Morphogenesis in early development involves complex and extreme deformations response to intra- intercellular forces. Zebrafish epiboly, the spreading of blastoderm cover engulf large yolk cell, is a key event that sets stage for gastrulation, but poorly understood. The enveloping layer (EVL), thin squamous outer epithelium blastoderm, bound at its edges cell by tight junctions, plays central role. marginal EVL cells receive through their forces generated propagate those rest EVL; resulting...

Simulations of tissue-specific effects primary acute viral infections like COVID-19 are essential for understanding disease outcomes and optimizing therapies. Such simulations need to support continuous updating in response rapid advances infection mechanisms, parallel development components by multiple groups. We present an open-source platform multiscale spatiotemporal simulation epithelial tissue, infection, cellular immune tissue damage, specifically designed be modular extensible...

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling simulation. allows users to create, simulate explore models virtual experiments based on soft condensed matter physics at multiple scales, from the molecular multicellular, using a simple, consistent interface. While designed simplify solving problems in complex subcellular, cellular tissue biophysics, it supports applications ranging classic dynamics agent-based multicellular...

An emerging approach in biofabrication is the creation of 3D tissue constructs through scaffoldfree, cell spheroid-only methods.The basic mechanism this technology spheroid fusion, which driven by minimization energy, same biophysical that governs formation.However, other factors such as oxygen and metabolite accessibility within spheroids impact on properties their ability to form larger-scale structures.The goal our work develop a simulation platform eventually capable predict conditions...

We extend our established agent-based multiscale computational model of infection lung tissue by SARS-CoV-2 to include pharmacokinetic and pharmacodynamic models remdesivir. remdesivir treatment for COVID-19; however, methods are general other viral infections antiviral therapies. investigate the effects drug potency, dosing frequency, initiation delay, half-life, variability in cellular uptake metabolism its active metabolite on outcomes a simulated patch infected epithelial tissue....

The pandemic outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly spread worldwide, creating a serious health crisis. virus is primarily associated with flu-like symptoms but can also lead to pathologies and death. We here present an ordinary differential equation model the intrahost immune response SARS-CoV-2 infection, fitted experimental data gleaned from rhesus macaques. calibrated nonlethal replicate behavior various lethal scenarios as well. evaluate...

Natural tissues are incorporated with vasculature, which is further integrated a cardiovascular system responsible for driving perfusion of nutrient-rich oxygenated blood through the vasculature to support cell metabolism within most cell-dense tissues. Since scaffold-free biofabricated being developed into clinical implants, research models, and pharmaceutical testing platforms should similarly exhibit perfused tissue-like structures, we generated generalizable biofabrication method...

Abstract Background The biophysics of an organism span multiple scales from subcellular to organismal and include processes characterized by spatial properties, such as the diffusion molecules, cell migration, flow intravenous fluids. Mathematical biology seeks explain biophysical in mathematical terms at, across, all relevant temporal scales, through generation representative models. While non-spatial, ordinary differential equation (ODE) models are often used readily calibrated...

Abstract Vertex models are a widespread approach for describing the biophysics and behaviors of multicellular systems, especially epithelial tissues. describe wide variety developmental scenarios like cell rearrangement tissue folding. Often, these implemented as single-use or closed-source software, which inhibits reproducibility decreases accessibility researchers with limited proficiency in software development numerical methods. We developed physics-based vertex model methodology Tissue...

Respiratory viruses present major public health challenges, as evidenced by the 1918 Spanish Flu, 1957 H2N2, 1968 H3N2, and 2009 H1N1 influenza pandemics, ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Severe RNA virus infections often correlate with high viral load excessive inflammation. Understanding dynamics of innate immune response its manifestations at cell tissue levels is vital to understanding mechanisms immunopathology developing strain-independent...

Abstract Summary Integrative biological modeling requires software infrastructure to launch, interconnect, and execute simulation components without loss of functionality. SimService is a library that enables deploying simulations in integrated applications as memory-isolated services with interactive proxy objects the Python programming language. supports customizing interface proxies so developers users alike can tailor generated instances according model, method, application. Availability...

Collectively migrating Xenopus mesendoderm cells are arranged into leader and follower rows with distinct adhesive properties protrusive behaviors. In vivo, leading row extend polarized protrusions migrate along a fibronectin matrix assembled by blastocoel roof cells. Traction stresses generated at the result in pulling forward of attached Mesendoderm explants removed from embryos provide an experimentally tractable system for characterizing collective cell movements behaviors, yet cellular...

Abstract PhysiCell, a mechanistic center-based agent-based modeling framework, describes sequences of cell behaviors in very elegant way with its phenotype submodel. However, phenotypes are not usable other frameworks, and the creation new is straight forward. PhenoCellPy an open-source Python package that implements PhysiCell’s their methods general way, easily extended embedded into python-based models. defines for states ( e.g. , cycle, or Phases cellular necrosis). classes Cell Volume...

Simulations of tissue-specific effects primary acute viral infections like COVID-19 are essential for understanding disease outcomes and optimizing therapies. Such simulations need to support continuous updating in response rapid advances infection mechanisms, parallel development components by multiple groups. We present an open-source platform multiscale spatiotemporal simulation epithelial tissue, infection, cellular immune tissue damage, specifically designed be modular extensible...

Multicellular aggregate growth is regulated by nutrient availability and removal of metabolites, but the specifics dynamics are dependent on cell type environment. Classical models based differential equations. While in some cases these classical match experimental observations, they can only predict a limited number types so be selectively applied. Currently, no model provides general mathematical representation for any This discrepancy limits their range applications, which modelling...

Abstract Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling simulation. allows users to create, simulate explore models virtual experiments based on soft condensed matter physics at multiple scales, from the molecular multicellular, using a simple, consistent interface. While designed simplify solving problems in complex subcellular, cellular tissue biophysics, it supports applications ranging classic dynamics agent-based...

Abstract Respiratory viruses present major health challenges, as evidenced by the 2009 influenza pandemic and ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Severe RNA virus infections often correlate with high viral load excessive inflammation. Understanding dynamics of innate immune response its manifestation at cell tissue levels are vital to understanding mechanisms immunopathology developing improved, strain independent treatments. Here, we a novel...

Reproducibility is a foundational standard for validating scientific claims in computational research. Stochastic models are employed across diverse fields such as systems biology, financial modelling and environmental sciences. Existing infrastructure software tools support various aspects of reproducible model development, application, dissemination, but do not adequately address independently reproducing simulation results that form the basis conclusions. To bridge this gap, we introduce...