ArticleNature computational science2025
Spatial modeling algorithms for reactions and transport in biological cells.
Article in Nature computational science, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
10 citing papers in PubMed.
- Mechanochemical modeling of exercise-induced skeletal muscle hypertrophy.PLoS computational biology · 2026Article
- Interplay between store-operated calcium entry and mitochondrial phosphate handling modulates force and fatigue during exercise.bioRxiv : the preprint server for biology · 2026Article
- Mathematical Modelling of the Mitochondrial Dicarboxylate Carrier (SLC25A10).Bulletin of mathematical biology · 2026Article
- Analytical comparisons for solving the modified fractional Kawahara equation: application on numerical simulation of chemical signaling processes.Scientific reports · 2026Article
- A predictive mechanochemical modeling framework for the deformation and remodeling of the nuclear lamina.bioRxiv : the preprint server for biology · 2026Article
- Calibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data.NPJ systems biology and applications · 2026Article
- Estimating physical conditions supporting gradients of ATP concentration in the eukaryotic cell.Biophysical journal · 2026Article
- A FINITE ELEMENT FRAMEWORK FOR BULK-SURFACE COUPLED PDES TO SOLVE MOVING BOUNDARY PROBLEMS IN BIOPHYSICS.bioRxiv : the preprint server for biology · 2025Article
- Systems modeling and uncertainty quantification of AMP-activated protein kinase signaling.NPJ systems biology and applications · 2025Article
- Nanoscale Curvature Regulates YAP/TAZ Nuclear Localization Through Nuclear Deformation and Rupture.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Here we present Spatial Modeling Algorithms for Reactions and Transport (SMART), a software package that takes in high-level user specifications about cell signaling networks and then assembles and solves the associated mathematical systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including yes-associated protein (YAP)/PDZ-binding motif (TAZ) mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.