteristic length is comparable with the molecular size of fluid, it should be considered. Molecular dynamics methods have been used to simulate the particle effects in nanoscale electroosmotic flows [23, 24]. However, it is too time-consuming to simulate a real electroosmotic micro- and nanofluidics by molecular dynamics. The multiscale modeling and analysis would be a possible research direction. 

This article reviews progress in the field of atomistic simulation of liquid crystal systems. The first part of the article provides an introduction to molecular force fields and the main simulation methods commonly used for liquid crystal systems molecular mechanics, Monte Carlo and molecular dynamics. The usefulness of these three techniques is highlighted and some of the problems associated with the use of these methods for modelling liquid crystals are discussed. The main section of the article reviews some of the recent science that has arisen out of the use of these modelling techniques. The importance of the nematic mean field and its influence on molecular structure is discussed. The preferred ordering of liquid crystal molecules at surfaces is examined, along with the results from simulation studies of bilayers and bulk liquid crystal phases. The article also discusses some of the limitations of current work and points to likely developments over the next few years. 

CNTs have extremely high stiffness and strength, and are regarded as perfect reinforcing fibers for developing a new class of nanocomposites. The use of atomistic or molecular dynamics (MD) simulations is inevitable for the analysis of such nanomaterials in order to study the local load transfers, interface properties, or failure modes at the nanoscale. Meanwhile, continuum models based on micromechan-ics have been shown in several recent studies to be useful in the global analysis for characterizing such nanomaterials at the micro- or macro-scale. 

The earliest fully atomistic molecular dynamic (MD) studies of a simplified Nation model using polyelectrolyte analogs showed the formation of a percolating structure of water-filled channels, which is consistent with the basic ideas of the cluster-network model of Hsu and Gierke. The first MD... 

This bimodal dynamics of hydration water is intriguing. A model based on dynamic equilibrium between quasi-bound and free water molecules on the surface of biomolecules (or self-assembly) predicts that the orientational relaxation at a macromolecular surface should indeed be biexponential, with a fast time component (few ps) nearly equal to that of the free water while the long time component is equal to the inverse of the rate of bound to free transition [4], In order to gain an in depth understanding of hydration dynamics, we have carried out detailed atomistic molecular dynamics (MD) simulation studies of water dynamics at the surface of an anionic micelle of cesium perfluorooctanoate (CsPFO), a cationic micelle of cetyl trimethy-lainmonium bromide (CTAB), and also at the surface of a small protein (enterotoxin) using classical, non-polarizable force fields. In particular we have studied the hydrogen bond lifetime dynamics, rotational and dielectric relaxation, translational diffusion and vibrational dynamics of the surface water molecules. In this article we discuss the water dynamics at the surface of CsPFO and of enterotoxin. 

In another paper in this issue [1], the molecular motions involved in secondary transitions of many amorphous polymers of quite different chemical structures have been analysed in detail by using a large set of experimental techniques (dynamic mechanical measurements, dielectric relaxation, H, 2H and 13C solid state NMR), as well as atomistic modelling. 

The final two chapters discuss modeling of PEFCs. Mukherjee and Wang provide an in-depth review of meso-scale modeling of two-phase transport, while Zhou et al. summarize both the simulation of electrochemical reactions on electrocatalysts and the transport of protons through the polymer electrolyte using atomistic simulation tools such as molecular dynamics and Monte Carlo techniques. 

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