The Laboratory of Computational Biology

Richard Pastor and Bernard Brooks


Aug. 3, 2022
"Modeling Conduction in Pentameric Cation Channels, and Understanding Charged Lipids (Gangliosides and PIP3) and Their Behavior in Electric Fields"
Nauman Sultan
The Laboratory of Computational Biology, NHLBI, NIH and The Johns Hopkins University

Jun. 16, 2022
"Prediction of Protein Side Chain pKa with Representation Learning"
Dr. Hatice Gökcan
Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania

May 19, 2022
"Deep Learning Approaches to Molecular Sampling"
Dr. Andreas Krämer
Frank Noé's group, Freie Universität Berlin

May 5, 2022
"Permeability from Path Sampling"
Prof. An Ghysels
IBiTech-Biommeda, Faculty of Engineering and Architecture, Ghent University, Belgium

Apr. 21, 2022
"Synergizing Enhanced Sampling and Machine Learning Strategies for Rapid Exploration and Generation of Complexree-energy Landscapes"
Prof. Mark E. Tuckerman
Department of Chemistry, New York University, New York

Apr. 14, 2022
"Machine Learning for Free Energy Calculations and Force Field Optimization, with Applications to Chromatin Folding"
Prof. Bin Zhang
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts

Apr. 7, 2022
"Modeling the Mesoscale Dynamics of Membrane and Peripheral Proteins"
Dr. Mohsen Sadeghi
Frank Noé's group, Freie Universität Berlin

Mar. 31, 2022
"JAX MD: A Framework for Differentiable Atomistic Physics"
Dr. Samuel Schoenholz
Google, Mountain View, California, United States

Mar. 29, 2022
"ProBiS-Fold-CHARMMing: Binding site detection for structural Human Proteome in Drug Discovery"
Prof. Dušanka Janežič
University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Koper, Slovenia

Mar. 24, 2022
"Investigating Biomolecular Rare Events with Artificial Intelligence Augmented Molecular Dynamics"
Yihang Wang
Tiwary Research Group, University of Maryland, College Park

Mar. 17, 2022
"The Thermodynamics of Polymorphism"
Dr. Frank Pickard
Pfizer, Cambridge, Massachusetts, United States

Mar. 10, 2022
"Current GAFF and GAFF-Based Scoring Function Development"
Dr. Junmei Wang
School of Pharmacy, University of Pittsburgh

Mar. 3, 2022
"Recent Advances in Machine-Learning and Coarse-Grained Force-Fields"
Dr. Aleksander Durumeric
Frank Noé's group, Freie Universität Berlin

Feb. 17, 2022
"Structure and Regulation of Membrane Transporters"
Dr. Cristina Fenollar Ferrer

Feb. 10, 2022
"Coarse-Grained Models for Intrinsically Disordered Proteins and Liquid-Liquid Phase Separation"
Dr. Thomas Dannenhoffer-Lafage
Robert Best's group, NIDDK, NIH


May 27, 2021
"Variational Embedding of Protein Folding Simulations using Gaussian Mixture Variational Autoencoders (GMVAEs)"
Mahdi Ghorbani

Apr. 29, 2021
"Can artificial intelligence help understand and predict molecular dynamics?"
Dr. Pratyush Tiwary
Department of Chemistry & Biochemistry and Institute for Physical Science & Technology, University of Maryland

Mar. 4, 2021
"Relative Binding Free Energy Calculations Toward Drug Discovery and Study of Contaminants"
Yigitcan Eken
Wilson Research Group, Department of Chemistry, Michigan State University

Sept. 10, 2020
"Machine Learning for Protein-Ligand Interactions"
Prof. David Sherrill
Georgia Institute of Technology

Aug. 27, 2020
"Exploring dynamics and Network analysis of spike glycoprotein in novel coronavirus"
Mahdi Ghorbani

Aug. 20, 2020
"Conductance of Ion Channels"
Ada Chen


Aug. 13, 2020
"Simulations of transport across the blood-brain barrier"
Dr. Christian Jorgensen
Johns Hopkins University

Aug. 6, 2020
"Modeling nucleosomes, protein unfolding, and the nuclear pore complex"
Dr. David Winogradoff
Center for the Physics of Living Cells and Physics Department, University of Illinois at Urbana-Champaign

Jul. 30, 2020
"QM/MM Free Energy Simulations and Application to pKa Prediction"
Fiona Kearns
Woodcock Research Group, USF

Jul. 23, 2020
"Computational Investigation of the PETase Reaction Mechanism"
Ben Pollard
Woodcock Research Group, USF

Jul. 9, 2020
"A recent update on the CHARMM36 united atom chain model for membrane simulations"
Yalun Yu
The Laboratory of Computational Biology. NHLBI, NIH

