Theory and Applications in Mathematical Cell Biology

Speaker: 

William Holmes

Institution: 

UC Irvine

Time: 

Wednesday, February 5, 2014 - 4:00pm to 5:00pm

Location: 

RH 306

I will give an overview of my work in mathematical cell biology.  First I will discuss topics related to polarity, specifically in the context of cell movement.  This and numerous other cell functions require identification of a “front” and “back” (e.g. polarity).   In some cases this can form spontaneously and in others sufficiently large stimuli are required.  I will discuss a mechanistic theory for how cells might transition between these behaviors by modulating their sensitivity to external stimuli.  In order to address this and analyze the systems being presented, I will describe a new non-linear bifurcation technique, the Local Perturbation Analysis, for analyzing complex, spatial biochemical networks.  This methodology fills a void between simple (but limited) stability techniques and more thorough (but in many cases impractical) non-linear PDE analysis techniques.  Additionally, I will discuss work related to early development of the mammalian embryo.  A vital first step in this process is the formation of an early placenta prior to implantation.  I will discuss a multi-scale stochastic model of this spatial patterning event and show that genetic expression noise is both necessary and sufficient for this event to occur robustly. 

Diffuse Decompositions of Polynomials

Speaker: 

Daniel Kane

Institution: 

Stanford University

Time: 

Wednesday, January 29, 2014 - 2:00pm to 3:00pm

Host: 

Location: 

DBH 6011

We study some problems relating to polynomials evaluated either at random Gaussian or random Bernoulli inputs.  We present a structure theorem for degree-d polynomials with Gaussian inputs. In particular, if p is a given degree-d polynomial, then p can be written in terms of some bounded number of other polynomials q_1,...,q_m so that the joint probability density function of q_1(G),...,q_m(G) is close to being bounded.  This says essentially that any abnormalities in the distribution of p(G) can be explained by the way in which p decomposes into the q_i.  We then present some applications of this result.

Dynamics of Ferromagnets: Averaging Methods, Bifurcation Diagrams, and Thermal Noise Effects

Speaker: 

Katie Newhall

Institution: 

New York University - Courant Institute

Time: 

Monday, January 13, 2014 - 2:00pm to 3:00pm

Host: 

Location: 

Nat Sci II Room 1201

Driving nanomagnets by spin-polarized currents offers exciting prospects in magnetoelectronics, but the response of the magnets to such currents remains poorly understood. For a single domain ferromagnet, I will show that an averaged equation describing the diffusion of energy on a graph captures the low-damping dynamics of these systems. Specifically, I obtain analytical expressions for the critical spin-polarized currents needed to induce stable precessional states and magnetization switching in the zero temperature system as well as for the mean times of thermally assisted magnetization reversals in the finite temperature system, giving explicit expressions for the effective energy barriers conjectured to exist. I will then outline the problem of extending the analysis to spatially non-unifrom magnets, modeled by an infinite dimensional Hamiltonian system.

Recent advances in First Passage Percolation

Speaker: 

Antonio Auffinger

Institution: 

University of Chicago

Time: 

Friday, January 10, 2014 - 2:00pm to 3:00pm

Host: 

Location: 

Nat Sci II Room 1201

First-passage percolation is a model of a random metric on a infinite network. It deals with a collection of points which can be reached within a given time from a fixed starting point, when the network of roads is given, but the passage times of the road are random. It was introduced back in the 60's but most of its fundamental questions are still open. In this talk, we will overview some recent advances in this model focusing on the existence, fluctuation and geometry of its geodesics. Based on joint works with M. Damron and J. Hanson.

Singularities of polynomials in characteristic 0 and characteristic p

Speaker: 

Karl Schwede

Institution: 

Pennsylvania State University

Time: 

Tuesday, January 21, 2014 - 2:00pm to 3:00pm

Host: 

Location: 

Nat Sci II Room 1201

I will discuss the singularities of the zero-locus of a polynomial equation. A particular focus will be payed to comparing different singularities. I will discuss two different approaches to this question: analytic (characteristic zero) and algebraic (positive characteristic).

Inverse boundary problems: recent advances and challenges

Speaker: 

Katya Krupchyk

Institution: 

University of Helsinki

Time: 

Friday, December 6, 2013 - 2:00pm to 3:00pm

Host: 

Location: 

Nat Sci II, Room 1201

In an inverse boundary value problem one is interesting in determining the internal properties of a medium by making measurements on the boundary of the medium. In mathematical terms, one wishes to recover the coefficients of a partial differential equation inside the medium from the knowledge of the Cauchy data of solutions on the boundary. These problems have numerous applications, ranging from medical imaging to exploration geophysics. We shall discuss some recent progress in the analysis of inverse boundary problems, starting with the celebrated Calderon problem, and point out how the methods of microlocal and harmonic analysis can be brought to bear on these problems.  In particular, inverse problems with rough coefficients and with measurements performed only on a portion of the boundary will be addressed.

