The Laboratory of Computational Biology

Richard Pastor and Bernard Brooks

2016-2017


Aug. 24, 2017
"New computational tools at the molecular scale for protein-ligand binding in drug discovery"
Prof. Dušanka Janežič
University of Primorska, Koper, Slovenia




Aug. 18, 2017
"Comparison & optimization of fixed-point charge & polarizable force fields for the simulation of water-alkane systems"
Andreas Krämer
Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany




Aug. 17, 2017
"Exploring protein allostery through systematic perturbation and machine-learning methods"
Prof. Peng Tao
Department of Chemistry, Southern Methodist University




July 27, 2017
"Using the Finite-Temperature String Method to Account for an Ensemble of Pathways"
Joe Persichetti
Pennsylvania State University




July 25, 2017
"Lipids as Pathways for Cellular Oxygen Diffusion: Molecular Simulation Studies"
Prof. Sally Pias
New Mexico Tech




July 6, 2017
"Position-dependent diffusion in and through membranes".
Prof. An Ghysels
Center for Molecular Modeling, Ghent University, Belgium




June 29, 2017
"Sample-based Models of (Altered) Protein Energy Landscapes Reveal much about (Dys)Function"
Prof. Amarda Shehu
Dept. of Computer Science, George Mason University




June 28, 2017
"Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations"
Dr. Juan Perilla
University of Delaware




June 27, 2017
"Comparison of direct simulation and model propagators for oxygen diffusion in membranes"
Ms. Oriana de Vos
Center for Molecular Modeling, Ghent University, Belgium




June 22, 2017
"Investigating the mechanism of ultra-fast energy transfer between Venus oligomers using time-resolved anisotropy, fluorescence correlation spectroscopy, and photon antibunching"
Dr. Youngchan Kim
NIAAA, NIH




June 15, 2017
"Quasiharmonic Analysis of P-T Effects on Local vs Collective Motions in Proteins"
Prof. Toshiko Ichiye
Georgetown University




May 25, 2017
"Estimating the defocus distance for each particle in a cryo-EM micrograph"
David Hurwitz
NCBI, NLM, NIH




May 11, 2017
"QM/MM Studies of Photosystem II and Visual Rhodopsin"
Dr. Victor Batista
Yale University




May 4, 2017
"A Physics-based van der Waals Functional Form for AMOEBA 2.0"
Dr. Joshua Rackers
Washington University in St. Louis




April 26, 2017
"Machine learning in quantum chemistry: the hype and the data. Is it time for the rise of the machines?"
Prof. Adrian Roitberg
University of Florida; Gainesville, Florida




April 25, 2016
"The Art of the Soluble: Predicting Hydration Free Energies and Distribution Coefficients".
Dr. Gerhard König
Department of Theory, Max-Planck-Institut für Kohlenforschung




April 20, 2017
"Free energy calculations: from cavitands to proteins"
Dr. Florentina Tofoleanu
LCB, NHLBI, NIH




April 13, 2017
Protein Binding Sites Dynamics in Drug Discovery
Prof. Dušanka Janežič
University of Primorska, Koper, Slovenia




April 4, 2017
"Finding multiple reaction pathways via global optimization of action"
Dr. Juyong Lee
LCB, NHLBI, NIH




March 30, 2017
"Transport Properties and Hydrodynamics in Coarse-Grained Models".
Andrew Zgorski.
Dept of Physics, University of Delaware.




March 21, 2017
"Development and use of molecular database for optimizing force"
Dr. Karl Kirschner
Bonn-Rhein-Sieg University of Applied Sciences Sankt Augustin, Germany




March 20, 2017
"Force Field Development methods for atomistic and mesoscopic models of soft matter systems"
Prof. Dirk Reith
Bonn-Rhein-Sieg University of Applied Sciences Sankt Augustin, Germany




Feb. 23, 2017
"Structure and mechanical properties of Cement and intermetallic compounds via ab-initio simulations"
Dr. chamila chathuranga dharmawardhana
Georgetown University




Feb. 16, 2017
"Computational Simulation and Design of Organic Photovoltaic Solar Cell".
Dr. Shuqiang Niu
Department of Chemistry, Texas A&M University




Jan. 12, 2017
"Automated Global and Local Optimization Methods for Atomistic Force Field Development"
Dr. Andreas Krämer
Bonn-Rhein-Sieg University of Applied Sciences in Sankt Augustin, Germany




Dec. 29, 2016
"Protein Structure Refinement"
Dr. Qianyi Cheng
Korean Institute for Advanced Studies




Dec. 8, 2016
"Redesigning Drug Design"
Dr. John Chodera
the Memorial Sloan Kettering Cancer Center, New York City, NY




Nov. 22, 2016
"Relative Resolution: A Hybrid Formalism for Fluid Mixtures".
Dr. Aviel Chaimovich
Max Planck Institute for Polymer Research, Mainz, Germany




Nov. 17, 2016
"Energy-Related Applications of Molecular Simulations"
Dr. Isaak Daniels
University of Kansas




Nov. 15, 2016
"AMOEBA 2.0: A first-principles force field for accurate simulation of biomolecules"
Josh Rackers
Washington University in St. Louis




Nov. 10, 2016
"New approaches for binding site and ligand prediction and their use in drug discovery".
Prof. Janez Konc
University of Ljubljana, National Institute of Chemistry, Ljubljana, Slovenia




Oct. 27, 2016
"Enabling long timescale sampling of protein motions".
Prof. Wei Yang
Florida State University




Oct. 20, 2016
"Predicting distribution coefficients in the SAMPL5 blind challenge".
Dr. Gerhard König
Max-Planck Institut for Kohlenforschung, Mulheim an der Ruhr, Germany




Oct. 13, 2016
"Reduction Potential Calculations of FeS Clusters in Thermus thermophilus Respiratory Complex I"
Ms. Kelly Tran
Georgetown University




Sept. 29, 2016
"Astatination of Aryliodonium Salts for alpha immunotherapy "
Dr. Yong Sok Lee
CMM, CIT, NIH




Sept. 22, 2016
"A Recent History of RNA Force Field Analysis and Development"
Dr. Christina Bergonzo
Cheatham Lab, University of Utah




Sept. 15, 2016
"Analytic Hessians for Particle Mesh Ewald electrostatics."
Dr. Andrew Simmonett
LCB, NHLBI, NIH




2015-2016


Aug. 4, 2016
"Folding Mechanisms of Small Proteins GB1 and LB1".
Dr. Qianyi Cheng
Korea Institute for Advanced Study, School of Computational Sciences, Seoul, Korea




July 29, 2016
"An implicit-solvent model with explicit-solvent accuracy: the solvation-layer interface condition (SLIC) approach".
Prof. Jaydeep P. Bardhan
Northeastern University




July 21, 2016
"SSMP: Progress on a Water Model for Computer Simulations of Biomolecules".
Dr. Jocelyn Rodgers and Kelly Tran
Georgetown University




July 14, 2016
"New Developments in CHARMM and Their Applications".
Dr. Milan Hodoscek
National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia




June 30, 2016
"Studies of Lipid-Involved Life-Phenomena: Whole Body, Organ, Cell, and Molecule Levels".
Dr. Kyungreem Han
LCB, NHLBI, NIH




June 23, 2016
"pH-dependent mechanism of sodium-proton transporter NhaA".
Dr. Yandong Huang
University of Maryland School of Pharmacy




Wednesday, June 22, 2016
"Accelerating Polarizable Multipole Free Energy Calculations: Application to Organic Crystal Thermodynamics".
Prof. Michael Schnieders
University of Iowa




June 16, 2016
"Exploring the Bioactive States of Macrocyclic Natural Products: Conformational Analysis, Permeability, and Target Identification".
Dr. Katrina Lexa
Merck




June 9, 2016
"mapping polarizable force fields from the Drude formalism into the multipole and induced dipole formalism".
Dr. Jing Huang
LCB, NHLBI, NIH




June 2, 2016
"Biological assembly of nascent HDL: What is the driving force?".
Prof. Jere Segrest
University of Alabama at Birmingham




May 12, 2016
"Structure and dynamics of apCAM and NCAM cell adhesion molecules".
Dr. Nicolae-Viorel Buchete
UCD School of Physics, Rm 111, Dublin 4, Ireland




April 28, 2016
"Polarizable Force Field for DNA and RNA Based on the Classical Drude Oscillator Model".
Dr. Justin Lemkul
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore




April 14, 2016
"Computing couplings with QM/MMpol models using the Q-Chem/CHARMM interface".
Qiao Zeng
LCB, NHLBI, NIH




April 11, 2016
"Solvation effect on the binding of hydrophilic amino saccharides to cucurbit[7]uril".
Dr. Chang Jun Lee
IBS Center for Self-assembly and Complexity, Korea




April 7, 2016
"Finding a dominant pathway via global action minimization".
Dr. Juyong Lee
LCB, NHLBI, NIH




Wednesday, March 30, 2016
"Quantifying Sampling in Molecular Dynamics Simulations".
Dr. Daniel Roe
Department of Medicinal Chemistry, University of Utah




Monday, March 28, 2016
"Atomistic simulations of biomolecular and polymeric systems in bulk and at interfaces".
Dr. Inchul Yeh
U.S. Army Research Laboratory (ARL)




Thursday, March 24, 2016
"Multidimensional Tunneling in Hydrogen Transfer Reactions".
Dr. Rubén Meana-Pañeda
Department of Chemistry, University of Minnesota




Wednesday, March 23, 2016
"Prediction and evaluation of protein binding sites in combination with molecular dynamics".
Prof. Dušanka Janežič
University of Primorska, Koper, Slovenia




Monday, March 21, 2016
"LIGO's discovery of the gravitational waves".
Dr. Igor Yakushin
Institute for CyberScience, Pennsylvania State University




March 18, 2016 (Friday, Noon)
"The intrinsic structure of fluid interfaces".
Marcello Sega
University of Vienna, Institute of Computational Physics




March 17, 2016
"Introduction to ion channel electrophysiology".
Prof. Bob Rosenberg
Earlham College, Richmond, IN




March 10, 2016
"Isotropic Periodic Sum For Multipole Interactions".
Dr. Xiongwu Wu
LCB, NHLBI, NIH




Feb. 25, 2016
"SAMPL5 recap".
Dr. Bernard R. Brooks
LCB, NHLBI, NIH




Feb. 18, 2016
"Study of lysine pKa shifts in SNase via VMMS Simulation in Explicit Water".
Dr. Xiongwu Wu
LCB, NHLBI, NIH




Feb. 8, 2016
"Compressed Sensing for the Fast Computation of Hessian Matrices in Electronic Structure Calculations".
Jacob Sanders and Thomas Markovich
Harvard University




Feb. 4, 2016
"Enhancing the coevolutionary signal".
Dr. Travis Hoppe
LCP, NIDDK




Jan. 21, 2016
"Generalized Ensemble Simulations to Discuss the Amyloid Fibril Formation".
Naohiro NISHIKAWA
Nagoya University, Japan




Jan. 14, 2016
"Conformational search methods using genetic crossover and development of force fields for protein systems".
Yoshitake Sakae
Nagoya University, Japan




Jan. 7, 2016
"A hybrid extended Lagrangian/self-consistent field scheme for solving classical polarization".
Alex Albaugh
Prof. Teresa Head-Gordon Lab, Dept. of Chemical Engineering, UC Berkeley




Wednesday, Jan. 6, 2016
"Explore the Third Dimension of Quantum Chemistry Calculations".
Dr. Yihan Shao
LCB, NHLBI, NIH/Q-Chem




Dec. 17, 2015
"Interplay between hydrophobic effect and dipole interactions in self-assembly processes".
Prof. Silvina R. Matysiak
Fischell Department of Bioengineering, University of Maryland




Dec. 10, 2015
"Development of Molecular Docking Program and its Application to Host-guest System".
Minkyung Baek
Seoul National University




Dec. 3, 2015
"Proteins Under Pressure: eXtreme Biophysics".
Prof. Toshiko Ichiye
Georgetown University




