video: This video shows a simulation created with SMART that showcases the calcium release dynamics within heart cells. This process is essential for heart muscles to contract.
Credit: Emmet Francis, Ph.D., an American Society for Engineering Education postdoctoral fellow in the research group supervised by Professor Padmini Rangamani, Ph.D., both affiliated with the Department of Pharmacology at UC San Diego School of Medicine and the Department of Mechanical and Aerospace Engineering at UC San Diego Jacobs School of Engineering.
Researchers at University of California San Diego have developed and tested a new software package, called Spatial Modeling Algorithms for Reactions and Transport (SMART), that can realistically simulate cell-signaling networks — the complex systems of molecular interactions that allow cells to respond to diverse cues from their environment. Cell-signaling networks involve many distinct steps and are also greatly influenced by the complex, three-dimensional shapes of cells and subcellular components, making them difficult to simulate with existing tools. SMART offers a solution to this problem, which could help accelerate research in fields across the life sciences, such as systems biology, pharmacology and biomedical engineering.
The researchers successfully tested the new software in biological systems at several different scales, from cell signaling in response to adhesive cues, to calcium release events in subcellular regions of neurons and cardiac muscle cells, to the production of ATP (the energy currency in cells) within a detailed representation of a single mitochondrion. By providing a flexible, accurate and efficient tool for modeling cell-signaling networks, SMART paves the way for more detailed simulations to advance our understanding of cellular behavior and drive the development of new treatments for human diseases.
The study, published in Nature Computational Science, was led by Emmet Francis, Ph.D., an American Society for Engineering Education postdoctoral fellow in the research group supervised by Professor Padmini Rangamani, Ph.D., both affiliated with the Department of Pharmacology at UC San Diego School of Medicine and the Department of Mechanical and Aerospace Engineering at UC San Diego Jacobs School of Engineering. The initial version of this software was written by Justin Laughlin, Ph.D., a former graduate student in Rangamani’s group.
SMART is part of an ongoing collaboration with a research team led by Marie Rognes, Ph.D., at Simula Research Laboratory in Oslo, Norway. This research was funded, in part, by the National Science Foundation, the Wu Tsai Human Performance Alliance, the Air Force Office of Scientific Research, the Hartwell Foundation, the Kavli Institute of Brain and Mind, the European Research Council, the Research Council of Norway, the K. G. Jebsen Center for Brain Fluid Research, and the Fulbright Foundation.
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Journal
Nature Computational Science