The simulation, analysis, and visualization of large photosynthetic membranes are replete with computational challenges due to the large size of these systems, the necessity for both quantum and classical mechanical modeling approaches, and due to the variety of timescales involved in individual molecular processes. The combination of experimental imaging, state-of-the-art molecular dynamics simulation, and high-fidelity visualization provides researchers with a powerful “computational microscope” that permits viewing of the dynamics of molecular processes with atomic detail. The energy conversion processes are summarized schematically in (H) (see Sec. The chromatophores densely populate the cell under low-light conditions, occasionally forming vesicular connections with one another (G) (the chromatophore shown in (A) is indicated by a circle). A minimal subunit of the four aforementioned primary protein groups is shown in (F) (proteins in cartoon representation same colors as in B-E).
In order of energy utilization, these proteins are: the LH2 (B) and LH1-RC-PufX (C) complexes for light capture, electronic excitation transfer, and charge separation the bc 1 complex (D) for generation of a proton gradient across the vesicle membrane and ATP synthase (E) for using the resultant proton gradient for ATP production (B, C, D: top view, i.e. sphaeroides (A) harvests solar energy for ATP production via a network of hundreds of cooperating proteins (see accompanying movies). The chromatophore from the purple bacterium Rba.
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The study of the chromatophore and its component proteins has been the subject of simulation efforts for three decades, driving software development and new methodologies in collaboration with experimental studies (see Sec. In the case of purple photosynthetic bacteria, the photosynthetic apparatus is the so-called chromatophore, now structurally known at atomic detail the chromatophore is a spherical membrane of 50 nm inner diameter, comprising over a hundred proteins and ~3,000 bacteriochlorophylls for photon absorption (see Fig. Light-harvesting in biological cells poses substantial computational challenges, since it involves many overlapping time and length scales, ranging from electronic excitation transfer on a picosecond timescale to diffusion events on a millisecond timescale.
Studies of natural light-harvesting systems provide insights for the engineering of bio-hybrid and artificial solar devices and may contribute substantially to the current 15 TW power demand of our civilization by better harvesting Earth’s 120,000 TW average solar irradiance. Nature has evolved devices that utilize quantum mechanics for conversion of light energy into stable chemical energy, which can be stored and consumed by living cells to power physiological processes. Solar energy, directly or indirectly, powers almost all life on Earth through photosynthesis. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movies, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers. The movies are the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We present, in two accompanying movies, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. Once you’ve created your ideal image, Canvas lets you import your work into Adobe Photoshop so you can continue to refine it or combine with other artwork.The cellular process responsible for providing energy for most life on Earth, namely photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. You can start from scratch, or get inspired by one of the sample scenes. Paint on different layers to keep elements separate. Canvas has nine styles that modify the look and feel of a painting and fifteen different materials ranging from sky and mountains to river and stone.
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