Nov. 19, 2015
"Comparison of simulations and NMR spectroscopy of sphingomyelin".
Dr. Alexander Sodt
LCB, NHLBI, NIH




Nov. 17, 2015
"Magnesium coordination in phosphate catalytic enzymes".
Dr. Edina Rosta
Department of Chemistry, King's College London




Nov. 12, 2015
"Some lessons from simple free energy simulations".
Dr. Gerhard König
LCB, NHLBI, NIH




Nov. 10, 2015
"Signatures of Molecular Motion in Energy & Biology".
Prof. Ryan Steele
University of Utah




Nov. 5, 2015
"In silico drug discovery: developer's perspective".
Dr. Janez Konc
National Institute of Chemistry, Laboratory for Molecular Modeling, Ljubljana, Slovenia




Oct. 29, 2015
"Simplified Modeling of the Cell Membrane: Lipid Phases and Lipid-Mediated Aggregation".
Dr. Jocelyn Rodgers
Georgetown University




Oct. 15, 2015
"Optimized, analytic induced dipole algorithms".
Dr. Andrew Simmonett
LCB, NHLBI, NIH




Oct. 8, 2015
"Towards a better understanding of electron polarization effects in QM/MM calculations".
Dr. Yihan Shao
LCB, NHLBI, NIH/Q-Chem




Oct. 1, 2015
"The disruptive state of the membrane active antimicrobial peptide piscidin 1 investigated by multi-microsecond all-atom simulations and solid-state NMR: surface defects are favored over stable pores".
Dr. Scott Perrin Jr.
LCB, NHLBI, NIH




Sept. 10, 2015
"Molecular Multipole Models for Water and Biological Macromolecules".
Prof. Toshiko Ichiye
Georgetown University




2014-2015


Aug. 4, 2015
"Computing pKa values in proteins".
Dr. Ernst-Walter Knapp
Department of Biology, Chemistry, Pharmacy, Institute of Chemistry & Biochemistry, Berlin




June 25, 2015
"The VMMS method for Constant pH Simulation in Explicit Water".
Dr. Xiongwu Wu
LCB, NHLBI, NIH




June 11, 2015
"Challenges and recent method developments in constant pH simulations".
Dr. Ana Damjanović
LCB, NHLBI




May 28, 2015
"Modeling the barrier function of mammalian skin in molecular detail".
Dr. Giacomo Fiorin
Temple University, PA




May 21, 2015
"Molecular Dynamic Studies of Interaction of Phospholipid membranes with Dehydroergosterol and Penetrating Peptides".
Dr. Mohsen Pourmousa
LCB, NHLBI, NIH




May 20, 2015
"How lipids mediate tumor suppressor function".
Prof. Arne Gericke
Department of Chemistry and Biochemistry, Worcester Polytechnic Institute




May 14, 2015
"Global Organization of Binding Site Network".
Dr. Juyong Lee
LCB, NHLBI, NIH




May 7, 2015
"Efficient treatment of induced dipoles".
Dr. Andrew Simmonett
LCB, NHLBI, NIH




May 5, 2015
"Studying Hydrogen-Bonded Systems: Modeling and Synergies with Spectroscopy".
Dr. Berhane Temelso
Dept. Chemistry, Bucknell University




April 30, 2015
"Computational investigation of transport mechanisms in AmtB and RhCG ammonium transporter proteins".
Dr. Esam Orabi
Concordia University in Montreal




April 28, 2015
"Condensed phase chemistry with the Effective Fragment Potential method".
Dr. Lyudmila V. Slipchenko
Purdue University




April 23, 2015
"Computational studies of organic electronic materials with DFT methods -- Inherent driving force for charge separation in organic photovoltaics".
Dr. Qin Wu
Brookhaven National Laboratory




April 16, 2015
"Continuum Models for Biomembrane Dynamics".
Dr. Frank Brown
University of California, Santa Barbara, CA




April 14, 2015
"Anisotropy in mechanical properties and diffusion of nanoporous flexible frameworks".
Dr. An Ghysels
Center for Molecular Modeling at Ghent University, Belgium




April 2, 2015
"The value of repetition: modeling studies of pseudo-symmetrical membrane transport proteins".
Dr. Lucy Forrest
NINDS, NIH




March 31, 2015
"Binding site prediction algorithms in pharmaceutical discovery".
Prof. Dušanka Janežč, Ph.D.
University of Primorska, Slovenia




Mar. 26, 2015
"Conformational Dynamics of a Ligand-Free Adenylate Kinase and Mhp1 Transporter".
Dr. Hyun Deok Song
Indiana University




Mar. 19, 2015
"Cofactor and protein dynamics in flavin-dependent enzyme reactions".
Prof. Pablo Sobrado
Department of Biochemistry, Virginia Tech




Mar. 12, 2015
"Reduction of all-atom folding dynamics to one-dimensional diffusion".
Dr. Robert Best
NIDDK, NIH




Feb. 26, 2015
"Predicting the biophysics of lipids from simulation: curvature, organization, and protein-lipid coupling".
Dr. Alexander Sodt
LCB, NHLBI, NIH




Feb. 19, 2015
"Dual allosteric inhibitors jointly modulate structure and dynamics in the HCV polymerase".
Prof. Ian F. Thorpe
Department of Chemistry and Biochemistry, University of Maryland, Baltimore County




Feb. 13 @ 4:00pm, 2015
"Conformational Dynamics and Structural Stability of Diabetes-related Human Amylin Protofilaments".
Ye Yuan
School of Physics, University College Dublin, Ireland




Feb. 13, 2015
"Improved sampling through collective variable biases: practical considerations".
Dr. Jerome Henin
Lab Biochimie Theorique, Inst. Biol. Physico-Chimique, Paris, France




Feb. 12, 2015
"Modeling the binding of the Histone-like Nucleoid Structuring protein H-NS to DNA".
Dr. Jocelyn Vreede
University of Amsterdam, The Netherlands




Feb. 11, 2015 @ 4:00 pm
"Ion Channels: From Structure Refinement and Remodeling to Functional Mechanisms".
Huan-Xiang Zhou
Florida State University




Feb. 6, 2015
"Elucidating the roles of protein dynamics on enzyme function by molecular simulations".
Prof. Kwangho Nam
Department of Chemistry, Umeå University, Umeå, Sweden




Feb. 5, 2015
"Multiscale Modeling of an Intrinsically Disordered Acid Stress-Sensing Chaperone".
Dr. Logan S. Ahlstrom
University of Michigan




Jan. 29, 2015
"Explore the space of quantum chemistry, and make a MESS!".
Dr. Yihan Shao
Q-Chem




Jan. 22, 2015
"Pipelining Molecular Dynamics: Python and Databases to control, analyze and stage simulations".
Prof. Tom Woolf
Johns Hopkins University




Jan. 15, 2015
1. "Recent developments in the CHARMMing Web interface"; 2. "Development at Supercomputing 2014: how they will affect simulation science and CHARMM".
Benjamin Miller
LCB, NHLBI, NIH




Dec. 16, 2014
"Activation mechanisms in RAF kinase dimers from MD simulations".
Dr. Edina Rosta
Department of Chemistry, King's College London




Dec. 11, 2014
"Kinetic analysis and enhanced sampling using coarse master equations: applications to amyloid-forming peptides".
Dr. Nicolae-Viorel Buchete
UCD School of Physics, Rm 111, Dublin 4, Ireland




Dec. 4, 2014
"Membrane remodeling in Gram negative bacteria important for pathogenesis".
Prof. Bob Ernst
Department of Microbial Pathogenesis, University of Maryland - Baltimore, School of Dentistry




Nov. 20, 2014
"When is a kink really a kink? Identifying and characterizing helix kinks".
Dr Henry Wilman
Department of Statistics, Oxford University




Nov. 6, 2014
"Multiscale free energy simulations: Moving towards quantitative predictions in biochemistry and nanotechnology".
Dr. Gerhard König
LCB, NHLBI, NIH




Oct. 30, 2014
"Computational Modeling of Hydrogenase Biomimetics".
Prof. Michael B. Hall
Texas A&M University




Oct. 23, 2014
"Protein Force Fields based on the Classical Drude Oscillator Model".
Dr. Jing Huang
Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Batlimore




October 17 Friday, 2014
"Subdiffusion in the liquid ordered phase of lipid bilayers".
Dr. Edward Lyman
University of Delaware




Oct. 3, 2014
"Modelling for Studying the Dynamics of Electronically Excited Protein-Chromophore Complexes".
Prof. Young Min Rhee
Postech, South Korea




Sept. 30, 2014
"A new look at some old methods: Electronic structure methods for electron correlation and NMR".
Dr. Shane Yost
UC Berkeley




Sept. 25, 2014
"Computational study on the cAMP modulation of the HCN2 ion channel".
Dr. Florentina Tofoleanu
LCB, NHLBI, NIH




Sept. 11, 2014
"New directions in systematic force field optimization".
Dr. Lee Ping Wang
Dept. of Chemistry, Stanford University




Sept. 4, 2014
"Multiscale Molecular Simulations of RNA Catalysis".
Dr. Brian Radak
University of Minnesota - Twin Cities




2013-2014



July 29, 2014
"Multiple-environment single-system quantum mechanical molecular mechanical (MESS-QM/MM) calculations: Can we estimate QM/MM polarization energies with a sub kcal/mol accuracy?".
Dr. Yihan Shao
Q-Chem, LCB, NHLBI, NIH




July 15, 2014
"Absolutely localized molecular orbitals for nanoscale simulations".
Dr. Rustam Z Khaliullin
UC Berkeley




July 10, 2014
"Mechanism of secondary transporter membrane proteins studied by computer simulations".
Prof. Oliver Beckstein
Arizona State University




June 26, 2014
"Virtual mixture approach for constant pH simulation in explicit water".
Dr. Xiongwu Wu
LCB, NHLBI, NIH




June 19, 2014
"Recent development and application of constant pH molecular dynamics".
Prof. Jana Shen
School of Pharmacy, University of Maryland, Baltimore




June 13, 2014, 9:00am-4:00pm
Computational Research Symposium
DC area Computational Biology groups




June 12, 2014
"Multiscale multiphysics and multidomain models for biomolecules".
Prof. Guowei Wei
Department of Mathematics, Michigan State University




June 10, 2014
"Replica-Permutation Method as a Better Alternative to Replica-Exchange Method".
Prof. Satoru Itoh
Dept. of Theoretical and Computational Molecular Science, National Institutes of Natural Science Okazaki, Japan




June 10, 2014
"Amyloid Disruption by Supersonic Wave in Non-Equilibrium Molecular Dynamics Simulation".
Prof. Hisashi Okumura
The Graduate University for Advanced Studies ,National Institutes of Natural Science Okazaki, Japan




June 5, 2014
"Toward Accurate Simulation and Prediction of Chemical and Physical Properties of Metalloproteins".
Dr. Shuqiang Niu
LCB, NHLBI; Dept. Chem., Texas A & M University




May 29, 2014
"Development of polarizable multipolar and density-based force fields for classical simulations".
Andrés Cisneros
Wayne State University




May 27, 2014
"Targeting biomolecular processes with self-learning simulation approaches".
Dr. Fabrizio Marinelli
LCB, NHLBI, NIH




May 22, 2014
"Atomic resolution cryo-electron microscopy: Recent progress and computational challenges".
Dr. Sriram Subramaniam
NCI, NIH




April 28, 2014
"Modeling Assemblies and Interactions at the Replication Fork: Sliding Clamps and Clamp Interacting Enzymes".
Dr. Max Xu
Georgia Statute University




April 24, 2014
"Fundamentals of Nanoscale Polymer-Protein Interactions and Their Potential Applications in Solid-state Nanobioarrays".
Prof. Jong-in Hahm
Department of Chemistry, Georgetown University




April 17, 2014
"A web-based tool for (Q)SAR modeling available from CHARMMing.org".
Iwona E. Weidlich
LCB, NHLBI, NIH




