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PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems

https://doi.org/10.1371/journal.pcbi.1005991
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Integrative physical oncology
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Modeling Multiscale Necrotic and Calcified Tissue Biomechanics in Cancer Patients: Application to Ductal Carcinoma In Situ (DCIS)
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Progress Towards Computational 3-D Multicellular Systems Biology
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Multiscale Computer Modeling in Biomechanics and Biomedical Engineering
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Individual-based and continuum models of growing cell populations: a comparison
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A New Ghost Cell/Level Set Method for Moving Boundary Problems: Application to Tumor Growth
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Multi-Scale Modeling of Tissues Using CompuCell3D
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The benefits and challenges associated with the use of drug delivery systems in cancer therapy
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Microvessel Chaste: An Open Library for Spatial Modeling of Vascularized Tissues
inferredcites →https://doi.org/10.1016/j.cels.2017.06.006openalex-snapshot
Semblance of Heterogeneity in Collective Cell Migration
inferredcites →https://doi.org/10.1016/j.cels.2017.08.005openalex-snapshot
When Seeing Isn't Believing: How Math Can Guide Our Interpretation of Measurements and Experiments
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43. Cell-based modeling of mechanical and chemical stress in tissues during cryoprotocols
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Use of multicellular tumor spheroids to dissect endothelial cell–tumor cell interactions: A role for T‐cadherin in tumor angiogenesis
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Analysis on the current status of targeted drug delivery to tumors
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Evolving interfaces via gradients of geometry-dependent interior Poisson problems: application to tumor growth
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Nonlinear simulation of the effect of microenvironment on tumor growth
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Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): From microscopic measurements to macroscopic predictions of clinical progression
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Improved patient-specific calibration for agent-based cancer modeling
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Biological background
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Targeting hypoxia in cancer therapy
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Hypoxia and metabolic adaptation of cancer cells
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A high-content image-based method for quantitatively studying context-dependent cell population dynamics
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Tumour surveillance: Missing peptides and MHC molecules
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Nonlinear modelling of cancer: bridging the gap between cells and tumours
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COPASI—a COmplex PAthway SImulator
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A cell-based simulation software for multi-cellular systems
inferredcites →https://doi.org/10.1093/bioinformatics/btt772openalex-snapshot
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
inferredcites →https://doi.org/10.1093/bioinformatics/btu498openalex-snapshot
Biocellion : accelerating computer simulation of multicellular biological system models
inferredcites →https://doi.org/10.1093/bioinformatics/btv363openalex-snapshot
libRoadRunner: a high performance SBML simulation and analysis library
inferredcites →https://doi.org/10.1093/bioinformatics/btv730openalex-snapshot
BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations
inferredcites →https://doi.org/10.1101/090456openalex-snapshot
MultiCellDS: a community-developed standard for curating microenvironment-dependent multicellular data
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Monte Carlo approach to tissue-cell populations
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Migration of breast cancer cells: Understanding the roles of volume exclusion and cell-to-cell adhesion
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Johnson-Kendall-Roberts Theory Applied to Living Cells
