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SPRING 2007 Monday February 5, 2007 Topic: Self-organized Structures in
Biological Systems: ABSTRACT: Self-organized ordered structures are wide spread in biology and common for membranes, cytoskeleton proteins, amino acids, and viruses. They form not only in vitro but even in vivo, ranging from the self-organized states of collagen in cornea to nematic-like actin and myosin organization in muscle fibers, and to ordered molecular structures in spermatozoa. The knowledge of physical mechanisms behind the biological expressions of molecular order has a potential to impinge broadly on understanding its function in the biological cells as well as on the treatment of relevant diseases. In this lecture, I will discuss the liquid crystalline phases and pattern formation in the concentrated DNA, when the extended molecular chains can trace out zigzags and form the periodic ordered structures. I will then show that even the live biological cells (such as Pseudomonas aeruginosa) can be orientationally ordered when placed into the matrices of biopolymers. Both experimental observations are modeled considering the elastic properties of the liquid crystalline states of the concentrated biopolymers; models correctly predict the experimentally measured parameters. Even though the studies are performed at artificial conditions, they help to better understand the partially ordered molecular self-organization in biological systems. These studies also shed light on the role played by the bacterial shape and extracellular biopolymers in important biological processes, such as cell-to-cell signaling and biofilm formation. Moreover, the controlled alignment has potential applications in biotechnology and nanotechnology. I will conclude the presentation with a summary of the main findings and their applications. Speakers: Dr. Ivan I. Smalyukh, University
of Illinois Wednesday February 7, 2006 Topic: Computational Modeling of Cardiovascular Diseases for Realistic Clinical Applications Abstract: Recent advances in computational modeling and imaging technology are making it possible that computational models can be built based on patient-specific image data and accurate predictions can be made for realistic clinical applications. In this talk, patient-specific MRI-based computational models for blood flow in arteries and blood flow in human heart (a right ventricle/left ventricle (RV/LV) model) will be presented. We will demonstrate how computational models can be used to a) understand fundamental biological and disease processes; b) assess atherosclerotic plaque rupture risk (plaque rupture often leads to stroke and heart attack); and c) conduct virtual surgery to optimize right ventricle volume reduction surgical procedures.
Speaker: Dalin Tang, Professor of Computational
Mathematics, Friday February 9, 2007 Topic: Instrumentation in Nuclear Medical
Imaging: ABSTRACT: The practice of medicine relies
on the ability to detect disease-related changes in anatomy, biochemistry,
and physiology. The development of imaging technologies and tomography
has provided the physician with unprecedented tools for detecting such
changes. Speakers: Dr. Woon-Seng Choong, Lawrence
Berkeley National Laboratory Monday February 12, 2007 Topic: Bergman spaces of the unit ball Abstract: Let B denote the open unit ball in the n-dimensional complex Euclidean space C^n. The subspace of holomorphic functions in L^p(B,dv), where dv is Lebesgue volume measure, is called a Bergman space and is denoted by A^p. I will give a brief history of the theory of Bergman spaces and discuss several recent characterizations of such spaces.. Speaker: Kehe Zhu, State University of New York at Albany Friday, February 16, 2007 Topic: Reconstructing and Making Use of Coherent Vibrations
Monday February 19, 2007 Topic: Hyperplane arrangements Abstract: During the last 30 years, the study of hyperplane arrangements has been a very active area of research in Combinatorics. Rather than attempting the impossible task of surveying this vast discipline, in this talk I will present some selected results and techniques that I believe convey the depth and beauty of the subject. Speaker: Hélène Barcelo, Arizona State University Tuesday February 20, 2007 Topic: Prime time for primes Abstract: As old as Euclid, prime numbers have recently started to yield their secrets. Mathematicians from California to India and elsewhere have shown us that primes regularly fall into strict patterns, they display unusual "clumping," and they are computationally easy to detect. While many mysteries remain, it does seem that this first decade of the new millennium is indeed a prime time for primes. Speaker: Dr. Carl Pomerance, Professor of Mathematics, Dartmouth College Wednesday February 21, 2007 Topic: Covering congruences Abstract: A famous old problem of Paul Erdös is whether for each number B the set of integers may be covered with a finite collection of congurence classes with distinct moduli each at least B. In fact, Erdös wrote of