Seminar Series

Carlos Simmerling organized the Laufer Center seminar series in the fall of 2008. In the summer of 2012, we began, with the permission of the speakers, to record videos of these events. Students and faculty are invited for refreshments before the talks at the Laufer Center Lounge. New seminar announcements are posted on our calendar and linked to our home page.

2014

SpeakerAffiliationTitleDate
Brandon S. Razooky Oak Ridge National Laboratory Nanofabrication Research Laboratory Group & Center for Nanophase Materials Sciences
Abstract      Video
07/25
Chris Sander Computational Biology Center Memorial Sloan Kettering Cancer Center, New York City

Laufer Distinguished Lecturer--Cancer systems biology and the design of combinatorial therapy

Abstract        Video

06/03
Chris Sander Computational Biology Center Memorial Sloan Kettering Cancer Center, New York City

Laufer Distinguished Lecturer--Physics meets biology

Abstract       Video

06/02
Firas Khatib University of Massachusetts Dartmouth Foldit: Scientific discovery by protein folding game players
Abstract     
05/27
Gabriel Rocklin University of Washington Designing protein structures de novo the Rosetta way
Abstract     
05/22
John D. Chodera Memorial Sloan-Kettering Cancer Center Redesigning Drug Design
Abstract      Video
04/29
Dave Thirumalai University of Maryland Stepping kinetics of Myosin motors: Moving forward, Backward, and foot Stomping
Abstract      Video
04/22
Marco Cosentino Lagomarsino Université Pierre et Marie Curie Statistical laws in genome evolution
Abstract      Video
04/15
Tack Kuntz UCSF
Peter Kollman Lecture
Computation, Modeling & Evolution at UCSF: Past, Present, Future

      Video or Original Video from UCSF
04/03
Shenshen Wang MIT Guiding Affinity Maturation to Generate Broadly Neutralizing Antibodies
Abstract      Video
04/01
Darrin York Rutgers University

Multiscale modeling methods to study RNA folding and catalysis
Abstract      Video

03/25
NYTaC3 Stony Brook University

Robert Rizzo, Stony Brook University: Strategies for lead discovery using footprint similarity scoring, Video

 

Ping Liu, BNL: Theoretical insight into heterogeneous catalysis at nanoscaleVideo

 

Scott Auerbach, University of Massachusetts, Multiscale Modeling of Inorganic Nanopore Formation, Video

 

Ken Dill, Stony Brook University, The Principle of Maximum Caliber: a new way to look at Nonequilibrium Statmech

 

Themis Lazaridis, City College, CUNY, Studies of peptide translocation and pore formation in lipid bilayers, Video

 

George Makhatadze, Rensselaer Polytechnic Institute, Modulation of protein folding energy landscape by charge‐charge interactions: Experimental and computational studies, Video

 

Vikas Nanda , Rutgers University, Molecular Design of Collagen Higher‐Order Assembly, Video

 

Nandini Ananth, Cornell University, Path‐integral based dynamics for multi‐electron processes

03/21
Seth Horne University of Pittsburgh Biomimetic Agents and Designer Materials from Protein-like Molecules Beyond Nature’s Covalent Structures
Abstract      Video
03/18
Andrés Cisneros Wayne State University Insights on liquid systems and DNA repair from computational simulations
Abstract      Video
03/11
Daniel S. Fisher Stanford Univeristy How much sex is enough?
Abstract
02/12
Ivet Bahar University of Pittsburgh Target flexibility, druggability and promiscuity: Major considerations in computer-aided drug discovery
Abstract      Video
01/14

