Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail - Brief TCBG UIUC 2015-03-05 | 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. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movie is the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movie, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers.A longer version of this video can be viewed at: http://youtu.be/cUHxfpPkN6ESC '14 Paper: http://sc14.supercomputing.org/sites/all/themes/sc14/files/archive/sci_vis/sci_vis_pages/svs115.htmlVisualization of energy conversion processes in a light harvesting organelle at atomic detail. Sener et al. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014.
Theoretical and Computational Investigations of Membrane Associated Pathology - Andres S. Arango TCBG UIUC 2023-05-15 | Doctoral defense presentation of TCBG member Andres Santiago Arango Isaza in the Center for Biophysics and Quantitative Biology at the University of Illinois at Urbana-Champaign. Doctoral advisor: Emad TajkhorshidTitle: Theoretical and Computational Investigations of Membrane Associated Pathology
Molecular Mechanism of Capsid Disassembly in Hepatitis B Virus TCBG UIUC 2021-11-29 | Worked published on PNAS September 7, 2021 118 (36) e2102530118; doi.org/10.1073/pnas.2102530118
Winner: Best Scientific Visualization SC19; Primary energy source of life from Birth of Planet Earth TCBG UIUC 2019-12-16 | Winner: Best Visualization Award, Scientific Visualization & Data Analytics Showcase, SC19 conference. "An accessible visual narrative for the primary energy source of life from the fulldome show Birth of Planet Earth" (Accompanying paper: sc19.supercomputing.org/proceedings/sci_viz/sci_viz_files/svs110s2-file1.pdf)Conversion of sunlight into chemical energy, namely photosynthesis, is the primary energy source of life on Earth. An explanatory visualization depicting this process 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.https://www.ks.uiuc.eduhttp://avl.ncsa.illinois.eduspitzcreativemedia.com
Visualization and analysis with VMD — David Winogradoff TCBG UIUC 2018-09-26 | Computational Biophysics Workshop - Urbana, September 24-26, 2018
Visualization and analysis with VMD — David Winogradoff TCBG UIUC 2018-09-26 | Computational Biophysics Workshop - Urbana, September 24-26, 2018
Multi-resolution Simulation of DNA nanostructures : Chris Maffeo TCBG UIUC 2018-09-25 | Computational Biophysics Workshop - Urbana, September 24-26, 2018
DNA Origami Design with CaDNAno ToolKit (CTK) - Turel Aksel TCBG UIUC 2018-09-25 | Computational Biophysics Workshop - Urbana, September 24-26, 2018
DNA Origami Design with CaDNAno ToolKit (CTK) - Turel Aksel TCBG UIUC 2018-09-25 | Computational Biophysics Workshop - Urbana, September 24-26, 2018
Introduction to MD simulations of DNA systems — Aleksei Aksimentiev TCBG UIUC 2018-09-24 | Computational Biophysics Workshop - Urbana, September 24-26, 2018
Introduction to Cadnano — Shawn Douglas TCBG UIUC 2018-09-24 | Computational Biophysics Workshop - Urbana, September 24-26, 2018
Exploring Complex Reaction Pathways Part II - Mahmoud Moradi TCBG UIUC 2018-09-14 | Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Exploring Complex Reaction Pathways Part I - Mahmoud Moradi TCBG UIUC 2018-09-14 | Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Test Stream TCBG UIUC 2018-09-14 | Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Accelerating Convergence of Free-Energy Calculation with Replica Exchange Solute Tempering,Wei Jiang TCBG UIUC 2018-09-13 | Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Specialized Algorithms for Enhanced Ergodic Sampling, Chris Chipot TCBG UIUC 2018-09-13 | Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Specialized Algorithms for Enhanced Ergodic Sampling, Chris Chipot TCBG UIUC 2018-09-13 | Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Specialized Algorithms for Enhanced Ergodic Sampling, Chris Chipot TCBG UIUC 2018-09-13 | Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
