Robustness Analysis Tools with Applications to
the Biological and Physical Sciences: The Challenge of Complexity
Kavli Institute for Theoretical Physics
University of California at Santa Barbara
March 20-21, 2003
Organizers: Andrew Doherty, Jorge Goncalves, John Doyle (Caltech).
URGENT: Please REGISTER now.
| Schedule | Registration | Abstract | Speakers | Materials | Visitor Info |
Schedule, Slides, and Video - NEW |
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Lectures will be 9-12:30 and 1:30-5:00 each day with breaks and
lunch, which are free and catered. Registration at website is required and
free.
Catered lunch 12:30-1:30. Thursday evening dinner will be at the Beachside Café, walking distance from UCSB. Drinks and appetizers at 6pm and dinner starting at 6:30, all in the rear east patio area by the pier, which can accommodate up to 50 people. Everyone will just order off the menu. The banquet is included in the registration fee (which is $0, so a good deal, eh?). |
Registration |
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It is essential that all attendees register HERE for planning purposes. There is no registration fee, but
there will be free catered food and we need headcounts. Those who wish
to or must may
contribute to the cost. |
Abstract |
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The now well-known vision and challenge in post-genomics biology
is to make the entire process of research scalable to large
networks using high-throughput techniques and large-scale
computation. Computational biology and bioinformatics have focused
attention on the need for sophisticated methods for handling large
databases and tools for modeling and simulating complex networks.
Not as widely recognized is that the scalability of the more
subtle processes of drawing meaningful and reliable scientific,
medical, and biological inferences from the wealth of data and
computation is equally important and requires the development of
fundamentally new theory and software. This tutorial workshop will
explore a new theoretical and software infrastructure for systems
biology, with concrete demonstrations using a variety of
biologically-motivated examples. The new theory builds on robust
control theory, dynamical systems, numerical analysis, operator
theory, real algebraic geometry, computational complexity theory,
duality and optimization, and semi-definite programming. While
some background in these areas will be helpful, the workshop will
aim for a newly unified and integrated presentation that should be
relatively accessible to biologists and physicists with little
previous exposure to these areas of mathematics. An extensive set
of notes and a set of software tools will be available both before
and after the workshop.
Systems level challenges in biology include predictive modeling
and analysis of complex multiscale dynamics, the most familiar
aspect being "vertically" across time and space scales in
connecting molecular interactions with higher level network
function. A less familiar and more abstract "horizontal" aspect
involves interconnection of modular components for sensing, signal
processing, communication, computation, and actuation into vast
regulatory networks with layers of feedback. This horizontal
interconnection happens within every vertical level, from
intra-macromolecular dynamics to intracellular regulation to
organism and ecosystem homeostasis, although the complexity
obviously grows at higher and larger scales. The most subtle and
arguably most important challenge involves the discovery and
characterization of higher-level organizational principles of
complex networks, without which the multiscale complexity becomes
overwhelming.
A central need is for a scalable and coherent scientific theory
and software infrastructure to address these challenges in systems
biology. Fortunately, insights about the fundamental nature of
biological complexity can now be drawn from the convergence of two
research themes with that of mainstream biology. The latter has
provided a detailed description of the components of biological
networks, and some "design" principles of these networks are
becoming increasingly apparent, even though the investigation and
elucidation of these principles is informal and ad hoc. In
addition, advanced technology has provided engineering examples of
networks with complexity approaching that of biology. While the
components are entirely different, there is striking convergence
at the network level of architecture and the role of protocols in
structuring complex system modularity. Finally, and most
importantly for this shortcourse, there is a new mathematical
framework being developed for the study of complex, multiscale
networks that suggests that this apparent network-level
evolutionary convergence both within biology and between biology
and technology is not accidental, and follows necessarily from the
requirements that both biology and technology be efficient and
robust.
Similar challenges exist throughout science and technology, such as the Internet, aerospace systems design, materials science, multiscale physics, stochastic multiscale chemistry, and disturbance ecology. This workshop will have a secondary focus on applications of the new theory to problems in multiscale physics that are motivated by biology, such as the structure of turbulence in the highly sheared flows around streamlined bodies and the statistical mechanics of systems persistently and robustly regulated far from thermodynamic equilibrium. On Saturday (March 22), there will be informal discussions among the theoreticians attending or presenting on the details of the current mathematics and algorithms research. All are welcome to attend. Back to top. |
Speakers (Tentative) |
| Pablo Parrilo (ETH-Zurich); Andrew Doherty, John Doyle, Dan Gillespie, Jorge Goncalves, Hideo Mabuchi, Antonis Papachristodoulou, Stephen Prajna, Tau-Mu Yi (Caltech); Bassam Bamieh, Hana El Samad, Mustafa Khammash, Linda Petzold (UCSB); Irina Grigorova (UCSF). |
Supplementary Materials |
| Printable information (pdf). Software tools implementing the algorithms described in this shortcourse are available: SOSTOOLS. Complex networks at Caltech: http://www.cds.caltech.edu/~doyle/CmplxNets. Internetworking at Caltech: http://netlab.caltech.edu/internet. Complex systems at UCSB: http://www.physics.ucsb.edu/~complex. Quantum entanglement application: http://www.arxiv.org/abs/quant-ph/0112007. Heat shock materials: http://www.public.iastate.edu/~helsamad/heatshock.html. |
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Last updated: Apr 7, 2003.  
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