INVITED TALKS:
  • Day of the living cell: Supercomputers reveal molecular design principles of photosynthesisGPU Technology Conference 2020 (03/26/2020)
  • Recipies for Discovery with VMD” SBGrid Consortium meeting, Harvard Medical School, Boston, MA, (01/28/2020)
  • How does self look like?” Scialog meeting by the Research Corporation, Tucson, AZ (10/11/2019)
  • Hybrid modeling of phenotypes from atoms” Chemistry, Georgia State University, Atlanta, GA (10/03/2019)
  • Molecular dynamics of Rotary Motor Mechanisms”, Bioenergetics Gordon Research Conference, Andover, NH, (06/03/2019)
  • Flexible Fitting into electron densities of heterogenous local resolution - the pros and cons of MD-based refinements”, SBGrid/NE-CAT Mini-symposium: Low-resolution model building in EM and X-ray crystallography, Harvard Medical School, Boston, MA, (03/20/2019)
  • Motormaker – A High-throughput Computational Evolution and Design tool for Synthetic Motors”, NSF Innovation laboratory, DC, (12/21/2018)
  • “Energy Metabolism in a Photosynthetic Organelle: From Proteins to Networks” ab initio, Biophest, University of Arizona, Tuscon, AZ (05/05/2018)
  • “Biomolecular Structure Determination with NAMD: Computational Cryo-EM on Titan”, OLCF Users Meeting, Oakridge National Research Laboratory, TN (05/16/2018)
  • “Free energy Calculations of molecular Motors: Chemomechanical Coupling in V-type ATPases”, University of Wisconsin, Miluwakee, WI (06/28/2018)
  • MD-Based Refinement and Validation at Sub-5 Å Resolution, Keystone Meeting, Lake Tahoe, CA (02/07/2018)
  • Femtosecon X-ray Scattering of Membrane Proteins with a Free Electron Laser, National BioXFEL Meeting, New Orleans, LA (02/13/2018)
  • Simulating biological energy transfer with NAMD: The Source, the sink and everything that happens in between. OLCF Users Meeting, Oak Ridge National Laboratory, May 2017.
  • How hexameric protein-protein interfaces harnesses energy within molecular motors: Chemo-mechanical coupling in V-type ATPases. Gordon Research Conference in Bioenergetics, Proctor Academy, NH, June 2017.
  • Structural Systems Biology of Respiratory Electron Transfer. School of Molecular Sciences, Arizona State University, February, 2017.
  • Free Energy Calculation of Molecular Motors: Chemomechanical Coupling in V-type ATPases, Telluride Free Energy Conference, Telluride, CO (7/11/2017)
  • Atom-Resolved View of a Cell Organelle on a Computational Microscope, 254th American Chemical Society National Meeting, Washington, DC (8/22/2017)
  • MD-Based Refinement and Validation at Sub-5 Å Resolution, Joint Cryo-EM Challenge, Stanford, CA (8/7/2017)
  • Energy Metabolism in Purple Bacteria: From Proteins to Networks ab initio, Cold Spring Harbor Symposium on Plant Genomes and Biotechnology, Cold Spring Harbor Laboratory, NY (11/30/2017)
  • Computer simulations of biology energy transfer: Proteins to complexes to cell organelle, jointly by U. Texas schools in Dallas (2016).
  • Biology through the computational microscope: One atom at a time, U. Louisville (2015).
ORAL PRESENTATIONS:
  • SBGrid Quo Vadis: Advanced Crystallography  “Structure Modeling and Data-guided Molecular Dynamics Simulations: The Flexible Fitting Paradigm” Harvard Medical School (2016).
  • DOE PARC All-hands Meeting Computer simulations of biology energy transfer: Proteins to complexes to cell organelle” Washington U. Saint Louis (2016).
  • Beckman Institute Director’s SeminarHow hexameric protein-protein interfaces harness energy within molecular motors: Revisiting ATP synthase” UIUC (2016).
  • 5th Annual Meeting of Membrane Protein Structure Dynamics Consortium "xMDFF refimenets of synthetic abiological molecules: macromolecular crystallography to the rescue of small-molecule structure determination", U. Chicago (2015).
  • Special Lecture on Simulation, Modeling, and Computation in Biophysics "Molecular Machines: Computational studies of ATP Synthase", U. Chicago (2015).
  • Keystone Conference on Hybrid Methods "Structure Determination with Data-Guided Molecular Dynamics: the flexible fitting paradigm", Lake Tahoe (2015).
  • Student Selected Nanohour Seminar Series, “Life on the Nanoscale Through a Computational Microscope”, Beckman Institute, UIUC (2014).
  • 4th Annual Meeting of Membrane Protein Structure Dynamics Consortium, “Resolution of Membrane Protein Structures with Data Guided MD Simulations: the Curious Cases of CiVSP and YidC, U. Chicago (2014).
  • 58th Biophysical Society, xMDFF: MDFF for low-resolution X-ray crystallography, San Fransisco (2014).
  • 246th American Chemical Society National Meeting, “Multiscale modeling of supramolecular assemblies for nanomedical sciences: Applications in computer-aided vaccine design Indianapolis (2013).
  • 3rd Annual Meeting of Membrane Protein Structure Dynamics Consortium, “xMDFF – Molecular Dynamics Flexible Fitting of Low Resolution X-ray Structures, U. Chicago (2013).
  • Physical Chemistry Seminar, “Multiscale Modeling of Macromolecular Assemblies: An Atomic-scale Perspective on Viruses and Vaccines”, IUB (2012).
  • Theoretical and Computational Biophysics Seminar, “Macromolecular Assemblies Understood via Coupled Evolution of Coarse-Grained and Atomistic Variables”, UIUC (2012).
  • 105th Statistical Mechanics Conference, Short talk on “Deductive Multiscale Analysis”, Rutgers University (2011).
  • Physics Colloquium, “Understanding Nanosystems the Multiscale Way: Applications to Macromolecular Assemblies and Quantum Nanosystems”, IUPUI (2011).
  • Physical Chemistry Seminar, “Electrostatics of Bionanosystems: The Multiscale way”, IUB (2010).
 PUBLIC LECTURE:
  • Chambana Science Café, “Biology on a Computer: Unraveling the Mysteries of Life Atom-by-Atom”, Champaign Public Library, Champaign (2013).

 

molecular-motors-umw.pdf62.45 MB
olcf-user-meeting-2018.pdf25.93 MB
keystone.pdf4.36 MB
coldspringharbor-singharoy.pdf37.48 MB
phillips-ab-gputech2020-s21500.pdf58.39 MB