New software unlocks secrets of cell signaling

Researchers at UC San Diego have developed and tested a new software package called the Spatial Modeling Algorithm for Reactions and Transport (SMART) that realistically simulates cellular signaling networks—the complex interactions of molecules. system that enables cells to respond to different cues from the environment. Cell signaling networks involve many different steps and are also greatly affected by the complex three-dimensional shapes of cellular and subcellular components, making them difficult to model with existing tools. SMART provides a solution to this problem, helping to accelerate research in life sciences such as systems biology, pharmacology, and biomedical engineering.

The researchers successfully tested the new software in multiple biological systems of varying scales, ranging from cell signaling in response to adhesion signals, to calcium release events in subcellular regions of neurons and cardiomyocytes, to ATP, the energy currency in cells. of generation in a detailed representation of a single mitochondrion. By providing flexible, accurate and efficient modeling tools for cell signaling networks, SMART paves the way for more detailed simulations to advance our understanding of cell behavior and drive the development of new treatments for human diseases.

The study was published in natural computational scienceled by Emmet Francis, Ph.D., an American Society for Engineering Education Postdoctoral Fellow, the research team is mentored by Padmini Rangamani, Ph.D., both affiliated with the Department of Pharmacology, UC San Diego School of Medicine, and Jacobs Engineering, UC San Diego Department of Mechanical and Aerospace Engineering, College. An initial version of the software was written by Dr. Justin Laughlin, a former graduate student in Rangamani’s group.

SMART is part of an ongoing collaboration with a research team led by Dr. Marie Rognes at the Simulation Research Laboratory in Oslo, Norway. This research was funded in part by the National Science Foundation, Wu Tsai Consortium on Human Performance, Air Force Office of Scientific Research, Hartwell Foundation, Kavli Institute for Brain and Mind Research, European Research Council, American Research Council Norway, KG Jebsen Cerebral Fluid Research Center and Fulbright Grant.