The Topology of DNA-Protein Interactions

Speaker: 

Dr. Dorothy Buck

Institution: 

Applied Mathematics, Imperial College London

Time: 

Monday, December 1, 2008 - 4:00pm

Location: 

RH 306

he central axis of the famous DNA double helix is
often topologically constrained or even circular.
The topology of this axis can influence which
proteins interact with the underlying DNA. Subsequently, in all cells there are
proteins whose primary function is to change the DNA axis
topology -- for example converting a torus link into an unknot.
Additionally, there are several protein families that change the axis
topology as a by-product of their interaction with DNA.

This talk will describe typical DNA conformations, and the families of
proteins that change these conformations. I'll present a few examples
illustrating how 3-manifold topology has been useful in understanding certain
DNA-protein interactions, and discuss the most common topological techniques
used to attack these problems.

Phase-filed models for multiphase complex fluids: modeling, numerical analysis and simulations

Speaker: 

Professor Jie Shen

Institution: 

Purdue University

Time: 

Monday, March 30, 2009 - 4:00pm

Location: 

RH 306

I shall present an energetic variational phase field model for
multiphase incompressible flows which leads to a set of coupled
nonlinear system consisting a phase equation and the Navier-Stokes
equations. We shall pay particular attention to situations with large
density ratios as they lead to formidable challenges in both analysis
and simulation.

I shall present efficient and accurate numerical schemes for solving
this coupled nonlinear system, and show ample numerical results (air
bubble rising in water, Newtonian bubble rising in a polymeric fluid, defect
motion in a liquid crystal flow, etc.) which not only demonstrate the
effectiveness of the numerical schemes, but also validate the
flexibility and robustness of the phase-field model.

Reflectionless measures

Speaker: 

Christian Remling

Institution: 

University of Oklahoma

Time: 

Thursday, November 13, 2008 - 2:00pm

Location: 

RH 306

Reflectionless measures are interesting objects because
they arise as limiting measures of spectral measures of arbitrary
Schr"odinger operators with some absolutely continuous spectrum.
In this talk, I'd like to review the definition and some background
material and then discuss more recent work, joint with Alexei Poltoratski,
on reflectionless measures.

Pisot tilings of the line and the discrete spectrum conjecture

Speaker: 

Professor Robert Williams

Institution: 

UT Austin

Time: 

Tuesday, November 18, 2008 - 3:00pm

Location: 

RH 440 R

I will present some of the results by Marcy Barge and Jaroslaw Kwapisz (based on their paper "Geometric Theory of unimidular Pisot substitutions", Amer. J. Math., vol. 128 (2006), no. 5, pp. 1219--1282).

There are two classical ways of studying substitution tilings of the line: symbolic dynamics, and endomorphisms of ``train tracks". The authors give a strikingly new geometric approach and in particular show that if the tiling has a unimodular Pisot matrix of dimension d, then there is a factor onto the d-dimensional torus. In fact, they have a preprint removing the unimodular assumption. I propose to begin defining tilings and the tiling space X of a tiling T. X is a compact metric space that contains all tilings which have the same local patterns as T. In dimension 1 (the subject of this talk) X is similar to a solenoid.

I will not assume any familiarity with tiling theory.

Cloaking by change of variables

Speaker: 

Professor Robert Kohn

Institution: 

Courant Institute of Mathematical Sciences New York University

Time: 

Monday, January 26, 2009 - 2:00pm

Location: 

RH 306

We say a region of space is "cloaked" with respect to electromagnetic measurements if its contents -- and even the existence of the cloak -- are inaccessible to such measurements. One recent proposal for such cloaking takes advantage of the coordinate-invariance of Maxwell's equations. As usually presented, this scheme uses a singular change of variables. That makes the mathematical analysis subtle, and the practical implementation difficult. This talk examines the correctness and robustness of the change-of-variable-based scheme, for scalar waves modelled by Helmholtz's equation, drawing on joint work with Onofrei, Shen, Vogelius, and Weinstein. The central idea is to use a less-singular change of variables. The quality of the resulting "approximate cloak" can be assessed by studying the detectability of a small inclusion in an otherwise uniform medium. We show that a small inclusion can be made nearly undetectable (regardless of its contents) by surrounding it with a suitable lossy layer.

Energy-driven Pattern formation

Speaker: 

Professor Robert Kohn

Institution: 

Courant Institute of Mathematical Sciences New York University

Time: 

Wednesday, January 28, 2009 - 4:00pm

Location: 

RH 306

Energy-driven pattern formation is difficult to define, but easy to recognize. I'll discuss two examples: (a) cross-tie wall patterns in magnetic thin films. (b) surface-energy-driven coarsening of two-phase mixtures. The two problems are rather different -- the first is static, the second dynamic. But they share certain features: in each case nature forms complex patterns as it attempts to minimize a suitable "free energy". The task of modeling and analyzing such patterns is a rich source of challenges -- many still open -- in the multidimensional calculus of variations.

Polynomial extensions in Sobolev spaces

Speaker: 

Professor Jay Gopalakrishnan

Institution: 

University of Florida

Time: 

Monday, February 23, 2009 - 4:00pm

Location: 

RH 306

Consider extension operators that extend certain given functions on the boundary of a tetrahedron into the interior of the tetrahedron, with continuity properties in appropriate Sobolev norms. While such extensions are a fundamental tool in Sobolev space theory, they are essential in finite element analysis. In fact, for the latter, one needs extensions with additional polynomial preservation properties. The talk is devoted to recent developments in the construction of such extension operators.

Method for the Linear Schroedinger Equation of N-interacting Particles

Speaker: 

Professor Claude Bardos

Institution: 

University of Paris 7

Time: 

Monday, October 27, 2008 - 4:00pm

Location: 

RH 306

This is a report on a joint work with Isabelle Catto, Norbert Mauser and Saber Trabelsi. The Multiconfiguration time dependent Hartree Fock Method (MCTDHF) is a nonlinear approximation of a linear system of /N/ quantum particles with binary interaction. It combines the principle of the Hartree Fock and the Galerkin approximation. The main difficulty is the introduction of a global (in space) density matrix $\Gamma(t) $ which may degenerate. By construction this approximation formally preserves the mass and the energy of the system. The conservation of energy can be used to balance the singularities Coulomb potential and to provide sufficient conditions for the global in time invertibility of $\Gamma(t)$.

In numerical computations this matrix is very often regularized (changed into $\Gamma(t) +\epsilon(t)$). In this situation the energy is no more conserved
and the mathematical analysis done in $L^2$ relies on Strichartz type estimates.

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