September 11-14, 2006
Workshop: "Principles of Fluorescence Techniques."
<Course Schedule>

April 24, 2006
Quantitative Analysis of Morphogen Gradients in Drosophila Oogenesis
by Stanislav Shvartsman, Ph.D.

Co-sponsored by the Center for Complex Biological Systems and Department of Developmental and Cell Biology

Reference:
Yakoby and Shvartsman, Systems-level questions in Drosophila Oogenesis (2005).

Spring 2005
Modeling Biochemical Systems with Differential Equations, Stochastic Processes, and Constraint-Based Optimization

Speaker: Hong Qian, Associate Professor, Department of Applied Mathematics; Associate Director, National Simulation Resource, University of Washington, Seattle.

With the demand from modeling systems level cellular biochemistry as a reaction network, different applied mathematical approaches are now being pursued. I will discuss three approaches based on (1) systems of ODE with nonlinearity, (1) stochastic processes with irreversibility, and (3) constraint-based optimization suggesting an oriented matroid. A unifying theme of these approaches is the nonequilibrium thermodynamics of living (open) systems.

Spring Quarter 2005

IGB DISTINGUISHED SPEAKER SERIES 2004-2005

February, 2005
ERIC S. LANDER, Ph.D.
Professor of Biology, Massachusetts Institute of Technology; Professor of Systems Biology, Harvard Medical School; Founding Director, Broad Institute, MIT/Harvard; Member, Whitehead Institute.

Lecture: "Interpreting Genomic Information"
Monday, February 28, 2005, at 10:00 a.m.
Student Center - Emerald Bay A/B, UC Irvine

The School of Biological Sciences in partnership with the Chancellor's Distinguished Fellows Series presents a public lecture by renowned scientist, Dr. Eric Lander, Director of the Broad Institute of MIT and Harvard, Professor of Biology at MIT, Professor of Systems Biology at Harvard Medical School and a member of the Whitehead Institute.

Lecture: "The Human Genome and Beyond".
Date/Time: Friday, February 25, 2005 at 8:00 p.m.
Place: Crystal Cove Auditorium

There will be a public reception before the lecture, from 7:00 - 8:00 p.m. in the lobby of the Student Center.

Dr. Lander is one of the driving forces behind today's revolution in genomics. He was among the leaders of the Human Genome Project and is founding director of the Broad Institute, a research collaboration between MIT, Harvard University and its affiliated hospitals and the Whitehead Institute for Biomedical Research. Its mission is to create comprehensive tools for genomic medicine and to pioneer applications of these tools to propel the understanding and treatment of disease. Dr. Lander has received many honors and awards for his scientific accomplishments and leadership in genomics.

University of California, Irvine Department of Mathematics Distinguished Lecture Series

Avner Friedman, Distinguished Professor, The Ohio State University; Director, NSF Mathematical Biosciences Institute.

Dr. Friedman is a Fellow of the National Academy of Arts and Sciences and a member of the National Academy of Sciences. He has also served as Director to the IMA at the University of Minnesota 1987-1997, Director of Minnesota Center for Industrial Mathematics and in 1996 became a Regents Professor at the University of Minnesota. His research interests include partial differential equations, stochastic processes, and control theory.

February 8, 2005
“How Useful is Mathematics to the Biosciences?”

The Mathematical Biosciences Institute (MBI) was established at The Ohio State University in 2002, with funding from the NSF. The MBI brings mathematicians and statisticians together with bio-scientists from all over the country and the world in order to work on significant problems in biology and medicine. In this talk, I shall give examples where mathematics does contribute to the solution of important problems in the biosciences. (i.e. tumor growth). I shall also briefly describe new mathematical problems, which arise from biological models.

February 7, 2005
“Mathematical Models in Tumor Growth”

For information call Gloria Coulston (949) 824-5502 or gcoulsto@math.uci.edu

http://www.math.uci.edu/

January 13, 2005
UCI Dynamical Systems Day
University of California, Irvine Department of Mathematics

"Data and Topology"
STEPHEN SMALE, Ph.D. – Professor of Mathematics and Economics, UC Berkeley. Distinguished University Professor, City University-Hong Kong. Dr. Smale has made significant contributions in the fields of dynamical systems, geometry, econometrics, operational research, topology and the mathematical theory of computer science. He is a member of the National Academy of Sciences. He received the Fields Medal, an International Medal, awarded every four years, in 1966. Important honors bestowed upon Professor Smale include the 1965 Veblen Prize for Geometry, the Chauvenent Prize in 1988 and the Van Neumann Award by the Society for Industrial and Applied Mathematics in 1989.

"Optimal decisions: From Neural Spikes, Through Stochastic Differential Equations, to Behavior."

