Credit: Department of Pharmacology at UC San Diego School of Medicine and Department of Mechanical and Aerospace Engineering at UC San Diego Jacobs School of Engineering.
Researchers at the University of California San Diego have developed and tested new software, called Spatial Modeling Algorithms for Reactions and Transport (SMART), capable of realistically simulating cellular signaling networks, complex systems of molecular interactions which allow cells to respond to various cues from their environment.
Cellular 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 areas of 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 signals, to calcium release events in the subcellular regions of neurons and heart muscle cells, until the production of ATP (the energy currency of cells). in a detailed representation of a single mitochondrion.
By providing a flexible, accurate and efficient tool for modeling cellular 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 Sciencewas led by American Society for Engineering Education postdoctoral researcher Emmet Francis, Ph.D., in the research group supervised by Professor Padmini Rangamani, Ph.D., both affiliated with the Faculty’s Department of Pharmacology of Medicine at UC San Diego and the Department of Mechanical and Aerospace Engineering at the Jacobs School of Engineering at UC San Diego. 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 the Simula Research Laboratory in Oslo, Norway.
More information:
Nature Computational Science (2024). DOI: 10.1038/s43588-024-00745-x. www.nature.com/articles/s43588-024-00745-x
Provided by University of California – San Diego
Quote: New software unlocks secrets of cell signaling, showing realistic simulations (December 19, 2024) retrieved December 19, 2024 from
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