2013

SpeakerAffiliationTitleDate
Robert Best NIDDK, National Institutes of Health How important are non-native interactions for protein folding? Insights from all-atom simulations
Abstract      Video
12/10
Heather Carlson University of Michigan MixMD: Development of Accurate Methods for Mapping Protein Surfaces
Abstract      
12/03
Jesmin Jahan Tithi Stony Brook University Fast Polarization Energy on Multicores, Clusters of Multicores and GPUs
Abstract      
11/26
Haw Yang Princeton University Insights from Single-Molecule Protein Dynamics—Conformation Bias, Local Unfolding, and Architectural Encoding
Abstract      
11/19
Sagar D. Khare Rutgers, The State University of New Jersey Computational design of novel protein functions
Abstract      
11/05
Shekhar Garde Rensselaer Polytechnic Institute Water, Proteins, Interfaces, and Assembly: A New Molecular Perspective
Abstract      
10/22
John Karanicolas University of Kansas Designing chemical tools to modulate protein function
Abstract      Video
10/10
Dima Kozakov Boston University Global sampling of macromolecular association energy landscapes using Fast Fourier Transforms and their generalizations.
Abstract      
09/18
Jose Onuchic Rice University From Protein Folding to Molecular Machines of Life
Abstract      Video
09/16
Joseph Morrone Columbia University The role of molecular scale hydrodynamics in the kinetics of hydrophobic assembly
Abstract      Video
07/24
Qing Nie UC Irvine Robust and Stochastic Dynamics in Signal Transduction and Developmental Patterning
Abstract       Video
04/30
Mike Keiser SeaChange Pharmaceuticals, Inc. Predicting unexpected off-targets for approved drugs
Abstract       Video
04/23
Sasha Levy Stanford University High-throughput lineage tracking reveals complex population dynamics in response to environmental change
Abstract       Video
04/09
Chenghang Zong Harvard Whole Genome Amplification and Sequencing of Single Human Cells
Abstract       Video
04/04
Kirill Korolev MIT Ecology and evolution of cancer tumors and expanding populations
Abstract       Video
03/28
Lucas Carey Weizmann Institute Understanding DNA encoded mechanisms of regulation using high-throughput measurements of cell-to-cell variability
Abstract       Video
03/13
Daniel Dwyer Boston University Quantitative exploration of antibiotic-induced bacterial cell death physiology
Abstract       Video
03/12
Danielle Basset University of California Santa Barbara Network Architecture and Predictive Dynamics of Brain Systems
Abstract      
03/07
Jianhua Xing Virgina Polytechnic Institute and State University Physics meets biology: Simplicity out of complexity
Abstract       Video
03/05
Zachary Pincus Yale University Variability in Longevity and the Origins of Individuality
Abstract       Video
02/26
Vikas Nanda Rutgers University Computational design of protein misfits
Abstract       Video
02/19
David Mobley University of California, Irvine Calculating binding free energies from molecular simulations: Blind predictions, model binding sites, and automated planning
Abstract       Video
02/12
Joanna Slusky Developmental Therapeutics Philadelphia The ins and outs of charges in membrane proteins
Abstract       Video
01/29
Cheemeng Tan Carnegie Mellon University Creating Synthetic Biological Systems with Coupled Genetic and non-Genetic Control Elements
Abstract       Video
01/22

2012

SpeakerAffiliationTitleDate
D. Allan Drummond University of Chicago Selection against protein aggregation at the proteome scale
Abstract      
12/11
Jie Xiao Johns Hopkins University Gene regulation at the single-molecule level: transcription factor and DNA looping
Abstract       Video
11/13
Gabor Balazsi The University of Texas MD Anderson Cancer Center Networks, noise and evolution: Lessons from synthetic gene circuits
Abstract       Video
11/06
Lingchong You Duke University The inoculum effect and band-pass bacterial response to periodic antibiotic treatment
Abstract       Video
10/09
Dave Mathews University of Rochester Medical Center 09/25
Guanyu Wang George Washington University Around Singularity, the Connections of Diseases
Video
09/18
Brandon Xia Boston University Biological Networks in Three Dimensions
Video
09/11
Ron Koder CCNY Engineering Artificial Protein Function
Video
09/04
Claus Wilke University of Texas at Austin A structural perspective on protein molecular evolution
Abstract       Video
08/28
Julia Hockenmaier University of Illinois at Urbana Champaign Dynamic programming for ab-initio prediction of protein folding routes
Abstract      
05/29
Willy Wriggers Weill Cornell Medical College Emergent Complexity of Multiscale Computational Modeling
Abstract      
04/24
Adrian Roitberg University of Florida,Gainesville Sometimes a pKa is not a pKA. Protein Simulations at Constant pH
Abstract      
04/17
Yuhai Tu IBM Watson Research Center Systems biology of a simple organism: On E. coli's memory, computation, and energy cost
Abstract      
03/20
Jeffrey Gore Massachusetts Institute of Technology Cooperation, cheating, and collapse in microbial populations
Abstract      
01/24