PHILIP HOLMES, Ph.D. – Charles N. Mellowes Professor Engineering and Applied Mathematics at Princeton University. He is a Fellow of the American Academy of Arts and Sciences. In 2001 he was elected an Honorary Member of the Hungarian Academy of Sciences. In 1993-94 he received a John Simon Guggenheim Memorial Fellow. Dr. Holmes works on nonlinear dynamics and differential equations, developing qualitative and analytical methods for studying mathematical models of solid, fluid, and biological systems.

For information call Gloria Coulston (949) 824-5502 or gcoulsto@math.uci.edu

http://www.math.uci.edu/

Fall Quarter 2005

December 7, 2005
Three-Dimensional Models of Morphogenesis

Mark Alber, Departments of Mathematics and Physics, The Center for the Study of Biocomplexity, University of Notre Dame

In this talk we will present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs [1]. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction diffusion model [2] and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows one to rapidly and compactly create computational models of a class of complex developmental phenomena. To illustrate model development, we describe simulations of the simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb. In the second half of the talk we will describe the first three-dimensional stochastic model [3,4] based on contact-mediated cell communication, for studying myxobacteria fruiting body development. The myxobacteria under starvation undergo several developmental stages including rippling, streaming, jamming, aggregation, and, finally, developing mature fruiting bodies. Combining contact signaling between cells and slime production mechanisms, our model reproduces all different stages in a transition from 3D traffic jams to aggregates and demonstrates possible structure of cell arrangement within the fruiting body.

References:
1. Chaturvedi, R., C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm, H.G.E. Hentschel, J. A. Glazier, S. A. Newman, M. Alber [2005], On Multiscale Approaches to 3-Dimensional Modeling of Morphogenesis, Journal of the Royal Society Interface 2 3, 237-253.

2. Alber, M., Glimm, T., Hentschel, H.G.E., Kazmierczak, B., and S. Newman [2005], Stability of n-Dimensional Patterns in a Generalized Turing System: Implications for Biological Pattern Formation, Nonlinearity 18 125-138.

3. Alber, M.S., M.A. Kiskowski, and Y. Jiang [2004], Two-stage aggregate formation via streams in myxobacteria, Phys. Rev. Lett. 93 068301.

4. Sozinova, O., Y. Jiang, D. Kaiser, and M. Alber [2005], A Three-Dimensional Model of Myxobacterial Aggregation by Contact-mediated Interactions, Proc. Natl. Acad. Sci. USA 102 No.32, 11308-11312.

January 7 - 10, 2005
Dynamic Days 2005

http://www.physics.uci.edu/dynamicsdays2005/

Dynamics Days is an annual conference organized to gather a
variety of researchers with overlapping interests in nonlinear dynamics. Participants span the fields of mathematics, physics, biology, chemistry, ecology, engineering, and geology.

This event is being co-organized by Michael Dennin and Vittorio Cristini.

There is money to provide support for UCI graduate students and postdocs to cover two nights lodging and the registration fee.

Fall Quarter 2004

BIOPHYSICS OF MOLECULES AND MOLECULAR MACHINES - PHYSICS 146A/230A

The course is organized in case studies, one per week. The first lecture will introduce the respective biological system, observation methods, and questions asked. Physical and mathematical concepts and methods that permit one to answer the questions raised will be discussed then. Every case study will end with discussion of a recent research publication that students are expected to have read beforehand.

http://www.physics.uci.edu/~tritz/BP/

October 6 , 2004
"Are bacteria individuals? And why should we care?"
Stan Leibler Talk in the McDonnell Douglas
Engineering Auditorium

Prof. Leibler is one of the world leaders in the emerging field of 'systems biology.' He combines theoretical physics and experimental molecular biological methods in a unique fashion to analyze the robustness and sensitivity of biological networks as well as to design artificial networks with desired functional properties. He is also interested in scaling properties of spatial pattern formation during Drosophila development. He is a member of the National Academy of Sciences and a Howard Hughes Medical Investigator.

Host: Thorsten Ritz, Department of Physics and Astronomy x-4345, tritz@uci.edu

November 10, 2004
"Bringing Genomes to Life: The Role of Genome-Scale in Silico Models"
Bernard Palsson, Professor, Department of Bioengineering, University of California, San Diego

November 12, 2004
"Whole Genome Sequencing, Comparative Genomics, and Systems Biology"
Gene Meyers, Professor of Computer Science, UC Berkeley.

November 12, 2004
"The Physics of Biological Ion Channels"
Klaus Schulten, Professor of Theoretical and Computational Biophysics, University of Illinois, Urbana.

December 1, 2004
"Robustness and Biological Complexity"
John Doyle, Professor of Control and Dynamical Systems, Caltech.

December 15, 2004
Michael Savageau, Professor, Biomedical Engineering, University of California, Davis