inferredcites →https://doi.org/10.1109/mcse.2014.2openalex-snapshot
Large-Scale Parallel Simulations of 3D Cell Colony Dynamics
inferredcites →https://doi.org/10.1109/mcse.2015.66openalex-snapshot
Large-Scale Parallel Simulations of 3D Cell Colony Dynamics: The Cellular Environment
inferredcites →https://doi.org/10.1146/annurev-bioeng-071910-124729openalex-snapshot
Multiscale Cancer Modeling
inferredcites →https://doi.org/10.1155/2011/803816openalex-snapshot
A Novel, Patient-Specific Mathematical Pathology Approach for Assessment of Surgical Volume: Application to Ductal Carcinomain situof The Breast
inferredcites →https://doi.org/10.1177/019262339702500116openalex-snapshot
The Pathways of Cell Death: Oncosis, Apoptosis, and Necrosis
inferredcites →https://doi.org/10.1177/2051013614525375openalex-snapshot
MHC class I antigen presentation and implications for developing a new generation of therapeutic vaccines
inferredcites →https://doi.org/10.1186/1479-5876-3-8openalex-snapshot
Revisiting immunosurveillance and immunostimulation: Implications for cancer immunotherapy
inferredcites →https://doi.org/10.1186/s12859-018-2510-xopenalex-snapshot
High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow
inferredcites →https://doi.org/10.1259/bjr.20130676openalex-snapshot
Defining normoxia, physoxia and hypoxia in tumours—implications for treatment response
inferredcites →https://doi.org/10.1371/journal.pcbi.1001045openalex-snapshot
A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt
inferredcites →https://doi.org/10.1371/journal.pcbi.1001048openalex-snapshot
Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings
inferredcites →https://doi.org/10.1371/journal.pcbi.1001120openalex-snapshot
The Morphology of the Rat Vibrissal Array: A Model for Quantifying Spatiotemporal Patterns of Whisker-Object Contact
inferredcites →https://doi.org/10.1371/journal.pcbi.1002970openalex-snapshot
Chaste: An Open Source C++ Library for Computational Physiology and Biology
inferredcites →https://doi.org/10.1371/journal.pcbi.1003115openalex-snapshot
Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus
inferredcites →https://doi.org/10.1371/journal.pcbi.1005387openalex-snapshot
Comparing individual-based approaches to modelling the self-organization of multicellular tissues
inferredcites →https://doi.org/10.1529/biophysj.104.041459openalex-snapshot
Modeling the Effect of Deregulated Proliferation and Apoptosis on the Growth Dynamics of Epithelial Cell Populations In Vitro
inferredcites →https://doi.org/10.2310/7290.2012.00012openalex-snapshot
Multicellular Tumor Spheroids as an in Vivo–Like Tumor Model for Three-Dimensional Imaging of Chemotherapeutic and Nano Material Cellular Penetration
inferredcites →https://doi.org/10.3233/acp-2011-0019openalex-snapshot
A novel, patient-specific mathematical pathology approach for assessment of surgical volume: application to ductal carcinoma in situ of the breast.
inferredcites →https://doi.org/10.3389/fonc.2013.00194openalex-snapshot
The Need for Integrative Computational Oncology: An Illustrated Example through MMP-Mediated Tissue Degradation
inferredcites →https://doi.org/10.6084/m9.figshare.5687197openalex-snapshot
High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow [Presented at SuperComputing SC17, Computational Approaches for Cancer Workshop]

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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A multiphysics hybrid continuum — agent-based model of in vitro vascularized organoids
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2024.109631openalex-snapshot
Mathematical modeling of impacts of patient differences on renin-angiotensin system and applications to COVID-19 lung fibrosis outcomes
inferred← citeshttps://doi.org/10.1016/j.copbio.2022.102702openalex-snapshot
Computational models in systems biology: standards, dissemination, and best practices
inferred← citeshttps://doi.org/10.1016/j.copbio.2022.102838openalex-snapshot
The dawn of interoperating spatial models in cell biology
inferred← citeshttps://doi.org/10.1016/j.copbio.2025.103398openalex-snapshot
Mapping multipathology via spatial omic integration
inferred← citeshttps://doi.org/10.1016/j.cpc.2019.05.005openalex-snapshot
LibreGrowth: A tumor growth code based on reaction–diffusion equations using shared memory
inferred← citeshttps://doi.org/10.1016/j.cpc.2026.110285openalex-snapshot
Efficient open-source GPU implementation for multi-agent autochemotactic 2D modeling
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.10.003openalex-snapshot
Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells
inferred← citeshttps://doi.org/10.1016/j.csbj.2023.01.044openalex-snapshot
Hybrid computational models of multicellular tumour growth considering glucose metabolism
inferred← citeshttps://doi.org/10.1016/j.foodres.2025.116408openalex-snapshot
Individual-based modelling (IbM) in food microbiology: A comprehensive guideline
inferred← citeshttps://doi.org/10.1016/j.gde.2020.05.039openalex-snapshot
Engineering and modeling of multicellular morphologies and patterns
inferred← citeshttps://doi.org/10.1016/j.heliyon.2024.e32546openalex-snapshot
Inspiring a convergent engineering approach to measure and model the tissue microenvironment
inferred← citeshttps://doi.org/10.1016/j.immuno.2023.100022openalex-snapshot
Modeling interaction of Glioma cells and CAR T-cells considering multiple CAR T-cells bindings
inferred← citeshttps://doi.org/10.1016/j.immuno.2024.100043openalex-snapshot
In silico modelling of CD8 T cell immune response links genetic regulation to population dynamics
inferred← citeshttps://doi.org/10.1016/j.imu.2020.100347openalex-snapshot
Novelty search employed into the development of cancer treatment simulations
inferred← citeshttps://doi.org/10.1016/j.imu.2026.101737openalex-snapshot
Who's afraid of synthetic data? Hybrid approaches to deliver medical digital twins
inferred← citeshttps://doi.org/10.1016/j.is.2025.102538openalex-snapshot
RATS: A resource allocator for optimizing the execution of tumor simulations over HPC infrastructures
inferred← citeshttps://doi.org/10.1016/j.isci.2021.102935openalex-snapshot
A persistent invasive phenotype in post-hypoxic tumor cells is revealed by fate mapping and computational modeling
inferred← citeshttps://doi.org/10.1016/j.isci.2022.104387openalex-snapshot
A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues
inferred← citeshttps://doi.org/10.1016/j.isci.2022.104395openalex-snapshot
Agent-based computational modeling of glioblastoma predicts that stromal density is central to oncolytic virus efficacy
inferred← citeshttps://doi.org/10.1016/j.isci.2022.105421openalex-snapshot
Multiscale modeling in the framework of biological systems and its potential for spaceflight biology studies
inferred← citeshttps://doi.org/10.1016/j.isci.2023.106897openalex-snapshot
An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia
inferred← citeshttps://doi.org/10.1016/j.isci.2023.107164openalex-snapshot
A hybrid physics-based and data-driven framework for cellular biological systems: Application to the morphogenesis of organoids
inferred← citeshttps://doi.org/10.1016/j.isci.2024.110968openalex-snapshot
Cell density couples tissue mechanics to control the elongation speed of the body axis
inferred← citeshttps://doi.org/10.1016/j.jmb.2022.167539openalex-snapshot
Probing the Interaction Between Supercarrier RBC Membrane and Nanoparticles for Optimal Drug Delivery
inferred← citeshttps://doi.org/10.1016/j.jocs.2023.102059openalex-snapshot
Establishing massively parallel models to examine the influence of cell heterogeneity on tumor growth
inferred← citeshttps://doi.org/10.1016/j.jocs.2023.102175openalex-snapshot
Mathematical modelling of cancer invasion: Phenotypic transitioning provides insight into multifocal foci formation
inferred← citeshttps://doi.org/10.1016/j.jocs.2025.102555openalex-snapshot
Establishing a massively parallel computational model of the adaptive immune response
inferred← citeshttps://doi.org/10.1016/j.jphotobiol.2023.112714openalex-snapshot
Suppressing cancer by damaging cancer cell DNA using LED irradiation
inferred← citeshttps://doi.org/10.1016/j.jtbi.2019.110052openalex-snapshot
Enhancing oncolytic virotherapy: Observations from a Voronoi Cell-Based model
inferred← citeshttps://doi.org/10.1016/j.jtbi.2022.111028openalex-snapshot
A mathematical model to study the impact of intra-tumour heterogeneity on anti-tumour CD8+ T cell immune response
inferred← citeshttps://doi.org/10.1016/j.jtbi.2022.111377openalex-snapshot
Designing experimental conditions to use the Lotka–Volterra model to infer tumor cell line interaction types
inferred← citeshttps://doi.org/10.1016/j.jtbi.2023.111434openalex-snapshot
A reduced model of cell metabolism to revisit the glycolysis-OXPHOS relationship in the deregulated tumor microenvironment
inferred← citeshttps://doi.org/10.1016/j.jtbi.2023.111592openalex-snapshot
Choice of spatial discretisation influences the progression of viral infection within multicellular tissues
inferred← citeshttps://doi.org/10.1016/j.jtbi.2024.111748openalex-snapshot
Kill rates by immune cells: Ratio-dependent, or mass action?