April 10, 2014
"Development of an efficient multipole algorithm".
Dr. Andrew Simmonett
LCB, NHLBI, NIH




April 3, 2014
"Polarizable force field for biomolecules based on the classical Drude oscillator that includes full treatment of induced-induced polarization terms".
Prof. Alex MacKarell
School of Pharmacy, University of Maryland, Baltimore




March 27, 2014
"Structurally conserved binding sites of hemagglutinin revisited by ProBiS".
Dr. Dušanka Janežič
University of Primorska, Slovenia




March 20, 2014
"Using simulations to understand the molecular basis of allosteric inhibition in the RNA polymerase from Hepatitis C virus".
Prof. Ian F. Thorpe
Department of Chemistry and Biochemistry, University of Maryland, Baltimore County




March 18, 2014
"Evaluation, Improvement and Application of Isotropic Periodic Sum Method".
Dr. Kazuaki Takahashi
Keio University, Japan




March 13, 2014
"Insights into the mechanism of the multidrug efflux pump acrB from computation".
Dr. Claudio Anselmi
LCB, NHLBI, NIH




March 7, 2014
"Molecular Mechanisms of Primary Energy Conversion".
Prof. Ville Kaila
Technical University of Munich (TUM), Garching, Germany




March 6, 2014
"Advances in Reservoir Replica Exchange Methodology".
Benjamin Miller
LCB, NHLBI, NIH




Feb. 27, 2014
"Many-Body Dispersion Interactions: Theory and Applications".
Dr. Robert A. DiStasio Jr.
Department of Chemistry, Princeton University




Feb. 4, 2014
"Computer simulations of protein aggregation in atomistic details".
Dr. Fahimeh Baftizadeh
MIT




Jan. 30, 2014
"Structure-based antibody probe engineering and implications for HIV-1 vaccine design".
Dr. Ivelin Georgiev
VRC, NIH




Jan. 23, 2014
"Theory and simulation of membrane curvature and protein/membrane curvature coupling".
Dr. Alexander Sodt
LCB, NHLBI, NIH




Jan. 16, 2014
"Structural refinement and conformational dynamics of cell adhesion molecules".
Catherine Kelly
University College Dublin, Ireland




Jan. 9, 2014
"A New Application to Estimate the Diversity of Molecular Databases".
Iwona E. Weidlich(a), Igor V. Filippov(b)
(a) CODDES LLC, (b) VIF Innovations LLC




Dec. 19, 2013
"Water at Hydrophobic Interfaces".
Prof. Toshiko Ichiye
Georgetown University




Dec. 12, 2013
"Mechanics and thermodynamics of biomembranes: ultrasoft condensed matter science".
Professor Evan Evans
Biomedical Engineering Dept., Boston University




Dec. 5, 2013
"Different directions to investigate protein conformational transitions through an adaptive biasing approach".
Dr. Fabrizio Marinelli
LCB, NHLBI




Nov. 21, 2013
"ProBiS - Binding site comparison for protein function prediction".
Dr. Janez Konc
LCB, NHLBI, NIH




Nov. 14, 2013
"Adapting the elastic network model for flexible fitting of low-resolution structural data and modeling conformational transition pathways".
Prof. Wenjun Zheng
Department of Physics,University at Buffalo




Nov. 5, 2013
"Molecular regulation of the kidney filtration barrier by phosphorylation and lipid binding".
Dr. Markus Rinschen
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Germany




Oct. 31, 2013
"High-accuracy protein structure modeling and its application to molecular replacement of crystal phasing".
Prof. Jooyoung Lee
KIAS, Korea




Sept 23, 2013
"Computer simulations of protein unfolding and translocation by AAA+ nanomachines".
Prof. George Stan
Dept. of Chemistry, University of Cincinnati




Sept 19, 2013
"Computational studies of the serotonin transporter (SERT): mechanism of serotonin transport and inhibition".
Dr Jerez Te
Weill Cornell School of Medicine, New York




Sept 12, 2013
"Ab Initio Dynamics and Cytochrome P450 Catalysis: Classical and Quantum Effects".
Justin Elenewski
VCU




Aug. 22, 2013
"Towards a new force field".
Dr. Ye Mei
ECNU & NHLBI




Aug. 20, 2013
"Conformational Changes involved in TopoII upon DNA binding, bending and cleavage".
Dr. Ahmet Mentes
University of CA, Irvine, Dept. of Chemistry




Aug. 16, 2013
"Transmembrane structures of amyloid precursor protein in biological membrane".
Dr. Yuji Sugita
Riken, Japan




Aug. 8, 2013
"Natural Bond Orbital Methods".
Prof. Eric Glendening
Indiana State University




2012-2013


July 11, 2013
"Enhanced sampling and kinetic analysis of peptide folding and peptide-peptide interactions".
Prof. Nicolae-Viorel Buchete
Indiana State University




June 27, 2013
"Improved network community structure improves function prediction".
Jooyoung Lee
University College Dublin, Ireland




June 25, 2013
"In the clutches of Maxwell's demon: below-equilibrium DNA topology simplification by type II topoisomerases".
Tamara Litwin
KIAS




June 20, 2013
"Umbrella Sampling Simulations of PAMAM Dendrimer-DNA Complexation".
Dr. Kathleen Maria Mills
NHLBI, NIH




June 13, 2013
"Neutron Diffraction and Simulation Studies of the Solvation of Complex Molecules".
Prof. John Brady
NHLBI,NIH




June 11, 2013
"UNRES force field".
Adam Sieradzan
Cornell University




June 10, 2013
"Structural mechanisms of conformational changes in Selectins: A molecular dynamics study".
Paul Cardenas-Lizana
Chemistry Department, University of Gdansk




June 6, 2013
"Modeling protein function coupling to membrane curvature".
Dr. Alexander Sodt
Wallace H. Coulter Dept. of Biomedical Engineering, Georgia Institute of Technology




May 30, 2013
"Insights from free energy calculations: protein conformational equilibrium, driving forces and ligand binding processes".
Chia-en A. Chang
LCB, NHLBI, NIH




May 23, 2013
"Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods".
Dr. Iwona Weidlich
UC, Riverside




May 16, 2013
"What can we learn about protein folding from atomistic simulations?".
Robert Best
Computational Drug Design Systems, Rockville, MD




May 9, 2013
"Current high performance computing hardware and software trends and their impact on molecular simulation science".
Benjamin Miller
Laboratory of Chemical Physics, NIDDK




May 2, 2013
"Through the Looking-Glass and what the Quantum Chemist Found There".
Prof. Daniel Crawford
LCB, NHLBI, NIH




April 25, 2013
"Towards an accurate treatment of many-body dispersion and polarization for chemical accuracy in the post-CMOS world".
Glenn J. Martyna
Dept. of Chemistry, Virginia Tech




April 18, 2013
"A Protein Conformational Entropy Meter from NMR Order Parameters".
Prof. Kim Sharp
IBM Research




April 16, 2013
"Structure-based Function Prediction for Proteins of Unknown Function".
Dr. Dušanka Janežič
University of Pennsylvania




April 4, 2013
"Model of Large Scale Conformational Mobility in Proteins".
Yaroslav Ryabov
National Institute of Chemistry, Slovenia




March 21, 2013
"Microsecond Simulations of a Peripheral Membrane Protein and Bilayer Properties as a Function of Temperature".
Prof. Jeffery Klauda
(CIT, NIH)




March 14, 2013
"Fast methods for computing intermolecular interactions in large systems".
Prof. John Herbert
University of Maryland




Feb 28, 2013
"Structure and Orientation of Antimicrobial Peptides Piscidin 1 and Piscidin 3 in Lipid Bilayers".
Dr. Scott Perrin Jr.
Ohio State University




Feb 21, 2013
"Accelerating QM and QM/MM calculations".
Dr. Yihan Shao
LCB, NHLBI, NIH




Feb 7, 2013
"pH driven conformational transitions of proteins".
Dr. Ana Damjanović
QCHEM




Jan 31, 2013
"An Efficient Multipole Implementation & Other Thoughts on CHARMM Development".
Dr. Frank Pickard
LCB, NHLBI




Jan. 24, 2013
"QM/MM Simulations for the Elucidation of Ionic Liquid Effects Upon Classical Organic Reactions".
Caley Allen
LCB, NHLBI, NIH




Jan 17, 2013
"The Hydrolysis Engine Concept for Motor Proteins".
Dr. Xiongwu Wu
Auburn University




Jan 10, 2013
"DNA-wrapped Carbon Nanotubes as Model Macromolecules".
Dr. Ming Zheng
LCB, NHLBI, NIH




Jan 3, 2013
"Protein structure prediction by dynamic fragment assembly".
Juyong Lee
NIST




Dec 20, 2012
"Nitrosative signaling in breast cancer".
Dr. Christopher Switzer
LCB, NHLBI, NIH




Dec 13, 2012
"Entropy and the Second Law, based Information Theory".
Dr. Arieh Ben-Naim
NCI, NIH




Dec 6, 2012
"Practical Redox Potential Calculations of Metalloproteins: Present and Future".
Prof. Toshiko Ichiye
Department of Physical Chemistry, The Hebrew University of Jerusalem




Nov 29, 2012
"Charge hydration asymmetry: the basic principle and its use in testing and improving solvation models".
Prof. Alexey Onufriev
Georgetown University




Nov 15, 2012 (4:00pm)
"Using molecular simulations to understand allosteric inhibition in the Hepatitis C virus polymerase".
Ian F. Thorpe
Virginia Tech




Nov 8, 2012
"Biopinspired catalytic homogeneous hydrogenation of dioxygen".
Zachariah M. Heiden, Ph.D.
UMBC




Nov 1, 2012
"Software development efforts in CHARMM and CHARMMing: drug design and replica exchange methods".
Benjamin Miller
Pacific Northwest National Laboratory




Oct 25, 2012
"Quantitative calculation of leaflet curvature induction by lipids and peptides".
Alexander Sodt
LCB, NHLBI, NIH




Oct 18, 2012
"Simulation of Oxygen Diffusion in Membranes".
Dr. An Ghysels
UC Berkely




Oct. 11, 2012
"Structure and dynamics of ternary bilayers by long-timescale simulation".
Edward Lyman, Ph.D.
Dept. of Physics, University of Delaware




Oct 4, 2012
"Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations".
Dr. Peng Tao
LCB, NHLBI,NIH




Sep 20, 2012
"Computational studies of activation of small molecules using Hydrogenation Transfer Catalysts and Nanostructures".
Dr. Sugata Chowdhury
LCB, NHLBI




Sep 13, 2012
"A QM/MC/FEP approach for the study of organic and enzymatic reactions in condensed phases".
Dr. Jakub Kostal
Yale Univeristy




2011-2012


Aug. 16, 2012
"Photons in and out proteins: the role of protein fluctuations".
Prof. Young Min Rhee
Postech, Korea




Aug. 9, 2012
"Mathematical models of branching actin networks: Results and methods".
Daniel Smith
LCB, NHLBI, NIH




July 9, 2012
"Molecular interactions of Alzheimer's amyloid-beta protofilaments with lipid membranes".
Dr. Florentina Tofoleanu
University College Dublin, Ireland




July 2, 2012
"1) Multireference systems with a single reference method: avoided crossings, conical intersections, multiradical character and more; 2) The role of the conjugated linker in organic dye sensitized solar cells".
Dr. David Casanova
University of Barcelona




June 21, 2012
"Orientation and Structure of Membrane Proteins Studied by Neutron Reflectivity and Molecular Dynamics".
Dr. Hirsh Nanda
CMU/NIST




June 7, 2012
"Nanopores as Versatile Single-molecule Sensors".
Dr. Arvind Balijepalli
LCB, NHLBI




May 31, 2012
"Linking the Movement of a Protein Domain to the Separation of a pair of Electrons in the Cytochrome bc1 Complex".
Dr. Lothar Esser
NCI, NIH




May 24, 2012
" ".
Dr. Youngchan Kim
Center for Computational Materials Science, Naval Research Laboratory




