Seminars
are held on Tuesdays from 4:00 p.m. at 114 Dana Research
Center, with refreshments served beforehand at 3:45.
All are welcome to attend!
May 9, 2006, 4:00 pm Tuesday CIRCS Seminar
TITLE: "Modularity, Synchronization, and What We May Learn From the Brain"
By:
Jean-Jacques Slotine
Nonlinear Systems Laboratory
MIT
ABSTRACT:
Although neurons as computational elements are 7 orders of magnitude
slower than their artificial counterparts, the primate brain grossly
outperforms robotic algorithms in all but the most structured
tasks. Parallelism alone is a poor explanation, and much recent
functional modelling of the central nervous system focuses on its
modular, heavily feedback-based computational architecture, the result
of accumulation of subsystems throughout evolution. We discuss this
architecture from a global stability and convergence point of view. We
then study synchronization as a model of computations at different
scales in the brain, such as pattern matching, temporal binding of
sensory data, and mirror neuron response. Finally, we derive a simple
condition for a general dynamical system to globally converge to a
regime where multiple groups of fully synchronized elements coexist.
Applications of such "polyrhythms" to some classical questions in
systems neuroscience and robotics are discussed.
The development makes extensive use of nonlinear contraction theory, a
comparatively recent analysis tool whose main features will be briefly
reviewed.
Host: Alain Karma, Physics Dept., Northeastern University
April 25, 2006, 4:00 pm Tuesday CIRCS Seminar
TITLE: "Recent Developments in Molecular Models of Biological Evolution"
By:
Professor C.K. Hu
Institute of Physics
Academia Sinica, Taipei
ABSTRACT:
Host: Professor Fa-Yueh Wu, Physics Dept., Northeastern University
April 20, 2006
4:00 pm Thursday SPECIAL CIRCS Seminar / Physics Colloquium
TITLE: "Physics of Genome Management
By:
Jane Kondev
Physics Department
Brandeis University
ABSTRACT:
April 18, 2006, 4:00 pm Tuesday CIRCS Seminar
TITLE: "Role of Sex in Cardiac Arrhythmias"
By:
Professor Guy Salama
Department of Cell Biology and Physiology
University of Pittsburg Medical School
ABSTRACT:
April 4, 2006, 4:00 pm Tuesday CIRCS Seminar
TITLE: "Physics of Polyelectrolytes with Connected Counterions"
By:
Per Lyngs Hansen
University of Southern Denmark
Harvard Medical School
ABSTRACT:
March 21, 2006, 4:00 pm Tuesday CIRCS Seminar
TITLE: "A Single-Molecule View of DNA Replication"
By:
Antoine van Oijen
Department of Biological Chemistry and Molecular Pharmacology
Harvard Medical School
ABSTRACT:
February 14, 2006, 4:00 pm Tuesday Joint CIRCS/Physics Seminar
TITLE: "Statistical Mechanics of Complex Networks: From the Internet to Cell Biology"
By:
Dr. Albert-Laszlo Barabasi
Dana Farber Cancer Institute & University of Notre Dame
ABSTRACT:
February 7, 2006, 4:00 pm Tuesday CIRCS Seminar
TITLE: "RNA Folding Energy Landscapes in Gene Splicing "
By:
Shi-Jie Chen
University of Missouri-Columbia
ABSTRACT:
December 1, 2005
12:00 pm Thursday SPECIAL CIRCS Seminar, MUGAR 412
TITLE: "Modeling and Mitigating Synaptic Plasticity Errors "
By:
Professor Paul Adams
MacArthur Award Winner and former Hughes Investigator and
member of the Royal Society
ABSTRACT:
Professor Adams will tackle one of the thorniest problems in neuroscience: What does the cortex do and how do we learn what we learn so quickly and so powerfully?
Modeling and mitigating synaptic plasticity errors.
Animals learn about their environments by selectively strengthening appropriate synapses – synapses at which coincident pre- and post-synaptic spikes often occur. However, experiments show that such “Hebbian” plasticity is not completely selective. What are the consequences of such plasticity “errors”, and how can they be avoided? We have modeled the effects of plasticity errors in simple linear neural network models. We suggest that errors might be particularly onerous for neocortical learning, and that certain enigmatic features of thalamocortical circuitry might minimize such problems. More generally, we suggest that if “intelligence” is ultimately generated by massively parallel application of “local” learning rules, then the selectivity of the rules may set limits to intelligence.