inferred← citeshttps://doi.org/10.1016/j.jtbi.2024.111806openalex-snapshot
A resource-based mechanistic framework for castration-resistant prostate cancer (CRPC)
inferred← citeshttps://doi.org/10.1016/j.jtbi.2024.111922openalex-snapshot
An adaptive numerical method for multi-cellular simulations of tissue development and maintenance
inferred← citeshttps://doi.org/10.1016/j.jtbi.2025.112266openalex-snapshot
Drug-loaded nanoparticles for cancer therapy: A high-throughput multicellular agent-based modeling study
inferred← citeshttps://doi.org/10.1016/j.jtbi.2025.112354openalex-snapshot
Emergent stable tissue shapes from the regulatory feedback between morphogens and cell growth
inferred← citeshttps://doi.org/10.1016/j.jtbi.2026.112592openalex-snapshot
Emergence of curvature-dependent tissue growth from cell crowding and mechanical interactions
inferred← citeshttps://doi.org/10.1016/j.mbs.2024.109369openalex-snapshot
Deficient cell-cell cohesion is linked with lobular localization in simplified models of lobular carcinoma in situ (LCIS)
inferred← citeshttps://doi.org/10.1016/j.mbs.2026.109683openalex-snapshot
Investigating the impact of adipose derived media on ovarian cancer: Insights from a 3D in-silico model
inferred← citeshttps://doi.org/10.1016/j.medengphy.2025.104369openalex-snapshot
Effects of mechanical stimuli on bone cells for regenerative medicine: A review of recent experimental and computational methods
inferred← citeshttps://doi.org/10.1016/j.media.2023.102991openalex-snapshot
Generative modeling of living cells with SO(3)-equivariant implicit neural representations
inferred← citeshttps://doi.org/10.1016/j.medj.2021.08.007openalex-snapshot
Forecasting cancer: from precision to predictive medicine
inferred← citeshttps://doi.org/10.1016/j.micpath.2026.108459openalex-snapshot
Virtual cell/virtual cell like: The key to unlocking a new era of HIV/AIDS treatment ?
inferred← citeshttps://doi.org/10.1016/j.nantod.2025.102918openalex-snapshot
Silico-driven drug discovery: A paradigm shift for nanomedicine science and industry
inferred← citeshttps://doi.org/10.1016/j.neo.2022.100796openalex-snapshot
Mathematical modeling of radiotherapy and its impact on tumor interactions with the immune system
inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2018.05.009openalex-snapshot
Mathematical models of dorsal closure
inferred← citeshttps://doi.org/10.1016/j.semcancer.2023.04.002openalex-snapshot
Clonal interactions in cancer: Integrating quantitative models with experimental and clinical data
inferred← citeshttps://doi.org/10.1016/j.smim.2020.101411openalex-snapshot
Interrogating the microenvironmental landscape of tumors with computational image analysis approaches
inferred← citeshttps://doi.org/10.1016/j.stem.2020.12.012openalex-snapshot
Computational Stem Cell Biology: Open Questions and Guiding Principles
inferred← citeshttps://doi.org/10.1016/j.tcb.2022.10.006openalex-snapshot
Agent-based methods facilitate integrative science in cancer
inferred← citeshttps://doi.org/10.1016/j.trecan.2020.01.004openalex-snapshot
The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View
inferred← citeshttps://doi.org/10.1016/j.yexcr.2022.113278openalex-snapshot
Application of deep learning methods: From molecular modelling to patient classification
inferred← citeshttps://doi.org/10.1016/j.yexcr.2022.113317openalex-snapshot
Thermodynamically-motivated chemo-mechanical models and multicellular simulation to provide new insight into active cell and tumour remodelling
