SimService: a lightweight library for building simulation services in Python.

SUMMARY: Integrative biological modeling requires software infrastructure to launch, interconnect, and execute simulation software components without loss of functionality. SimService is a software library that enables deploying simulations in integrated applications as memory-isolated services with interactive proxy objects in the Python programming language. SimService supports customizing the interface of proxies so that simulation developers and users alike can tailor generated simulation instances according to model, method, and integrated application. AVAILABILITY AND IMPLEMENTATION: SimService is written in Python, is freely available on GitHub under the MIT license at https://github.com/tjsego/simservice, and is available for download via the Python Package Index (package name "simservice") and conda (package name "simservice" on the conda-forge channel).

Mathematical Modeling of the Lethal Synergism of Coinfecting Pathogens in Respiratory Viral Infections: A Review.

Influenza A virus (IAV) infections represent a substantial global health challenge and are often accompanied by coinfections involving secondary viruses or bacteria, resulting in increased morbidity and mortality. The clinical impact of coinfections remains poorly understood, with conflicting findings regarding fatality. Isolating the impact of each pathogen and mechanisms of pathogen synergy during coinfections is challenging and further complicated by host and pathogen variability and experimental conditions. Factors such as cytokine dysregulation, immune cell function alterations, mucociliary dysfunction, and changes to the respiratory tract epithelium have been identified as contributors to increased lethality. The relative significance of these factors depends on variables such as pathogen types, infection timing, sequence, and inoculum size. Mathematical biological modeling can play a pivotal role in shedding light on the mechanisms of coinfections. Mathematical modeling enables the quantification of aspects of the intra-host immune response that are difficult to assess experimentally. In this narrative review, we highlight important mechanisms of IAV coinfection with bacterial and viral pathogens and survey mathematical models of coinfection and the insights gained from them. We discuss current challenges and limitations facing coinfection modeling, as well as current trends and future directions toward a complete understanding of coinfection using mathematical modeling and computer simulation.

Modeling the roles of cohesotaxis, cell-intercalation, and tissue geometry in collective cell migration of Xenopus mesendoderm.

Collectively migrating Xenopus mesendoderm cells are arranged into leader and follower rows with distinct adhesive properties and protrusive behaviors. In vivo, leading row mesendoderm cells extend polarized protrusions and migrate along a fibronectin matrix assembled by blastocoel roof cells. Traction stresses generated at the leading row result in the pulling forward of attached follower row cells. Mesendoderm explants removed from embryos provide an experimentally tractable system for characterizing collective cell movements and behaviors, yet the cellular mechanisms responsible for this mode of migration remain elusive. We introduce an agent-based computational model of migrating mesendoderm in the Cellular-Potts computational framework to investigate the relative contributions of multiple parameters specific to the behaviors of leader and follower row cells. Sensitivity analyses identify cohesotaxis, tissue geometry, and cell intercalation as key parameters affecting the migration velocity of collectively migrating cells. The model predicts that cohesotaxis and tissue geometry in combination promote cooperative migration of leader cells resulting in increased migration velocity of the collective. Radial intercalation of cells towards the substrate is an additional mechanism to increase migratory speed of the tissue. Summary Statement: We present a novel Cellular-Potts model of collective cell migration to investigate the relative roles of cohesotaxis, tissue geometry, and cell intercalation on migration velocity of Xenopus mesendoderm.

Tissue Forge: Interactive biological and biophysics simulation environment.

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.

General, open-source vertex modeling in biological applications using Tissue Forge.

Vertex models are a widespread approach for describing the biophysics and behaviors of multicellular systems, especially of epithelial tissues. Vertex models describe a wide variety of developmental scenarios and behaviors like cell rearrangement and tissue folding. Often, these models are implemented as single-use or closed-source software, which inhibits reproducibility and decreases accessibility for researchers with limited proficiency in software development and numerical methods. We developed a physics-based vertex model methodology in Tissue Forge, an open-source, particle-based modeling and simulation environment. Our methodology describes the properties and processes of vertex model objects on the basis of vertices, which allows integration of vertex modeling with the particle-based formalism of Tissue Forge, enabling an environment for developing mixed-method models of multicellular systems. Our methodology in Tissue Forge inherits all features provided by Tissue Forge, delivering open-source, extensible vertex modeling with interactive simulation, real-time simulation visualization and model sharing in the C, C++ and Python programming languages and a Jupyter Notebook. Demonstrations show a vertex model of cell sorting and a mixed-method model of cell migration combining vertex- and particle-based models. Our methodology provides accessible vertex modeling for a broad range of scientific disciplines, and we welcome community-developed contributions to our open-source software implementation.

