The University of California, San Diego (UCSD) has the right mix of outstanding faculty and interdisciplinary research initiatives to set a new world standard for interdisciplinary modeling in the physical and biological sciences.  Scientifically, we now have many of the tools and techniques to develop a synthesis of a physics-based theory of living organisms. 

To make the maximum progress in this important area of science, we are proposing to create a unique theoretical center, the Trans-scale Theory Institute (TTI) at UCSD, which will serve as an intellectual center for the coming revolution in biology and medicine that is coming by bringing to bear all of tools from the disciplines of biology, chemistry, mathematics, medicine, and physics to the key problems of modern biology.  In addition to deepening our understanding of the natural sciences, discoveries made by leading physicists, mathematicians and biological scientists working collaboratively in the UCSD tradition hold the potential for profound advances in medicine, technology, and environmental sciences.

The advent of large-scale computing has added a new set of tools for scientific discovery.  The change that has occurred in physics and the other natural sciences as the result of modern computational technology has been profound.  Computational simulation has taken its place as a third method of doing science in addition to theory and experiment.  Scientists may understand the basic laws that govern a system such as Newton’s law or Schrodinger’s equation, and these have been well tested in simple situations.  However, with the advent of modern computers, the rapid increase in both computational speed and memory, and the development of new numerical algorithms, we can now explore the properties of complex systems such as weather patterns or the effect of new species on local environmental systems through simulations. Computational simulations provide us with ways to explore new phenomena when either it is impossible to perform experiments as in the case of star or galaxy formation, it is not feasible to perform experiments as in the case of nuclear reactors and weapons, or it is too costly to run experiments such as in the case of the design of new cars and planes.  Thus the new discipline of computational science has emerged as an important research area in modern science.

The rise of computational science has led to a whole new set of scientific and computational questions.  As one starts to explore more complex systems, a key problem that immediately arises is how to connect multiple length and time scales.  Climate modeling provides an example of these challenges.  The earth’s climate system consists of many interacting components: the ocean, atmosphere, cryosphere, biosphere, etc.  To build a successful computational climate model, we must break the system into manageable elements that can be quantified and whose interactions can be treated numerically.  We face a tremendous challenge in translating our understanding of DNA and the basic chemical building blocks of cells to provide a thorough understanding of the behavior of cells, organs, and individual organisms.  Again, a key to understanding complex systems is to be able to develop new models, mathematical tools, and numerical algorithms which will allow us to understand complex systems at different length and time scales. 

Indeed, we all know that life can be studied at many scales.  There are rich and complex systems at every level which is why the field of biology has been partitioned into fields such as molecular biology, cellular biology, population biology, evolutionary biology, ecology, etc. Biology, like physics, and other natural sciences also requires us to develop new ways to analyze massive amounts of data which has lead to new fields of biological research like bioinformatics and systems engineering.  To make rapid progress in our understanding of emergent behavior of biological systems, which, in turn, can lead to new tools to attack a wide variety of diseases, we firmly believe that we need to develop new methods that can transcend the inherent difficulties of merging simulations at different time and length scales where different modeling, mathematical, and numerical techniques are often used.

Thus we need new models and techniques to deal with phenomena at multiple scales or what we shall term a new trans-scale theory. We believe that this will require us to develop a new and deeper understanding of multi-scale phenomenon, new models and mathematical methods, and new numerical methods. This effort will require us to combine the skills of biologists, chemists, physicists, mathematicians, and computer scientists. The potential payoff of such an effort is tremendous as it can lead to new tools to attack a large variety of health and environmental problems.

To compliment this initiative and to create a third sort of science to blend with theory and experiment, UCSD created a doctoral program in Computational Science, Mathematics, and Engineering (CSME) and has also created a Center for Computational Mathematics.  The term computational scientist has been coined to describe scientists, engineers and mathematicians who apply high-performance computer technology in innovative and essential ways to advance the state of knowledge in their respective disciplines. 

What this means for the students, the University and the region, is that UCSD is positioned at the forefront of producing the highest-level mathematical/computational thinkers in Chemistry and Biochemistry, Computer Science and Engineering, Mathematics, Mechanical and Aerospace Engineering and Physics.  The establishment of the CSME program at UCSD is the result of articulated demand from regional visionaries who recognize the nation’s growing and continuing need for broadly trained advanced computational scientists in academic, industry and government labs. 

With its San Diego Supercomputer Center, School of Medicine, superb faculty and programs in science and engineering, UCSD is uniquely positioned to build a trans-scale theory center that can exploit the linkages with a wide variety of frontier experimental science. This will continue UCSD's remarkable stimulation of industrial growth.