this as his "favorite problem". In recent work with Filaseta, Ford, Konyagin, and Yu, we have found some new results in this area; for example, if such finite collections should exist, the largest modulus cannot be O(B). These new results settle some conjectures of Erdös, Graham, and Selfridge. Speaker: Dr. Carl Pomerance, Professor of Mathematics, Dartmouth College Monday February 21, 2007 Topic: Elliptical Galaxies: ABSTRACT: I will discuss the formation of elliptical galaxies within the LambdaCDM scenario using semi-analytical modeling of galaxy formation. The focus will be on the assembly of elliptical galaxies with special attention to the role of dissipation during their formation and the consequences for the size distribution and evolution. Furthermore, I will discuss the need for feedback within galaxy formation models using recent observational tests on AGN-feedback to derive a critical black hole mass above which star formation is shut off in galaxies of a given velocity dispersion. As an alternative to AGN-feedback I will present a model based on environmental effects including dynamical friction heating in clusters and gravitational heating from infalling satellites. The combined environmental effects reproduce several observations of the galaxy population like the luminosity function colour-magnitude relation or the cosmic star formation history and thus provide an interesting alternative approach to AGN-feedback. Speakers: Dr. Sadegh Khochfar, University of Oxford Friday February 23, 2007 Topic: Planet Embryos in Vortex Wombs: ABSTRACT: The past 15 years have witnessed the discovery of planets in the most unexpected of places: terrestrial-size planets around such "dead" stars as pulsars (Wolszczan 1991), gas giant planets that orbit their parent stars much closer than Mercury does our Sun (Mayor & Queloz 1995), and now even planets around "failed" stars known as brown dwarfs (Chauvin et al. 2005). Besides these unusual systems, astronomers have now discovered more than 200 planets around other Sun-like stars (Marcy et al. 2006, Fischer et al. 2006), and the search continues as we try to find a system that looks just like our own. Clearly, the mechanisms of planet formation are far more robust than we had first imagined. These new discoveries have sparked a Renaissance in planet formation theory, an understanding of which is inherently interdisciplinary, drawing on mechanics (both solid & fluid), thermodynamics, electromagnetism, astrophysics, and geophysics. I will present recent computational simulations of the settling of dust sub-layers in the protoplanetary disks of gas & dust out of which planets must form. Such dust sub layers can be unstable to Kelvin-Helmholtz instabilities which can re-mix the gas and dust and prevent further settling, potentially inhibiting the formation of planetesimals, the first building blocks of planets. I will also describe alternative mechanisms to concentrate dust, including 3D vortices ("giant hurricanes") in protoplanetary disks, which trap dust grains in the "eyes" of such storms. Speakers: Dr. Joseph A. Barranco, Harvard-Smithsonian Center for Astrophysics Monday February 26, 2007 Topic: Like-Charge Attraction of Biological Rod-Like ABSTRACT: Structure formation by like-charged bio-polymers is ubiquitous within eukaryotic cells. Condensation of DNA by oppositely charged histone proteins forms the basis for the cell nucleus, and bundles of condensed filamentous actin proteins form the basis of the cell cytoskeleton. By using small angle x-ray scattering to study the in-vitro structures and phase transitions of biological polyelectrolytes under condensing conditions, we learn more about their in-vivo structure and function. Determining the structure of biological polyelectrolye aggregates has lead to a better understanding of multiple genetic diseases ranging from Cystic Fibrosis to deafness. One form of genetic deafness is caused by mutations in the actin bundling protein espin, which are involved in the formation of large actin parallel bundles in stereocilia of cochlear hair cells. Sterocilia are vital for the mechano-electrical transduction of sound in hearing. We found that mutations in one of the two F actin binding sites of espin, which have been implicated in deafness, can tune espin actin interactions and radically transform the system's phase behavior. The paracrystalline F-actin bundle structure found in the presence of wild type espin destabilizes in favor of an unanticipated nematic actin-espin network. These results and others related to discerning and dissolving the unwanted polyelectrolyte structures in the airways of Cystic Fibrosis patients will be presented. Speakers: Dr. Kirstin Purdy, University of Illinois Monday February 26, 2007 Topic: What is Finsler geometry? Abstract: This talk consists of three parts. First, it points out the presence of Finsler geometry in everyday life and gives a case study of geodesics. Second, it presents a pedestrian definition of flag curvatures and illustrates with a practical example. Third, it