Past Seminars

• Fall 2010

  October 19, 2010: Tudor Oprea, University of New Mexico, Computer-Aided Drug Repurposing

  October 26, 2010: Bette Korber, T-6, LANL, Variability in HIV Vaccine Design

  November 2, 2010: Yunzhou Sophia Shi, Purdue University Nanomedicine and chemical imaging approaches for traumatic spinal cord injury

  November 8, 2010: Rajan Lamichhane, Wayne State University Study of protein-RNA interactions by using fluorescence resonance energy transfer (FRET) and single-molecule FRET (smFRET) Special Time: Monday at 11:00-12:00

  November 16, 2010: Geoffrey Waldo, LANL. Special Time: 3:00-4:00pm Protein tagging and labeling systems for protein chemistry and cellular biology.

  November 23, 2010: No Seminar Thanksgiving week

  November 30, 2010: No Seminar this week

  December 7, 2010: Dmitry Novikov, NYU Medical Center NMR relaxation and diffusion in biological tissues and heterogeneous media

  December 14, 2010: No Seminar this week

  December 21, 2010: Cesar Lopez Bautista, University of Groningen, The Martini force field: Different flavors for molecular simulations Special Time: 10AM

• Summer 2010

  Aug 24: Srabanti Chaudhury, University of Texas, Austin, Dynamic disorder in single enzyme kinetics: effects of conformational fluctuations

  Aug 17: Chunbo Lou, University of California at San Francisco*:Jul 20: Alvin Tamsir, University of California at San Francisco Robust multicellular computing using genetically-encoded NOR gates and chemical “wires”

  Aug 10: Chris Bystroff, Rensselaer Polytechnic Institute, GFP-based Biosensors NB: this talk will take place in Room 203A/B, Building 4200, TA-3; this room is on the same floor as Hot Rocks Java Cafe in the Los Alamos Research Park building.

  Aug 3: Arjun Raj, University of Pennsylvania A single molecule view of cell fate: FISHing for worm guts NB: this talk will take place in Room 203A/B, Building 4200, TA-3; this room is on the same floor as Hot Rocks Java Cafe in the Los Alamos Research Park building.

  Jul 27: Jasmin Fisher, Microsoft Research Cambridge

• Spring 2010

  Jun 2: Cécile Fradin, McMaster University,Diffusion in living cells: simple or anomalous? NB: this talk is scheduled for a Wednesday 2:00 pm

  May 25: Lydia Tapia, University of Texas, Austin, From Robots to Molecules: Intelligent Motion Planning and Analysis with Probabilistic Roadmaps, NB: this talk is scheduled to start at 2:30 pm

  May 18: Jon Houtman, University of Iowa, Characterization of the Complexity of Signaling Complexes in Human T Cells

  May 11: Vittorio Cristini, University of Texas Health Science Center, Houston, Multiparameter Computational Modeling of Tumor Invasion

  May 4: Gurol Suel, UT Southwestern Medical School, Noisy out of necessity: the relationship among gene circuit architecture, dynamics and biological function

  Apr 20: Simona Cocco, Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods

  Apr 6: Itai Cohen, Cornell University, A Mechanism for Shear Energy Dissipation in Articular Cartilage

• Winter 2010

  Mar 23: Linda Petzold, University of California, Santa Barbara, Discrete Stochastic Simulation of Spatially Inhomogeneous Biochemical Systems

  Mar 9: Jin Yang, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Sensory estimation of ligand concentrations by a single receptor and a receptor array

  Mar 2: Eric Klavins, University of Washington, Feedback Control with Bio-molecular Circuits

  Jan 26: Graham Mackay, University of Melbourne, Expression and Function of Antibody Fc Receptors on Human Airway Smooth Muscle Cells

  Jan 12: Cynthia A. Derdeyn, Emory University,Neutralizing antibody responses in HIV-1 and nonpathogenic SIV infection

  Jan 5: Bin Hu, University of New Mexico

  Dec 22: Erwin Van Meir, Emory University

• Fall 2009

  Dec 16: Guy Dimonte, X-1, A cell kinetics model for prostate cancer and its application to clinical data and individual patients NB: this seminar talk is on a Wednesday, 1 PM - 2 PM

