Researchers at the University of California (UC), San Diego, have introduced Spatial Modeling Algorithms for Reactions and Transport (SMART), an innovative software tool designed to realistically simulate complex cell-signaling networks. Published in Nature Computational Science, this technology provides accuracy and flexibility, addressing the challenges of modeling molecular interactions within the intricate, three-dimensional environments of cells.
Cell signaling, the process by which cells respond to environmental cues, involves highly dynamic biochemical reactions that are influenced by cellular geometry and spatial organization. SMART leverages finite element analysis through the FEniCS Project software to simulate these processes across realistic cell and subcellular structures. This capability allows researchers to gain deeper insights into cellular behavior and explore the mechanisms underlying a range of biological phenomena.
“SMART provides a significant advancement in modeling cellular processes,” said Emmet Francis, PhD, lead author of the study and a postdoctoral fellow at UC San Diego. By automating the assembly and solution of mathematical models for signaling networks, SMART offers researchers a powerful tool to investigate complex biological systems with efficiency and precision.
The research team demonstrated SMART’s versatility by applying it to a variety of biological scenarios. Simulations included calcium signaling in neurons and heart cells, mechanotransduction pathways, and ATP production in mitochondria. Each application showcased SMART’s ability to model processes across different spatial and temporal scales, providing insights that could drive advances in systems biology, pharmacology, and biomedical engineering.
“Understanding the spatial and temporal dynamics of cellular processes is critical for developing targeted therapies and uncovering the principles that govern cellular function,” said Padmini Rangamani, PhD, a professor at UC San Diego who supervised the study.
SMART was developed in collaboration with researchers at Simula Research Laboratory in Oslo, Norway, under the leadership of Marie Rognes, PhD. The project received support from numerous international organizations, including the National Science Foundation, the European Research Council, and the Kavli Institute of Brain and Mind.
The researchers believe that by overcoming the limitations of existing modeling tools, SMART opens new avenues for exploring cell-signaling networks with unprecedented accuracy. This development holds promise for advancing our understanding of cellular mechanisms and driving innovations in disease treatment and therapeutic development.