May 17, 2012
"Combined Quantum Mechanics and Molecular Mechanics:
Prof. Jinzhi Pu
Department of Chemistry and Chemical Biology




May 4, 2012
"Computational Enzymology: QM/MM, Reaction Path, and Beyond".
Dr. Peng Tao
LCB, NHLBI, NIH




May 3, 2012
"Orientations of Piscidin 1 and Piscidin 3 in Lipid Bilayers".
Dr. Scott Perrin
LCB, NHLBI, NIH




April 26, 2012
"Molecular interactions of Alzheimer's Aβ protofilaments with lipid membranes".
Dr. Nicolae-Viorel Buchete
University College Dublin, Ireland




April 19, 2012
"Imaging the nanometer scale architecture of vesicle release and recapture".
Dr. Justin Taraska
NHLBI, NIH




April 12, 2012
"Protons, electrons, and photo-excitations in biology".
Dr. Ville Kaila
NIDDK, NIH




March 26, 2012
"Chemistry-driven protein evolution in the alkaline phosphatase superfamily.".
Dr. Lynn Kamerlin
Uppsala University, Uppsala, Sweden




March 22, 2012
"".
Dr. Mingliang Tan
Chemistry Dept. Georgetown University




March 15, 2012
"Evaluating the performance of reservoir replica exchange methods through transition state theory".
Dr. Asim Okur
LCB, NHLBI




March 8, 2012
"Conformation of the Retinal Ligand in the GPCR Rhodopsin: Insights from NMR and MD Simulation".
Dr. Preethi Chandran
NIBIB/NICHD, NIH




Feb. 16, 2012
"Conformations of water hexamer at low temperatures.".
Dr. Volodymyr Babin
North Carolina State University




Feb. 15, 2012
"Conformation of the Retinal Ligand in the GPCR Rhodopsin: Insights from NMR and MD Simulation".
Prof. Scott Feller
Wabash College




Feb. 14, 2012
"pH replica exchange with discrete protonation states".
Ana Damjanović
LCB, NHLBI




Feb. 10, 2012
"Dynamic proteins and protein complexes. Investigations by x-ray crystallograhpy, NMR spectroscopy and Molecular Dynamics on systems that regulate cell migration.".
Prof. Matthias Buck
Department of Physiology and Biophysics,Case Western Reserve University, Cleveland, Ohio




Feb. 9, 2012
"Molecular Hygroscopy of Ethanol: From the Bartender's Conundrum to Biological Solvation".
Prof. Toshiko Ichiye
Dept. Chemistry, Georgetown University




Feb. 2, 2012
"Stochastic Modeling of Clathrin-coated Pit Assembly".
Dr. Anand Banerjee
NICHD, NIH




Jan. 31, 2012
"Study of the Hepatitis Delta Virus (HDV) Ribozyme using Theoretical Tools".
Mr. Abir Ganguly
Penn State University




Jan. 26, 2012
"Experimental and theoretical study of the Mycobacterium tuberculosis dUTPase enzyme".
Anna Lopata, BSc
Institute of Enzymology, Hungarian Academy of Sciences and




Jan. 19, 2012
"Putting the Statistics back in Statistical Mechanics".
Dr. Michael Shirts
University of Virginia




Jan. 6, 2012
"The surprising dynamics of adenosine receptor agonists".
Prof. Edward Lyman
The University of Delaware




Jan. 3, 2012
"Dynamics on biomolecule surfaces at atomic resolution by solution NMR".
Dr. Nicolas Fawzi
NIDDK, NIH




Dec. 22, 2011
"Molecular dynamics and docking study of collagenolysis mechanism of matrix metalloproteinase 1".
Dr. Chien Nguyen
LCB, NHLBI, NIH




Dec. 20, 2011
"The ProBiS tools (algorithm, web-server, and database) for predicting and modeling of pharmaceutically interesting proteins".
Dr. Dušanka Janežič
National Institute of Chemistry, Slovenia




Dec. 15, 2011
"Exploring the Nature of the Off-diagonal Coupling Element in SN2 Reactions and the Origin of Linear Free Energy Relationships".
Dr. Edina Rosta
NIDDK, NIH




Dec. 12, 2011
"Practice talk".
Dr. Joe Larkin
LCB, NHLBI, NIH




Dec. 8, 2011
"".
Earl Stadtman NIH-wide tenure-track seminars




Dec. 1, 2011
"Determination of Inner-Sphere Reduction Free Energies of Iron-Sulfur Proteins".
Dr. Shuqiang Niu
Chemistry Dept. Georgetown University




Nov. 18, 2011
"Generalized Deformations and the Role of Viscous Dissipation in Lipid Bilayers".
Max C. Watson
Dept of Chemistry, University of California, Santa Barbara




Nov. 17, 2011
"Development of the Psi4 Software Package".
Dr. Andy Simmonett
Center for computational Chemistry, U. Georgia




Nov. 11, 2011
"Pools of PIP2 in the Plasma Membrane".
Stuart McLaughlin
Stony Brook University




Nov. 10, 2011
"Open-boundary QM/MM for multi-scale molecular dynamics simulations".
Dr. Hai Lin
Chemistry Department, University of Colorado Denver




Nov. 8, 2011
"Biomolecular Simulations using Implicit Solvent Models".
Prof. David A. Case
Rutgers University




Nov. 3, 2011
"Langevin dynamics simulations of protein fencing of PIP2".
Dr. Kyu Il Lee
Dept. Mol. Biosciences and Center for Bioinformatics, University of Kansas




Oct. 27, 2011
"Bilayer spontaneous curvature from simulation".
Dr. Alexander Sodt
LCB, NHLBI, NIH




Oct. 20, 2011
"Redox Properties of Blue Copper Proteins".
Dr. Carrie S. Miller
Georgetown University




Oct. 13, 2011
"The Perfect Penicillin Protonation Puzzle".
Dr. Jacqueline C. Hargis
University of South Florida




Sept. 29, 2011
"Estimation of inter-domain flexibility in N-terminal modules of factor H using residual dipolar couplings".
Dr. Mateusz Maciejewski
NHLBI, NIH




Sept. 22, 2011
"A study of excited states of oligocarbazole and firefly luciferin".
Shushu Zhang
LCB, NHLBI/NIBIB, NIH




Sept. 8, 2011
"Solvent-mediated electrostatics and liquid-structure forces: how much Physics can be described by a continuum representation of the aqueous solvent? A review of the SCPISM".
Dr. Sergio Hassan
CIT, NIH




Sept. 1, 2011
"Enzymatic activity of MMP-1 on collagen molecule".
Dr. Chien Nguyen
LCB, NHLBI




Aug. 25, 2011
"Monte Carlo simulations to explain adsorption-induced structural transitions of porous materials".
Dr. An Ghysels
UC Berkely




Aug. 23, 2011
"ProBiS algorithm and ProBiS web-tool for detection of protein binding sites".
Dr. Dušanka Janežič
National Institute of Chemistry, Slovenia




2010-2011


July 12, 2011
"Toward understanding of Min system pattern formation".
Dr. Vassili Ivanov
NIDDK/NIH




June 30, 2011
"Replica Exchange Accelerated Molecular Dynamics and Binding Cooperativity in Protein Kinase A".
Dr. Mikolai Fajer
University of California, San Diego




June 28, 2011
"1: Why do carbon nanotubes suck up water? 2: Density functional theory made close to chemical accuracy and fast using the opposite-spin ansatz".
Prof. Yousung Jung
KAIST, Korea




June 23, 2011
"Computational Dielectric spectra of polarizable ionic liquids".
Dr. Christian Schroeder
Institute of Computational Biological Chemistry, University of Vienna, Austria




June 16, 2011
"Development and test of AMBER additive and polarizable force fields".
Dr. Junmei Wang
Department of Pharmacy, University of Texas Southwestern Medical Center at Dallas




June 9, 2011
"Group-theoretic methods in protein structure determination".
Prof. Gregory S Chirikjian
Department of Mechanical Engineering, Johns Hopkins University




June 2, 2011
"Approaches and Methods to Multiscale Modeling with CHARMM".
Miller, Tim
LCB, NHLBI, NIH




May 26, 2011
"Redox Properties of Fe-S Proteins".
Dr. Scott Perrin
Dept of Chemistry, Georgetown University




May 19, 2011
"Molecular simulations of certain model human membranes and secondary active transport proteins".
Prof. Jeffery Klauda
University of Maryland




May 12, 2011
"Internal ionizable groups in proteins: pKa values and ionization triggered conformational relaxation".
Dr. Ana Damjanović
LCB, NHLBI, NIH




May 10, 2011
"Improved conformational sampling through combining conformational space annealing method with replica exchange".
Dr. Asim Okur
LCB, NHLBI, NIH




May 5, 2011
"What's Wrong with the Water (Model)? Insights from Quantum Chemical Calculations".
Prof. Ichiye Toshiko
Georgetown University




April 21, 2011
"Continuum modeling of cell motility".
Dr. Nyugen Chien
LCB, NHLBI, NIH




April 14, 2011
"Protein-protein interactions in a crowded cellular environment: Simulation and theory".
Dr. Youngchan Kim
Naval Research Laboratory, Washington, DC




April 7, 2011
"Computational Methods in Enzymatic Reaction Mechanism Study".
Dr. Peng Tao
LCB, NHLBI




April 5, 2011
"Discrete molecular dynamics with coarse grained peptide model and implicit solvent model: Comparison to all atom molecular dynamics".
Dr. Sijung Yun
NCI, NIH




April 1, 2011
"Computational and experimental analysis of oligosaccharide conformation and dynamics".
Prof. Goran Widmalm
Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University




March 31, 2011
"Probing the kinetic network of folding—unfolding transitions in proteins".
Dr. Nicolae-Viorel Buchete
Physics Dept., University College Dublin, Ireland




March 24, 2011
"Alternative tubulin lateral interactions with functional roles in microtubules mechanics and assembly dynamics".
Dr. Zhanghan Wu
1Department of Biological Sciences, Virginia Polytechnic Institute and State University




March 22, 2011
"Nanoscale virtual cell with minimum genome".
Dr. Yu Xu
NCI, NIH




March 18, 2011
"Computer simulations of lipid bilayers and protein multimers".
Dr. Michael Lerner
LCB, NHLBI




March 17, 2011
"Load-sharing mechanism governs the force-velocity relationship of branching actin networks".
Daniel Smith
LCB, NHLBI




March 10, 2011
"Spatial regulation by microtubule spindle".
Dr. Jing Chen
LCB, NHLBI, NIH




March 3, 2011
"Transmembrane Helix Dynamics: Is It An Artifact of Molecular Dynamics Simulation?".
Prof. Wonpil Im
University of Kansas




Feb. 24, 2011
"Molecular Imaging of Cancer".
Dr. Shawn Chen
NIBIB




Feb. 17, 2011
"A comparison of bilayer stress profiles and lipid shape".
Dr. Alxander Sodt
LCB, NHLBI




Feb. 11, 2011
"Molecular dynamics simulations of transmembrane helices in lipid bilayers".
Dr. Liqun Zhang
Department of Physiology and Biophysics,Case Western Reserve University, Medical School




Feb. 10, 2011
"Role of Water in Protein-Protein Interactions".
Prof. Sihyun Ham
Sookmyung women's University, South Korea




Feb. 3, 2011
"Application and Development of SGMD/SGLD".
Dr. Xiongwu Wu
LCB, NHLBI,NIH




Jan. 20, 2011
"Membrane diffusion of tethered dimer and trimer systems".
Dr. Michael Lerner
LCB, NHLBI, NIH




Jan. 13, 2011
"Asymmetric Engagement of Molecular Clutch across Focal Adhesion is Essential for Cell Mechanosensing and Durotaxis".
Dr. Sergey Plotnikov
NHLBI, NIH




Jan. 6, 2011
"Roles of slow protein conformational changes in cellular dynamics".
Dr. Jianhua Xing
Virginia Tech




Dec. 22, 2010
"Computational Studies of Rubredoxin-type Electron Transfer Proteins".
Dr. Dušanka Janežič
National Institute of Chemistry, Ljubljana, Slovenia