June 25, 2020
"A Generalized Self-Guided Molecular Simulation Method: SGMDg/SGLD"
Dr. Xiongwu Wu
The Laboratory of Computational Biology, NHLBI, NIH

June 18, 2020
"Revisiting the Double Link Atom Approach for QM/MM Simulations"
Dr. Michael Jones
The Laboratory of Computational Biology, NHLBI, NIH

June 11, 2020
"OpenMM and friends"
Dr. Andrew Simmonett
The Laboratory of Computational Biology, NHLBI, NIH

June 4, 2020
"Breakthroughs in Obtaining QM/MM Free Energies"
Dr. Phillip Hudson
The Laboratory of Computational Biology, NHLBI, NIH

May 28, 2020
"Molecular dynamic simulation and in-silico ala-scanning unravel critical hot-spots for binding of nCOV-2019 to its receptor ACE2"
Mahdi Ghorbani
The Laboratory of Computational Biology, NHLBI, NIH

Mar. 12, 2020
"Coarse-grained approaches to understanding I-BAR domain organization"
Dr. Zachary Jarin
Pritzker School of Molecular Engineering, University of Chicago

Mar. 10, 2020
"Towards the automation of the design and construction of protein QM-models"
Thomas Summers
Chemistry Dept., University of Memphis

Mar. 10, 2020
"Application of RINRUS in Studying Enzymatic Reactions"
Dr. Qianyi Cheng
Chemistry Dept., University of Memphis

Jan. 31, 2020
"Asymmetry, metastable phases, and flip-flip in lipid bilayers"
Prof. Peter Olmsted
Dept of Physics, Georgetown University

Jan. 27, 2020
"Enhanced Sampling of Peptide and Small-molecule Insertion into Membranes"
Andreas Krämer
Laboratory of Computational Biology

Jan. 23, 2020
"Modifying the CHARMM C36 lipid force field for LJPME simulation"
Yalun Yu
University of Maryland

Dec. 19, 2019
"How pH Modulates the Conductance of A Sodium Channel"
Ana Damjanović
Johns Hopkins University

Dec. 12, 2019
"Automated Optimization of the CHARMM Lipid Force Field"
Dr. Andreas Krämer
Laboratory of Computational Biology

Nov. 21, 2019
"Quantum and Molecular Mechanics Studies of the Ring Puckering of Cyclopentane, Methylcyclopentane and Ethylcyclopentane"
Martin R. Schenk
Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin

Nov. 15, 2019
"Machine Learning and Markov State Modeling Applied to Simulation Studies of Proteins"
Dr. Brooke E. Husic
Department of Mathematics and Computer Science, Freie Universität Berlin

Nov. 14, 2019
"Challenge in Deeply Understanding Hypotheses of Alzhaimer's Diseases Pathophysiology"
Dr. Shuqiang Niu
Texas A&M University

Oct. 31, 2019
"Lateral pressure in asymmetric membranes"
Dr. Soohyung Park
Lehigh University, Pennsylvania

Oct. 31, 2019
"Localization and Dynamics of Quinone in Archaeal Membranes"
Dr. Shasha Feng
Lehigh University, Pennsylvania


Sept. 12, 2019
"Gasotransmitter Permeability of Plasma and Mitochondrial Membranes using Bayesian Analysis"
Prof. Christopher Rowley
Dept of Chemistry, Memorial University of Newfoundland

Aug. 8, 2019
"Surface viscosity and interleaflet friction of membranes from all-atom simulations"
Prof. Edward Lyman
Dept of Physics, University of Delaware

Jun. 6, 2019
"Exploring Convergence of Thermodynamic and Kinetic Properties of QM-cluster Enzyme Models"
Nathan J. DeYonkers
Department of Chemistry, University of Memphis

Jun. 6, 2019
"RINRUS Toolkit and its Applications"
Qianyi Cheng
Department of Chemistry, University of Memphis

May. 30, 2019
"Enhanced sampling methods for simulations of amyloid-forming peptides"
Prof. Nicolae-Viorel Buchete
School of Physics, University College Dublin

May. 23, 2019
"Recent evolutions in polarizable MD simulations"
Felix Aviat
Laboratoire de Chimie Théorique, Sorbonne Université, Paris, France

Apr. 23, 2019
"Binary Bilayer Simulations for Quantitative Characterization of Membrane Protein-Lipid Interactions"
Dr. Soohyung Park
Lehigh University

Apr. 11, 2019
"Synthetically Accessible Virtual Inventory (SAVI): Billions of Easily Synthesizable Compounds for Drug Design"
Dr. Marc C. Nicklaus
Computer-Aided Drug Design (CADD) Group, National Cancer Institute NIH

