Brown University
Center for Statistical Sciences
2007 Lectureship Series
Biostatistics in the Post-genomic Era:
Statistical Methodology & Applications in Bioinformatics
Division of Biostatistics Yale School of Public Health | |
Refreshments beginning at 3:15 p.m. |
Abstract: Transcription regulation is a fundamental biological process, and extensive efforts have been made to dissect its mechanisms through direct biological experiments and regulation modeling based on physical-chemical principles and mathematical formulations. Recent advances in high throughput technologies have provided substantial amounts and diverse types of genomic data that reveal valuable information on transcription regulation, including DNA sequence data, protein-DNA binding data, microarray gene expression data, and others. In this talk, I will present a Bayesian modeling framework to integrate diverse data types, e.g. protein-DNA binding data and gene expression data, to reconstruct transcriptional regulatory networks. The usefulness of this general modeling approach is demonstrated through its application to infer transcriptional regulatory networks in the yeast cell cycle.
This is joint work with Ning Sun and Ray Carroll.
Sponsored by: The Charles K. Colver Lectureship and Publication Fund
Brown University --
Joint Materials/Solid Mechanics Seminar Series
Department of Organismic and Evolutionary Biology, Harvard University | |
What We Have Learned From Rubber Balloons and Soap Bubbles | |
Abstract: Although most cells have complex shapes, many of their characteristic geometrical features are dictated by well-known physical laws. I will present examples of cell morphogenesis where cellular and molecular processes can be distilled into strikingly simple physical or geometrical models. The first example is the folding of pollen grains. The pollen wall is mechanically designed so that the grain can fold and unfold neatly. I will outline some of the design features that support the folding process and present an exact solution for the simplest mode of folding observed in these cells. A second example is cell division. In many plant tissues, the plane of cell division seems to be determined according to the same laws that specify the equilibrium geometry of soap films. I will show how this simple model explains intricate cellular patterns with surprising accuracy.
Center for Fluid Mechanics
And
The Fluids, Thermal And Chemical Processes Group
Of
The Division of Engineering
Seminar Series
Department of Mechanical Engineering, Polytechnic University Brooklyn, NY | |
Abstract: Flow in the human body is designed to be laminar and regular. A few exceptions where turbulence plays a role are speech production and pathological flow in the circulatory system. Speech production involves unsteady pulsatile flow and turbulent structures that affect the aeroacoustics. Examples of pathological blood flow in which unsteadiness, separation and turbulence are important include regurgitant heart valves, stenoses or blockages, and branches and bifurcations. Pulsatile unsteady phenomena, coherent vortical structures and transitional flow or turbulence occurring at low Reynolds numbers are common to these biological flows. An overarching motivation for studying hemodynamics and speech production is to facilitate surgical planning, i.e. to enable physicians to assess the outcomes of surgical procedures by using faithful computer simulations. Such simulations are on the horizon with the advent of increasingly more powerful high performance computing and cyberinfrastructure, but they still lack all the appropriate models. This seminar will emphasize our cardiovascular-flow-related research program, where the goal is to investigate the fluid dynamics stimuli of pathological flows on the endothelial cells lining the intima of the arteries. The motivation is to understand the cycle of plaque formation that occurs in the disease atherosclerosis. A multidisciplinary effort with colleagues in Biomedical Engineering enables study of the fluid dynamics in the presence of live cells. Because actual cells are subjected to the flow and then analyzed for biochemical and genetic response, the facility cannot be scaled-up. Thus, techniques such as micro-PIV and MEMS-based wall shear stress sensors are required to characterize the flow. Another important objective is to enable computations with realistic inlet and boundary conditions. Our work on perturbations addresses the sensitivity of pulsatile flow in arteries to changes in inlet conditions such as curvature and velocity profile distortion.
Biographical Sketch: Dr. Michael W. Plesniak is the Eugene Kleiner Professor for Innovation in Mechanical Engineering at Polytechnic University in Brooklyn, NY and an Adjunct Professor of Mechanical Engineering at Purdue University. He recently completed a term as the Director of the Fluid Dynamics & Hydraulics program at the National Science Foundation. Prof. Plesniak earned his Ph.D. degree from Stanford University, and his M.S. and B.S. degrees from the Illinois Institute of Technology; all in Mechanical Engineering. Dr. Plesniak was elected a Fellow of ASME in 2006. His current research interests include: bio fluid mechanics, turbulence transport and mixing enhancement, cavitation, three-dimensional boundary layers, gas turbine cooling, environmentally-benign consumer aerosol sprays, and entrainment control. Dr. Plesniak has authored one hundred refereed archival publications and conference papers, over fifty non-refereed publications and presentations, and has presented numerous invited seminars and keynote addresses. He has served as an Associate Editor for the ASME Journal of Fluids Engineering.
CCMB Seminar Series Lecture
Sandia National Laboratories, Albuquerque, New Mexico | |
Applications, Algorithms and Architectures | |
Refreshments will be served at 3:45 p.m. |
Abstract: In its relatively short lifespan, computational biology has had an enormous impact on high performance computing. The computing requirements of biological applications have altered the research and business landscape of advanced computing in myriad ways. In this talk, I will review some of these synergistic developments and speculate about the even more dramatic changes ahead.
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Brown Analysis Seminar
Brown University
Division of Applied Mathematics
TRANSATLANTIC SEMINAR
Abstract: This work is the result of a collaboration between around 12 people from both dynamical systems and analytic geometry work groups. We have been considering convex symetric lens-shaped networks in the plane and let them evolve under curve shortening flow. We impose a 120 degree angle condition at the two triple points. The enclosed convex domain will shrink to a point in finite time. We proved the existence of a self-similarly shrinking network, but we are still working to prove the uniqueness of this. Once it is done, it is possible to show that the general convex symmetric lens-shaped domain shrinks in this unique self-similar way to a point. Furthermore, we will see an attempt to replace the convexity assumption by a weaker one (graphicality of the lens).
Brown University
Graduate School
Dissertation Defense Information
Brown University
Graduate School
Dissertation Defense Information
Convergence for Hyperbolic Conservation Laws and Applications in Computational Cosmology | |
Special Department of Mathematics
Extreme Geometry Colloquium
Brown University, Division of Applied Mathematics,
Graduate Student Pizza Seminar
Introduction, Analysis and Use in Hybrid Schemes | |
Abstract: The discontinuous Galerkin (DG) method has become quite a hotbed of research in this department as well as in the rest of the scientific computing community. In the first part of this talk I will outline the basic formulation of the method, comparing its attributes to other methods such as the finite difference, finite volume and standard Galerkin methods. In the second part of my talk I will discuss high-order limiting, one of DG's main weaknesses, and how my research addresses this topic. Specifically, my research focuses on creating a hybrid scheme which imposes the DG method in smooth regions of a solution, but "switches" to a finite-volume scheme in nonsmooth regions.
PDE Seminar
Brown University
Department of Mathematics
Brown Distinguished Lectures
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