Special PDE/LCDS Seminar
Center for Computational Molecular Biology Seminar
Department of Biological Statistics and Computational Biology Faculty Search Candidate | |
Abstract: A critical mass of DNA polymorphism data is now available to comprehensively scan the human genome for evidence of different types of natural selection. However, such an analysis requires new statistical methods that correct for the confounding effects of demographic history, such as population growth, subdivision, and divergence. In this talk I will present two studies which use novel, robust methods to describe natural selection in the human genome. In the first study, I search for evidence of recent selective sweeps, finding many genomic regions that have recently experienced Darwinian adaptation. Selected regions of biological interest include pigmentation candidate genes, centromeric regions, and clusters of olfactory receptors. In the second, I measure the general effect of selection on different types of mutations, finding widespread evidence of negative selection acting against non-synonymous variation. Importantly, even though non-synonymous mutations tend to be deleterious, I find that selection is weak enough that selected variants can reach observable frequencies (1-10%) through genetic drift, suggesting that they may significantly contribute to variation in human phenotypes, such as genetic diseases.
Brown University
Joint Materials/Solid Mechanics Seminar Series
Abstract: Polycrystalline thin films are often deposited under energetic particle bombardment, which strongly affects their microstructure. We have investigated the effect of deposition angle on the crystallographic orientation distribution (texture) of metal and compound thin films (Ag, Nb, Al, AlN) prepared by magnetron sputtering. These films all show strong fiber texture, however, the effect of deposition angle on the texture angle depends on the type of material. Additionally, varying the N content in Al from Al to AlN shows an abrupt shift in texture angle even after the film composition is fully nitrided. Mechanisms responsible for these effects will be discussed, along with possible applications.
James Harper is a Professor of Physics and Director of the Materials Science Program at the University of New Hampshire. He joined UNH three years ago, after a career in IBM Research in microelectronic materials. He is active in the Materials Research Society and the American Vacuum Society, and carries out research in thin film materials science.
Center for Fluid Mechanics
And
The Fluids, Thermal and Chemical Processes Group
Of
The Division of Engineering
Seminar Series
Department of Mechanical Engineering, University of California, Santa Barbara, CA | |
Abstract: In this talk I will describe three recent studies of novel Marangoni flows, i.e., flows that are driven by tangential stresses due to temperature, compositional, or electrical fields. These stresses can drive bulk flows that are vigorous and in many cases, counter-intuitive.
The first two studies involve gradients of concentration of surfactants arising from variation in the rate of chemical reaction producing them. We study the effect of in-situ production of surfactants on viscous fingering instabilities. We find that Maragoni stresses result in wider fingers, a larger fractal dimension of the pattern, and an increase in displacement efficiency. We then describe a surprising phenomenon of spontaneous, self-sustained chemically driven oscillations at the tip of a drop suspended from a needle. We connect this phenomenon with the well-known tip-streaming in drops subjected to extensional flows. Plausible physical mechanisms are proposed for both of these phenomenon.
Finally we describe theory and experiment on internal circulations in drops that are driven by a combination of translation and tangential electrical stresses. Modulation of the electric field responsible for the latter then results in chaotic advection and good mixing within the drop. Theory and experiment for the mixing patterns are found to be in good agreement. Transport of heat (or mass) to such chaotically stirred drops has a surprisingly non-monotonic dependence on the frequency of modulation. Visualization of the temperature (concentration) fields by means of movies explains why.
Center for Computational Molecular Biology -- Chalk Talk
Department of Computer Science and Engineering Faculty Search Candidate | |
Towards a Cancer Genome Project | |
Abstract: Cancer is a disease driven by mutations in the genome that alter the structure, function, and regulation of genes. These mutations range from single letter changes in the DNA sequence to more drastic rearrangements, gains, or losses of large pieces of DNA. In some types of cancer these large-scale alterations are directly implicated in the pathogenesis of cancer and provide targets for cancer diagnostics and therapeutics.
I will describe computational methods for reconstructing tumor genome architectures and analyzing rearrangements in tumor genomes at high resolution using a technique called End Sequence Profiling (ESP). These methods are inspired by techniques in comparative genomics and view a tumor genome as a rearranged version of the normal human genome. In this framework, both the human and tumor genomes are represented by permutations and the problem is to find a parsimonious sequence of rearrangement operations that transform one permutation into another. I will also describe how computational analysis of ESP data suggests mechanisms that produce complicated patterns of overlapping rearrangement and duplication events that are observed in some tumor genomes.
Another experimental technique called array comparative genomic hybridization (aCGH) has become indispensable in the identification of duplicated and deleted segments of DNA in tumor genomes. However, aCGH gives no information about the location or organization of the duplicated segments within the tumor genome. ESP provides an effective complement to aCGH, and I will discuss how to combine data from both types of experiments using network flow techniques in order to obtain a comprehensive view of tumor genome architecture. I will demonstrate the application of these methods to ESP and aCGH data from breast cancers. Finally, I will describe the implications of this work for the recently proposed Cancer Genome Atlas, a genome project for cancer.
Brown Analysis Seminar
Brown University
Joint Materials/Solid Mechanics Seminar Series
and Department of Mechanical and Aerospace Engineering Princeton University | |
Abstract: This talk presents the results of a combined experimental, theoretical and computational study of contact damage in dental multi-layers. The talk is divided into three parts. In the first part, mechanism-based mechanics models are presented for the prediction of loading rate effects, and failure of dental multi-layers under cyclic loading. In both cases, the critical conditions for failure are predicted by considering the combined effects of slow crack growth and viscous deformation. Subsequently, the mechanisms of interfacial fracture are explored using Brazil disk geometries of model epoxy/glass bi-layers that enable the basic study of interfacial fracture over a wide range of mode mixities. The measured mode mixity dependence of interfacial fracture toughness is shown to be well predicted by cohesive zone models and zone contact models. A microstructure-based finite element model is then used to explain the crack path selection in the model bi-layer system. Finally, the presentation explores the potential for the bio-inspired design of dental multi-layers with improved resistance to contact damage.
PDE Seminar
Department of Mathematics Colloquium
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