TCBG UIUC Live Stream TCBG UIUC 2018-09-12 | Designing, Implementing and Optimizing Collective Variables in VMD and NAMD, Jérôme Hénin - Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Geometrical Free-Energy Methods: Strengths and Limitations, Jérôme Hénin TCBG UIUC 2018-09-12 | Geometrical Free-Energy Methods: Strengths and Limitations, Jérôme Hénin - Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Mechanism of Bacterial Adhesion in Staphylococcal Infection Revealed with Atomic detail TCBG UIUC 2018-03-29 | What makes pathogenic bacteria so persistent? Researchers from the Beckman Institute at the University of Illinois and the University of Munich (LMU) decipher the physical adhesion mechanism of a widespread pathogen virulence factor. Staph infections are caused by staphylococcus bacteria, types of germs commonly found on the skin of healthy individuals. Most of the time, these bacteria cause no problems or result in relatively minor skin infections. However, according to the Mayo Clinic, septicemia (also known as blood poisoning) can occur when staph bacteria enter a person’s bloodstream. The bacteria can travel to locations deep within the body causing infections. Particularly vulnerable regions are medical devices such as artificial joints or cardiac pacemakers. Not surprisingly, staph infections are the leading cause of healthcare-related, so called nosocomial infections.Read more:http://science.sciencemag.org/content/359/6383/1527
NAMD goes quantum TCBG UIUC 2018-03-26 | The Computational Microscope got new lenses for subatomic resolution. Our center used it to investigate the setting of the genetic code. Using a combination of Classical and Quantum Mechanics - commonly known as QM/MM - researchers worldwide can now investigate biomolecular interactions with a higher level of accuracy using NAMD and VMD, two of the most popular molecular dynamics and visualization software.Read more:nature.com/articles/nmeth.4638https://news.illinois.edu/view/6367/630024
Contact Analysis with PyContact TCBG UIUC 2018-01-31 | This demo video shows how our tool, PyContact, can be used to analyze contacts in molecular dynamics simulation trajectories in anintuitive and comprehensive manner. For more information, please visit: http://www.ks.uiuc.edu/Research/pycontact/ or github.com/maxscheurer/pycontact
Applications of Enhanced Sampling and Free Energy Calculation Methods - Emad Tajkhorshid TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Applications of Enhanced Sampling and Free Energy Calculation Methods Emad Tajkhorshid:http://csbmb.beckman.illinois.edu/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day1_EmadTajkhorshid.pdf
Exploring Complex Reaction Pathways I - Mahmoud Moradi TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Exploring Complex Reaction Pathways I presented by Mahmoud Moradi:http://www.comp.uark.edu/~moradi/members.htmlPresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day5_MahmoudMoradi.pdf
Specialized Algorithims for Enhanced Ergodic Sampling - Chris Chipot TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Specialized Algorithims for Enhanced Ergodic Sampling Chris Chipot:http://www.ks.uiuc.edu/~chipot/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day2_ChrisChipot.pdf
Accelerating Convergence of Free Energy Calculations - Wei Jiang TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Accelerating Convergence of Free Energy Calculations Wei Jiang:alcf.anl.gov/staff-directory/wei-jiangPresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day4_WeiJiang.pdf
Introduction to Free Energy Calculations - Chris Chipot TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to Free Energy Calculations Chris Chipot:http://www.ks.uiuc.edu/~chipot/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day1_ChrisChipot.pdf
Adaptive Multilevel Splitting Method Isomerization - Laura Lopes TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Adaptive Multilevel Splitting Method Isomerization presented by Laura Lopes:https://cermics.enpc.fr/~silva-ll/contacts_en.htmlPresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day4_LauraLopes.pdf
Designing Implementing and Optimzing Collective Variables in VMD and NAMD - Giacomo Fiorin TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Designing Implementing and Optimzing Collective Variables in VMD and NAMD Giacomo Fiorin:giacomofiorin.github.ioPresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day3_GiacomoFiorin.pdf
Constant pH Molecular Dynamics with NAMD - Brian Radak TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Constant pH Molecular Dynamics with NAMD Brian Radak:alcf.anl.gov/staff-directory/brian-k-radakPresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day2_BrianRadak.pdf