2011

SpeakerAffiliationTitleDate
Regis Pomes University of Toronto Aggregated Yet Disordered: Towards a Unified Model of Structure and Function in Self-Assembled Elastomeric Proteins
Abstract      
12/13
Markus Seeliger Stony Brook University Medical School Mechanism of a New Class of Highly Specific Src Inhibitors
Abstract      
11/29
Hue Sun Chan University of Toronto Cooperativity, Local-Nonlocal Coupling, and Nonnative Interactions in Protein Folding
Abstract      
11/15
Gregory A. Voth University of Chicago Theory and Simulation of Biomolecular Systems: Surmounting the Challenge of Bridging the Scales
Abstract      
11/08
Joel L. Sussman Weizmann Institute of Science Intrinsically Disordered Proteins: Why are they More Abundant in Higher Organisms?
Abstract      
10/25
Joanna Masel University of Arizona Molecular errors, cryptic genetic variation, and evolvability
Abstract      
10/04
Hong Qian University of Washington Mesoscopic Open Biochemical Reaction Systems and Delbruck-Gillespie Processes for Stochastic Biochemical Population Dynamics
Abstract      
09/23
Jhih-Wei Chu University of California, Berkeley Multiscale Simulation for Biomolecular Engineering: Protein Allostery and Cellulose Deconstruction
Abstract      
09/14
Koby Levy Weizmann Institute of Science Biophysics and evolution of post-translation modification
Abstract      
06/13
Purushottam Dixit John Hopkins University Thermodynamics of metal-protein interactions
Abstract      
05/24
Jiang Zhu NIAID/NIH Analyzing CD4 binding site-directed broadly neutralizing HIV-1 antibodies by 454 pyrosequencing and computational bioinformatics
Abstract      
05/17
Paul Matsudaira National University of Singapore Dynamics of nm-size droplets of water at the confined-bulk transition
Abstract      
05/12
Jorg Schwender Brookhaven National Laboratory Quantitative Analysis of Metabolic Fluxes in Plants
Abstract      
05/03
Ross Walker University of California, San Diego Supercomputer in a Desktop: Extreme Acceleration of Scientific Applications Using NVIDIA GPUs
Abstract      
04/26
Hao Ge Fudan University Stochastic dynamics in biochemical systems: from single-molecule kinetics to Chemical master equation
Abstract      
04/21
Sebastian Bernhardsson Copenhagen University Structural correlations in bacterial metabolic networks
Abstract      
04/19
Alexey Onufriev Virginia Tech The Simple Approaches to Complex Biology
Abstract      
04/12
Themis Lazaridis City College of New York Modeling Membrane Binding and Permeabilization by Antimicrobial Peptides
Abstract      
03/22
Ronald M. Levy Rutgers University Exploring landscapes for protein binding and folding using replica exchange dynamics, kinetic networks and Markov state models
Abstract      
03/15
Yan Li Brookhaven National Laboratory First-Principles Studies of Cellulose I: crystal structure, intermolecular interactions and water adsorption
Abstract      
03/08
Michael Schatz Cold Spring Harbor Laboratory Cloud Computing and the DNA Data Race
Abstract      
02/15

2010

SpeakerAffiliationTitleDate
Marco Ceruso The City College of New York, CUNY Elnedin: a mixed coarse-grained molecular model for the simulation of protein dynamics and protein interactions 11/30
David R. Langley Bristol-Myers Squibb Co., R&D Three-dimensional models of the HIV-1 integration complex 11/16
Lee H. Woodcock University of South Florida Multiscale Modeling as an Avenue to Explore Enzyme Reactivity and Structure 11/02
Kenneth Foreman Astellas Pharma Industrial Strength Computational Chemistry 10/19
Wei Yang Florida State University High Order Generalized Ensemble Methods: A Possible Path to Quantitative Biomolecular Simulations 10/12
Bud Mishra New York University Detectability of Certain Dark-Genome-Matter Candidates: Algorithms for Assembling Genomes Correctly 09/28
Chris Sander Memorial Sloan-Kettering Cancer Center Systems Biology of Cancer Cells 09/21
Bill Jorgensen Yale University NYAS Chemical Biology Discussion Group Meeting 06/08
Emmanuel Mongodin University of Maryland School of Medicine Pan Genome of Borrelai burgdorferi 05/18
Marta Filizola Mount Sinai School of Medicine Molecular Recognition, Activation, and Functional Specificity of G-Protein Coupled Receptors as Assessed by Biased Molecular Dynamics 05/04
Distinguished Speakers Stony Brook University Cancer Center and Department of Molecular Genetics & Microbiology Symposium Cancer Stem Cells, Differentiation and Metastasis Symposium 04/27
Ken A. Dill University of California, San Francisco Nonequilibrium statistical mechanics of few-particle systems, such as in biology and nanotechnology 04/13
Roberto Sanchez Mount Sinai School of Medicine Identifying protein-ligand binding sites: combining physics and evolution 04/06
Tomas Lindahl London Research Institute 2010 ZICKLER LECTURE 03/30
Daniel Bogenhagen, MD Pharmacological Sciences, Stony Brook University Mitochondrial Molecular Systems Biology: From the Origins of Life to Human Disease 03/16
James Glimm Applied Mathematics and Statistics, Stony Brook University Parallel Computing: A Tutorial--Everything you wanted to know but were afraid to ask. 03/15
Danny Bluestein Bioengineering, Stony Brook University Numerical modeling approaches for optimizing cardiovascular devices and enhancing cardiovascular disease diagnostics 03/09
Yingkai Zhang Chemistry, New York University Multiscale Simulation of Histone Modifications
Abstract      
03/02
Wei Zhu Applied Mathematics and Statistics, Stony Brook University New Development in Pathway zhang 02/23
John R. True Ecology and Evolution, Stony Brook University The genome as an environment: the role of epistatic genes and networks in adaptation and speciation. 02/09