explains what Ricci curvatures are, states a question due to Chern, and proposes a notion of Ricci flow for answering this question. Speaker: David Bao, University of Houston Wednesday February 28, 2007 Topic: iJava: A New Direction in Online Education Abstract: The iJava textbook is an online, interactive text for elementary Java instruction. The textbook narrative is punctuated with about 200 embedded problems, most of which involve programming. These exercises are placed in the text in such a way as to make students competent readers. Did you understand the last two paragraphs? Consolidate your understanding: try this problem. iJava judges the correctness of student answers in real-time, and provides feedback when submissions are incorrect. The text also comes with hundreds of standard end-of-chapter homework problems and mini-projects, most of which are also programming problems. These, too, are judged in real-time, as students make submissions. The system provides extensive instructor tools, including an electronic gradebook. Thus, an instructor might choose a homework set for a certain week, and then, on the due-date, simply view the automated gradebook tabulation to assess student progress. We have had considerable success using the text over the last eighteen months, both in traditional lecture courses and in online distance-learning classes. This project has been funded, in part, by the National Science Foundation. It is currently being supported by the U.S. Department of Education via a FIPSE grant, for the purpose of establishing a third aspect of iJava, an online community of instructors who share ideas, teaching tactics, examples, exam questions, and a variety of other teaching and learning resources. In this talk I’ll discuss details of the book, my experiences teaching with it, how the system works, and my plans for creating the proposed iJava user’s community. Speaker: Robert Moll, University of Massachusetts, Amherst Wednesday March 7, 2007 Topic: Moore's Law and Microcomputer History Abstract: Moore's law is in the news and is a way of describing the historic growth in density of integrated circuits. Several of the factors that contributed to the increased density of IC's during 1960-2000 are described, some of which are applicable today. Additionally, the influence of chip density on early microprocessor architecture and design, particularly the "LSI constraints" which confronted the chip designer are discussed. Stan will describe his experiences in the design of the early Intel chips. Speaker: Stanley Mazor Friday, March 9, 2007 Topic: Long 2 Electron - 4 Centered 2.9 Å Carbon-Carbon Bonds-
Monday March 9, 2007 Topic: Quasar Feedback in Structure Formation ABSTRACT: While many components and reaction steps necessary for bidirectional transport across the nuclear envelope (NE) have been characterized, the mechanism and control of cargo migration through nuclear pore complexes (NPCs) remains poorly understood. Here, we demonstrated that single cargo molecules could be visualized interacting with nuclear pore complexes in permeabilized cells by single molecule narrow-field epifluorescence microscopy. At low importin concentrations, about half of the signal-dependent cargos that interacted with an NPC were translocated across the NE, indicating a nuclear import efficiency of ~50%. The NPC interaction times for cargos that actually transported through the NPC and those that underwent abortive transport were both ~8.3 ms under these conditions. At high importin concentrations, the import efficiency increased to ~80% and the transit speed increased ~7-fold. The transit speed and import efficiency of 10 kDa dextran, a signal-independent cargo, was also increased by high importin concentrations. These results demonstrate that maximum nucleocytoplasmic transport velocities can be modulated by at least ~10-fold by the importin â concentration. Thus, we postulate that cargo trafficking rates depend on pore occupancy, a model explicitly recognizing that the number, identity, and distribution of molecules within the pore affects cargo translocation through the pore. Factors that could be affected by changes in pore occupancy include: i) the accessible volume for the transiting cargo; ii) the concentration and distribution of RanGTP in the NPC; and iii) the structure and physical properties of the permeability barrier. Speaker: Dr. Evan Scannapieco, University of California, Santa Barbara Monday March 12, 2007 Topic: Single Molecule Studies of Translocation ABSTRACT: For the past 10 billion years, the typical mass of star-forming galaxies has been decreasing, seemingly in direct conflict with the prevailing model of cosmological structure formation. Using analytic arguments and reviewing recent observations, I will demonstrate that the solution to this mystery is likely to lie in the formation of supermassive black holes, which exert strong feedback on their environments as they pass through an active phase, known as a quasar. Next, I will present the results of one of the largest