LATTICE BOLTZMANN AND MOLECULAR DYNAMICS STUDIES IN MATERIALS AND BIOMOLECULAR

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We propose to investigate problems in materials and biomolecular sciences. In the materials science domain, we plan to quantitatively study the emergent properties of complex materials by performing simulations with very large system models, using massively parallel codes, hitherto not possible due to computational resource limitations. Such large scale simulations allow us to calculate materials properties which are not accessible with simulations of smaller models and to quantitatively assess the role of finite size effects. In the biomolecular sciences domain, our projects are concerned with understanding biologically relevant processes based on free energy calculations. In the projects proposed here, we build on earlier work where we have developed and validated novel computational algorithms and grid computing infrastructure, allowing access to physical timescales via molecular dynamics simulations, which have so far been very difficult to achieve. We shall focus on projects on four specific scientific research areas - i) Large-scale lattice-Boltzmann simulations of liquid crystalline materials ii) Material properties of clay-polymer nanocomposites iii) Drug resistance in HIV-1 proteases and iv) Nucleic acid translocation through alpha-hemolysin protein nanopores. In project (i), our objective is to investigate the rheological and morphological properties of mesoscopic cubic phases of oil/water surfactant systems. In particular, we plan to examine the effect of defects on the rheological properties of self-assembled gyroid mesophases. In project (ii), we propose to calculate the materials properties of clay-polymer nanocomposite systems. We will use physically realistic-sized models and perform molecular dynamics simulations in order to calculate material properties, including the bending modulus, Young.s modulus and Poisson.s ratio, directly from emergent undulating motions observed in these simulations. The objective of the work in project (iii), is to study the effect of pairwise complementary mutations on HIV-1 protease activity and drug resistance. Calculation of differential dynamics and differences in binding affinities in protease-inhibitor(drug) and protease-substrate complexes will allow increasingly accurate inferences to be made about the basis of HIV protease drug resistance. In project (iv), our objective is to compute the free energy profile of the translocation process of DNA along the vertical axis of a transmembrane protein pore buried in a lipid membrane bilayer. We use scalable codes LB3D, LAMMPS and NAMD which have been extensively benchmarked and used in our previous work on the TeraGrid. The codes LB3D and NAMD have been used in our award winning simulations of the TeraGyroid and SPICE projects. We intend to use grid middleware, called the Application Hosting Environment (AHE), which provides easy, uniform access to distributed computational resources, including the TeraGrid. The AHE has proved to be a powerful tool; it is currently being used by scientists to manage their simulations and workflows on the TeraGrid. AHE capabilities can be further exploited if used in conjunction with roaming access on the TeraGrid. In this proposal, in the first section, we present a precis for the Principal Investigator and for the Co-Investigators as well as the main research topics we wish to investigate. In the next section of this proposal, we describe the background for our research and provide details of previous research using TeraGrid resources. We then briefly describe AHE and how it enables scientists to utilize grid resources. In the penultimate section of this proposal we described the specifics of the scientific issues and simulations that we wish to perform with this MRAC allocation. In the final section of this proposal, we provide a summary of the TeraGrid resources requested in this MRAC proposal.