inferred← citeshttps://doi.org/10.1016/j.ymeth.2020.01.006openalex-snapshot
An in silico hybrid continuum-/agent-based procedure to modelling cancer development: Interrogating the interplay amongst glioma invasion, vascularity and necrosis
inferred← citeshttps://doi.org/10.1021/acs.analchem.3c04444openalex-snapshot
Tailored Mass Spectral Data Exploration Using the SpecXplore Interactive Dashboard
inferred← citeshttps://doi.org/10.1021/acs.chemrev.0c00356openalex-snapshot
Engineering in Medicine To Address the Challenge of Cancer Drug Resistance: From Micro- and Nanotechnologies to Computational and Mathematical Modeling
inferred← citeshttps://doi.org/10.1021/acsbiomaterials.5c01998openalex-snapshot
A Review on AI-Based Data-Driven Models for Optimization of Nanocarriers as Drug Delivery Systems
inferred← citeshttps://doi.org/10.1021/acssynbio.5c00402openalex-snapshot
An LLM-Based Tool for Automated Generation of 3D Model Organism Colony Simulations
inferred← citeshttps://doi.org/10.1021/acssynbio.5c00704openalex-snapshot
Prompt-Only Gene-Circuit Modeling with a Large Language Model Simulates the synNotch Spheroids
inferred← citeshttps://doi.org/10.1038/s41467-022-31138-1openalex-snapshot
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling
inferred← citeshttps://doi.org/10.1038/s41467-022-35484-yopenalex-snapshot
Evolutionary rescue of resistant mutants is governed by a balance between radial expansion and selection in compact populations
inferred← citeshttps://doi.org/10.1038/s41524-020-00366-8openalex-snapshot
In silico modelling of cancer nanomedicine, across scales and transport barriers
inferred← citeshttps://doi.org/10.1038/s41524-021-00614-5openalex-snapshot
Evolutionary computational platform for the automatic discovery of nanocarriers for cancer treatment
inferred← citeshttps://doi.org/10.1038/s41540-023-00314-4openalex-snapshot
PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
inferred← citeshttps://doi.org/10.1038/s41540-024-00397-7openalex-snapshot
A comprehensive review of computational cell cycle models in guiding cancer treatment strategies
inferred← citeshttps://doi.org/10.1038/s41540-024-00419-4openalex-snapshot
Spatial computational modelling illuminates the role of the tumour microenvironment for treating glioblastoma with immunotherapies
inferred← citeshttps://doi.org/10.1038/s41540-024-00472-zopenalex-snapshot
A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins
inferred← citeshttps://doi.org/10.1038/s41540-025-00508-yopenalex-snapshot
Exploring the role of EMT in ovarian cancer progression using a multiscale mathematical model
inferred← citeshttps://doi.org/10.1038/s41540-025-00518-wopenalex-snapshot
Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures
inferred← citeshttps://doi.org/10.1038/s41540-025-00642-7openalex-snapshot
Mathematical modeling of combinatorial antigen targeting with multiple CAR T-cell products for glioblastoma treatment
inferred← citeshttps://doi.org/10.1038/s41540-026-00648-9openalex-snapshot
Simulation-based inference of cell migration dynamics in complex spatial environments
inferred← citeshttps://doi.org/10.1038/s41540-026-00669-4openalex-snapshot
Experimentally calibrated multiscale model predicts schedule dependent drug combination effects
inferred← citeshttps://doi.org/10.1038/s41540-026-00736-wopenalex-snapshot
tugMedi: simulator of cancer-cell evolution for personalized medicine based on the genomic data of patients
inferred← citeshttps://doi.org/10.1038/s41540-026-00767-3openalex-snapshot
Intelligent tool orchestration for rapid mechanistic model prototyping: MCP servers as AI-biology interfaces