General, Open-Source Vertex Modeling in Biological Applications Using Tissue Forge.

Vertex models are a widespread approach for describing the biophysics and behaviors of multicellular systems, especially of epithelial tissues. Vertex models describe a wide variety of developmental scenarios and behaviors like cell rearrangement and tissue folding. Often, these models are implemented as single-use or closed-source software, which inhibits reproducibility and decreases accessibility for researchers with limited proficiency in software development and numerical methods. We developed a physics-based vertex model methodology in Tissue Forge, an open-source, particle-based modeling and simulation environment. Our methodology describes the properties and processes of vertex model objects on the basis of vertices, which allows integration of vertex modeling with the particle-based formalism of Tissue Forge, enabling an environment for developing mixed-method models of multicellular systems. Our methodology in Tissue Forge inherits all features provided by Tissue Forge, delivering opensource, extensible vertex modeling with interactive simulation, real-time simulation visualization and model sharing in the C,C++ and Python programming languages and a Jupyter Notebook. Demonstrations show a vertex model of cell sorting and a mixed-method model of cell migration combining vertex- and particle-based models. Our methodology provides accessible vertex modeling for a broad range of scientific disciplines, and we welcome community-developed contributions to our open-source software implementation.

Age-Related Changes to the Immune System Exacerbate the Inflammatory Response to Pandemic H1N1 Infection.

Age-induced dysregulation of the immune response is a major contributor to the morbidity and mortality related to influenza a virus infections. Experimental data have shown substantial changes to the activation and maintenance of the immune response will occur with age, but it remains unclear which of these many interrelated changes are most critical to controlling the survival of the host during infection. To ascertain which mechanisms are predominantly responsible for the increased morbidity in elderly hosts, we developed an ordinary differential equation model to simulate the immune response to pandemic H1N1 infection. We fit this model to experimental data measured in young and old macaques. We determined that the severity of the infection in the elderly hosts is caused by a dysregulation in the innate immune response. We also simulated CD8+ T cell exhaustion, a common consequence of chronic and extensive infections. Our simulations indicate that while T cell exhaustion is possible in both age groups, its effects are more severe in the elderly population, as their dysregulated immune response cannot easily compensate for the exhausted T cells. Finally, we explore a therapeutic approach to reversing T cell exhaustion through an inflammatory stimulus. A controlled increase in inflammatory signals can lead to a higher chance of surviving the infection, but excess inflammation will likely lead to septic death. These results indicate that our model captures distinctions in the predominant mechanisms controlling the immune response in younger and older hosts and allows for simulations of clinically relevant therapeutic strategies post-infection.

Building digital twins of the human immune system: toward a roadmap.

Digital twins, customized simulation models pioneered in industry, are beginning to be deployed in medicine and healthcare, with some major successes, for instance in cardiovascular diagnostics and in insulin pump control. Personalized computational models are also assisting in applications ranging from drug development to treatment optimization. More advanced medical digital twins will be essential to making precision medicine a reality. Because the immune system plays an important role in such a wide range of diseases and health conditions, from fighting pathogens to autoimmune disorders, digital twins of the immune system will have an especially high impact. However, their development presents major challenges, stemming from the inherent complexity of the immune system and the difficulty of measuring many aspects of a patient's immune state in vivo. This perspective outlines a roadmap for meeting these challenges and building a prototype of an immune digital twin. It is structured as a four-stage process that proceeds from a specification of a concrete use case to model constructions, personalization, and continued improvement.

Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2.

We extend our established agent-based multiscale computational model of infection of lung tissue by SARS-CoV-2 to include pharmacokinetic and pharmacodynamic models of remdesivir. We model remdesivir treatment for COVID-19; however, our methods are general to other viral infections and antiviral therapies. We investigate the effects of drug potency, drug dosing frequency, treatment initiation delay, antiviral half-life, and variability in cellular uptake and metabolism of remdesivir and its active metabolite on treatment outcomes in a simulated patch of infected epithelial tissue. Non-spatial deterministic population models which treat all cells of a given class as identical can clarify how treatment dosage and timing influence treatment efficacy. However, they do not reveal how cell-to-cell variability affects treatment outcomes. Our simulations suggest that for a given treatment regime, including cell-to-cell variation in drug uptake, permeability and metabolism increase the likelihood of uncontrolled infection as the cells with the lowest internal levels of antiviral act as super-spreaders within the tissue. The model predicts substantial variability in infection outcomes between similar tissue patches for different treatment options. In models with cellular metabolic variability, antiviral doses have to be increased significantly (>50% depending on simulation parameters) to achieve the same treatment results as with the homogeneous cellular metabolism.

