Variational Implicit Solvent Modeling and Level-Set Calculation of Biomolecular Structure and Interaction

Speaker: 

Associate Professor Bo Li

Institution: 

UCSD

Time: 

Monday, October 8, 2007 - 4:00pm

Location: 

MSTB 254

Understanding biomolecules, their structures and interactions
with solvent such as water, is essential to revealing mechanisms
and functions of biological systems. While atomistic simulations
that treat both solvent and solute molecules explicitly are
usually more accurate, implicit or continuum solvent models for
biomolecules are far more efficient. In this talk, I will first
introduce a new class of accurate implicit solvent models, termed variational implicit solvent models, for biomolecules. Central in this model is a free energy functional of all admissible
solute-solvent interfaces, coupling both nonpolar and polar
contributions of an underlying system. An energy-minimizing
interface then defines a molecular surface in solution. I will
then describe a level-set method for the numerical calculation of equilibrium solvent-solute interface and free-energy for the
solvation of nonpolar molecules, and present extensive numerical results with comparison to molecular dynamics simulations. This is joint work with Jianwei Che, Li-Tien Cheng, Joachim Dzubiella, J. Andy McCammon, and Yang Xie.

Some Fast Numerical Methods Based on Semiseparable Rank Structured Matrices

Speaker: 

Adjunct Assistant Professor Jianlin Xia

Institution: 

UCLA

Time: 

Monday, October 1, 2007 - 4:00pm

Location: 

MSTB 254

This talk discusses some fast numerical methods using certain rank
structured matrices: sequentially semiseparable (SSS) matrices
and hierarchically semiseparable (HSS) matrices. I will first
briefly show an example using semiseparable matrices: to find
polynomial roots and to estimate their conditions in $O(n^2)$ flops
instead of classical $O(n^3)$, where $n$ is the degree of the
polynomial. Then I will discuss in detail a superfast multifrontal
type direct method for large discretized linear systems. Rank
structures in the multifrontal method for certain discretized
matrices are exploited. Then semiseparable matrices are used
to approximate dense frontal and update matrices in the elimination.
A generalized semiseparable type factorization is obtained in linear
time. The overall sover has nearly linear complexity, linear storage,
and good potential for parallelization. It can also work as an
effective preconditioner.

Fun with zeta and L-functions of graphs

Speaker: 

Audrey Terras

Institution: 

UCSD

Time: 

Saturday, October 27, 2007 - 4:00pm

Location: 

McDonnell Douglas Engineering Auditorium

I will present an introduction to zeta and L-functions of graphs by comparison with the zeta and L-functions of number theory. Basic properties will be discussed, including: the Ihara formula saying that the zeta function is the reciprocal of a polynomial. I will then explore graph analogs of the Riemann hypothesis, the prime number theorem, Chebotarev's density theorem, zero (pole) spacings, and connections with expander graphs and quantum chaos. References include my joint papers with Harold Stark in Advances in Mathematics. There is also a book I am writing on my website.

Serre's conjecture

Speaker: 

Chandrashekhar Khare

Institution: 

UCLA

Time: 

Saturday, October 27, 2007 - 2:30pm

Location: 

McDonnell Douglas Engineering Auditorium

I will spend most of the time formulating Serre's conjecture and explaining some of its applications: for instance, it implies Artin's conjecture for 2-dimensional odd complex representations of the absolute Galois group of Q. I will sketch some of the main ideas in the recent proof of the conjecture in joint work with Wintenberger, as completed by Kisin. I will also explain, if time permits, how our work offers a fresh perspective on Wiles' proof of Fermat's Last Theorem (FLT). For instance it gives a diiferent, in a sense more elementary, aproach to Ribet's level lowering results, a key ingredient in the proof of FLT.

Integral models for toroidal compactifications of Shimura varieties

Speaker: 

Elena Mantovan

Institution: 

Caltech

Time: 

Saturday, October 27, 2007 - 11:30am

Location: 

McDonnell Douglas Engineering Auditorium

In the case of good reduction, smooth integral models for Shimura varieties of PEL type have been constructed by Faltings and Chai. In my talk I'll describe how their construction can be extended to the cases of bad reduction at unramified primes, and discuss the geometry of the resulting spaces. A useful tool in this context is provided by the language of 1-motives. This is joint work with Ben Moonen.