inferred← citeshttps://doi.org/10.1038/s41559-023-02000-4openalex-snapshot
State-dependent evolutionary models reveal modes of solid tumour growth
inferred← citeshttps://doi.org/10.1038/s41568-025-00796-wopenalex-snapshot
Using mathematical modelling and AI to improve delivery and efficacy of therapies in cancer
inferred← citeshttps://doi.org/10.1038/s41598-019-39636-xopenalex-snapshot
The impact of proliferation-migration tradeoffs on phenotypic evolution in cancer
inferred← citeshttps://doi.org/10.1038/s41598-020-69862-7openalex-snapshot
An in-silico study of cancer cell survival and spatial distribution within a 3D microenvironment
inferred← citeshttps://doi.org/10.1038/s41598-020-73866-8openalex-snapshot
Multicompartment modeling of protein shedding kinetics during vascularized tumor growth
inferred← citeshttps://doi.org/10.1038/s41598-020-78780-7openalex-snapshot
Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach
inferred← citeshttps://doi.org/10.1038/s41598-023-39150-1openalex-snapshot
BMX: Biological modelling and interface exchange
inferred← citeshttps://doi.org/10.1038/s41598-024-59773-2openalex-snapshot
Machine learning approach for recognition and morphological analysis of isolated astrocytes in phase contrast microscopy
inferred← citeshttps://doi.org/10.1038/s41598-024-63125-5openalex-snapshot
In silico study of heterogeneous tumour-derived organoid response to CAR T-cell therapy
inferred← citeshttps://doi.org/10.1038/s41598-025-86805-2openalex-snapshot
Numerical modeling of oxygen diffusion in tissue spheroids undergoing fusion using function representation and finite volumes
inferred← citeshttps://doi.org/10.1038/s41746-025-02198-6openalex-snapshot
AI-driven virtual cell models in preclinical research: technical pathways, validation mechanisms, and clinical translation potential
inferred← citeshttps://doi.org/10.1038/s42003-023-05653-wopenalex-snapshot
Stochastic biological system-of-systems modelling for iPSC culture
inferred← citeshttps://doi.org/10.1038/s43588-021-00154-4openalex-snapshot
A rigid body framework for multicellular modeling
inferred← citeshttps://doi.org/10.1038/s43588-022-00377-zopenalex-snapshot
Mathematical modeling of cancer immunotherapy for personalized clinical translation
inferred← citeshttps://doi.org/10.1038/s43588-023-00427-0openalex-snapshot
Unraveling non-genetic heterogeneity in cancer with dynamical models and computational tools
inferred← citeshttps://doi.org/10.1038/s44222-023-00089-7openalex-snapshot
Computational approaches to modelling and optimizing cancer treatment
inferred← citeshttps://doi.org/10.1038/s44222-023-00105-wopenalex-snapshot
Synthetic living materials in cancer biology
inferred← citeshttps://doi.org/10.1038/s44222-024-00245-7openalex-snapshot
Synthetic data in biomedicine via generative artificial intelligence
inferred← citeshttps://doi.org/10.1038/s44387-026-00157-4openalex-snapshot
Reinforcement Failing guides the discovery of emergent physical dynamics in adaptive tumor therapy
inferred← citeshttps://doi.org/10.1039/c9me00036dopenalex-snapshot
Learning-accelerated discovery of immune-tumour interactions
inferred← citeshttps://doi.org/10.1051/mmnp/2019026openalex-snapshot
Hybrid data-based modelling in oncology: successes, challenges and hopes
inferred← citeshttps://doi.org/10.1051/mmnp/2025012openalex-snapshot
Spatial organization of mediated-macrophage chemoprotective niches in solid tumors: A mathematical analysis
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