Dec. 16, 2010
"Computational Studies of Rubredoxin-type Electron Transfer Proteins".
Dr. Yan Luo
Georgetown Univeristy




Dec. 9, 2010
"Site-Specific Semiempirical Models for Metalloenzymes".
Prof. Guillaume Lamoureux
Department of Chemistry and Biochemistry, Concordia University




Dec. 2, 2010
"Allosteric Regulation: The Cullin-RING E3 Ubiquitin Ligases and Beyond".
Dr. Jin Liu
NCI, NIH




Nov. 18, 2010
"High Order Generalized Ensemble Simulation Techniques: Starting with the Orthogonal Space Random Walk Algorithm".
Prof. Wei Yang
Florida State University




Nov. 9, 2010
"Accurate simulation with non-polarizable models: high quality pair-wise force-field from adaptive force matching".
Prof. Feng Wang
Department of Chemistry, Boston University




Nov. 4, 2010
"Simulation-based Validation of the CHARMM Additive Force Field for Carbohydrates".
Rick Venable
LCB, NHLBI




Oct. 28, 2010
"Conformational Sampling and Free Energy Estimation of Molecules using Low Order Distribution Functions".
Sandeep Somani
Center for Advanced Research in Biotechnology, University of Maryland




Oct. 21, 2010
"P450-Catalyzed Aromatization: A Case for Dual Oxidants".
Prof. John C Hackett
Virginia Commonwealth University, School of Pharmacy




Oct. 19, 2010
"The chemical biology of NO and HNO".
Dr. David A. Wink
Radiation Biology Branch, Division of Clinical Sciences,NCI




Oct. 14, 2010
"Polarizable Force Field for Biomolecular Simulation".
Prof. Jay W Ponder
Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine




Oct. 13, 2010
"A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins".
Prof. Yingkai Zhang
Department of Chemistry, New York University




Oct. 7, 2010
"Prediction of ligand binding site on protein surface and MD simulation of flexible compound with multiple chains".
Dr. Shijun Zhong
University of Maryland




Sept. 30, 2010
"The Unified reaction valley approach: New insights into chemical reaction mechanism".
Prof. Elfi Kraka
Dept. Chem., Southern Methodist University,




Sept. 23, 2010
"MD simulation study of osmotic pressure and mobility of electrolyte solutions".
Dr. Yun Luo
Dept. Biochem & Mol. Biol., University of Chicago




2009-2010


July 1, 2010
"The initial and final states of electron and energy transfer processes: quantum chemistry methods applied to dynamics".
Prof. Joseph Subotnik
University of Pennsylvania




June 24, 2010
"On Self-Guided Langevin Dynamics".
Dr. Bernard R. Brooks
LCB, NHLBI




June 17, 2010
"Application of Computational Simulations in Studying Dynamics and Energetics of Biomolecules".
Huan Rui
Kansas University




June 10, 2010
"Design and automation of the CHARMM General Force Field".
Dr. Kenno Vanommeslaeghe
Maryland University




June 8, 2010
"QM/MM free energies with the Mobile Block Hessian approach".
Dr. An Ghysels
Center for Molecular Modeling, Ghent University and MolSim group, University of California — Berkeley




June 3, 2010
"Non-classical nucleation mechanisms and their role in nanocrystal formation: implications for novel drug-delivery strategies and biomineralization processes".
Dr. Sergio A. Hassan
CIT, NIH




May 25, 2010
"On Free Energy Simulations".
Dr. Gerhard König
Dep. Of Computational Biological Chemistry, University of Vienna, Vienna, Austria




May 18, 2010
"Modeling Bacterial Gliding Motility".
Dr. Jing Chen
UC Berkeley




May 13, 2010
"Residue-specific Fluorescent Probes of α-synuclein Interactions with Lipids, Metals, and Itself".
Dr. Jennifer Lee
LMB, NHLBI, NIH




April 29, 2010
"Computational Analysis and Design of Host-Guest Complexes with Protein-Ligand-Like Affinities".
Dr. Sarvin Moghaddam
Dept Chem Eng, University of Maryland




April 27, 2010
"Effects of Blast Overpressure on Phospholipid-Cholesterol Bilayers".
Dr. Jeffery Mason
Traumatic Brain Injury Center, Armed Forces Institute of Pathology




April 22, 2010
"Structures and Reactivity of Diaryliodonium Salts".
Dr. Yong Sok Lee
CIT, NIH




April 8, 2010
"QM Studies of Boronic acids in Proteasome Inhibition and a Glucose Sensing".
Dr. Joseph Larkin
NHLBI, NIH




March 26, 2010
"Density Matrix Renormalization Group (DMRG) and its Chemical Applications".
Dr. Sandeep Sharma
Cornell University




March 25, 2010
"Vibrational Probes of Amino Acid Protonation State".
Carrie Miller
University of Notre Dame




March 23, 2010
"Quantum statistical properties and dynamics of cold atoms-light system".
Wenzhou Chen
University of Arizona




March 19, 2010
"Coarse master equations for protein folding".
Dr. Vio Buchete
University College Dublin, Ireland




March 18, 2010
"Interface problems in vascular mechanics and the mechanics of multilayer systems".
Chien Nguyen
Syracuse University, NY




March 11, 2010
"Membrane-cytoskeleton interaction through curved membrane proteins".
Roie Shlomovitz
Weizman Institute, Israel




March 4, 2010
"Energy minimization for spatially varying dielectrics".
Dr. Oleg Obolensky
NIH, NLM, NCBI




Feb. 18, 2010
"QM/MM Study of Several Enzymatic Systems".
Dr. Tao Peng
NIH, NHLBI




Feb. 4, 2010
"Molecular interactions in physics and biology: from Poisson's equation to derivation of the universal density functional".
Dr. Yi-Kuo Yu
NIH, NLM, NCBI




Jan. 28, 2010
"Iron-Sulfur Proteins: Where Are We Now and Where Are We Going?".
Prof. Toshiko Ichiye
Georgetown University




Jan. 21, 2010
"When does the GxxxG transmembrane alpha-helix motif suggest helix dimerization?".
Dr. Alexander Sodt
NHLBI, NIH




Jan. 14, 2010
"Coarse-grained Modeling of Biopolymers in Aqueous Solution via Multipole Electrostatics".
Prof. Toshiko Ichiye
Georgetown University




Dec. 3, 2009
"Random walks and the structure of macromolecules".
Dr. Hwan Kyu Lee
NHLBI




Nov. 12, 2009
"What Can We Learn about Iron-Sulfur Proteins from PES, Ligand K-edge XAS, and QM Calculations?".
Dr. Shuqiang Niu
Dept. Chemistry, Georgetown University




Nov. 5, 2009
"Dynamic Pattern Formation by Bacterial Cell Division Proteins is Controlled by Dynamic Instability of Oligomers and Lipid Membrane Properties".
Dr. Vassili Ivanov
LMB, NIDDK, NIH




Oct. 29, 2009
"Kinetic model of replica exchange: Two-state protein folding".
Dr. Edina Rosta
NIDDK, NIH




Oct. 22, 2009
"Electron tomography and molecular modeling study of chemoreceptor organization".
Dr. Xiongwu Wu
LCB, NHLBI, NIH




Oct. 1, 2009
"Multiscale simulations of peptides, nanoparticles, polymers, and membranes for drug delivery and nanopore applications".
Dr. Hwan Kyu Lee
LCB, NHLBI, NIH




Sept. 24, 2009
"Information theory and molecular biology".
Dr. Thomas D. Schneider
the Molecular Information Theory Group, NCI, Frederick




Sept. 17, 2009
"Single molecule size spectrometry".
Dr. John Kasianowicz
NIST




Sept. 3, 2009
"Pathways in protein-protein association by paramagnetic relaxation enhancement NMR".
Dr. Nicolas Fawzi
NIDDK, NIH, and University of Maryland




2008-2009


Aug. 13, 2009
"Coarse grained simulations of alpha-helix association in a lipid bilayer".
Dr. Alex Sodt
UC Berkeley




Aug. 6, 2009
"CHARMM-GUI: Automated Setup for Molecular Dynamics Simulation".
Sunhwan Jo
Dept. of Mol. Bioscience and Center for Bioinformatics, Univ. of Kansas




July 30, 2009
"Understanding Protein Misfolding and Molecular Function".
Prof. Sihyun Ham
Department of Chemistry, Sookmyung Women's University, Korea




July 23, 2009
"Mechanisms and Energetics of Protein/Peptide Interactions in Biological Membranes".
Prof. Wonpil Im
Dept. of Mol. Bioscience and Center for Bioinformatics, Univ. of Kansas




July 9, 2009
"Mesoscopic Simulaitons of Membranes".
Prof. Berend Smit
Dept of Chemical Engineering and Dept of Chemistry




June 4, 2009

Dr. Bernard R. Brooks and Dr. Richard W. Pastor
NHLBI, NIH




May 7, 2009
"Enzymatic symmetry breaking: How does topoisomerase IV distinguish left from right?".
Dr. Keir C. Neuman
Laboratory of Molecular Biophysics, NHLBI, NIH




April 16, 2009
"Density Functional Theory: 1. Accelerating with GPU, 2. van der Waals dispersion correction".
Dr. Zhengting Gan
Q-Chem, Inc.




April 2, 2009
"New protein-protein docking methodology".
Dr. Dušanka Janežič
National Institute of Chemistry, Slovenia




April 1, 2009
"Statistical behavior of the self-guided dynamics algorithms".
Daniel Smith
Dept. of Mathematics, University of Pittsburgh




March 26, 2009
"Computer simulations of lipid bilayers" and "Computer simulations of crystalline cellulose".
Dr. Jakob Wohlert and Dr. Malin Bergenstrahle
Cornell University, Dept of Food Science




March 12, 2009
"Artificial Reaction Coordinate "Tunneling" In Free Energy Calculations: Nucleic Acid Cleavage By RNase H.".
Dr. Edina Rosta
NIDDK




March 4, 2009
"Multiscale method in bimolecular simulations".
Dr. Jhih-Wei Chu
UC Berkeley




Feb. 26, 2009
"NIST Computational Chemistry Group, though a Biological Lens".
Dr. Karl Irikura
NIST




Feb. 19, 2009
"Challenges in calculations of pKa values - part II".
Dr. Satoru Itoh
NHLBI




Feb. 12, 2009
"Temperature and Pressure Dependence of the Soft Sticky Dipole-Quadrupole-Octupole (SSDQO) Water Model".
Dr. Jerez Te
Georgetown University




Feb. 5, 2009
"Regulation and mechanics of unconventional myosins".
Dr. James Sellers
NHLBI, NIH




Jan. 22, 2009
"Challenges in calculations of pKa values - part I".
Dr. Ana Damjanović
NHLBI, NIH




Jan. 15, 2009
"Exploring QM/MM paths for mapping reaction mechanisms".
Dr. Lee Woodcock
NHLBI, NIH




Jan. 8, 2009
"Improvement to 3D IPS for the calculation of long-range interactions in homogeneous and heterogeneous systems".
Dr. Xiongwu Wu
NHLBI, NIH




Dec. 18, 2008
"Dynamic Importance Sampling within CHARMM: Computing Transitions".
Prof. Thomas B. Woolf
Department of Physiology, Johns Hopkins University School of Medicine




Dec. 4, 2008
"Fold vs. Sequence: Nature's Control of Fe-S Protein Reduction Potentials".
Dr. Scott Perrin
Grogetown University




Nov. 20, 2008
"Metallic Systems: Metal Ions, Metal-Organic Copmplexes, and Metalloproteins".
Dr. Orkid Coskuner-Weber
Grogetown University/NIST




Nov. 13, 2008
"Protein-mediated Electron Transfer".
Prof. Toshiko Ichiye
Grogetown University




Nov. 6, 2008
"Combined QM/MM Studies of Ligand-Thrombin Interaction".
Dr. Marek Freindorf
University at Buffalo




Nov. 6, 2008
"Density Functional Theory Made Faster and More Accurate:New XC Algorithm and Density Functional Dispersion".
Dr. Jing Kong
Q-Chem Inc.