Special values of L functions modulo p

Speaker: 

Vinayak Vatsal

Institution: 

University of British Columbia

Time: 

Saturday, October 27, 2007 - 10:00am

Location: 

McDonnell Douglas Engineering Auditorium

It has been known since Euler that the values of the Riemann zeta function at negative integers are certain rational numbers, namely the Bernoulli numbers Bk. Similarly, the values of Dirichlet L-functions at s=0 are related to class numbers of certain number fields. These are simple instances of a common phenomenon, namely that the values of L-functions at critical points are algebraic, up to a simple factor, and that these algebraic numbers are related to algebraic quantities such as class numbers and Selmer groups. The present talk will be a survey talk on the algebraicity of special values of L-functions and their divisibility properties modulo primes.

Mathematical theory of solids: From atomic to macroscopic scales

Speaker: 

Professor Weinan E

Institution: 

Princeton

Time: 

Thursday, November 29, 2007 - 4:00pm

Location: 

MSTB 254

There are no analogs of Navier-Stokes equations for solid mechanics. One reason is that information at the atomic scale seems to play a much more important role for solids than for fluids. A satisfactory mathematical theory for solids has to taken into account the behavior of solids at different scales, from electronic to atomic, to macroscopic scales.

I will discuss some of the fundamental problems that we have to resolve in order to build such a theory. I will start by reviewing the geometry of crystal lattices, the quantum as well as classical atomistic models of solids. I will then focus on a few selected problems:

(1) The crystallization problem -- why the ground states of solids are crystals and which crystal structure do they select?

(2) the microscopic foundation of elasticity theory;

(3) stability and instability of crystals;

(4) the electronic structure and density functional theory.

Metric Degeneration and Spectral Convergence

Speaker: 

Professor Julie Rowlett

Institution: 

UCSB

Time: 

Tuesday, March 4, 2008 - 4:00pm

Location: 

MSTB 254

Consider a family of smooth compact connected $n$ dimensional Riemannian manifolds. What can one say about the spectral geometry of a limit of these?

This question has interested many spectral geometers; my talk focuses on conical metric degeneration in which the family converges "asymptotically conically'' to an open manifold with conical singularity. I will present spectral convergence results and discuss techniques including microlocal analysis on manifolds with corners and geometric blowup constructions. I will also summarize spectral convergence results for other geometric contexts and discuss applications and open questions.

Subelliptic Cordes estimates

Speaker: 

Professor Juan Manfredi

Institution: 

University of Pittsburgh

Time: 

Thursday, March 13, 2008 - 4:00pm

Location: 

MSTB 254

The classical Friedrichs identity states that for $u\in C_0^{\infty}(\mathbb{R}^n)$ we have
$$\int_{\mathbb{R}^n} |D^2 u|^2\, dx = \int_{\mathbb{R}^n} |\Delta u|^2\, dx.$$
From this inequality we immediately get $W^{2,2}$-estimates for
solutions of $\Delta u =f$ and also for solutions of measurable perturbations
of the form $\sum_{ij}a_{ij}(x) u_{ij}(x)=f(x)$, when the matrix
$A=(a_{ij})$ is closed to the identity in sense made precise
by Cordes.
In this talk we first explore extensions of the Friedrichs identity in
the form of sharp inequalities
$$\int_{X} |\mathfrak{X}^2 u|^2\, dx \le C_1 \int_{X} |\Delta_{\mathfrak{X}} u|^2\, dx +C_2\int_{X} |\mathfrak{X}u|^2 \, dx $$
where $X$ is a Riemannian manifold, the Heisenberg group, and certain types of CR manifolds.
\par
We then show how to use these estimates to study quasilinear subelliptic equations.\par

This is joint work with Andr\`as Domokos (PAMS 133, 2005) and Sagun
Chanillo (2007 preprint.)

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