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Previous CIRCS seminars (2003-2001) |
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Previous Seminars
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Tuesday, October 31, 2000 Title: ""Why It is So Difficult to Explain the Universal Occurrence of Static Friction and How to Resolve this Difficulty" by Professor J. B. Sokoloff, Physics Department and CIRCS, Northeastern University ABSTRACT: Several workers have established that the Larkin domains for two three dimensional nonmetallic elastic solids in contact with each other at a disordered interface are enormously large, implying that there should be negligible static friction per unit area in the macroscopic solid limit. The present work argues that the fluctuations in the heights of the random asperities at the interface that occur in the Greenwood-Williamson model can account for static friction. In fact, for light loads, even typical height asperities (as opposed to height fluctuations) can easily be in the "strong pinning limit," for which there is static friction. |
October 17th, 2000 Title:"Embryo Survival and the Genomics Revolution" by Prof. C. Warner, Biology Department, Northeastern University ABSTRACT: All mammals undergo a period of development between fertilization and implantation that is called the preimplantation period. Embryo survival during this preimplantation period is dependent on both environmental and genetic factors and is crucial for a successful pregnancy. The elucidation of the genes that control preimplantation embryo survival is complex. Revolutionary new methods in biology, including whole Gerome DNA sequence analysis, detection of single nucleotide polymorphisms (SNPs) and mRNA expression with DNA chips and microarrays, cloning of animals by nuclear transfer, and creation of gene knockout mice and embryonic stem cells, should all aid in furthering the understanding of the genetic control of preimplantation embryo survival. In this seminar I will focus on two species, the mouse and the human. The reasons are that the mouse is the most thoroughly studied mammalian system with respect to preimplantation development, and that the advent of in vitro fertilization . |
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10th, 2000 Title: "Pattern formation in non-linear optical systems" by Dr. Jean Bragard, Department of Physics, CIRCS, Northeastern University ABSTRACT: Pattern forming instabilities occurring in systems formed by an optically nonlinear component inserted in a feedback loop are presently a subject of wide experimental and theoretical investigations. We describe one of these optical systems where the nonlinear component is a liquid crystal light valve (LCLV) where a wavefront horizontal translation is introduced in the feedback loop. A series of transitions between different two-dimensional patterns (hexagons, rolls, and zig-zags) are displayed for increasing values of the displacement. A linear stability analysis is sufficient to describe these patterns, except for the large displacement values, where we can use a phenomenological model analysis. This model is also of interest for other dynamical systems where diffusion and drift act. |
Tuesday,
May 16th, 2000 Title: Molecular Class Discovery and Prediction in Cancer Using Micro-Array Gene Expression Data by Dr. Pablo Tamayo, #000000Fhead/MIT Center for Genome Research, Massachusetts Institute of Technology ABSTRACT: We review computational approaches to the problem of biological class discovery and prediction using micro-array expression data. The problem of class prediction appears when one tries to use an initial collection of samples belonging to known classes (phenotypes) to create a predictor to classify new, unknown samples. For example, class predictors can be constructed for known pathological categories ^× reflecting a tumor's cell of origin, stage or grade etc.^× and then applied to new clinical samples to facilitate classification and diagnosis. We will also discuss the problem of class discovery where biological classes and phenotypes are discovered automatically. Class discovery entails two challenges: i) developing algorithms to cluster samples by gene expression patterns, and ii) validation: determining whether those putative classes are meaningful and reflect true biological structure in the data rather than aggregation by chance. |
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Tuesday, May 9th, 2000 Title: "Viscous nonlinear dynamics of elastic filaments: twist, kinks, and drag." by Thomas R. Powers, Division of Engineering and Applied Sciences Harvard University ABSTRACT: As D'Arcy Thompson emphasized (1), growth and form in the biological world are governed by simple physical laws. Using ideas from elasticity theory, fluid dynamics, pattern formation, and geometry, I study the shape and motion of a flexible filament rotating in a viscous fluid. Motivated by recent experiments that show large torsional stress in linear DNA during transcription, I first consider the dynamics of a rod with a single kink. I describe how kinks block speedometer-cable motion and trap torsional stress, and give simple scaling laws for shape and stress vs. rotation rate. I argue that the bent rod should exhibit bistability between extended and folded states at high rotation rate, and present experimental results confirming this expectation. Then I turn to the interplay between speedometer-cable and crankshaft motion in naturally straight rods. At a critical rotation rate, there is a Hopf bifurcation from "twirling" motion, in which the centerline of the rod remains straight, to "whirling" motion, in which the centerline crankshafts about a single axis much more slowly then the speedometer-cable motion of each rod element about the local tangent. The connection to #000000F's theorem relating link, twist and writhe for closed ribbons is explained. |