Oct. 23, 2008
"Molecular dynamics studies of the interactions of membranes with peptides, synthetic polymers and nanoparticles".
Dr. Hwan Kyu Lee
LCB, NHLBI, NIH




Oct. 16, 2008
"Ligand-driven conformational rearrangements of proteins: insights from simulations".
Dr. Ana Damjanović
LCB, NHLBI, NIH




Oct. 2, 2008
"Predicting osmolyte and pH effects on proteins with the Molecular Transfer Model - Application to single molecule FRET and AFM experiments".
Edward O'Brien
LCB, NHLBI, NIH




Sept. 18, 2008
Unlocking the Secrets of Proteins: Stories Told in Computational Chemistry.
Dr. Peng Tao
Dept. Chemistry, Wayne State University




Sept. 4, 2008
Carbohydrate mini-symposium
Dr. Richard Pastor, Prof. Alexander D. MacKerell, Rick Venable,Lee Woodcock, Jeff Klauda, Liz Hatcher, Olgun Guvench, Daron Freedberg, Willie Vann
Laboratory of Computational Biology, NHLBI, NIH, and University of Maryland




2007-2008


July 24, 2008
"Computational assessment of protein nanotubes based on symmetry".
Idit Buch
Tel Aviv University, Israel




June 12, 2008
"Applications of Systems Biology Approaches".
Dr. Eric Billings
Bioinformatics and Systems Biology Core facility of NHLBI, NIH




June 5, 2008
"Electronic vs Electrostatic Effects on Redox Potentials of Proteins: How Important is Quantum Mechanics?".
Prof. Toshiko Ichiye
Dept. Chemistry, Georgetown University




May 29, 2008
"Dynamics and Vibrational Spectra of Rhodobacter capsulatus [2Fe-2S] Ferredoxins VI by Normal Mode Analysis".
Dr. Mingliang Tan
Dept. Chemistry, Georgetown University




May 15, 2008
"Toward Assembly/Disassembly Mechanism of [4Fe-4S] Protein Active Sites".
Dr. Shuqiang Niu
Dept. Chemistry, Georgetown University




May 8, 2008
"Acclerating RI-MP2 quantum chemistry calculations with graphical processing units".
Roberto Olivares-Amaya
Department of Chemistry, Harvard University




May 1, 2008
"Toward Realizing a PRAM-on-a-Chip Vision".
Dr. Uzi Vishkin
University of Maryland Institute for Advanced Computer Studies (UMIACS) and Electrical and Computer Engineering Department




April 24, 2008
"Muscle contraction and protein folding".
Dr. Julien Davis
Lab of Mol Cardiology , NHLBI, NIH




April 17, 2008
"Membrane-based action of antimicrobial oligomers: an atomistic view from simulations".
Dr. Jerome Henin
Center for Molecular Modeling, University of Pennsylvania




April 10, 2008
"Binding-Sites Prediction Assisting Protein-Protein Docking".
Dr. Dušanka Janežič
National Institute of Chemistry, Slovenia




April 8, 2008
"Catalytic mechanism of human DNA polymerase lambda with MgII and MnII from ab initio QM/MM studies".
Dr. G. Andrés Cisneros
NIEHS, NIH




April 3, 2008
"Point Multipole Electrostatics For Coarse-Grained Models".
Prof. Toshiko Ichiye
Georgetown University




March 27, 2008
"Identification of the Transition Sates in the Inversion of Benzodiazepines".
Dr. Yong Sok Lee
CIT, NIH




March 20, 2008
"Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy".
Dr. Hwan Kyu Lee
LCB, NHLBI, NIH




March 6, 2008
"A universal IPS method for molecular simulation of heterogeneous systems".
Dr. Xiongwu Wu
LCB, NHLBI, NIH




Feb. 28, 2008
"Modeling and docking IgE and anti-IgE".
Dr. Jon Wright
Institute of Biomedical Sciences, Academia Sinica, Taipei




Feb. 21, 2008
"Entropic effect in protein-ligand docking/Zipper model of B and Z DNA transition".
Juyong Lee
Dept. Chemistry, Seoul national university




Feb. 7, 2008
"Iterative Refinement of a Continuum-Solvent Energy Function for Peptide Structure Prediction".
Dr. Peter Steinbach
CIT, NIH




Jan. 17, 2008 and Jan.24, 2008
"Ion Clusters Formation in Concentrated Aqueous Solutions: Statistical, Structural, and Dynamic Properties at Ambient Conditions".
Dr. Sergio A. Hassan
CIT, NIH




Jan. 10, 2008
"NMR relaxation in lipid bilayers".
Dr. Richard W. Pastor
LCB, NHLBI, NIH




Dec. 21, 2007
"Temperature Intervals with Global Energy Reassignment" (TIGER).
Prof. Robert A. Latour
Rhodes Engineering Research Center,Clemson University




Dec. 13, 2007
"Protein-Protein Binding Site Prediction".
Dr. Dušanka Janežič
National Institute of Chemistry(Slovenia)




Nov. 29, 2007
"Calculation of Vibronic Couplings For Proton-Coupled Electron Transfer".
Dr. Jonathan H. Skone
Department of Chemistry, Pennsylvania State University




Nov. 27, 2007
"Using GPUs for molecular dynamics simulations".
Tim Miller
LCB, NHLBI




Nov. 15, 2007
"Systematic analysis of motions and communication networks in a benchmark of allosteric proteins".
Dr. Michael Daily
The Program in Molecular and Computational Biophysics, Johns Hopkins University




Nov. 13, 2007
"Protein switches".
Dr. Ana Damjanović
LCB, NHLBI




Nov. 8, 2007
"QM/MM Minimum Free Energy Path Calculations: The Mechanism of Cdc25b with Para-Nitrophenyl Phosphate".
Dr. Jerry Parks
Duke University




Nov. 6, 2007
"Normal modes in partially optimized molecular structures: the mobile block Hessian (MBH) approach".
An Ghysels
Center for Molecular Modeling, Ghent University, Belgium




Nov. 1, 2007
"Quantitative Explorations of Free Energy Surfaces In Biomolecular Simulations".
Prof. Wei Yang
Florida State University




Oct. 25, 2007
"Computational Protein Design: Toward stereochemically adaptable form and chemically adaptable function".
Dr. Ranjit S Ranbhor
Georgetown University




Oct. 18, 2007
"Modeling and predicting the effect of osmolytes on the thermodynamics and folding kinetics of a globular protein".
Edward O'Brien
LBC,NHLBI/Maryland University




Sept. 27, 2007
"High accuracy template based modeling by global optimization".
Prof. Jooyoung Lee
Computational Sciences, Korea Institute for Advanced Study




Sept. 20, 2007
"Computational studies of E. coli DHFR: Drug design and dynamics".
Dr. Michael G. Lerner
Biophysics Research Division, University of Michigan




Sept. 13, 2007
"Combinations of genomic analysis and structural modeling in computational study of p53-DNA recognitions".
Dr. Buyong Ma
NCI-Frederick




Sept. 6, 2007
"Vibrational Free Energy Partitioning".
Dr. Bernard R. Brooks
Laboratory of Computational Biology, NHLBI, NIH




2006-2007


July 19, 2007
"Applications of Density functional theory: Rasiation-induced DNA damage".
Dr. Sunghwan Kim
Department of Chemistry, University of Georgia




July 5, 2007
"Computational Analysis of the Recognition Mechanism of DNA Repair Enzyme Fpg".
Dr. Kun Song
Stony Brook University




June 28, 2007
"Reduction Potentials of Iron-Sulfur Proteins by Continuum Electrostatics".
Bradley Scott Perrin
Department of Chemistry, Georgetown University




June 21, 2007
"Structural Studies of Human Leukocyte Antigens and their Peptide Ligands." and "A new CHARMM command: MSCALE, for multi-scale molecular simulations".
Dr. Christian Parry and Dr. Bernard Brooks
LCB, NHLBI




June 7, 2007
"Optimization of Soft Sticky Dipole-Quadrupole-Octupole Water Model".
Jerez Angcom Te
Department of Chemistry, Georgetown University




May 31, 2007
" Dynamics in Electron Transfer of Clostridrium acidurici Ferredoxin".
Yan Luo
Department of Chemistry, Georgetown University




May 24, 2007
"Combined Broken-Symmetry DFT and Photoelectron Spectroscopy to Determine Intrinsic Reduction Potentials of Iron-Sulfur Proteins".
Dr. Shuqiang Niu
Department of Chemistry, Georgetown University




May 17, 2007
"Development of an additive empirical force field for hexopyranose monosaccharides".
Dr. Olgun Guvench and Dr. Ganesh Kamath
University of Maryland School of Pharmacy




May 10, 2007
"Enhanced Conformational Sampling Methods for Molecular Simulations".
Dr. Asim Okur
Chemistry Dept., Stony Brook University




May 3, 2007
"Ligand-driven conformational rearrangements of proteins".
Dr. Ana Damjanović
NHLBI




April 26, 2007
"Nanotube confinement can stabilize or denature protein helices: Lessons for helix formation in the ribosome tunnel".
Edward O'Brien
NHLBI




April 12, 2007
"Insights into protein folding from single molecule experiments and molecular simulations".
Dr. Robert Best
Laboratory of Chemical Physics, NIDDK




April 5, 2007
"Small-Molecules Mimics of Superoxide Dismutase as Therapeutics".
Dr. Ye Che
NHLBI, LCB




March 22, 2007
"Estimating the relative stability of drug-DNA complexes using free energy calculations".
Dr. Jozica Dolenc
Laboratory of Physical Chemistry, ETH Zurich, Switzerland




March 20, 2007
"Thermodynamics of functional RNA's and low resolution structure of a riboswitch".
Prof. Sebastian Doniach
Stanford Univeristy




March 15, 2007
"Structure basis of autoimmune diabeties".
Dr. Christian Parry
NHLBI,NIH




March 1, 2007
"Slow Conformational Dynamics and Unfolding of the Calmodulin C-Terminal Domain".
Dr. Yng-Gwei Chen
NIDDK




Feb. 22, 2007
"Macromolecular Docking of Large Systems Using the EMAP Program of CHARMM: A Map and Grid Based Approach".
Dr. Jim Gruschus
LCB, NHLBI




Feb. 1, 2007
1. "Distributed Diagonal Force Decomposition Method"; 2. "CHARMM and Grid Computing".
1. Urban Borstnik; 2. Ana Damjanović and Tim Miller
1. National Institute of Chemistry, Ljubljana, Slovenia. 2. LCB, NHLBI




Jan. 25, 2007
"Hydrophobic and Ionic Interactions in Nanosized Water Droplets".
Dr. Subramanian Vaitheeswaran
University of Mariland




Jan. 18, 2007
"Folding and Misfolding Peptides: A Refined SCP Implicit Solvent Model, Replica Exchange, and the Search for the Grail".
Dr. Peter Steinbach
CIT, NIH




Jan. 11, 2007
"Structure, Dynamics, and Small Molecule Transport through Cell Membranes: How can Simulations Aid Experiments?".
Dr. Jeffery Klauda
LCB, NHLBI




Jan. 4, 2007
"Multi-scale molecular modeling".
Dr. Bernard R. Brooks
LCB, NHLBI




Dec. 21, 2006
"Normal Mode Analysis of Rubredoxins and [2Fe-2S] Ferredoxins".
Dr. Mingliang Tan
Dept. Chemistry, Georgetown University




Dec. 14, 2006
"Protein structure evolution, a challenge".
Prof. Jean Garnier
INRA/MIG(Mathematique Informatique et Genome- Unite MIG), Jouy-en-Josas, France




Dec. 7, 2006
"Computational Insights into the Radical Generation Step in B12-dependent Methylmalonyl-CoA Mutase and Short-Strong Hydrogen Bonds in Thrombin Active Site through Molecular Dynamic Studies".
Dr. Renata Kwiecien
The Catholic University of America