Minimal submanifolds in differential geometry

Speaker: 

Richard Schoen, Bass Professor of Humanities and Sciences

Institution: 

Stanford University

Time: 

Tuesday, March 12, 2013 - 2:00pm to 3:00pm

Location: 

RH 306

The theory of minimal surfaces arose historically from work of J. L. Lagrange and physical observations of J. Plateau almost 200 years ago. Rigorous mathematical theory was developed in the 20th century. In more recent times the theory has found important applications to diverse areas of geometry and relativity. In this talk, which is aimed at a general mathematical audience, we will introduce the subject and describe a few recent applications of the theory.

Asymptotic and bifurcation analysis of a travelling wave based mechanism for cell polarization

Speaker: 

Alexandra Jilkine

Institution: 

University of Arizona

Time: 

Thursday, January 24, 2013 - 4:00pm to 5:00pm

Location: 

RH 306

The ability of eukaryotic cells to polarize is essential for their division, differentiation into distinct tissues, and migration. During polarization various polarity proteins segregate to form a distinct front and rear. To understand a mechanism for polarization we consider a simplified PDE model describing the interchange of a polarity protein,  between an active membrane-bound form and an inactive cytosolic form. An initial transient signal results in a traveling front of activation that stops at some point in the domain, representing segregation of the cell into front and back. Using phase plane methods and numerical continuation we analyze the transition from a spatially heterogeneous (pinned wave) to a spatially homogeneous steady state as the ratio of the diffusion coefficients of the two forms and the total amount of material in the domain is varied. We discover a second spatially heterogeneous solution that acts as a threshold for polarity establishment, and give biological interpretation for this phenomenon.

Actin traveling waves in motile cells

Speaker: 

Jun Allard

Institution: 

UC Davis

Time: 

Wednesday, January 30, 2013 - 4:00pm to 5:00pm

Host: 

Location: 

RH 306

Traveling waves in actin have recently been reported in many cell types. Fish keratocyte cells, which usually exhibit rapid and steady motility, exhibit traveling waves of protrusion when plated on highly adhesive surfaces. We hypothesize that waving arises from a competition between actin polymerization and mature adhesions for VASP, a protein that associates with growing actin barbed ends. We developed a mathematical model of actin protrusion coupled with membrane tension, adhesions and VASP. The model is formulated as a system of partial differential equations with a nonlocal integral term and noise. Simulations of this model lead to a number of predictions, for example, that overexpression of VASP prevents waving, but depletion of VASP does not increase the fraction of cells that wave. The model also predicts that VASP exhibits a traveling wave whose peak is out of phase with the F-actin wave. Further experiments confirmed these predictions and provided quantitative data to estimate the model parameters. We thus conclude that the waves are the result of competition between actin and adhesions for VASP, rather than a regulatory biochemical oscillator or mechanical tag-of-war. We hypothesize that this waving behavior contributes to adaptation of cell motility mechanisms in perturbed environments.

Integro-differential Equations for Biomedical Image Processing and Modeling

Speaker: 

Associate Professo Chiu-Yen Kao

Institution: 

The Ohio State University

Time: 

Monday, January 30, 2012 - 3:00pm

Location: 

Natural Sciences 2 #3201

Differential and Integral Equations are powerful tools to model and analyze biological problems. In this talk, two different biological applications will be discussed: one is in biomedical images and the other is in cellular biology.

The basic medical science research and clinical diagnosis and treatment have strongly benefited from the development of various noninvasive biomedical imaging techniques and modeling, e.g. magnetic resonance imaging (MRI) and computed tomography (CT). We introduce integro-differential models to the morphology and connectome study of human brains from brain images, as well as the shape analysis of ciliary muscles from human eyes.

In the application of cellular biology, we investigate the cell differentiation model of T cells. T cells of the immune system, upon maturation, differentiate into either Th1 or Th2 cells that have different functions. The decision to which cell type to differentiate depends on the concentrations of transcription factors T-bet and GATA-3. We study a population density model of the T cells and show that, under some conditions on the parameters of the system of integro-differential equations, various T cells differentiation scenarios occur.

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