2009

SpeakerAffiliationTitleDate
David Case Chemistry & Chemical Biology, Rutgers University Critical tests of the quality of protein molecular dynamics simulations in solution and crystals 12/15
Bernard Brooks Laboratory of Computational Biology, National Institutes of Health/National Heart, Lung, and Blood Institute Examining Protein Structure and Function using Multi-scale Methods 12/08
Steven Skiena Computer Science, Stony Brook University Genome Sequence Assembly and Synthetic Design: Better Reading and Writing through Algorithmetic 12/01
Ellen Li Department of Medicine, Division of Gastroenterology and Hepatology; Stony Brook University A novel pathway discovery and analysis paradigm for inflammatory bowel diseases 11/24
Charles M. Fortmann Materials Science & Engineering; Stony Brook University The biomechanics of protein folding and applications 11/17
Ken A. Dill University of California at San Francisco Exploring the physical principles of protein folding 11/03
Alex MacKerell University of Maryland School of Pharmacy Optimizing ligand-protein interactions via SILCS: Site Identification by Ligand Competitive Saturation 10/27
Eugene V. Koonin National Institutes of Health Systems biology and universals of genome evolution 10/13
DISTINGUISHED SPEAKERS ICB&DD Symposium Frontiers in Chemical Biology and Drug Discovery 10/06
Robert Jernigan Iowa State University Functional protein motions
Abstract      
09/29
DISTINGUISHED SPEAKERS Laufer Center Inaugural Symposium 09/25
Randy Jirtle Department of Radiation Oncology, Duke University, Durham, NC Epigenetics: The New Genetics of Disease Susceptibility 05/19
John Moult Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute SNPs, Protein Structure, and Disease 05/12
William Studier Brookhaven National Laboratory, Upton, NY Learning from genome sequences of E. coli B and K 05/05
Andrea Califano Center for Computational Biology and Bioinformatics, Columbia University Medical Center, New York, NY Molecular Network analysis reveals master regulators of physiologic and pathologic human phenotypes 04/28
Nicholas Patterson The Broad Institute, Cambridge, MA Learning the Genetic History of South Asia from Genome-wide Data 04/14
Michael Hadjiargyrou Stony Brook University, Stony Brook, NY Unraveling the Molecular Basis of Bone Regeneration 03/17
Dax Fu Brookhaven National Laboratory, Upton, NY Novel metallochemistry in zinc transporters: integration of structural, functional and computational analyses 03/10
Steffen Mueller Stony Brook University, Stony Brook, NY Synthetic DNA technologies - perils and promise for the future of bioscience 02/24
Mickey Atwal Cold Spring Harbor Laboratory, Cold Spring Harbor, NY Natural Selection of Genetic Fidelity 02/10
Jin Wang Stony Brook University, Stony Brook, NY Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations 02/03

2008

SpeakerAffiliationTitleDate
Michael Zhang Cold Spring Harbor Laboratory, Cold Spring Harbor, NY Computational Dissection of Mammalian Regulation Subnetworks 12/16
Weigang Qiu Department of Biological Sciences, Hunter College, New York, NY Lineage-specific genomic variations in Lyme disease bacteria and implications for pathogenesis 12/09
David S. Eisenberg University of California, Los Angeles, CA Structural Insights into Amyloid and Prion Diseases 11/25
David Baker Department of Biochemistry, University of Washington, Seattle, WA 2008 ADRIEN ALBERT LECTURE - From prediction of structure to design of function 11/21
Arnold J. Levine The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 2008 ZICKLER LECTURE - The p53 Pathway: Cancer, Fertility, Metabolic Control and the Central Nervous System 11/11
Bruce Futcher Stony Brook University, Stony Brook, NY Transcription Circuits, in Shades of Green and Red 11/04
Robert C. Rizzo Stony Brook University, Stony Brook, NY Characterization of drug resistance at the atomic level 10/28
Eli Hatchwell Stony Brook University, Stony Brook, NY The Future of Personalized Medicine 10/21
Stanley Fields University of Washington, Seattle, WA Footprinting the Genome 10/17
Uri Alon Weizmann Institute of Science, Rehovot, Israel Design Principles of Biological Circuits 10/07
John Reinitz Stony Brook University, Stony Brook, NY Canalization of transcription in the Drosophila blastoderm: from data to dynamical systems 09/23
Sergei Maslov Brookhaven National Laboratory, Upton, NY Modeling biomolecular networks: from metabolism and its regulation to protein-protein interactions 09/16
David F. Green Stony Brook University, Stony Brook, NY Applied protein design: Engineering molecular interactions in complex systems 09/09