A5067249389- Protein Structure and Dynamics
- Force Microscopy Techniques and Applications
- Photosynthetic Processes and Mechanisms
- Photoreceptor and optogenetics research
- Mitochondrial Function and Pathology
- ATP Synthase and ATPases Research
- Cellular Mechanics and Interactions
- Molecular Junctions and Nanostructures
- Advanced Electron Microscopy Techniques and Applications
- Bacteriophages and microbial interactions
- Spectroscopy and Quantum Chemical Studies
- Enzyme Structure and Function
- Cardiomyopathy and Myosin Studies
- RNA and protein synthesis mechanisms
- Mechanical and Optical Resonators
- Advanced Fluorescence Microscopy Techniques
- Cell Adhesion Molecules Research
- Advanced biosensing and bioanalysis techniques
- Biochemical and Molecular Research
- Mass Spectrometry Techniques and Applications
- Chemical Synthesis and Analysis
- Advanced Data Storage Technologies
- Scientific Computing and Data Management
- Light effects on plants
- Genomics and Phylogenetic Studies
University of Illinois System
2014-2023
University of Illinois Urbana-Champaign
2000-2021
Urbana University
2014
University of Washington
1999-2003
The 10th type III module of fibronectin possesses a β -sandwich structure consisting seven -strands (A–G) that are arranged in two antiparallel sheets. It mediates cell adhesion to surfaces via its integrin binding motif, Arg 78 , Gly 79 and Asp 80 (RGD), which is placed at the apex loop connecting F G. Steered molecular dynamics simulations tension applied protein’s terminal ends reveal -strand G first break away from on forced unfolding whereas remaining fold maintains structural...
Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures large biomolecular complexes. Evaluating quality-of-fit obtained hybrid is computationally demanding, particularly in context a multiplicity structural conformations that must be evaluated. Existing tools analysis visualization have previously targeted small are too slow to used interactively complexes...
This paper introduces Cybershuttle, a new type of user-facing cyberinfrastructure that provides seamless access to range resources for researchers, enhancing their productivity. The Cybershuttle Research Environment is built on open source Apache Airavata software and uses hybrid approach integrates locally deployed agent programs with centrally hosted middleware. enables end-to-end integration computational science engineering research across resources, including users' local centralized...
F(1)-ATPase is the catalytic domain of F(1)F(o)-ATP synthase and consists a hexameric arrangement three noncatalytic α β subunits. We have used unbiased molecular dynamics simulations with total simulation time 900 ns to investigate dynamic relaxation properties isolated β-subunits as step toward explaining function integral F(1) unit. To this end, we simulated open (β(E)) closed (β(TP)) conformations under conditions for up 120 each using several samples. The confirm that nucleotide-free...
Pataskala molecular dynamics simulations provide a powerful tool for probing the of cellular processes at atomic and nanosecond resolution not achievable by experimental methods alone. Extraction details about bimolecular from terabytes simulation output requires user-extensible analysis visualization tools. trajectories are so large that it is now necessary to perform many tasks formerly handled off-site computational facilities in-place on supercomputer itself. We report ongoing progress...
We report the first 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from purple bacterium, which reveals cascade energy-conversionsteps culminating into generation ATP sunlight. Molecular dynamics simulations ofthis elucidate how integral-membrane complexes influences local curvature as ployto tune photoexcitation pigments. Brownian small-molecules within probe mechanisms directional charge transport under various pH and salinity conditions....
Over the past 18 months, need to perform atomic detail molecular dynamics simulations of SARS-CoV-2 virion, its spike protein, and other structures related viral infection cycle has led biomedical researchers worldwide urgently seek out all available biomolecular structure information, appropriate modeling simulation software, necessary computing resources conduct their work. We describe our experiences from several COVID-19 research collaborations challenges they presented in terms software...
This visualization of the quantum-mechanical process photosynthesis involved combining structural models from atomic, protein, organelle, and cell scales. We descend into a prehistoric hot spring, revealing primitive bacteria which use an early form to turn sunlight chemical energy in structures called chromatophores. fulldome animation follows through progressively more stable forms: captured photon, electronic excitation, pumped protons, finally, synthesis ATP molecules. The team used VMD,...
The forced unfolding of fibronectin's tenth type III module (FnIII/sub 10/) was simulated by steered molecular dynamics (SMD) indicating that mechanical tension applied to the module's termini renders its RGD loop inaccessible cell surface integrins. FnIII/sub 10/ possesses a /spl beta/-sandwich motif consisting seven beta/-strands (A-G) are arranged in two antiparallel sheets with peptide sequence located at apex FG loop. Computer simulations now reveal beta/-strand G separates from an...