Thursday, May 4th, 2000 NOTE SPECIAL DAY, JOINT COLLOQUIUM/CIRCS SEMINAR Title: "Modeling of the visual cortex." by Dr. Michael J. Shelley Courant Institute |
| THURSDAY,
April 27th, 2000 NOTE SPECIAL DAY, JOINT COLLOQUIUM/CIRCS SEMINAR Title: "Oscillatory cluster patterns in a homogeneous chemical system with global feedback" by Prof. Irving R. Epstein Provost and Senior Vice President for Academic Affairs Brandeis University ABSTRACT: Oscillatory clusters consist of sets of domains in which nearly all of the elements in a domain oscillate with the same amplitude and phase. While clusters have received considerable attention in arrays of coupled neurons, they are rare in chemical systems. In the simplest case, a system consists of two clusters that oscillate in antiphase; each cluster can occupy multiple fixed spatial domains. Such clusters resemble standing waves, except that clusters lack a characteristic wavelength. I shall describe a family of cluster patterns that arise in the Belousov-Zhabotinsky (BZ)reaction-diffusion system with photochemical global feedback. Standing clusters have fixed spatial domains and oscillate periodically in time. Irregular clusters show no periodicity either in space or in time. Localized clusters display periodic antiphase oscillations in one part of the medium, while the remainder appears uniform. Numerical simulations based on a model of the BZ reaction supplemented with global feedback show good agreement with our experimental data. The results may have significance for neural as well as chemical and physical systems with global feedback. |
Tuesday,
April 11th, 2000 Title: "Noise-Based Control of Gene Expression" by Dr. Jeff Hasty, Center for BioDynamics and Department of Biomedical Engineering, Boston University ABSTRACT: The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own expression or the production of protein in another network. Engineered control of cellular function through the design and manipulation of such networks lies within the constraints of current technology. I will show how one develops a model describing the regulation of gene expression, and elucidate the effects of noise on the formulation. In the context of a single network derived from bacteriophage $\lambda$, I will discuss the derivation of a two-parameter deterministic model describing the temporal evolution of the concentration of $\lambda$ repressor protein. Bistability in the steady-state protein concentration arises naturally, and I will show how the bistable regime is enhanced with the addition of the first operator site in the promotor region. I will then demonstrate how additive and multiplicative external noise can be used to regulate expression, and highlight the utility of such control through the construction of a protein switch. These novel results suggest that an external noise source could be used as a control mechanism for gene expression |
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Tuesday, February 29th, 2000 "Interface dynamics for the Allen-Cahn equation with memory" by Dr. Horacio G. Rotstein, Chemistry Department, Brendeis University ABSTRACT: We consider an integrodifferential partial differential equation as a mathematical model for phase transition dynamics when memory effects are present. By taking appropriate kernels, this convolution equation can be reduced to both the Klein-Gordon equation and the bistable equation. By means of a formal asymptotic analysis we derive an equation governing the dynamics of a front, an interface separating between two phases. It turns out that to the leading order, under suitable assumptions on the kernels and constraining the interface to move with non-vanishing velocity, the motion of interfaces is similar to that governed by the damped Klein-Gordon equation. |
THURSDAY,
February 24th, 2000 NOTE SPECIAL DAY, JOINT COLLOQUIUM/CIRCS SEMINAR "The physics of collective microorganism patterns" by Professor H. Levine, Physics Department, University of California, La Jolla ABSTRACT: Research over the past decade has elucidated many mechanisms whereby physical and chemical systems can form spatial patterns when driven far from equilibrium. Remarkably, these concepts can help us unravel structures that arise in a biological setting, namely the collective dynamics of microorganism colonies. Some examples that have been studied to date include fractal growth in Bacillus, spot patterns in E. Coli and chemical wave dynamics and rotating aggregate formation in Dictyostelium. This talk will provide an introduction to some of these systems and explain how one can use nonequilibrium physics to understand their behavior. |
