Hello, A yearly allocation for the LCRC cluster has been requested with the following updated information: Submitter/PI: Oleksandr Kokhan Project Name: biomimetic_systems Division: CSE Project title: Solar energy conversion in biomimetic molecular architectures Associated funding: DOE Division of Chemical Sciences, Geosciences, and Biosciences Other Systems: N/A Science: This computational project will supplement our experimental work on construction and characterization of water-splitting catalysts and biomimetic molecular architectures for solar energy conversion. The first aim is to use all-atom Molecular Dynamics (MD) simulations to better understand conformational dynamics and structural impact of various photosensitizers and photosensitizer-catalyst dyads covalently linked to PpcA, a multi-heme c-type cytochrome from Geobacter sulfurreducens. These results will facilitate interpretation of kinetic electron transfer rates as well as Small- and Wide-Angle X-ray Scattering (SAXS, WAXS) data to provide an insight into strategies for optimization of electron transfer rates within biomimetic hybrids. The second aim is to continue our work on understanding of shortcomings of popular all-atom force fields for protein simulations (CHARMM, AMBER) and develop tools facilitating interpretation of protein SAXS/WAXS data. Finally, we plan to explore a possibility of using ab initio molecular dynamics for refinement and getting better fits of structural and hydration models of water splitting catalysts derived for our High Energy X-ray Scattering data. Project description: We are developing biomimetic molecular architectures for efficient solar energy conversion using artificial and natural photosensitizers combined with natural and genetically engineered host systems capable to support long-lived charge-separated states and conduct charges away from the photosensitizers. We recently developed a series of cysteine mutants of PpcA, a multiheme redox protein from Geobacter sulfurreducens, and synthesized a number of photosensitizers which can be selectively attached to the engineered residues. These bio-hybrids demonstrate light-induced electron transfer (ET) but the observed rates and quantum yields are far from optimal. Furthermore, there is no agreement in scientific community on whether the donor-acceptor distance, driving and re-organization energies are the only factors responsible for control of ET rates (Moser et al. Nature, 355:796; Page et al. Nature, 402:47) or frameworks of internal bonds and protein dynamics can also have a significant impact on the ET in protein systems (Balabin and Onuchic, Science, 290:114; Lin et al. Science, 310, 1311). During FY2012 we have developed CHARMM force field parameters for several photosensitizers and obtained promising preliminary results for some of PpcA mutants in their oxidized form linked to Ru(bpy)3. In FY2013 our main focus will be on significantly extending those simulations as well as adding other types of photosensitizers. We expect that MD simulations will provide a sufficient sampling of protein conformational space and help us to better rationalize the collected kinetic data on electron transfer rates and SAXS/WAXS scattering profiles. To achieve this goal we plan to run a series of 100-500 ns MD simulations on all 6 available PpcA mutants. At the initial stages of the project we will focus on the systems with all three PpcA hemes either oxidized or reduced. All MD simulations will be performed with NAMD 2.8 and CHARMM force field. We will use standard for protein MD conditions: nPT, PME electrostatics, explicit TIP3 water boxes sufficiently large to keep interaction energy negligible between protein mirror images. The analysis of MD trajectories, computational docking and calculation of X-ray scattering profiles will be carried out on our lab computers. The second goal is to continue our work in collaboration with Dr. Xiaobing Zuo (XSD) on developing methods and techniques for generating sufficiently large protein conformational ensembles and rapidly matching X-ray scattering profiles calculated from MD snapshots with the actual experimental data. For this project we also plan to run all-atom MD and Steered MD simulations with CHARMM force field. Project URL: http://www.cse.anl.gov/fundamental_interactions/solar_conversion.html Current FY Hours Used: undetermined amount New FY Requested allocation: 600000 Q1: 150000 Q2: 150000 Q3: 150000 Q4: 150000 Justification: NAMD is a highly scalable molecular dynamics simulations code. Benchmarks on Fusion with wild-type PpcA in a water box (~13,000 atoms) showed more than 99% speed-up efficiency with ~1,600 atoms/CPU core and ~80% efficiency with ~400 atoms/core and yielded 5.1 and 15.7 ns/day, respectively. NAMD can be dramatically accelerated (~5-fold for typical protein simulations) with GPU support. Thank You, The LCRC Accounts System