Geometrical Free Energy Methods - Giacomo Fiorin TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Geometrical Free Energy Methods Giacomo Fiorin:giacomofiorin.github.ioPresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day3_GiacomoFiorin.pdf
Exploring Complex Reaction Pathways II - Mahmoud Moradi TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Exploring Complex Reaction Pathways II presented by Mahmoud Moradi:http://www.comp.uark.edu/~moradi/members.htmlPresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day5_MahmoudMoradi.pdf
Transition Path Sampling and Free Energy Calculations - Chris Chipot TCBG UIUC 2018-01-19 | Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation - Urbana, September 25-29, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Transition Path Sampling and Free Energy Calculations Chris Chipot:http://www.ks.uiuc.edu/~chipot/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017b/slides/TCBG_Urbana_2017_Day2_ChrisChipot.pdf
Accurate Calculation of Protein Ligand Binding Energies - Chris Chipot TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Accurate Calculation of Protein Ligand Binding Energies presented by Chris Chipot:http://www.ks.uiuc.edu/~chipot/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/FreeEnergy.Introduction.pdf
Introduction to Classical Force Fields: Topology, Parameters, and Structure Files - Emad Tajkhorshid TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to Classical Force Fields: Topology, Parameters, and Structure Files presented by Emad Tajkhorshid:http://csbmb.beckman.illinois.edu/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/Day3-ForceFieldParameters.pdf
Introduction to Force Field Toolkit - Christopher Mayne TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to Force Field Toolkit presented by Christopher Mayne:http://www.ks.uiuc.edu/~maynePresentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/2017_fftk-nih-workshop-urbana.pdf
Introduction to Modeling and Simulation of DNA Systems - Alek Aksimentiev TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to Modeling and Simulation of DNA Systems presented by Alek Aksimentiev:http://bionano.physics.illinois.edu/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/AlekAksimentiev_DNA_Urbana21_2017.pdf
Introduction to Molecular Dynamics Flexible Fitting - Ryan McGreevy TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to Molecular Dynamics Flexible Fitting presented by Ryan McGreevy:http://www.ks.uiuc.edu/~ryanmcgreevy/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/Ryan_McGreevy_MDFF_Urbana21_2017.pdf
Introduction to Simulations of Bacterial Cells - Zan Luthey-Schulten TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to Simulations of Bacterial Cells presented by Zan Luthey-Schulten:http://www.scs.uiuc.edu/chem/faculty/Zaida_Luthey_Schulten.html
Introduction to QwikMD and Amazon Cloud - João Ribeiro TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to QwikMD and Amazon Cloud presented by João Ribeiro:http://www.ks.uiuc.edu/~jribeiro/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/UsingAWS.pdf
Visualizing Biomolecules in VMD - John Stone TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Visualizing Biomolecules in VMD presented by John Stone:http://www.ks.uiuc.edu/~johns/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/VMD-UrbanaSpring2017.pdf
A General Overview of Free Energy Methods - Chris Chipot TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/A General Overview of Free Energy Methods presented by Chris Chipot:http://www.ks.uiuc.edu/~chipot/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/FreeEnergy.Introduction.pdf
Introduction to Molecular Dynamics with NAMD - Emad Tajkhorshid TCBG UIUC 2017-06-13 | Computational Biophysics Workshop - Urbana, April 17-21, 2017For more information please see:http://www.ks.uiuc.edu/Training/Workshop/http://www.ks.uiuc.edu/Training/Tutorials/Introduction to Molecular Dynamics with NAMD presented by Emad Tajkhorshid:http://csbmb.beckman.illinois.edu/Presentation slides: http://www.ks.uiuc.edu/Training/Workshop/Urbana2017a/slides/Day1-EmadTaj-MD-Introduction.pdf
