Exact stochastic behavior of molecular networks and realistic simulation of cellular pattern formation

Speaker: 

Jie Liang

Institution: 

Dept of Bioengineering, University of Illinois at Chicago

Time: 

Wednesday, September 26, 2007 - 4:00pm

Location: 

MSTB 254

Many biochemical networks involve molecular species of small copy
numbers. Of fundamental importance in systems biology is to understand
the nature of stochasticity intrinsic in these networks. The chemical
master equation (CME) provides a general framework for studying such
networks. Although Fokker-Planck/Langevin equations give useful
approximations, Gillespie Monte Carlo algorithm is often used to
simulate stochasticity. Here we describe a new method to directly
solve the CME to account for full stochasticity without either
Fokker-Planck or Gillespie for nontrivial systems. We characterize
the exact state space of a molecular network of small copy numbers
with arbitrary stochiometry at a given initial concentration
condition. We show how our method works for toggle-switch, MAPK, and
lambda-phage networks. We then show how to compute the steady state
probablistic landscape of these networks, and infer biological conditions
for bistability and the mechanism of lysis-lysogeny switch. We also
demonstrate how time evolution of concentration dynamics of molecular
species in a nework at large time span across many orders of scale can be
computed. Finally, we demonstrate a novel method for simulating
stochastic behavior of dynamic pattern formation of cell populations.
Unlike
cellular automata which provides only caricatures of cell pattern
formation, our geometric model captures the shape and size of cells
more realistically, accounts for topological events in the dynamic
re-arrangement of spatial cells, and incorporates many biochemical
forces. Example in cell differentiation will be given
(Joint work with Youfang Cao, Hsiao-Mei Lu, and Sema Kachalo. Relevant
publications can found following URL: www.uic.edu/~jliang)

Funding Opportunities in the Mathematical Sciences at the National Science Foundation

Speaker: 

Professor Henry A. Warchall

Institution: 

NSF

Time: 

Thursday, October 11, 2007 - 4:00pm

Location: 

MSTB 254

I will describe current opportunities for funding in mathematics and statistics at the National Science Foundation, as well as issues that arise in proposal preparation. There will be ample opportunity for questions from the audience.

Complemented subspaces of symmetric Banach spaces

Speaker: 

Professor Matthew Neal

Institution: 

Denison University, Ohio

Time: 

Friday, September 28, 2007 - 3:00pm

Location: 

MSTB 254

A symmetric Banach space (SBS) is one whose dual ball is a bounded symmetric domain. It is a deep fundamental result that a contractively complemented subspace of an SBS is linearly isometric to another SBS. We prove the converse: if a subspace of a SBS is linearly isometric to an SBS, then that subspace is contractively complemented. Examples of SBSs are L^1-spaces and preduals of von Neumann algebras. (Joint work with B. Russo)

Phenotypic Evolutionary Models in Stem Cell Biology: Replacement, Quiescence, and Variability

Speaker: 

Professor Marc Mangel

Institution: 

University of California, Santa Cruz

Time: 

Monday, December 10, 2007 - 4:00pm

Location: 

MSTB 254

Stem cells have the ability to renew and to differentiate into progenitor cells that ultimately form all of the tissues in an organism. The current interest in stem cells C both adult and embryonic C is through the promise that they hold for regenerative medicine.
That promise, however, relies on the assumption that stem cells will respond to our modifications of them in ways that we desire. However, experience with interventions in other natural systems C from fishing to antibiotics C shows that acting without thinking about evolutionary consequences is fraught with danger. The time for an evolutionary ecology of stem cells is now. I will show how this can be done, using the hematopoeitic system as an example. To begin, we model the system of stem, progenitor, and fully differentiated cells using a combination of stochastic simulation and associated ordinary differential equations. These models must capture the feedback controls C both positive and negatve C on the stem cell system. Once this framework is organized, it is possible to ask a variety of questions. In this talk, I will focus on two. First, I will use evolutionary invasion analysis to ask if modifications of stem cell parameters will have the effects that we desire. Second, I will use state dependent life history theory, implemented through stochastic dynamic programming, to understand why stem cells are mainly quiesencent and compare this result with the classic experiment of Till and colleagues. This work reminds us that nothing in biology makes sense except in the light of evolution.

Recent progress and remaining challenges in computational rheology

Speaker: 

Professor Raz Kupferman

Institution: 

The Hebrew University

Time: 

Monday, November 26, 2007 - 4:00pm

Location: 

MSTB 254

Since its early days in the early 1970, the field of computational rheology (the flow of complex fluids) has experienced a number of insurmountable stumbling blocks, notably, the high Weissenberg number problem (HWNP); it is a term coined to describe the breakdown of computations at a moderately high values of the elasticity parameter. In this lecture I will report a number of recent advances in an effort to elucidate the HWNP, and describe some of the remaining problems.

Numerical Methods for Inverse Transport Problems and Applications

Speaker: 

L. E. Dickson Instructor Kui Ren

Institution: 

University of Chicago

Time: 

Monday, November 19, 2007 - 4:00pm

Location: 

MSTB 254

We present a few numerical methods for inverse problems related to the
radiative transport equation. We consider two specific applications of those inverse problems: optical tomography and incoherent imaging in random media. Numerical examples based on synthetic and experimental data will be presented.