Host: Don O'Malley, Biology Dept., Northeastern University
November 29, 2005
4:00 pm Tuesday CIRCS Seminar
TITLE: "A Paradigm for Biolubrication"
By:
Jacob Klein
Oxford University and the Weizmann Institute
ABSTRACT:
November 22, 2005
4:00 pm Tuesday CIRCS Seminar
TITLE: "Decoding the Geochemical Record of Biological and Environmental Coevolution"
By:
Professor Daniel Rothman
MIT
ABSTRACT:
November 8, 2005
4:00 pm Tuesday CIRCS Seminar
TITLE: "Dynamics of Cell Motility: Growing Networks and Flexible Membranes"
By:
Professor Wolfgang Losert
Physics Department
University of Maryland
ABSTRACT:
October 20,
2005 Joint Physics Colloquium and Special CIRCS Seminar
TITLE: "Biophysics of the DNA Molecule"
By:
Maxim Frank-Kamenetskii
Boston University
ABSTRACT:
Biophysical studies of DNA and their relevance to DNA functioning are overviewed. Several simplified theoretical models are discussed. The elastic rod model has proven to be especially fruitful in treating the DNA behavior in single-molecule experiments and in studying DNA topological properties. DNA functioning critically depends on the ability of the double helix for looping, which makes it possible for proteins bound to different sites on DNA to interact with each other. The design of molecular pliers, versatile and sequence-specific benders of the DNA double helix, is presented. Molecular pliers promise to make it possible to modulate gene activity via looping and bending DNA. The nature of intermolecular interactions holding the two DNA strands together is discussed. This question has remained unanswered before very recently. A new approach to the issue is described, which is based on studies of DNA molecules carrying single-strand breaks in specific sites. These studies make it possible the direct determination of stacking free energy between adjacent base pairs in DNA. As a result, the separate contribution of base paring and base stacking into stability of the DNA double helix can be determined. The separate determination of base stacking and base pairing parameters makes it possible to theoretically predict the probability of base-pair opening in DNA (DNA breathing). Results of such calculations and their comparison with NMR experiments are discussed.
October 3, 2005, CIRCS Seminar
TITLE: "The Game of Life. How Protein Universe Emerged"
By: Eugene Shakhnovich
Department of Chemistry
Harvard University
ABSTRACT:
September 29, 2005, Joint Physics Colloquium and CIRCS Seminar
TITLE: "How Does A Protein Find Its Site on DNA"
By: Leonid Mirny
MIT
ABSTRACT:
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a long DNA molecule and then strongly binds this site. We aim to find a mechanism that can provide both a fast search (1-10 sec) and high stability of the specific protein-DNA complex.
Earlier studies have suggested that rapid search involves the sliding of a protein along the DNA. Here we consider sliding as a one-dimensional (1D) diffusion in a sequence-dependent rough energy landscape. We demonstrate that, in spite of the landscape's roughness, rapid search can be achieved if 1D sliding is accompanied by 3D diffusion. We estimate the range of the specific and non-specific DNA-binding energy required for rapid search and suggest experiments that can test our mechanism. We show that optimal search requires a protein to spend half of time sliding along the DNA and half diffusing in 3D. We also establish that, paradoxically, realistic energy functions cannot provide both rapid search and strong binding of a rigid protein. To reconcile these two fundamental requirements we propose a search-and-fold mechanism that involves the coupling of protein binding and partial protein folding. Proposed mechanism has several important biological implications for search in the presence of other proteins and nucleosomes, simultaneous search by several proteins etc. Proposed mechanism also provides a new framework for interpretation of experimental, chromatin-IP and structural data on protein-DNA interactions.
September 13, 2005, CIRCS Seminar
TITLE: "A Biophysical Approach to Worm Behavioral Neuroscience"
By: Aravinthan Samuel
Physics Department
Harvard Unversity
ABSTRACT:
July 22, 2005 Special CIRCS Seminar
TITLE: "Material Behavior at the Nano-scale: Thermodynamic and Dynamic Considerations"
By: Gregory Mckenna
Texas Tech University
ABSTRACT:
