NSF DBI04-20980: "Acquisition of the Notre Dame Biocomplexity Computer Cluster," National Science Foundation, 8/1/2004 - 07/31/2007. This grant supports a Beowulf type Biocomplexity Cluster (62 dual processors nodes with 64-bit architecture), which provides computer infrastructure for the Notre Dame Interdisciplinary Center for the Study of Biocomplexity (ICSB) to meet its broad research and educational goals. Establishment of the Cluster resulted in a dramatic increase in the range and complexity of the biological computations on Notre Dame's campus. The Biocomplexity Cluster supports a variety of projects, which require a high-end computational environment. These projects (Molecular Dynamics, Multiscale Simulation of Avian Limb Development, Microscale Modeling of Cancellous Bone Damage, and Environmental Biocomplexity) cover all interacting scales of Biocomplexity phenomena from molecular to environmental.
NIH 1 RO1 GM065420: "Supplement for the Study of Complex Biological Systems," National Institutes of Health, 08/01/2005 - 07/31/08. This grant supports an ongoing collaboration between cell biologist Holly Goodson and mathematician Mark Alber to use a coupled program of iterative computational modeling and experiments to investigate key aspects of dynamic microtubule systems. The microtubule (MT) cytoskeleton is one of the fundamental organizing forces in biology: it directs cell motility, partitions the chromosomes during mitosis, and denes the localization of internal membranes. One way to gain an understanding of MT function is to identify and characterize the proteins that regulate dynamic instability. However, classic biochemistry and cell biology are not sufficient to address this problem: dynamic instability is an emergent property of the system of MTs and soluble subunits.
NIH 1 RO1 GM076692-1: "Interagency Opportunities in Multiscale Modeling in Biomedical, Biological and Behavioral Systems" (collaboration with IU Bloomington and Medical School, University of Kansas), National Institutes of Health, 09/01/2005 - 08/31/2008.
NSF IBN-0344647: "Testing a Developmental Mechanism by an Integrated Empirical Computational Approach" (collaboration with New York Medical College), National Science Foundation, 04/15/2004 - 03/31/2008.
NSF IBN-0083653: "BIOCOMPLEXITY Multiscale Simulation of Avian Limb Development" (collaboration with IU Bloomington, New York Medical College, University of Missouri, and Emory University, 9/1/2000-8/31/2006. The goal is to develop a model of avian limb structural development based on physical processes, including cell adhesion, chemotaxis and haptotaxis, mitosis, and cell differentiation. The Notre Dame team includes 2 postdocs, 4 graduate students, and 4 undergraduates. The Biocomplexity Group at Notre Dame introduced unified, object-oriented, three-dimensional framework, which includes composite discrete and continuous modeling and computation, and used it for developing the computer package CompuCell3D for simulating chondrogenesis in an avian limb.
NSF DMS05-17864: "Workshop on Applications of Methods of Stochastic Systems and Statistical Physics in Biology," National Science Foundation, 09/01/2005 - 08/31/2006.