A multiscale multicellular spatiotemporal model of local influenza infection and immune response.

Respiratory viral infections pose a serious public health concern, from mild seasonal influenza to pandemics like those of SARS-CoV-2. Spatiotemporal dynamics of viral infection impact nearly all aspects of the progression of a viral infection, like the dependence of viral replication rates on the type of cell and pathogen, the strength of the immune response and localization of infection. Mathematical modeling is often used to describe respiratory viral infections and the immune response to them using ordinary differential equation (ODE) models. However, ODE models neglect spatially-resolved biophysical mechanisms like lesion shape and the details of viral transport, and so cannot model spatial effects of a viral infection and immune response. In this work, we develop a multiscale, multicellular spatiotemporal model of influenza infection and immune response by combining non-spatial ODE modeling and spatial, cell-based modeling. We employ cellularization, a recently developed method for generating spatial, cell-based, stochastic models from non-spatial ODE models, to generate much of our model from a calibrated ODE model that describes infection, death and recovery of susceptible cells and innate and adaptive responses during influenza infection, and develop models of cell migration and other mechanisms not explicitly described by the ODE model. We determine new model parameters to generate agreement between the spatial and original ODE models under certain conditions, where simulation replicas using our model serve as microconfigurations of the ODE model, and compare results between the models to investigate the nature of viral exposure and impact of heterogeneous infection on the time-evolution of the viral infection. We found that using spatially homogeneous initial exposure conditions consistently with those employed during calibration of the ODE model generates far less severe infection, and that local exposure to virus must be multiple orders of magnitude greater than a uniformly applied exposure to all available susceptible cells. This strongly suggests a prominent role of localization of exposure in influenza A infection. We propose that the particularities of the microenvironment to which a virus is introduced plays a dominant role in disease onset and progression, and that spatially resolved models like ours may be important to better understand and more reliably predict future health states based on susceptibility of potential lesion sites using spatially resolved patient data of the state of an infection. We can readily integrate the immune response components of our model into other modeling and simulation frameworks of viral infection dynamics that do detailed modeling of other mechanisms like viral internalization and intracellular viral replication dynamics, which are not explicitly represented in the ODE model. We can also combine our model with available experimental data and modeling of exposure scenarios and spatiotemporal aspects of mechanisms like mucociliary clearance that are only implicitly described by the ODE model, which would significantly improve the ability of our model to present spatially resolved predictions about the progression of influenza infection and immune response.

Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics.

Respiratory viruses present major public health challenges, as evidenced by the 1918 Spanish Flu, the 1957 H2N2, 1968 H3N2, and 2009 H1N1 influenza pandemics, and the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Severe RNA virus respiratory infections often correlate with high viral load and excessive inflammation. Understanding the dynamics of the innate immune response and its manifestations at the cell and tissue levels is vital to understanding the mechanisms of immunopathology and to developing strain-independent treatments. Here, we present a novel spatialized multicellular computational model of RNA virus infection and the type-I interferon-mediated antiviral response that it induces within lung epithelial cells. The model is built using the CompuCell3D multicellular simulation environment and is parameterized using data from influenza virus-infected cell cultures. Consistent with experimental observations, it exhibits either linear radial growth of viral plaques or arrested plaque growth depending on the local concentration of type I interferons. The model suggests that modifying the activity of signaling molecules in the JAK/STAT pathway or altering the ratio of the diffusion lengths of interferon and virus in the cell culture could lead to plaque growth arrest. The dependence of plaque growth arrest on diffusion lengths highlights the importance of developing validated spatial models of cytokine signaling and the need for in vitro measurement of these diffusion coefficients. Sensitivity analyses under conditions leading to continuous or arrested plaque growth found that plaque growth is more sensitive to variations of most parameters and more likely to have identifiable model parameters when conditions lead to plaque arrest. This result suggests that cytokine assay measurements may be most informative under conditions leading to arrested plaque growth. The model is easy to extend to include SARS-CoV-2-specific mechanisms or to use as a component in models linking epithelial cell signaling to systemic immune models.