  Dec 15: Elaine L. Bearer, University of New Mexico School of Medicine, Computational modeling of tumor progression: from physical laws to biological prediction

  Dec 8: Gregor Neuert, Massachusetts Institute of Technology

  Dec 1: Feng Gai, University of Pennsylvania, Kinetics of peptide folding in dehydrated and crowded environments

  Nov 24: Jaeymeong Jung, Howard Hughes Medical Institute, Stanford University, Single molecule study of disassembly of SNARE complex by NSF/α−SNAP

  Nov 17: Srinivas Iyer, Bioscience Division, Los Alamos National Laboratory, Proteomic analysis on a MALDI-MS platform

  Nov 9: Hanna Salman, University of Pittsburgh,Escherichia coli Cultures in Temperature Gradients This seminar is on MONDAY Nov 9th

  Nov 3: Rusty Lansford, California Institute of Technology, Structural and cellular dynamics in vascular development

  Nov 2: Dipak Barua, University of Wisconsin, Rule-Based Computational Modeling of Modular Signaling Protein Interactions This seminar is at 11 AM on Monday, November 2

  Oct 29: Robert D. Young, Northern Arizona University, Conformation relaxation dynamics of biomolecules NB: this seminar talk is on a Thursday, 10 AM - 11 AM

  Oct 20: Tijana Jovanovic-Talisman, National Institutes of Health, Artificial Nanopores that Mimic the Transport Selectivity of the Nuclear Pore Complex

  Oct 6: Sigfried Musser, Texas A&M University, Single Molecule Fluorescence Studies of Nucleocytoplasmic Transport

  Oct 1: Boguslaw Stec, Burnham Institute for Medical Research, How proteins acquired their tricks: Physical basis of protein structure and function This seminar is at 10 AM on Thursday, October 1

  Sep 22: Dr. Nikolaos G. Sgourakis, Protein Conformational and Interaction Dynamics by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments, Center for Biotechnology and Interdisciplinary studies, RPI

  Sep 15: Dr. Anurag Sethi, Development of Methods to Combine Sequence, Structure, and Network Analyses to Study Gene Annotation, Coevolution, and Allostery in Protein:RNA Complexes, Theoretical Division, Los Alamos National Laboratory

• Summer 2009

  Aug 4: Andrew H. Clayton, Ludwig Institute for Cancer Research, EGF receptor in the lime light

  July 28: Ruy M. Ribeiro, Los Alamos National Laboratory, Unraveling a pandemic: from avian to swine influenza

  July 21: Anton Zilman, Los Alamos National Laboratory, Selectivity of transport through the nuclear pore complex: from nuclear import to bio-sensors

  July 14: Linus J. Schumacher, University of Cambridge, How liquid is biological signaling? - using random graphs to study protein networks

  July 7: Omar Saleh, University of California, Santa Barbara, Single-molecule meets scaling: the low-force elasticity of single-stranded DNA

  June 30: Kim Ø. Rasmussen, Los Alamos National Laboratory, Dynamical signature of the core promoter

  June 23: Michael Samoilov, QB3/University of California, Berkeley and Lawrence Berkeley National Laboratory, Quantitative Analysis of Constructive Stochastic Designs in Biological Systems

  June 16: Christopher A. Voigt, University of California, San Francisco, Programming Cells: Using a Synthetic Light Sensor as a Fast, High-Resolution Input to Signaling Networks

  June 9: Aaron R. Dinner, University of Chicago, Genetic circuit architectures underlying cell-fate choices for immunity

  June 2: Joshua Shaevitz, Princeton University, Mechanical roles of the bacterial cytoskeleton

• Winter/Spring 2009

  May 26: Paul D. Adams, Lawrence Berkeley National Laboratory, The Joint BioEnergy Institute

  May 12: Wallace Marshall, University of California, San Francisco, The Flagellar Length Control System

  May 5: Christina D. Smolke, Stanford University, Programming RNA Devices to Control Cellular Information Processing

  Apr 28: Michael W. Deem, Rice University, Vaccine Design for Influenza and Dengue Fever

  Apr 21: Arup K. Chakraborty, Massachusetts Institute of Technology, Understanding adaptive immunity: a crossroad of the physical and life sciences

  Apr 14: Hana El-Samad, University of California, San Francisco, Stochastic Biological Circuits: Noise as a Phenotype