Interface dynamics and shape control in fluids, materials and bio-systems

Speaker: 

Visiting Assistant Professor Shuwang Li

Institution: 

UCI

Time: 

Monday, November 5, 2007 - 4:00pm

Location: 

MSTB 254

Many multiphysics problems involve time-dependent free boundaries (or
interfaces) where the interface motion is controlled by interactions
among microscopic forces (e.g. surface tension) and external
macroscopic driving forces (e.g. far-field temperature or heat flux
for solidification problems, external flow for biomembranes). During
the evolution, the moving interface experiences instability due to the
imbalance of forces. In the first part of this talk, we consider the
Hele-Shaw problem (Saffman-Taylor instability) and crystal growth
problem (Mullins-Sekerka instability). We will show how these
instabilities can be suppressed using appropriate boundary
conditions. In particular, we demonstrate the existence of
self-similar evolving, symmetric universal patterns. In the second
part of this talk, we consider a bio-membrane problem. We will discuss
the model and show how surface tension can be used to control the
phase decomposition along the surface of the membrane. In particular,
we demonstrate how flow, morphology and phase decomposition are
coupled during the dynamics.

Numerical Methods of Electromagnetics for Complex Inhomogenous Systems

Speaker: 

Professor Wei Cai

Institution: 

University of North Carolina at Charlotte

Time: 

Monday, October 29, 2007 - 4:00pm

Location: 

MSTB 254

Fast and accurate computation of electromagnetic phenomena plays an important role in understanding the underlying physics for many complex physical and biological systems, such as lasing in optical fiber lasers, electrostatics forces in solvation model of biomolecules, and irradiation damage in materials under extreme conditions. In this talk, we will present two new algorithm developments with applications in these areas.

Image Charge Approximations of Reaction Fields and FMM for Charges inside a Dielectric Sphere

The reaction field of a charge inside a dielectric sphere, induced by a surrounding dissimilar dielectric medium, has applications in the study of electrostatic forces in the defect evolutions in material under extreme neutron irradiation, and hybrid explicit/implicit solvation models for biomolecules. In both cases, the long range Coulomb interactions have been identified as of primary influence in materials resistance to amorphorization under extreme conditions in the first case, and the free energy and the solvation study of biomolecules for the second. We have developed new discrete image charge approximations for the reaction field of a charge inside a dielectric sphere at high accuracy with only 2-3 image charges. Based on this result, we have extended the Fast Multipole Method to calculate the electrostatic interactions of charges inside or outside a dielectric sphere. The resulting O(N) algorithm has applications in computational materials and biology.

A Generalized Discontinuous Galerkin (GDG) Method based on Split Distributions for PDE with Nonsmooth Solutions

To model optical wave propagations in inhomogenous waveguides under the paraxial approximation, we need to solve time dependent Schrödinger equations with nonsmooth solutions as a result of field discontinuities at material interfaces. We will present a new type of discontinuous Galerkin method based on split distributions and their incorporations into the PDEs to account for jumps in solutions and derivatives. Special integration by parts formula for the split distributions is developed. The resulting generalized discontinuous Galerkin (GDG) method will be flexible to handle various types of interface jump conditions (time dependent and nonlinear) with high accuracy and easy to extend to multi-dimensional and other type PDEs with nonsmooth solutions. A full vector GDG-BPM (beam propagation method) will be developed to study gain guided fiber laser for efficient generations of high energy power sources.

A Posteriori Error Estimation in Finite Element Method

Speaker: 

Professor Zhiqiang Cai

Institution: 

Purdue University

Time: 

Monday, October 22, 2007 - 4:00pm

Location: 

MSTB 254

All computational results obtained from computer simulations of
physical phenomena involve numerical error. Discretization error can
be large, pervasive, unpredictable by classical heuristic means, and
can invalidate numerical predictions. The {\it a posteriori} error
estimation is a mathematical theory for estimating and quantifying
discretization error based on information gained during the current
stage of the computation. In this talk, I will first give an
introductory review of existing {\it a posteriori} error estimators,
and then introduce two new estimators. One of them is a modification
of the recovery-based estimator and the other is exactly equal to
the true error in an ``energy'' norm on any given mesh. Numerical
examples will also be presented.

Multi-scale Geometric Modeling of 3D Cardiac Myocytes from Light/Electron Microscopy Imaging Data

Speaker: 

Postdoctoral Scholar Zeyun Yu

Institution: 

UCSD

Time: 

Monday, October 15, 2007 - 4:00pm

Location: 

MSTB 254

The geometries of sub-cellular structures in cardiac myocytes play a critical role in regulating the cells' functions. We present a chain of image and geometric processing approaches for constructing multi-scale and realistic models of 3D cardiac cells. Two types of imaging data are considered: one is the confocal light microscopy images of whole cells and the other is the electron microscopy images of individual calcium release units (CRUs). Images are pre-processed by anisotropic filtering and contrast enhancement techniques. Sub-cellular structures are extracted by automatic image analysis approaches including 3D image segmentation and skeletonization. High quality surface and volumetric meshes are generated for finite element simulation of excitation-contraction (E-C) coupling in cardiac myocytes.

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