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. In this supplemental request, we propose to extend our investigations carried out within the MRAC allocation(DMR070014N and DMR070013N). We shall focus on four projects in the materials and biomolecular sciences domain. In the materials science domain we will extend our lattice-Boltzmann mesoscale simulations to study shear-induced transitions between the sponge phase and the lamellar and multi-lamellar vesicle phase. This work continues from our current simulation studies of the rheological transitions between cubic and non-cubic mesophases of amphiphilic mixtures. In the materials science domain, we will also extend our fully-atomistic molecular dynamics studies of clay-polymer nanocomposites of large-scale models at unprecedented sizes. We will now carry out atomistic molecular dynamics simulations of clay-polymer nanocomposites with explicit edges which replicate the experimental system and calculate their characteristic material properties. In the biomolecular sciences domain, we have made significant progess in our molecular dynamics simulations of the binding affinities of HIV-1 proteases to drug substrates using advanced grid middleware capabilities, We now propose to extend this work to a variety of proteases and associated resistance-conferring mutations and to carry out analogous studies for the HIV-1 reverse transcriptases. We are also proposing a project which utilizes replica exchange molecular dynamics to elucidate the dynamics of the gating mechanism of the flaps in HIV-1 protease. This project will utilize grid middleware that provides automatic co-allocation of TeraGrid resources and launching of cross-site simulations.