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Clay minerals belong to a wider class of solids known as layered materials, which may be defined as ‘crystalline materials wherein the atoms in the layers are cross-linked by chemical bonds, while the atoms of adjacent layers interact by physical forces' [1]. Both clay sheets and interlayer space have one dimension in the nanometre range. Cationic clays are the predominant naturally occurring minerals with aluminosilicate sheets carrying a negative charge. Therefore, the interlayer guest species are positively charged to compensate the layer charge [2]. In anionic clays, also known as layered double hydroxides (LDHs), the interlayer guest species carry a negative charge and the inorganic mixed metal hydroxide sheets are positively charged. In recent times, there has been a growing interest in anionic clays, although initial attention was focussed almost exclusively on the cationic clay materials. Reviews have appeared that often emphasise interesting properties and the use of experimental techniques to determine or at least infer the local structure of the clay sheet or intercalated material [3-5]. However, clays are polycrystalline materials and precise experimental location of interlayer species is extremely difficult. [ABSTRACT FROM AUTHOR]

The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation [ABSTRACT FROM AUTHOR]

Drug resistant mutations have severely limited the success of HIV therapy. Here we provide insight into the molecular basis of drug resistance in HIV-1 protease with the inhibitor saquinavir. We employ protocols consisting of chained molecular dynamics simulations that allow preparation of desired mutants from an available wildtype structure. By conducting ensembles of molecular dynamics simulations we report differing frequencies of adoption of four stable conformations of the P2 subsite of saquinavir. The P2 subsite hydrogen bonds more frequently with the catalytic aspartic acid dyad in the wildtype, whilst preferring to bind with the flaps of the protease in three chosen mutants. Previously such simulations have been demanding to perform on computational grids due to the difficulty in tracking large numbers of simulations. Using the Application Hosting Environment, a lightweight grid middleware solution, we present a simple way to construct chained ensembles of simulations seamlessly across multiple grid resources. [ABSTRACT FROM AUTHOR]

Until recently, theoretical hydrodynamics has largely dealt with relatively simple fluids which admit or are assumed to have an explicit macroscopic description. It has been highly successful in describing the physics of such fluids by analyses based on the Navier-Stokes equations, the classical equations of fluid dynamics which describe the motion of fluids, and usually predicated on a continuum hypothesis, namely that matter is infinitely divisible [1]. On the other hand, many real fluids encountered in our daily lives, in industrial, biochemical, and other fields are complex fluids made of molecules whose individual structures are themselves complicated. Their behavior is characterized by the presence of several important length and time scales. It must surely be among the more important and exciting research topics of hydrodynamics in the 21st century to properly understand the physics of such complex fluids. Examples ofcomplex fluids arewidespread - surfactants, inks, paints, shampoos, milk, blood, liquid crystals, and so on. Typically, such fluids are comprised ofmolecules and/or supramolecular componentswhich have a non-trivial internal structure. Suchmicroscopic and/or mesoscopic structures lead to a rich variety of unique rheological characteristics which not only make the study of complex fluids interesting but in many cases also enhance our quality of life. [ABSTRACT FROM AUTHOR]