Mar. 28, 2019
"Protein interaction atlas for prediction of genetic variations involved in drug interactions and disease development"
Prof. Dušanka Janežič,
University of Primorska, Slovenia

Mar. 7, 2019
"Predicting protein-ligand binding affinity using 3D convolutional neural network"
Prof. Juyong Lee
Assistant Professor, Dept. of Chemistry, Kangwon National University, South Korea

Mar. 7, 2019
"Hydrogen-deuterium exchange and ab initio protein structure determination"
Prof. Emanuele Paci
Biological Sciences, University of Leeds, UK

Feb. 28, 2019
"Surveying the sequence space landscape of fold-switching proteins"
Dr. Lauren Porter
Looger Lab, Howard Hughes Medical Institute, Janelia

Jan. 31, 2019
"The MolSSI Driver Interface: Software Interoperability Made Simple"
Taylor Barnes
MolSSI, Virginia Tech

Jan. 31, 2019
"An Overview of The Molecular Sciences Software Institute"
Eliseo Marin-Rimoldi
MolSSI, Virginia Tech

Jan. 10, 2019
"Lipid Membranes of the Stratum Corneum and How Lipids can Influence Ion Permeation in alpha-Hemolysin"
Prof. Jeffery Klauda
Department of Chemical and Biomolecular Engineering, University of Maryland

Dec. 20, 2018
"Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer' Protofilaments"
Prof. Nicolae-Viorel Buchete
University College Dublin, Ireland

Dec. 13, 2018
"Coarse-grained molecular dynamics simulations of proteins with UNRES force field assisted by knowledge-based information"
Agnieszka Karczynska
University of Gdańsk

Dec. 6, 2018
"Computational modeling of G protein-coupled receptors"
Dr. Kenneth A. Jacobson and Dr. Veronica Salmaso
Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, NIH

Nov. 29, 2018
"Toward a comprehensive atomistic view of bacterial outer membrane remodeling"
Amy Rice
Illinois Institute of Technology

Nov. 15, 2018
"Non-equilibrium coupling of protein structure and function to translation elongation kinetics"
Prof. Ed O´Brien
Department of Chemistry, Pennsylvania State University

Nov. 08, 2018
"Fragment Molecular Orbital study of Excitonic Interactions in Fenna-Matthews-Olson Complex"
Dr. Danil Kaliakin
Department of Chemistry, Purdue University

Nov. 1, 2018
"Mechanics and Dynamics of Simulated Membranes: Extraction of Bending Moduli and Difficulty in the Extraction of Diffusion Coefficients"
Prof. Frank Brown
University of California, Santa Barbara

Oct. 19, 2018
"On the accuracy and convergence of multi-scale free energy simulations"
Dr. Gerhard König
Laboratory of Biomolecular Simulation Research, Rutgers University


July 19, 2018
"Molecular Mechanisms of Biological Energy Conversion"
Ville Kaila
Technical University of Munich

July 9, 2018
"A comparative study of forcing schemes in a multicomponent lattice Boltzmann model"
Knut Küllmer
Department of Electrical Engineering, Mechanical Engineering, and Technical Journalism (EMT)

July 9, 2018
"Multistep Integration in the Lattice Boltzmann Method: Application and Limitations"
Dominik Wilde
Department of Electrical Engineering, Mechanical Engineering, and Technical Journalism (EMT)

June 14, 2018
"Building Blocks of the Outer Membrane: Calculating a general elastic energy model for beta-barrel membrane proteins"
Prof. Henry Lessen
Johns Hopkins University

June 11, 2018
"Two-point microrheology and correlated motions: a better way to calculate diffusion coefficients for membrane simulations"
Prof. Michael Lerner
Earlham College, IN

June 7, 2018
"Constant pH simulations of an ion channel"
Prof. Ana Damjanović
Johns Hopkins University

May 10, 2018
"Kinetic conformational networks for folding and protein-protein interactions: From amyloid peptides to kinase signaling"
Prof. Nicolae-Viorel Buchete
University College Dublin

May 3, 2018
"pKa Prediction using DFT + SMD Approach"
Dr. Qiao Zeng

April 26, 2018
"Understanding Prenyltransferase Selectivity via Computational Simulations"
Dr. Daniel R. Roe

March 29, 2018
"ProBiS tools at the PDB scale for drug discovery"
Prof. Dušanka Janežič
University of Primorska, Koper, Slovenia

March 7, 2018
"Pre-pores and pores in membranes bilayers"
Dr. Neha Awasthi

Feb. 5, 2018
"Reaction coordinate for enhanced sampling of biomolecules: fool's gold or an actionable concept?"
Prof. Pratyush Tiwary
Department of Chemistry and Biochemistry & Institute for Physical Science and Technology, University of Maryland

