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 LRAC request, we propose to investigate problems in turbulence, haemodynamics, materials research and the biomolecular science. In the materials science domain, we plan to quantitatively study the emergent properties of liquid crystalline materials and of clay-polymer nanocomposites which have immense scientific and technological relevance. This work will be carried for very large system models, using massively parallel codes, hitherto not possible due to computational resource limitations. In the biomolecular sciences domain, our projects are concerned with understanding biologically relevant processes based on drug binding affinity 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 six specific projects in this proposal: (i) Identification of Unstable Periodic Orbits (UPOs) in the Navier-Stokes equations: The objective of this work is to identify Unstable Periodic Orbits for the characterisation of turbulent flows using a novel four-dimensional spacetime parallelisable approach. (ii) Patient-specific whole brain blood flow simulations: Our objective in this project is to provide an efficient computational environment to assist interventional neuroradiologists in neurovascular surgery by providing information on patient-specific haemodynamics within clinically relevant timeframes. (iii) Large-scale lattice-Boltzmann simulations of liquid crystalline materials: In this project we will study the rheological response and self-assembly dynamics of cubic liquid crystals in ternary amphiphilic mixtures using our tried and tested kinetic lattice-Boltzmann approach. (iv) Materials properties of clay-polymer nanocomposites: The objective of this work is to calculate the bulk materials properties of clay-polymer nanocomposites using molecular dynamics simulations using unprecedented model sizes. (v) Drug resistance in HIV-1 proteases and reverse transcriptases: The objective of this work is to elucidate and predict the effect of patient-specific mutations in HIV-1 Proteases and Reverse Transcriptases on drug-binding affinities. This work will be carried using NAMD building on novel simulation methodologies developed in our previous work on the TeraGrid. (vi) Predicting affinity of EGFR kinase domain for drug inhibitors using high performance computing molecular dynamics: The objective this work is to elucidate and predict the effect of patient-specific mutations in the cancer-specific protein, epidermal growth factor receptor (EGFR) on drug-binding affinities. This work will be carried using NAMD and novel ensemble molecular dynamics simulations. We use scalable codes HYPO4D, HemeLB, LB3D, LAMMPS and NAMD which have been extensively benchmarked and used in our previous work on the TeraGrid, particularly on Ranger, where we have achieved scalability on up to 32768 cores. The HemeLB code has been used to conduct simulation studies within the GENIUS project for which we received the """"""""Transformational Science Challenge"""""""" award at TeraGrid'08. We have also received 5K Club awards for the HYPO4D and LB3D codes. We will use NAMD for our molecular dynamics studies which is a widely used community-code and has been previously used in award winning simulations of the SPICE project.
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