MULTISCALE SIMULATIONS OF BIOMOLECULAR DYNAMICS

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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. An emerging view of biomolecular structure is that of an ensemble of conformations, some of which determine specific functions. Biomolecular dynamics determines how often these functionally important conformations appear in the course of biomolecules life, and, therefore, modulates its functional activity. Areas, such as protein folding, biomolecular design, cell regulation, and biotechnology, often require deep understanding of molecular conformations. Despite recent revolutionary advances in experimental methodologies, we are still restrained in our ability to sample and decipher the structural and dynamic aspects of biomolecules that are critical for sustaining cellular processes. Thus, there is a crucial need for novel and unconventional techniques to uncover the fundamentals of biomolecular structure and interactions. Our indigenously developed simulation engine - discrete molecular dynamics (DMD) has been pivotal in accessing biologically relevant time and length scales. It is faster than traditional molecular dynamics simulations by 5 to 10 orders of magnitude. The goal of this proposal is to utilize multiscale simulations in a grid computing environment towards studies of biomolecular dynamics, stability and aggregation. We have created a web-portal, called iFold: http://ifold.dokhlab.org providing the first online gateway for exploring protein dynamics using DMD. However, extensive computational resources are needed to support iFold simulations. So far, a UNC based local cluster resource was used for iFold backend. Due to universal appeal of iFold, Renaissance Computing Institute (RENCI) at North Carolina has extended their support for making iFold a TeraGrid Science Gateway. This proposal aims at utilizing the TeraGrid resources towards computational needs of iFold.