Nov. 30, 2006
"Decrypting protein conformational dynamics with coarse-grained elastic models".
Dr. Wenjun Zheng
NHLBI, NIH




Nov. 16, 2006
"Osmolyte Effects on Protein Structure: The Medium is the Message".
Prof. D. Wayne Bolen
Dept. of Human Biological Chemistry & Genetics, the University of Texas Medical Branch




Nov. 9, 2006
"Molecular dynamics simulations of peptide-lipid and nanoparticle-lipid interactions".
Dr. Hwankyu Lee
University of Michigan




Nov. 2, 2006
"Peptide hydrolysis in zinc enzymes studied with classical and QM/MM molecular dynamics".
Dr. Guillaume Lamoureux
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania




Oct. 26, 2006
"Structural analysis of an aqueous Cl— model at high temperatures by ab initio-classical free energy perturbation method".
Dr. Haitao Dongh
Department of Chemistry, Oregon State University




11:00am, Oct. 19, 2006
"Dynamics of Lipids in Membranes".
Dr. Richard Pastor
LCB, NHLBI




Oct. 12, 2006
"Theoretical Study of the Rhenium-Alkane Interaction in s-Complexes".
Erika Cobar
LCB, NHLBI




2:00pm-3:00pm, Oct. 4, 2006
"Faster Density Functional Theory Calculation Through Multiresolution".
Dr. Jing Kong, CEO & Chief Scientist
Q-Chem Inc




Sept. 28, 2006
"Isotropic Periodic Sum (IPS) for the Calculation of Long-Range Interactions in Periodic Membrane Systems".
Dr. Xiongwu Wu
NHLBI, NIH




2005-2006


July 13, 2006
"Simulating conformational changes triggered by ionization of a residue buried in the protein interior".
Dr. Ana Damjanović
NHLBI, NIH




June 22, 2006
"Development of the GROMACS-CPMD Quantum-Mechanical-Molecular-Mechanical Interface and a Polarizable Force Field for the QM/MM".
Dr. P. K. Biswas
Department of Chemistry, Cleveland State University




June 21, 2006
"Prediction of Protein Structure, Function and Druggability on a Proteomic Scale".
Dr. Jeffrey Skolnick
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology




June 8, 2006
"Mechanism of Titin Unfolding by Force: Insight from Quasi-equilibrium Molecular Dynamics Calculations".
Dr. German Pabon
Dept. of biophysics and biophysical chemistry, the Johns Hopkis univeristy




May 25, 2006
"Experimental-Computational Study on Lipid Bilayer Structure and a Finite Size Effect of Lipid Diffusion".
Dr. Jeffery Klauda
LCB, NHLBI




May 18, 2006
"The Effect of Confinement, Crowding and Cosolutes on Equilibrium Properties of Proteins and Polypeptides".
Edward O'brien
LCB, NHLBI




May 11, 2006
"Yin-Yang atom: a simple classical-mechanical/quantum mechanical interface".
Dr. Yihan Shao
Q-Chem




May 4, 2006
"Development and application of hybrid QM/MM reaction path methods".
Dr. Lee Woodcock
LCB, NHLBI




April 20, 2006
"Allostery of Actin Filaments: Atomistic Simulations and Coarse-Grained Modeling".
Dr. Jhih-Wei Chu
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah




April 13, 2006
"Biological Nanomachines at Work: Chaperonin-Mediated Protein Folding".
Dr. George Stan
NHLBI




April 6, 2006
"Molecular dynamics integration and molecular vibrational theory".
Dr. Dušanka Janežič
National Institute of Chemistry, Ljubljana, Slovenia




March 16, 2006
"Structural Model of CCR5 for the discovery of entry inhibitors for the therapeutic intervention of HIV-1 infection".
Dr. Debananda Das
HIV and AIDS Malignancy Branch, NCI




March 9, 2006
"Ab initio Characterization of Boronic Acids".
Mr. Joseph Larkin
NHLBI




Feb. 23, 2006
"Proton Translocation in Bacteriorhodopsion".
Dr. Yong Sok Lee
CIT




Feb. 16, 2006
"Automatic refinement of 3D tomography volume data".
Dr. Xiongwu Wu
NHLBI




Feb. 9, 2006
"Membrane Stretching, Lysozyme Flexing and Bismarck's Grid".
Dr. Richard Pastor
FDA/NHLBI




Feb. 2, 2006
"Molecular dynamics simulation of cyclooxygenases".
Terry P. Lybrand
Center for structural biology, Vanderbilt Univeristy




Jan. 26, 2006
"Quantitative Structure Activity Relationship of Spirosuccinimide Type Aldose Reductase Inhibitors, II".
Youngdo Won
NHLBI visiting professor




Jan. 19, 2006
"Quantitative Structure Activity Relationship of Spirosuccinimide Type Aldose Reductase Inhibitors".
Youngdo Won
NHLBI visiting professor




Jan. 12, 2006
"Study of the bioprotective action of sugars: an investigation by molecular dynamics and Raman spectroscopy".
Adrien Lerbret
Department of Food Science, Cornell University




Dec. 8, 2005
"The Plastic Network Model of Conformational Change: application to adenylate kinase and GroEL".
Paul Maragakis
Department of Chemistry and Chemical Biology, Harvard University




Dec. 1, 2005
"The Two Aspects of the Protein Folding Problem".
Prof. Harold A. Scheraga
Baker Lab of Chemistry, Cornell University




Nov. 3, 2005
"Dimerization of an Amyloidogenic Peptide: The Effects of Sequence Shuffling, Crowding, Confinement and Force-Field".
Edward O'Brien
University of Maryland/NHLBI




Oct. 27, 2005
"A Quantum-Mechanical Framework for bio-molecular simulations and structure based drug design".
Dr. Victor Anisimov
University of Maryland




Oct. 20, 2005
"Normal Mode Analysis of Pyrococcus furiosus rubredoxins".
Dr. Mingliang Tan
Georgetown University




Oct. 6, 2005
"A Polarizable Atomic Multiple-based Potential for Protein Modeling".
Prof. Pengyu Ren
The University of Texas at Austin




Sept. 29, 2005
"Stabilizing and Destabilizing Lipid Bilayers".
Dr. Richard Pastor
Biophysics Laboratory, CBER, FDA




Sept. 22, 2005
"Effects of the Structure and Dynamics of the Solvent in Molecular Dissociation: Competition of Forces in 0-2 M NaCl Solutions at T
Dr. Sergio A. Hassan
CIT, NIH




Sept. 15, 2005
"Use map objects for efficient protein-protein docking".
Dr. Xiongwu Wu
NHLBI, NIH




2004-2005


Sept. 15, 2005
"Use map objects for efficient protein-protein docking".
Dr. Xiongwu Wu
NHLBI, NIH




Aug. 25, 2005
"Simulation of phase transformations of lipid aggregates".
Prof. Alex H de Vries
University of Groningen




July 14, 2005
"A new approach to electrostatics and a domain decomposition model for CHARMM".
Dr. Robert J. Petrella
Dept of Chemistry and Chemical Biology, Harvard University




June 30, 2005
"Mechanism of proton transfer in bacteriorhodopsin".
Dr. Nicoleta Bondar
The Computational Molecular Biophysics Group, IWR, Uni-Heidelberg, Germany




June 23, 2005
"Many-body polarization and dispersion effects in molecular and atomic liquids".
Dr. Troy Whitfield
IBM




May 26, 2005
"Simulation Studies of Protein Folding and Aggregation".
Dr. Teresa Lyn Head-Gordon
Lawrence Berkeley National Laboratory




May 5, 2005
"Local molecular theory for nonuniform ionic fluid".
Dr. Yng-Gwei Chen
NIDDK, NIH




April 28, 2005
"Interpreting Single-Molecule Fluorescence Measurements of Forster Resonance Energy Transfer with Simulated Dynamics of Polyproline".
Dr. Peter Steinbach
CIT, NIH




April 21, 2005
"Computational study of asparagine deamidation".
Dr. Baron Peters
MIT




April 14, 2005
"Effect of salicylate on microscopic and mesoscopic properties of a DPPC bilayer with molecular dynamics simulation".
Dr. Yuhua Song
Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine




April 7, 2005
"Flat-Histogram Sampling Methods in Molecular Simulation: Equilibrium Properties of Mixtures".
Dr. Vincent K. Shen
National Institute of Standards and Technology




March 31, 2005
"Toward a better understanding of protein function based on structure and dynamics".
Dr. Grzegorz Iwo Jezierski
Dept. Of Biology, University of Maryland




March 24, 2005
"Molecular dynamics simulations of amyloid fibrils".
Dr. Nicolae-Viorel Buchete
NIDDK




March 10, 2005
"Molecular dynamics integration and molecular vibrational theory. New symplectic integrators".
Dr. Dušanka Janežič
National Institute of Chemistry, Slovenia




March 3, 2005
"Molecular Dynamics of Peptides, Nucleic Acids, and Membrane Channels".
Dr. In-Chul Yeh
Laboratory of Chemical Physics, NIDDK




Feb. 24, 2005
"Annealing mechanism of chaperonin molecules".
Dr. George Stan
NHLBI, NIH




Feb. 17, 2005
"Probing the Solution Structure of Sucrose via the Evaluation of Residual Dipolar Coupling NMR Data with Multiple MM Force Fields".
Mr. Rick Venable
FDA




Feb. 10, 2005
"Identifying dynamically relevant reaction coordinates for protein folding".
Dr. Robert Best
NIDDK, NIH




Feb. 3, 2005
"1. Development and Application of QM/MM methodology; 2. Exploring Energy Surfaces: Can model carbohydrates be used to gain understanding?".
Dr. H. Lee Woodcock
NHLBI




Jan. 27, 2005
"The Search for Trehalose's Function in Lipid Bilayers".
Dr. Anna Skibinsky
FDA




Jan. 13, 2005
"Molecular Dynamics Study of Water Penetration in Wild Type and Mutants of Staphylococcal Nuclease".
Dr. Ana Damjanović
Department of Biophysics, Johns Hopkins University




Jan. 6, 2005
"Modulation of Protein-Protein with Small Molecules" and "Functional Mimetics of Superoxide Dismutase Enzymes".
Dr. Ye Che
NHLBI, NIH




Dec. 16, 2004
"Properties of polyunsaturated lipids from molecular dynamics computer simulations".
Dr. Scott Feller
Department of Chemistry, Wabash College




Dec. 9, 2004
"Trans-Cis Isomerization of Geldanamycin Catalyzed by Heat Shock Protein 90".
Dr. Yong Sok Lee
CIT, NIH, Bethesda, MD




Dec. 2, 2004
"Understanding Intramolecular Electron Transfer in Ferredoxin: Free Energy Curves by MD Study".
Dr. Mingliang Tan
Department of Chemistry, Georgetown University, Washington, DC




Nov. 18, 2004
"Method to Predict All Classes of Proteins from Homology to Ab Initio Targets".
Prof. Jooyoung Lee
School of Computational Sciences, Korea Institute for Advanced Study




Nov. 4, 2004
"Probing dynamics using residual dipolar coupling data".
Dr. Charles Schwieters
CIT




Oct 28, 2004
"How chair-like is the structure of glucose?".
Dr. Russell Negin
FDA




Oct 21, 2004
"An Ab Initio Study on the Torsional Surface of Alkanes and its Effect on Molecular Simulations of Alkanes and DPPC Bilayers".
Dr. Jeffery Klauda
Laboratory of Computational Biology, NHLBI, NIH




Oct 13, 2004
"Developments in the Classical Drude Oscillator Model for Electronic Polarizability".
Dr. Victor Anisimov and Dr. Igor Vorobyov
School of Pharmacy, University of Maryland




September 16, 2004
"Hydrogen bond properties and Dynamics of molecular solutions at ambient and non-ambient conditions: A computational study".
Snehasis Chowdhuri
Dept. Chemistry, Georgetown University




September 9, 2004
"Mechanistic Insight into the Symmetric Fission of [4Fe-4S] Analogue Complexes and Implications for Cluster Conversions in Iron—Sulfur Proteins".
Dr. Shuqing Niu
Chemistry Department, Georgetown University




September 2, 2004
"Conservation of dynamically important residues computed from an elastic network model".
Dr. Wenjun Zheng
LBC, NHLBI/NIH




2001-2004


10/4/2001
Richard Pastor
FDA
"Lipid Bilayers, NMR Relaxation, and Computer Simulation".