  Apr 7: Harmen Bussemaker, Columbia University, Learning mechanistic models of gene expression regulation from natural sequence variation

  Mar 31: Holger Conzelmann, Harvard Medical School, Model Reduction of Rule-based ODE Models: Exact vs. Approximate Approach

  Mar 24: Mingzhou Song, New Mexico State University, Computational Modeling of Interactions in Dynamic Biological Networks

  Mar 17: Ekaterina Nestorovich, NIH, Biophysics of anthrax toxin inhibition by derivatives of beta-cyclodextrin

  Mar 10: Katia Koelle, Duke University, Simple mathematical models to understand influenza’s complex evolutionary dynamics This lecture will begin at 2:30 instead the usual time of 2:15.

  Mar 3: Aleksandra M. Walczak, Princeton University, Learning design principles from noisy small gene regulatory networks

  Feb 24: Christopher V. Rao, University of Illinois, Urbana-Champaign, Coordinate regulation of virulence in Salmonella typhimurium

  Feb 17: Andrea Califano, Columbia University, Cellular Network Based Identification of Master Regulators of Physiological and Oncogenic Processes

  Feb 10: Jim Werner, LANL, Tracking single quantum dots in three dimensions: Following cell receptor traffic and membrane topology

  Feb 3: Meredith Betterton, University of Colorado, Theory of microtubule depolymerization by kinesin-8 motors

  Jan 27: Chris Myers, Cornell University, Specificity and satisfiability in biological information processing networks

  Jan 20: Pablo Iglesias, Johns Hopkins University, Theoretical and Experimental Analysis of Chemotactic Systems in Biology

  Jan 13: Yinjie Tang, Washington University, St. Louis, 13C-based Metabolic Flux Analysis of Environmental Microorganisms

  Jan 6: Harel Dahari, University of Illinois, Chicago, Modeling hepatitis C virus (HCV) dynamics: Relating intracellular (in vitro) and extracellular (in vivo) HCV kinetics under treatment

• Fall 2008

  Dec 9: Jean Krivine, Harvard Medical School, Modeling dynamic molecular compartments: the bigraphical approach

  Dec 2: William Ryu, University of Toronto, The thermal response and motor behavior of E. coli and C. elegans

  Nov 25: Tomasz Lipniacki, Polish Academy of Sciences, Exploring mechanisms of oscillations in p53 and NF-κB systems

  Nov 18: Karen Sachs, Stanford University, Learning signaling pathway structure from high throughput, multivariate single cell data

  Nov 12: Jin Yang, Chinese Academy of Sciences-Max Planck Society Partner Institute for Computational Biology, Genome-scale analysis of protein-protein interaction networks NB: this seminar will be 3:15-4:15 PM on WEDNESDAY, November 12 because of the Veterans Day holiday on Tuesday

  Nov 4: Calin Guet, University of Chicago, A Single-Cell View of Multiple Antibiotic Resistance in Escherichia coli

  Oct 28: Haw Yang, University of California, Berkeley, The Energetics and Mechanistic Roles of Protein Conformational Dynamics

  Oct 21: Lingchong You, Duke University, Biology by design: reduction and synthesis of cellular networks

  Oct 14: Jerome K. Percus, Courant Institute of Mathematical Sciences, New York University, The Ubiquity of Power Law Extrapolation of Sub-Threshold Data

  Oct 7: Sotiria Lampoudi, University of California, Santa Barbara, Adapting stochastic simulation to suit biology and biological data to suit simulation

  Sep 30: Ricardo Paxson, The MathWorks, Inc., Modelling of the Mitotic Spindle Assembly Checkpoint using SimBiology

  Sep 23: Frank Brown, University of California, Santa Barbara, Simple Models for Biomembrane Structure and Dynamics

  Sep 16: John Wikswo, Vanderbilt University, The Possibility of Automated Experiments for Inference of Metabolic Models

  Sep 9: Charlie E. M. Strauss, Bioscience Division, Los Alamos National Laboratory, On the origin of symmetry in biology: Protein oligomers

  Sep 2: Kathleen B. Hall, Washington University School of Medicine, St. Louis, Discovering the role of Protein Dynamics in RNA recognition motifs

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