SMART, a cutting-edge software tool, simplifies the study of signaling processes in biology. Its findings might speed up research across various life sciences disciplines, including systems biology, pharmacology, and biomedical engineering.
Researchers from the University of California San Diego have created and evaluated a new software tool known as Spatial Modeling Algorithms for Reactions and Transport (SMART). This tool effectively simulates cell-signaling networks, which are intricate systems of molecular interactions that enable cells to respond to various signals from their surroundings. The complexity of cell-signaling processes encompasses numerous distinct steps and is heavily influenced by the three-dimensional structures of cells and their components, making them challenging to simulate with current software. SMART addresses these challenges, potentially accelerating advancements across the life sciences, including systems biology, pharmacology, and biomedical engineering.
The team successfully tested this new software in biological systems at multiple levels, ranging from cell signaling reactions to adhesive factors, calcium release in specific areas of neurons and cardiac muscle cells, and ATP (the cellular energy molecule) production within a detailed model of an individual mitochondrion. By offering a versatile, precise, and efficient modeling tool for cell-signaling networks, SMART facilitates more comprehensive simulations that enhance our understanding of cellular activities and contribute to the development of new treatments for human diseases.
This research is documented in the journal Nature Computational Science, led by Emmet Francis, Ph.D., a postdoctoral fellow with the American Society for Engineering Education, under the guidance of Professor Padmini Rangamani, Ph.D., both of whom are part of the Department of Pharmacology at UC San Diego School of Medicine and the Department of Mechanical and Aerospace Engineering at Jacobs School of Engineering. The original software was developed by Justin Laughlin, Ph.D., a former graduate student in Rangamani’s lab.
SMART is the result of ongoing collaboration with a research team led by Marie Rognes, Ph.D., at Simula Research Laboratory in Oslo, Norway. This research has received partial funding from various organizations, including the National Science Foundation, Wu Tsai Human Performance Alliance, Air Force Office of Scientific Research, Hartwell Foundation, Kavli Institute of Brain and Mind, European Research Council, Research Council of Norway, K. G. Jebsen Center for Brain Fluid Research, and the Fulbright Foundation.