10/11/2001
Mr. Jhih-Wei Chu
Department of Chemical Engineering, MIT
"Stabilization of Therapeutic proteins via molecular understanding: Oxidation of methionine groups in G-CSF".





10/25/2001
Dr. Bernard Brooks
NHLBI, NIH
"Replica Path Method in CHARMM(I)".





11/1/2001
Dr. Bernard Brooks
NHLBI, NIH:
"Replica Path Method in CHARMM(II)".





11/8/2001
Dr. Morris Krauss
"Enzyme Active Site: Structure, Spectroscopy, Reactivity".





11/15/2001
Dr. Debananda Das
"QM/MM methods using CHARMM".





11/29/2001
Dr. Mingliang Tan
"Soft-sticky dipole water: a single-site water model".





12/6/2001:
Speaker= Prof. Toshiko Ichiye
Affiliation=
"Computational studies of iron-sulfur proteins".





12/13/2001
Dr. Peter Steinbach,CIT
"Modeling Mutation-Induced Drug Resistance with Soft-Core Potentials and a 'Monte-Carlo / Minimization' Search".





12/20/2001
Dr. George Stan
NHLBI,NIH
"Chaperonin-mediated protein folding".





1/3/2002
Dr. Xiongwu Wu
NHLBI, NIH
"Direct observation of two-state b-hairpin folding in water through computer simulation".





1/10/2002
Dr. Yong Lee
Affliation
"Hydrogen Bonding Interactions between Potent Inhibitor Tolrestat and Aldose Reductase".





1/17/2002
Dr. Kyung-Hoon Lee
Department of Medicinal Chemistry, Purdue University
"Molecular Dynamics Simulations and Thermodynamic Studies of Hemoprotein Model Compounds".





1/24/2002: Dr. Andrey Kajava
CIT
"A Christmas eve story about 26S proteasome".





2/7/2002
Dr. Charles Schwieters
CIT
"Molecular Dynamics in Internal Coordinates - What's it good for?".





2/14/2002
Dr. Xiongwu Wu
NHLBI, NIH
"Molecular modeling using cryoelectron microscopy images: method and CHARMM implementation".





2/28/2002
Prof. William M. Southerland
Howard University College of Medicine
"The dynamics of ligand binding to dihydrofolate reductase".





7/18/2002
Dr. Dusanica Janezic
National Institute of Chemistry, Ljubljana, Slovenia:
"Symplectic MD integration".





9/12/2002
Dr. Gopalan Raghunathan
San Diego Supercomputer Center
"Protein Modeling - Some recipes and an application".





10/3/2002
Prof. Kevin Cahill
"On the Kinematics of Protein Folding".





10/10/2002
Journal club.





10/17/2002
Dr. Gerhard Hummer
Laboratory of Chemical Physics, NIDDK
"Carbon Nanotubes as Molecular Channels".





10/24/2002
Nicolae-Viorel Buchete, a postdoctoral candidate
"Spherical Harmonic Analysis of Orientation Dependent Statistical Potentials Derived from Protein Structural Databases".





10/31/2002
Mr. Wenjun Zheng
"Protein structure prediction aided by Solution X-ray Scattering data".





11/14/2002
Dr. Paul Sherwood
CLRC Daresbury Laboratory, Warrington, UK:
"Facing the Challenge of Computational Chemistry on HPC(x),the UK's first TeraScale Academic Supercomputer".





11/21/2002
Mr. Lee Woodcock
"The Problematic Energy Differences Between Cumulenes and Poly-ynes: Does this Point to a Systematic Improvement of Density Functional Theory?".





12/17/2002
Mr. Jhih-Wei Chu
Department of Chemical Engineering, MIT:
"Progress in advancing the nudged elastic band method".





1/9/2003
Dr. Xiongwu Wu
NHLBI, NIH:
"b-hairpin folding mechanism uncovered from reversible folding simulations".





1/16/2003
Mr. Jeffery B. Klauda, University of Delaware:
"Intermolecular Potentials from ab initio Quantum Mechanics and their Applications to Gas Hydrates and Nanoporous Carbon Systems".





1/23/2003
Prof. Youngdo Won
"Molecular Dynamics Simulations of Atomic Layer Deposition Processes".





2/13/2003
Dr. Rick Venable
FDA
"Micelle-Bound Conformation of a Hairpin-Forming Peptide: Combined NMR and Molecular Dynamics Study".





2/27/2003
Rich, Toshiko, and Bernie
Journal club.





3/13/2003
Dr. Sanjib Senapati
"Molecular Dynamics Simulation Studies of Fluorosurfactant Based Reverse Micelles in Supercritical Carbon Dioxide".





3/19/2003
Dr. Milena Shahu
Department of Chemistry, American University
"Theoretical Studies of the Dynamics of Electronically Excited Vinyl, Allyl and Propargyl Radicals".





3/20/2003
Mr. Ye Che
Center for Computational Biology, Washington University, School of Medicine
"A Path To The Power Ball: Drug Design On Protein-Protein Interfaces".





4/10/2003
Dr. Morris Krauss
"Two Two-Metal Enzyme Mechanisms: Zinc Lactamase and Adenylyl Cyclase".





5/1/2003
Dr. Anna Skibinsky
Center for Polymer Studies,Boston University
"Generic mechanism for generating a liquid-liquid phase transition".





5/8/2003
Dr. Yong Sok Lee
"Dynamics of the Proton Transport".





6/24/2003
Prof. Alex Mackerell
"Computational studies of base flipping in DNA alone and complexed to the cytosine-5-methyltransferase from Hhal".





9/11/2003
Dr. Margaret Cheung
Univ. of Maryland
"Solvation in protein folding analysis--combination of theoretical and experimental approaches".





9/18/2003
Dr. Dusanha Janezic
National Institute of Chemistry, Ljubljana, Slovenia:
"Analytical treatment of high-frequency motions in molecular dynamics".





9/25/2003
Dr. Richard Pastor
Chief, Laboratory of Biophysics, FDA
"Two new things you should know about: LRC and CMAP".





10/2/2003
Dr. Michael S. Lee
U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD:
"Solvation Energies: From Implicit to Explicit".





October 9, 2003
Dr. Peter Steinbach, chief of the Center for Molecular Modeling, CIT
"Predict protein structures using implicit solvation models".





October 16, 2003
Prof. Tom Woolf from Departments of Physiology and of Biophysics, Johns Hopkins University
"Simulations of membrane:protein, membrane:ion, and membrane:membrane systems".





October 30, 2003
Dr. Shuqiang Niu from Department of Chemistry, Georgetown University
"Deeper Insight into the Redox Site of Iron-Sulfur Proteins".





November 6, 2003
We have Prof. Dmitri Klimov from Institute for Physical Science and Technology, University of Maryland
"Assembly of Aβ16-22 oligomers: Role of sequence and environment".





November 13, 2003
We have Prof. John Brady from Cornell University
"Studies of Structure in Aqueous Solutions of Complex Biomolecular Solutes".





December 4, 2003
We have Prof. Diana Murray from Department of Microbiology and Immunology and the Institute for Computational Biomedicine Weill Medical College of Cornell
"Computational analysis of phosphoinositide signaling: Limits of current approaches and plans for incorporating dynamical methods".





December 11, 2003
Dr. Mingliang Tan from Dept. Chemistry, Georgetown University:
"Understanding reduction potential changes in rubredoxins".





January, 15, 2004
Prof. Lai-Sheng Wang, Department of Physics, Washington State University and W.R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
"Probing the Electronic Structures of Multiply-Charged Anions and Fe-S Clusters".





January 22, 3004
Dr. Sergio A. Hassan, Center for Molecular Modeling, CIT
"Toward the development of a comprehensive continuum description of biomolecules for large-scale Molecular Mechanics simulations".





January 29, 2004
Dr. George Stan
NHLBI
"Computational studies of chaperonin-mediated protein folding".





February 5, 2004
Dr. Jeffery Klauda
NHBLI
"The evaluation and improvement of force fields: Alkanes and their relation to lipid tails and beta-hairpin folding".





February 12, 2004
Dr. Gary Holtom
PNL
"CARS microscopy: not just Raman imaging of live cells".





February 20, 2004
Professor Austen Angell
Department of Chemistry and Biochemistry, Arizona State University:
"Cold Folding Studies Of Lysozyme Using A Novel Solvent In Which Folding Energetics Are Unchanged, Unfolded Protein Does Not Aggregate, And Ice Never Forms".





February 26, 2004
Dr. Christine Peter
Laboratory of Chemical Physics, NIDDK:
"Effects of different treatments of electrostatic interactions in molecular dynamics simulation".





March 4, 2004
Rick Venable from Biophysics Lab of FDA:
"Alpha- and beta-Octyl-Glucoside as Probes of Exocyclic Conformation and Dynamics in Simple Sugars".





March 11, 2004
Dr. Christian S. Parry
University of Massachusetts Medical School, Department of Pathology, Worcester, Massachusetts:
"Crystallographic structure of the human leukocyte antigen DR52a (DRB3*0101) at 2.2A resolution: Functional and comparative analysis of class II MHC molecules".





March 18, 2004
Rick Venable
Biophysics Lab of FDA:
"Alpha- and beta-Octyl-Glucoside as Probes of Exocyclic Conformation and Dynamics in Simple Sugars".





March 19, 2004
Prof. Robert A. Latour Jr.
Clemson University, Clemson, SC
"Molecular Simulation of Protein Adsorption to Materials Surfaces".





March 25, 2004
Prof. Toshiko Ichiye
Georgetown University:
Water, Water Everywhere!





April 1, 2004
Prof. Wah Chiu, Alvin Romansky
Professor of Biochemistry, Director of National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX
"Structural Polymorphism of Molecular Components in Biological Complexes revealed by Electron Cryomicroscopy".





April 8, 2004
Dr. Zhexin Xiang
Center for Molecular Modeling, CIT, NIH
"Bridging physical chemistry and bioinformatics in high resolution structure modeling".





April 15, 2004
Prof. Steve Rick,
Department of Chemistry, University of New Orleans, and Department of Chemistry, Southern University of New Orleans, New Orleans, LA
"Water in Protein Interiors".





May 6, 2004
Prof. Jeffrey Gray
Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD.
"Developments in protein-protein docking".





May 13, 2004
Dr David M Belnap
National Institute of Arthritis and Musculoskeletal and Skin Disease, NIH.
"Three-Dimensional, Cryo-Electron Microscopy: Something from (Nearly) Nothing".





May 20, 2004
Prof. Ozlem Keskin
Chemical and Biological Engineering, Koc University, Istanbul, and currently at Laboratory of Experimental and Computational Biology, NCI-Frederick, MD.
"Hot Regions in Protein-Protein Interactions".





May 27, 2004
Dr. Robert Best
Laboratory of Chemical Physics, NIDDK
"Investigating protein side-chain dynamics by simulation and experiment".





June 10, 2004
Dr. Brooks is planning to give a CHARMM course in the coming months. He will discuss the content and schedule of this course.





June 17, 2004
Dr. Xiongwu Wu
NHLBI
"Isotropic periodic sum: an efficient and accurate approach to calculating long range interactions of homogenous systems".





July 1, 2004
Prof. Yuko Okamoto
Dept. of Theoretical Studies, Institute for Molecular Science, Okazaki, Japan
"Comparisons of protein force fields by generalized-ensemble simulations".





August 5, 2004
Prof. Ahmed E. Ismail
Department of Chemical Engineering, Massachusetts Institute of Technology
"Multiresolution methods for materials modeling".