ArticleCommunications in applied mathematics and computational science2010
A Cut Cell Method for Simulating Spatial Models of Biochemical Reaction Networks in Arbitrary Geometries.
Article in Communications in applied mathematics and computational science, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Development and calibration of digital twins for human skin growth in tissue expansion.Acta biomaterialia · 2025Article
- Variations in plume activity reveal the dynamics of water-filled faults on Enceladus.Nature communications · 2024Article
- Evaluation of Sampling Algorithms Used for Bayesian Uncertainty Quantification of Molecular Dynamics Force Fields.Journal of chemical theory and computation · 2024Article
- Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo.Journal of chemical theory and computation · 2024Review
- Monte Carlo samplers for efficient network inference.PLoS computational biology · 2023Article
- A Stochastic Mobility-Driven Spatially Explicit SEIQRD covid-19 Model with VOCs, Seasonality, and Vaccines.Applied mathematical modelling · 2023Article
- Bayesian parameter estimation for dynamical models in systems biology.PLoS computational biology · 2022Article
- Bayesian causal inference in visuotactile integration in children and adults.Developmental science · 2022Article
- Multimeric structure enables the acceleration of KaiB-KaiC complex formation induced by ADP/ATP exchange inhibition.PLoS computational biology · 2022Article
- A Hybrid Semi-Lagrangian Cut Cell Method for Advection-Diffusion Problems with Robin Boundary Conditions in Moving Domains.Journal of computational physics · 2022Article
- Embedding optimization reveals long-lasting history dependence in neural spiking activity.PLoS computational biology · 2021Article
- A particle flow filter for high-dimensional system applications.Quarterly journal of the Royal Meteorological Society. Royal Meteorological Society (Great Britain) · 2021Article
- A MATLAB toolbox for modeling genetic circuits in cell-free systems.Synthetic biology (Oxford, England) · 2021Article
- Deciphering the regulatory genome ofeLife · 2020Article
- Parametric emulation and inference in computationally expensive integrated urban water quality simulators.Environmental science and pollution research international · 2020Article
- Gas phase Elemental abundances in Molecular cloudS (GEMS) II. On the quest for the sulphur reservoir in molecular clouds: the HAstronomy and astrophysics · 2020Article
- Gravity-dominated Collisions: A Model for the Largest Remnant Masses with Treatment for "Hit and Run" and Density Stratification.The Astrophysical journal · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Cells use signaling networks consisting of multiple interacting proteins to respond to changes in their environment. In many situations, such as chemotaxis, spatial and temporal information must be transmitted through the network. Recent computational studies have emphasized the importance of cellular geometry in signal transduction, but have been limited in their ability to accurately represent complex cell morphologies. We present a finite volume method that addresses this problem. Our method uses Cartesian cut cells and is second order in space and time. We use our method to simulate several models of signaling systems in realistic cell morphologies obtained from live cell images and examine the effects of geometry on signal transduction.
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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.