Paraphrasing Douglas Adams, cells are "big ... vastly, hugely, mind-bogglingly big"
—
especially when looked at it in atomistic detail. Telling the story of a cellular process often requires a multitude of scales, spanning electronic, atomic, protein, and organelle sized structures before integrating them into an entire cell. The story of how light powers life is one such story
—
in fact, the oldest story of humanity, now retold in a multi-scale atoms-to-cell computational model built upon a decade-long experimental collaboration.
Visualization of such cell-scale models is recently made possible by the addition of instancing support for molecules into VMD.
The new VMD instancing feature permits molecular scientists to create an arbitrary number of graphical copies or instances of user-selected molecular components, proteins, or entire complexes, thereby facilitating cell-scale visualization. The set of instances to be visualized are described by assigning a set of transformation matrices and graphical representations that VMD uses to the complete visualization.
VMD's instancing capabilities are illustrated in the cover design of
Molecular Mechanisms of Photosynthesis
(Wiley, 2021)
by
Robert Blankenship.
The structural model
employed for the cover is that of a low light adapted
Rba. sphaeroides cell featuring 985 chromatophores
with a radial distribution consistent with cryoEM tomography.
Combined with
award winning advances in multi-scale simulation techniques,
these visualization methods enable the quantification of cellular processes
from individual atoms to organizing principles.
The Future of Biomolecular Modeling
A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee.
Read more
VMD Illuminated
The software program VMD is a visualization and analysis tool that goes where no microscope can. Trace the trajectory of its development over the last two decades. By Lisa Pollack.
Read more
Announcements
Research Programmer Position AvailableCongratulations to Defne Gorgun for securing Beckman Institue fellowshipCongratulations to Moeen Meigooni for securing biophysics fellowship @ UOFIBiology Simulations to Receive a Big Boost from ORNL's Frontier Exascale Computer
Seminars
Remembering Klaus Schulten
Recent Publications All Publications
- py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD. J. Chem. Theory Comput. 2022.
- Phthalate monoesters act through peroxisome proliferator-activated receptors in the mouse ovary. Reproductive Toxicology, 110:113-123. 2022.
- Experiences porting NAMD to the Data Parallel C++ programming model. Association for Computing Machinery, IWOCL22. 2022.
- ANARI: A 3D Rendering API Standard. Comput. Sci. Eng. 2022.
- Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins. Chem. Sci., 13:4150-4169. 2022.
- Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. J. Clin. Invest., e154891. 2022.
- Use of Microscale Thermophoresis to Measure Protein-Lipid Interactions. J. Vis. Exp., 180:e60607. 2022.
- Microscopic Characterization of the Chloride Permeation Pathway in the Human Excitatory Amino Acid Transporter 1. ACS Chem. Neurosci., 13:776-785. 2022.
- Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. J. Biol. Chem., 298:101676. 2022.
- A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls. J. Chem. Theory Comput., 18:1406-1422. 2022.