Center for Macromolecular Modeling and Bioinformatics

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Project Summary / Abstract The Biomedical Technology Research Resource for Macromolecular Modeling and Bioinformatics, hereafter referred to simply as the “Center,” develops software tools to model cellular processes at both the atomic and coarse- grained level. An experienced, multidisciplinary team of researchers at the Center provides for the biomedical research community a “computational microscope” and collaborates with leading experimental laboratories. The computational microscope, equipped with molecular visualization, sequence, structure and dynamics analysis capabilities, presently consists of NAMD, VMD, and Lattice Microbes software programs that are free and open- source. The Center will expand the use of its computational tools to a broad range of biomedical research problems and provide easy access to these tools for the biomedical research community. In the next funding period, the Center will pursue the following goals: · Raise performance, efficiency, and accuracy of simulations for cellular processes at long time and large length scales; · Facilitate innovation in the biomedical research community by providing accessible simulation tools support- ing, in particular, advanced multi-copy enhanced sampling protocols, QM/MM, multi-resolution methods, coarse-grained models, stochastic simulations of large networks of biochemical reactions, Brownian dynamics, and whole cell simulations; · Lead the implementation of state of the art technologies in GPU, petascale, and pre-exascale computing into biomedical research at the molecular and cellular level; · Support visualization and analysis of biomolecular systems with powerful, customizable software packages, integrating multi-modal experimental imaging (e.g., cryo-electron microscopy and tomography, X-ray, NMR) and -omics data with model building and simulation tools; · Enhance performance for visualization, analysis, and modeling of large-size and long-timescale cellular pro- cesses by exploiting emerging technologies such as GPU acceleration, remote visualization, and non-volatile memory; · Develop methods to model whole cell behavior and large cellular components such as membrane environments and chromatin; · Scale coarse-grained simulation methods to eukaryotic-sized cells; · Drive the development of novel computational tools and methods through collaborations with both theoretical and experimental laboratories; · Enhance service, training, and dissemination with the use of electronic text books and videos, providing a cutting edge computational laboratory, cloud computing resources, hands-on training, first-rate educational material, and an extensive, widely-used website to biomedical researchers.