cosmological smooth particle hydrodynamic simulations every carried out, which includes this feedback process and can be used to make detailed observational comparisons. In particular, our modeling places us in a unique position to interpret joint measurements of the distributions of quasars, galaxies, and small-scale distortions in the microwave background. Finally, I will summarize other aspects of my ongoing research, focusing on studies that constrain the properties of the first stars. Speaker: Dr. Wei-Dong Yang, Texas A&M University Wednesday March 14, 2007 Topic: A non-parametric approach to the geometry of statistical models Abstract: Statistical models exhibit interesting mathematical structures that can be alternatively classified as differential geometry, conxex analysis, commutative algebra. Statistical models are usually presented as parameterized families of probability densitities. A fully non parametric presentation is possible, leading to an interesting approach even in the case of a finite state space model. Some work is in progress to generalize this theory to extended exponential models. Speaker: Giovanni Pistone, Politecnico di Torino DIMAT Thursday March 15, 2007 Topic: Warm Upwelling Regions During the Pliocene Warm Period Speaker: Petra Dekens, Ocean Sciences Department Wednesday March 28, 2007 Topic: Matching games and theirs generalizations Abstract: The Matching Game is a game designed for teaching 4th graders in California about probability. It is a two-player game, each player draws a ball from a bag of balls with 2 different colors. The first player wins if the balls drawn are of the same color, otherwise the second player wins. We will examine some generalizations of the Matching Game and find the "fair games" in those situations. Speaker: Wai Yan Pong, California State University, Dominguez Hills Monday April 2, 2007 Topic: Energy for All in the 21st Century ABSTRACT: Energy is the key to development and is the basis of modern technological societies. Fossil fuels -- Oil, coal, and gas -- were the dominant sources of energy in the 20th century and major contributors to pollution and green house gasses. The urgent question is -- what energy portfolio will provide affordable clean energy to 8 billion people? This talk will examine the current challenges and the technological breakthroughs required to realize the potential of fossil fuels, nuclear energy, and alternates (hydro, solar, wind). I will make the case for why the US must lead the efforts to develop and deploy cheap clean energy for all. Speaker: Dr. Rajan Gupta, Los Alamos National Lab Saturday, April 14, 2007 Topic: The Fourteenth Bay Area Discrete Math Day (BAD Math Day) BAD Math Days are one-day meetings aimed at facilitating communication between researchers and graduate students of discrete mathematics around the San Francisco Bay Area. These days happen twice a year and strive to create an informal atmosphere to talk about discrete mathematics. The term "discrete mathematics" is chosen to include at least the following topics: Algebraic and Enumerative Combinatorics, Discrete Geometry, Graph Theory, Coding and Design Theory, Combinatorial Aspects of Computational Algebra and Geometry, Combinatorial Optimization, Probabilistic Combinatorics, and Combinatorics in Mathematical Physics. The speakers for the meeting will be: Time: 10am - 5pm Monday April 16, 2007 Topic: Photonic Crystals: Surface Effects ABSTRACT: In this talk I will review my recent works related to photonic crystals. I will focus to surface states, which might appear in photonic crystals due to their termination. We investigated the surface states of a defect chain embedded in a host photonic crystal. Our analytical and numerical analysis showed that the surface states of the defect chain could be classified in terms of the Tamm-like or the Shockley-like states known in surface physics of solids. However, the analogy between the surface states of photonic crystals and solids is not complete. I will demonstrate the effect of transformation of the Shockley-like surface states into the Tamm-like states, which is non-typical for solids. Speakers: Dr. Natalia Malkova, NASA Ames Nanotechnology Center Monday May 14, 2007 4:05 p.m., TH 411 Topic: Epsilon Eridani: A Nearby Young Solar System Analog ABSTRACT: Epsilon Eridani, a young solar-type star only 10 light years from us, has been known since the IRAS mission to have a circumstellar debris disk, a more massive version of our solar system's outer Kuiper Belt, consisting of remnant planetary construction material. Spitzer Space Telescope images of the eps Eri system, supplemented by ground-based sub-millimeter data, that allow modeling the debris disk's structure in search of evidence for gravitational influence of planets. We have discovered an inner debris zone, similar in position to our solar system's asteroid belt, close to the orbit of eps Eri's reported radial velocity planet. Speaker: Dr. Dana Backman, NASA Ames Research Center
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