Feb. 1, 2018
"Hydrogen bond dynamics of ubiquitin under elevated temperature and pressure"
Dr. Jinghuang
Westlake Institute for Advanced Study, Westlake University, Hangzhou, China

Jan. 25, 2018
"Regulatory Roles of Weak Encounter Complexes Between Proteins"
Dr. Seyit Kale

Jan. 18, 2018
"Kinetic Conformational Networks of Amyloid-Forming Peptides".
Prof. Nicolae-Viorel Buchete
School of Physics, University College Dublin

Dec. 21, 2017
"Updates to Biowulf with Applications to Simulation Science"
Benjamin Miller

Dec. 7, 2017
"The reason behind the high apparent dielectric constants in the interior of proteins"
Dr. Xiongwu Wu

Nov. 20, 2017
"Quantitative Characterization of Cholesterol-lipid Interactions: Partitioning of Cholesterol in Binary Bilayers"
Dr. Soohyung Park
Lehigh University

Oct. 27, 2017
"Mechanism of kinesin dimers walking on microtubules"
Alicia Pan and Allen Pan
Madison High School

Oct. 19, 2017
"Using iTTM model with REMD to Alkali-Metal-Water-Clusters/Using MD simulations with PEG-coated Nanoparticles to Study BBB Diffusivity and Targeted Drug Delivery"
Mr. Jude Tunyi
NIH NHLBI/University of Washington PRG/University of California San Diego CAICE program

Sept. 21, 2017
"From molecules to proteomes to mechanisms: A systems approach to glomerular kidney disease."
Dr. Markus Rinschen
Nephrolab Cologne / Nephrologisches Forschungslabor University, Kóln, Germany

Sept. 14, 2017
"Mechanical analysis of collagen and DNA"
Dr. Xiaojing Teng
Georgetown University


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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

Jan. 21, 2016
"Generalized Ensemble Simulations to Discuss the Amyloid Fibril Formation".
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

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

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

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

Oct. 8, 2015
"Towards a better understanding of electron polarization effects in QM/MM calculations".
Dr. Yihan Shao

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.

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


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

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

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

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

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

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

March 31, 2015
"Binding site prediction algorithms in pharmaceutical discovery".
Prof. Dušanka Janežč
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

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

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

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

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

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

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


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

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

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

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

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".
Iwona E. Weidlich

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Dec. 12, 2011
"Practice talk".
Dr. Joe Larkin

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

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

Sept. 22, 2011
"A study of excited states of oligocarbazole and firefly luciferin".
Shushu Zhang

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


Richard Pastor
"Lipid Bilayers, NMR Relaxation, and Computer Simulation".

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

Dr. Bernard Brooks
"Replica Path Method in CHARMM(I)".

Dr. Bernard Brooks
"Replica Path Method in CHARMM(II)".

Dr. Morris Krauss
"Enzyme Active Site: Structure, Spectroscopy, Reactivity".

Dr. Debananda Das
"QM/MM methods using CHARMM".

Dr. Mingliang Tan
"Soft-sticky dipole water: a single-site water model".

Speaker= Prof. Toshiko Ichiye
"Computational studies of iron-sulfur proteins".

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

Dr. George Stan
"Chaperonin-mediated protein folding".

Dr. Xiongwu Wu
"Direct observation of two-state b-hairpin folding in water through computer simulation".

Dr. Yong Lee
"Hydrogen Bonding Interactions between Potent Inhibitor Tolrestat and Aldose Reductase".

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
"A Christmas eve story about 26S proteasome".

Dr. Charles Schwieters
"Molecular Dynamics in Internal Coordinates - What's it good for?".

Dr. Xiongwu Wu
"Molecular modeling using cryoelectron microscopy images: method and CHARMM implementation".

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

Prof. Dušanka Janežič
National Institute of Chemistry, Ljubljana, Slovenia:
"Symplectic MD integration".

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

Prof. Kevin Cahill
"On the Kinematics of Protein Folding".

Journal club.

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

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

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

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

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

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

Dr. Xiongwu Wu
"b-hairpin folding mechanism uncovered from reversible folding simulations".

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

Prof. Youngdo Won
"Molecular Dynamics Simulations of Atomic Layer Deposition Processes".

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

Rich, Toshiko, and Bernie
Journal club.

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

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

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

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

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

Dr. Yong Sok Lee
"Dynamics of the Proton Transport".

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

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

Prof. Dušanka Janežič
National Institute of Chemistry, Ljubljana, Slovenia:
"Analytical treatment of high-frequency motions in molecular dynamics".

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

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

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

December 4, 2003
Prof. Diana Murray 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
"Computational studies of chaperonin-mediated protein folding".

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

February 12, 2004
Dr. Gary Holtom
"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
"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".