Literature DB >> 34824485

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales.

Stuart Levy1, John E Stone2, Melih Sener2, A J Christensen1, Barry Isralewitz2, Robert Patterson1, Kalina Borkiewicz1, Jeffrey Carpenter1, C Neil Hunter3, Zaida Luthey-Schulten4, Donna Cox2.   

Abstract

Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. A visualization depicting this process, based on multiscale computational models from electronic to cell scales, is presented in the form of an excerpt from the fulldome show Birth of Planet Earth. This accessible visual narrative shows a lay audience, including children, how the energy of sunlight is captured, converted, and stored through a chain of proteins to power living cells. The visualization is the result of a multi-year collaboration among biophysicists, visualization scientists, and artists, which, in turn, is based on a decade-long experimental-computational collaboration on structural and functional modeling that produced an atomic detail description of a bacterial bioenergetic organelle, the chromatophore. Software advancements necessitated by this project have led to significant performance and feature advances, including hardware-accelerated cinematic ray tracing and instanced visualizations for efficient cell-scale modeling. The energy conversion steps depicted feature an integration of function from electronic to cell levels, spanning nearly 12 orders of magnitude in time scales. This atomic detail description uniquely enables a modern retelling of one of humanity's earliest stories-the interplay between light and life.

Entities:  

Year:  2020        PMID: 34824485      PMCID: PMC8612599          DOI: 10.1016/j.parco.2020.102698

Source DB:  PubMed          Journal:  Parallel Comput        ISSN: 0167-8191            Impact factor:   0.986


  26 in total

Review 1.  Proton-coupled electron transfer at the Qo-site of the bc1 complex controls the rate of ubihydroquinone oxidation.

Authors:  Antony R Crofts
Journal:  Biochim Biophys Acta       Date:  2004-04-12

2.  Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle.

Authors:  Melih K Sener; John D Olsen; C Neil Hunter; Klaus Schulten
Journal:  Proc Natl Acad Sci U S A       Date:  2007-09-25       Impact factor: 11.205

3.  Accelerating molecular modeling applications with graphics processors.

Authors:  John E Stone; James C Phillips; Peter L Freddolino; David J Hardy; Leonardo G Trabuco; Klaus Schulten
Journal:  J Comput Chem       Date:  2007-12       Impact factor: 3.376

4.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

5.  Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering.

Authors:  John E Stone; William R Sherman; Klaus Schulten
Journal:  IEEE Int Symp Parallel Distrib Process Workshops Phd Forum       Date:  2016-08-04

Review 6.  Förster energy transfer theory as reflected in the structures of photosynthetic light-harvesting systems.

Authors:  Melih Şener; Johan Strümpfer; Jen Hsin; Danielle Chandler; Simon Scheuring; C Neil Hunter; Klaus Schulten
Journal:  Chemphyschem       Date:  2011-02-25       Impact factor: 3.102

7.  Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

Authors:  Abhishek Singharoy; Christophe Chipot; Mahmoud Moradi; Klaus Schulten
Journal:  J Am Chem Soc       Date:  2016-12-23       Impact factor: 15.419

8.  Connectivity of centermost chromatophores in Rhodobacter sphaeroides bacteria.

Authors:  Jade M Noble; Johann Lubieniecki; Benjamin H Savitzky; Jürgen Plitzko; Harald Engelhardt; Wolfgang Baumeister; Lena F Kourkoutis
Journal:  Mol Microbiol       Date:  2018-09-15       Impact factor: 3.501

9.  Membrane organization of photosystem I complexes in the most abundant phototroph on Earth.

Authors:  C MacGregor-Chatwin; P J Jackson; M Sener; J W Chidgey; A Hitchcock; P Qian; G E Mayneord; M P Johnson; Z Luthey-Schulten; M J Dickman; D J Scanlan; C N Hunter
Journal:  Nat Plants       Date:  2019-07-22       Impact factor: 15.793

10.  Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides.

Authors:  Michaël L Cartron; John D Olsen; Melih Sener; Philip J Jackson; Amanda A Brindley; Pu Qian; Mark J Dickman; Graham J Leggett; Klaus Schulten; C Neil Hunter
Journal:  Biochim Biophys Acta       Date:  2014-02-13
View more
  1 in total

1.  #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.

Authors:  Abigail Dommer; Lorenzo Casalino; Fiona Kearns; Mia Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo; Sofia Oliveira; Clare Morris; Anthony Bogetti; Anda Trifan; Alexander Brace; Terra Sztain; Austin Clyde; Heng Ma; Chakra Chennubhotla; Hyungro Lee; Matteo Turilli; Syma Khalid; Teresa Tamayo-Mendoza; Matthew Welborn; Anders Christensen; Daniel G A Smith; Zhuoran Qiao; Sai Krishna Sirumalla; Michael O'Connor; Frederick Manby; Anima Anandkumar; David Hardy; James Phillips; Abraham Stern; Josh Romero; David Clark; Mitchell Dorrell; Tom Maiden; Lei Huang; John McCalpin; Christopher Woods; Alan Gray; Matt Williams; Bryan Barker; Harinda Rajapaksha; Richard Pitts; Tom Gibbs; John Stone; Daniel Zuckerman; Adrian Mulholland; Thomas Miller; Shantenu Jha; Arvind Ramanathan; Lillian Chong; Rommie Amaro
Journal:  bioRxiv       Date:  2021-11-15
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.