Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: David Tiede Applicant's institution: ANL Applicant's division: Project Name: protein_e-wire Project title: Solar energy conversion in biomimetic molecular architectures Associated funding: This project is supported by three funding programs within the DOE-BES Division of Chemical Sciences, Geosciences, and Biosciences: i) Solar Photochemistry; ii) Photosynthetic Systems; iii) Energy Frontier Research Center: Argonne Northwestern Solar Energy Research (ANSER) Center 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. Multi-heme cytochromes function as "molecular wires" for long range electron transfer in Geobacter. We are investigating these materials for opportunities to engineer novel solar energy conversion function. The MD molding results will be critical for 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 to develop tools facilitating interpretation of protein SAXS/WAXS 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). In the past 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 which closely matched X-ray scattering data. However, in some instances the complete equilibration of photosensitizer-cytochrome complexes required 50-75 ns trajectories. In FY2015 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 charge 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. The latter is particularly interesting as it r esults in a significant change of the total protein change from +4 to +1. 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. NAMD is a highly scalable molecular dynamics simulations code. Our past benchmarks on Fusion with 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 on 8 and 32 cores, respectively. We expect at least comparable scaling performance on Blues. Project URL: http://www.cse.anl.gov/fundamental_interactions/solar_conversion.html Requested allocation: 800000 Q1: 200000 Q2: 200000 Q3: 200000 Q4: 200000 Justification: As described above, we have used the NAMD code extensively previously in a Fusion program with Oleksandr Kokhan as PI on the project "biomimetic_systems". Our past benchmarks on Fusion with 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 on 8 and 32 cores, respectively. We expect at least comparable scaling performance on Blues The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System