Mathematical Biology
Mathematical biology seeks to establish a deep theoretical understanding, detailed modeling, and quantitative experimentation directed at understanding the behavior of particular regulatory systems and/or elucidating general principles of cellular information processing. Within molecular systems, our most most significant investments have been the q-bio summer school and conference. Additionally, we supported a world recognized HIV conference in Santa Fe. The vision workshop, held in Santa Fe in May, has been a primary vehicle for establishing collaborations with out-of-state researchers in the field. In computational neuroscience, we funded a mentoring program for students and a workshop. These events put New Mexico on the international map as a recognized leader in quantitative biology and mathematical biology.
This program produced numerous grant proposals that demonstrate our leadership in this area. A grant to the National Institutes of Health (NIH) for subsidized travel to the q-bio conference for junior research from across the U.S. has been recommended for funding, underscoring NIH's recognition of the q-bio conference as an important venue for scientific training and communications. A National Science Foundation (NSF) proposal for federal funding for the q-bio Summer School is being considered now. Building on the success of the q-bio series, it was possible to assemble a University of California-Los Alamos National Laboratory (LANL) collaborative structure in quantitative biology, which served as a backbone for the Center for Nonlinear Studies (CNLS)-led University of California Office of the President (UCOP) proposal, currently in review.
The q-bio series was also the cornerstone of a major $20M proposal to the NSF for a Center of Mathematical Biology. This proposal was unsuccessful, but made it through the first stages of the selection process. It has played an important role in affirming New Mexico's leadership in quantitative biology in the nation. Importantly, the proposal has established a collaborative infrastructure among the University of New Mexico (UNM), New Mexico State University (NMSU), LANL, Los Alamos County, and the State of New Mexico, which is leading to tighter integration of research initiatives across the state, and will allow the institutions involved to use the infrastructure for future proposals. Finally, the New Mexico Consortium won a $1.2M NSF grant to develop the primitives that underlie the processing in biological neural circuits.
As a direct result of the vision workshop, a UCOP proposal between LANL and UC Berkeley has been submitted, and a Cyber-Enabled Discovery and Innovation (CDI) Type II proposal is being considered by the same participants. The work under Neuroscience Mentoring has been instrumental in bridging the gap between psychophysical models of human vision and detailed High Performance Computing (HPC) neural simulation models, which were the first scientific application to break the petaflop barrier early in the summer of 2008. As a result of this investment, we are now positioned to take a full advantage of the Roadrunner architecture computers for neuroscience applications when they arrive on-site in October.
Katharine Chartrand, New Mexico Consortium, knc@newmexicoconsortium.org, 412-4177
HIV Dynamics & Evolution 2008
This conference facilitated communication of the most recent results relating to HIV dynamics and pathogenesis, HIV evolution and phylogenetics, immune responses, T cell dynamics and viral escape. The conference also provided a forum for debate and discussion of alternative hypotheses in these areas. A key objective was the integration of new bio-mathematical approaches into research in HIV pathogenesis and vaccine development. Bio-mathematical studies contribute not only to the understanding of the relationships between viruses, but the understanding of selection and viral interplay with the immune system, factors that have bearing on host-pathogen interactions, issues in pathogen forensics and molecular epidemiology and vaccine development.
2008 q-bio Summer School on Cellular Information Processing
The 2008 q-bio Summer School on Cellular Information Processing seeks to advance predictive modeling of cellular regulatory systems. Participants in the School included 21 undergraduate and graduate students and postdoctoral researchers from 19 different research institutions, such as Cornell University, Columbia University and MIT. Lecturers in the Summer School included 19 Los Alamos National Laboratory (LANL) researchers, five of whom are Laboratory Fellows (Hans Frauenfelder, James P. Freyer, Byron Goldstein, Alan S. Perelson, and Arthur F. Voter), two University of New Mexico faculty members (Professors Nitant Kenkre and Bridget Wilson), and seven external lecturers.
2008 q-bio Conference
The annual q-bio conference advances predictive modeling of cellular regulation, decision making, formation of response, and other information processing phenomena. The emphasis is on deep theoretical understanding, detailed modeling, and quantitative experimentation directed at understanding the behavior of particular regulatory systems and/or elucidating general principles of cellular information processing. Unlike many biological conferences, which focus on specific model systems, q-bio focuses on understanding of phenomena, which manifest themselves in many biological systems.
Undergraduate Education at the Interface of Mathematics and Biology
This program seeks to investigate educational models and strategies that will inform national efforts to enhance undergraduate education and training at the intersection of mathematics and biology. Los Alamos National Laboratory (LANL) and New Mexico State University (NMSU) have partnered to provide intensive, multidisciplinary mentored research experiences for undergraduates supported by relevant coursework. To date, they have recruited three students for research stipends: Ryan Hatch, Tori Barron, and Jesus Perez and they are developing a new course that will be offered next spring entitled, Introduction to Mathematical Biology. This program continues in FY ’09.
Computational Neuroscience Mentoring
After decades of exponential growth in power, existing computer architectures still fail to match the ability of the mammalian brain to interpret, respond to, and learn from natural sensory inputs. Rapid progress in neuroscience suggests an alternative strategy for achieving brain-like behavior: identifying the computational primitives that underlie the processing in biological neural circuits. The New Mexico Consortium supports a National Science Foundation (NSF) research program to develop high-performance neural simulation tools and to use them to find these primitives. The primitives make the brain much more powerful than the familiar von Neumann computer or artificial neural networks (ANNs). The IAS supported Garrett Kenyon to mentor five students in this program for the summer.
Center at the Interface of Mathematics and Biology Proposal
The IAS supported a statewide response to the National Science Foundation (NSF) Center at the Interface of Mathematics and Biology at the New Mexico Consortium. The proposed q-Bio center would create a mathematical foundation for a quantitative, mechanism-based predictive modeling of biological processes focusing on infectious diseases. This five-year, $16M proposal to the NSF attracted ~$5M in matching funds and involved over 20 scientists from across the state. The proposal made it to the final round, but was ultimately not selected. The effort, however, is a model for statewide partnering on proposal response, which is a priority for the IAS. The Center would have brought to the state a new scientific initiative that would not have been possible without the involvement of all IAS partners.
High-Level Perception and Low-Level Vision: Bridging the Semantic Gap
The "semantic gap" describes the current inability of computer vision systems to connect low-level visual descriptions with the high-level conceptual schemas and analogies. Similarly, neuroscientists and psychophysicists have uncovered many of the physiological and perceptual mechanisms underlying various stages of visual processing. Yet the interactions and transformations between levels remains obscure. The purpose of this workshop was to address how the semantic gap might be bridged, both in natural and computer vision, and to see if a set of common principles of visual understanding can be discovered from the collective, multidisciplinary knowledge of the participants.
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