Some Mathematical Problems in Computational Systems Biology

Speaker: 

Prof Eric Mjolsness

Institution: 

UCI

Time: 

Monday, March 14, 2005 - 4:00pm

Location: 

MSTB 124

Biochemical reaction networks provide a paradigm for many dynamical systems in biology. The paradigm can be generalized to describe "variable-structure systems" in which objects larger than molecules (such as cells) also change in number and in their relationships over time. In the course of building mathematical and software tools for understanding such networks and dynamical systems, we have identified some interesting applied mathematical problems whose reformulation and solution would be very useful in current computational biology. For example, we can identify partial differential equations whose solution would be especially instructive for enzyme kinetics. These problems arise at the level of small reaction networks, multimolecular complexes, and the development of multicellular tissues. Developmental examples include modeling the shoot meristem of a plant.

A common mathematical framework for models at these different spatial scales can be given in terms of "dynamical grammars". In a dynamical grammar, an input/output syntax for an elementary chemical or biological processes is mapped to an operator algebra expression for the generator of the temporal dynamics associated with that process. Many processes act simultaneously (in parallel) if their generators are summed. Contingent spatial relationships are expressed in terms of dynamical graph grammars, whose formulation could perhaps be improved by use of ideas from topology and differential geometry. By solving such problems, we may hope to construct a useful modeling language of sufficient generality to describe multiscale, variable-structure dynamical systems that arise naturally in biology.

A mathematical model for the regulation of tumor dormancy based on enzyme kinetics

Speaker: 

Prof Howard Levine

Institution: 

Iowa State University

Time: 

Monday, April 4, 2005 - 4:00pm

Location: 

MSTB 124

We present a two compartment model for tumor dormancy based on an idea of Zetter to wit: The vascularization of a secondary (daughter) tumor can be suppressed by inhibitor originating from a larger primary (mother) tumor. We apply this idea at the avascular level to develop a model for the remote suppression of secondary avascular tumors via the secretion of primary avascular tumor inhibitors. The model gives good agreement with experimental observation (Derm. Surg. 29(2003) 664-667). The authors reported on the emergence of a polypoid melanoma at a site remote from a primary polypoid melanoma after excision of the latter . The authors observed no recurrence of the melanoma at the primary site, but did observe secondary tumors at secondary sites five to seven centimeters from the primary site within a period of one month after the excision of the primary site. We attempt to provide a reasonable biochemical/cell biological model for this phenomenon. We show that when the tumors are sufficiently remote, the primary tumor will not influence the secondary tumor while, if they are too close together, the primary tumor can effectively prevent the growth of the secondary tumor, even after it is removed. It should be possible to use the model as the basis for a testable hypothesis which could be checked in a controlled in vitro experiment.

Quenching of reaction by fluid flow

Speaker: 

Prof Alexander Kiselev

Institution: 

Wisconsin

Time: 

Monday, March 21, 2005 - 4:00pm

Location: 

MSTB 124

We consider the problem of quenching the flame in a framework of passive reaction-diffusion model. We ask which flows are more efficient in supressing reaction, and prove bounds on the relationship between flow strength and the initial flame size for different classes of flows. The estimates we prove agree very well with numerical experiments carried out in collaboration with astrophysics ASC group at the University of Chicago. The problem is closely related to proving norm bounds for the evloution semigroup corresponding to the passive scalar model. The techniques involve PDE and probability tools, and further natural questions indicate interesting links with spectral theory of elliptic operators and dynamical systems.

Towards the quantum Brownian motion

Speaker: 

Professor Laszlo Erdos

Institution: 

University of Munich

Time: 

Tuesday, April 5, 2005 - 2:00pm

Location: 

MSTB 256 - NOTE DIFFERENT ROOM

Einstein's kinetic theory of the Brownian motion, based upon light
water molecules continuously bombarding the heavy pollen, provided an explanation of diffusion from the Newtonian mechanics. Since the discovery of quantum mechanics it has been a challenge to verify the emergence of diffusion from the Schrodinger equation. In this talk I will report on a mathematically rigorous derivation of a diffusion equation
as a long time scaling limit of a random Schr\"odinger equation in a weak, uncorrelated disorder potential. This is a joint work with M. Salmhofer and H.T. Yau.

TBA

Speaker: 

Laszlo Erdos

Time: 

Wednesday, May 4, 2005 - 2:00pm

Location: 

MSTB 256 - NOTE DIFFERENT ROOM

Infinite Groups

Speaker: 

Zelmanov

Institution: 

UCSD

Time: 

Thursday, April 21, 2005 - 4:00pm

Location: 

MSTB 254

I will try to give a broad review of the amasing
developments in the theory of infinite groups during the last 25 years. These include the
emergence of Monsters and flourishing of the Asymptotic Theory of Finite Groups. We will focus on important examples and formulate some open problems.

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