stalk rotation of V-type ATPase TCBG UIUC 2017-06-02 | Zoomed in view of stalk rotation in V-type ATPases. The research reported has been supported by the National Science Foundation through Grants MCB1616590 and PHY1430124, and the National Institute of Health through Grants 9P41GM104601 and R01-GM067887-11. (Credit: Barry Isralewitz, University of Illinois at Urbana-Champaign)Publication: "Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V-Type ATPases" Authors: Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi , and Klaus SchultenJournal: Journal of American Chemical Society (http://pubs.acs.org/doi/full/10.1021/jacs.6b10744)
Rotatory catalysis in V-type ATPase TCBG UIUC 2017-06-02 | ATP hydrolysis-driven rotation of the central stalk in the V-type ATP synthase of the bacteria Enterococcus hirae depicts chemo-mechanical coupling of the molecular motor. These simulations were carried out on the Titan supercomputer using NAMD2.12. Visualization and movie rendering were completed on VMD1.9.3. The research reported has been supported by the National Science Foundation through Grants MCB1616590 and PHY1430124, and the National Institute of Health through Grants 9P41GM104601 and R01-GM067887-11. (Credit: Barry Isralewitz, University of Illinois at Urbana-Champaign)Publication: "Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V-Type ATPases" Authors: Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi , and Klaus SchultenJournal: Journal of American Chemical Society (http://pubs.acs.org/doi/full/10.1021/jacs.6b10744)
Developing a Complete In Silico Model of a Minimal Cell TCBG UIUC 2016-12-04 | This video illustrates the vision of the Center in developing a complete in silico model of a minimal cell. It was submitted as part of the Center's collaborative application to the MacArthur Foundation's 100&Change program. In collaboration with geneticists and microscopists, the Center will leverage its large-scale modeling software and expertise to completely describe a 400 nm cell on all time and length scales, helping to usher in a new era in biomedicine.Materials taken from Center work or collaborators, except for the Biochemical Pathways poster (created by Dr. Gerhard Michal; electronic version: © 2014 F. Hoffmann-La Roche Ltd).
HIV-1 Capsid VR visualization TCBG UIUC 2016-08-09 | Molecular dynamics simulation of an entire HIV-1 capsid, a total of 64 million atom. The immersive visualization shows the ions in yellow (sodium) and cyan (chloride). The simulations were performed in Oakridge's Titan super computer. Movie made by Juan R. Perilla.
Structure determination with cascade MDFF TCBG UIUC 2016-07-25 | New hybrid structure determination methods leveraging the inherent biophysical properties of a biomolecule through molecular dynamics simulations provide accurate and cost-efficient ways of achieving atomic structures from high resolution cryo-EM density maps.
Example VMD VR movie: inside the HIV-1 capsid TCBG UIUC 2016-03-24 | This video is an early example of VR movies that can be produced with the latest versions of the popular molecular visualization program VMD.For best 3-D viewing, use the YouTube player app for your smartphone with a Google Cardboard VR viewer, or similar (g.co/cardboard), and set the video quality to the highest setting that your device can play smoothly.The movie will also play in a standard desktop or tablet web browser, however it will not be shown in stereo 3-D, although you can still use the mouse to rotate the view around you as the movie plays.About the movie:This movie shows the interior of the HIV-1 capsid and solvent bath, but with only 1% of the ions shown in the solvent for ease of viewing.Learn more about the HIV-1 capsid and other retroviruses here:http://www.ks.uiuc.edu/Research/HIVThe omnidirectional stereoscopic ray tracing techniques used for production of this movie are described in our paper: "Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing":http://dx.doi.org/10.1016/j.parco.2015.10.015The movie was rendered a 4096x4096 resolution using an omnidirectional stereoscopic projection, with ambient occlusion lighting and shadows. The movie was produced running VMD in parallel on the Blue Waters Cray XK7 supercomputer at NCSA, U. Illinois, using 256 NVIDIA Tesla K20X GPUs with the TachyonL-OptiX GPU-accelerated ray tracing engine implemented in VMD 1.9.3.For more information about VMD, please visit the VMD home page:http://www.ks.uiuc.edu/Research/vmd/