| Tuesday,
February 22nd, 2000 "Fluctuation-dissipation relations during aging in structural glass" by Dr. Tomas Grigera, Physics Department, Northeastern University ABSTRACT: Physical aging is a distinctive feature of the glassy state. It means that, after a temperature quench, response and correlation functions continue to evolve for a long time even after the energy has reached a constant value. This behavior has been experimentally observed in structural and spin glasses alike. For some years, it has been expected on theoretical grounds that aging be accompanied by non-universal violations of the fluctuation-dissipation theorem. Very recently, these violations have been observed experimentally for the first time. Experiments of this kind provide a new probe of aging dynamics and are likely to produce information essential to a full understanding of the aging process. Important similarities as well as differences between structural and spin glasses emerge from aging studies. |
Tuesday, February 15th,
2000 "Novel aproaches to diagnosis and therapy in acute coronary syndromes" by Professor Ban-an Khaw, Pharmaceutical Science Department, Northeastern University, ABSTRACT: Although, clinical history, ECG and cardiac serum proteins are usually sufficient for diagnosis of run-of-the-mill acute myocardial, very acute and specific diagnosis is often equivocal. Furthermore, earlier diagnosis could lead to better therapy. Therefore, new methods have been developed that can be used to visualize the actual areas of myocardial injury by gamma scintigraphic imaging techniques. Initially we developed a monoclonal antibody based method for unequivocal differentiation of irreversible myocardial cell injury associated with ischemic compromise. However, it being a protein based technique, required about one day delay for unequivocal diagnosis. Therefore, a non-protein-based method utilizing Glucaric acid labeled with technetium-99m was developed. This method is as specific as the monoclonal antimyosin method for diagnosis of myocardial necrosis, however, since it is a small carbohydrate molecule, it can localize at the targets quickly at the same time clear from the blood quickly to enable visualization of the targets within minutes. This decrease in the time for diagnosis would allow thrombolytic therapy to be initiated earlier for better therapeutic outcome. Yet thrombolytic therapy alone may not provide adequate therapeutic advantage. Therefore, we have initiated a potential acute therapeutic intervention that might preserve the viability of the myocardium above that provided by reperfusion alone. We had hypothesized that if the cell membrane lesion of the myocardium at risk were sealed at the time of reperfusion, viability of more cells will be preserved. This should lead to better outcome in patients. We had demonstrated that such cell membrane lesion sealing can be achieved with cytoskeleton specific immunoliposomes, initially in in vitro assays and finally in in vivo acute experimental myocardial infarct model. Therefore, the diagnostic methods that allowed very acute detection of ischemic injury may also allow acute intervention where cell membrane lesions induced by ischemia may be sealed with a novel "cellular band-aid" technology. |
| Wednesday,
January 19th, 2000 NOTE SPECIAL DAY!!!! "Can one hear the shape of a pore?" by Dr. Pabitra Sen, MIT and Schlumberger Doll ABSTRACT: The motion of water molecules diffusing in pore-space can be interrogated by NMR relaxation and pulsed gradient spin echo techniques. Determination of surface to pore volume ratio and other geometrical factors using combination of NMR experimental techniques and Kac's mathematical ideas will be described. |
Tuesday, January 18,
2000 "Discrete 1-D Maps and Cardiac Electrophysiology" by Dr. Mari Watanabe, Department of Physics, CIRCS, Northeastern University ABSTRACT: The duration of excitation of the heart is dependent upon its duration of rest, a useful characteristic that assures an optimal ratio of diastolic filling and systolic ejection times. This dependence of action potential duration on diastolic interval is called the restitution function, and it can be described as a simple one dimensional discrete dynamical system that can be iterated simmilarly to the logistic equation, the equation that describes long term population dynamics. Despite its simplicity, dynamics of the restitution function can simulate experimental data well. A one variable equation can also describe conduction times through the AV node of the heart, and dynamics of that equation are also well suited to explain classical electrocardiographic phenomena. These are two of the examples that I will use to describe the usefulness of discrete 1-D maps for understanding cardiac electrophysiology. |
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THURSDAY, January
13, 2000, CANCELED DUE TO WEATHER |
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