This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.Photosynthesis is the bioenergetic process by which the majority of Earths biosphere derives energy from sunlight. This efficient sub-cellular process depends on the complex organization of the photosynthetic unit (PSU) at multiple scales spanning from sub-nanoscale atomic processes to macroscale multi-protein and lipid assemblies that are integral components of PSU organelles. One such organelle found in the purple bacterium Rhodobacter sphaeroides is the chromatophore, a 70 nm wide bulbous invagination of the inner membrane containing a total of approximately 200 proteins, 5,000 chlorophylls, and 1,700 carotenoids that permit efficient photosynthesis. These 200 chromatophore proteins consist of several multi-protein complexes, including 20 photosynthetic reaction centers (RC) [1, 2], 20 light harvesting complexes 1 (LH1) [3, 4], 150 light harvesting complexes 2 (LH2) [5, 6], five bc1 complexes (bc1) [7] and cytochrome c2s [8], and usually one ATP synthase [9]. Involving 70 million atoms, continued development of coarse-graining tools and the extension of VMD and NAMD capabilities will be necessary to accommodate such a large system computationally. Representing one of the first simulations at the near-cellular level, the chromatophore system will also strenuously test the scalability of VMD and NAMD while providing unique opportunities to investigate one of the most fundamental processes necessary for life on Earth, namely the conversion of light into bioenergy.
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