One of the primary sources of energy to earth life is the sun energy and photosynthesis is the first fundamental step in the ecosystem to make this energy available to other life forms. It is therefore crucial to study photosynthesis in various scale to understand the archecture and process of this robust energy supply method. Researchers in the Theoretical and Computational Biophysics Group are particularly interested in studying this bioenergetic process with atomic details, including the archecture of pigment-protein units in the membrane level, the overall functioning process from exciation to ATP in PSU of purple bacteria and short-time dynamics of excitation migration under various protein environments.
Most life on Earth is powered directly or indirectly by harvesting the energy of sunlight. Plants and bacteria convert solar energy into chemical energy, which is used, ultimately, for producing food. Compared to the complicated energy harvesting apparatus of plants, the primitive purple bacteria display a far simpler instance of photosynthesis. In purple bacteria, the energy harvesting processes are performed by a spherical vesicle, called the chromatophore, featuring hundreds of cooperating proteins assembled together on a membrane. A team of experimental and computational scientists have recently reported the overall efficiency of this energy conversion process based on a structural model. The energy conversion process in the chromatophore shows that the bacteria adapted to efficiently harvest light at the dim light conditions typical of their habitat. At bright light conditions, the bacteria instead dissipate the harvested energy to protect against damage. A step-by-step summary of the energy conversion processes in the chromatophore can be viewed in a video produced by high performance computing (YouTube video; discussed further in article 1 and article 2.) More on energy harvesting by bacteria can be found on our photosynthesis page and the
chromatophore page.
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing.
John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, Joao V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. Parallel Computing, 55:17-27, 2016.
Visualization of energy conversion processes in a light harvesting organelle at atomic detail.
Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy, Ivan Teo, Kirby L. Vandivort, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014. (4 pages).
Self-assembly of photosynthetic membranes.
Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih Sener, Johan Strumpfer, and Klaus Schulten. ChemPhysChem, 11:1154-1159, 2010.
A chemical compass for bird navigation.
Ilia A. Solov'yov, P. J. Hore, Thorsten Ritz, and Klaus Schulten. In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio, editors, Quantum Effects in Biology, chapter 10, pp. 218-236. Cambridge University Press, 2014.