Generation of multicellular spatiotemporal models of population dynamics from ordinary differential equations, with applications in viral infection.

BACKGROUND: The biophysics of an organism span multiple scales from subcellular to organismal and include processes characterized by spatial properties, such as the diffusion of molecules, cell migration, and flow of intravenous fluids. Mathematical biology seeks to explain biophysical processes in mathematical terms at, and across, all relevant spatial and temporal scales, through the generation of representative models. While non-spatial, ordinary differential equation (ODE) models are often used and readily calibrated to experimental data, they do not explicitly represent the spatial and stochastic features of a biological system, limiting their insights and applications. However, spatial models describing biological systems with spatial information are mathematically complex and computationally expensive, which limits the ability to calibrate and deploy them and highlights the need for simpler methods able to model the spatial features of biological systems. RESULTS: In this work, we develop a formal method for deriving cell-based, spatial, multicellular models from ODE models of population dynamics in biological systems, and vice versa. We provide examples of generating spatiotemporal, multicellular models from ODE models of viral infection and immune response. In these models, the determinants of agreement of spatial and non-spatial models are the degree of spatial heterogeneity in viral production and rates of extracellular viral diffusion and decay. We show how ODE model parameters can implicitly represent spatial parameters, and cell-based spatial models can generate uncertain predictions through sensitivity to stochastic cellular events, which is not a feature of ODE models. Using our method, we can test ODE models in a multicellular, spatial context and translate information to and from non-spatial and spatial models, which help to employ spatiotemporal multicellular models using calibrated ODE model parameters. We additionally investigate objects and processes implicitly represented by ODE model terms and parameters and improve the reproducibility of spatial, stochastic models. CONCLUSION: We developed and demonstrate a method for generating spatiotemporal, multicellular models from non-spatial population dynamics models of multicellular systems. We envision employing our method to generate new ODE model terms from spatiotemporal and multicellular models, recast popular ODE models on a cellular basis, and generate better models for critical applications where spatial and stochastic features affect outcomes.

Advancing therapies for viral infections using mechanistic computational models of the dynamic interplay between the virus and host immune response.

The COVID-19 pandemic has highlighted a need for improved frameworks for drug discovery, repurposing, clinical trial design and therapy optimization and personalization. Mechanistic computational models can play an important role in developing these frameworks. We discuss how mechanistic models, which consider viral entry, replication in target cells, viral spread in the body, immune response, and the complex factors involved in tissue and organ damage and recovery, can clarify the mechanisms of humoral and cellular immune responses to the virus, viral distribution and replication in tissues, the origins of pathogenesis and patient-to-patient heterogeneity in responses. These models are already improving our understanding of the mechanisms of action of antivirals and immune modulators. We discuss how closer collaboration between the experimentalists, clinicians and modelers could result in more predictive models which may guide therapies for viral infections, improving survival and leading to faster and more complete recovery.

Compartmental Model Suggests Importance of Innate Immune Response to COVID-19 Infection in Rhesus Macaques.

The pandemic outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly spread worldwide, creating a serious health crisis. The virus is primarily associated with flu-like symptoms but can also lead to severe pathologies and death. We here present an ordinary differential equation model of the intrahost immune response to SARS-CoV-2 infection, fitted to experimental data gleaned from rhesus macaques. The model is calibrated to data from a nonlethal infection, but the model can replicate behavior from various lethal scenarios as well. We evaluate the sensitivity of the model to biologically relevant parameters governing the strength and efficacy of the immune response. We also simulate the effect of both anti-inflammatory and antiviral drugs on the host immune response and demonstrate the ability of the model to lessen the severity of a formerly lethal infection with the addition of the appropriately calibrated drug. Our model emphasizes the importance of tight control of the innate immune response for host survival and viral clearance.

A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.

Simulations of tissue-specific effects of 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 to rapid advances in understanding of infection mechanisms, and parallel development of components by multiple groups. We present an open-source platform for multiscale spatiotemporal simulation of an epithelial tissue, viral infection, cellular immune response and tissue damage, specifically designed to be modular and extensible to support continuous updating and parallel development. The base simulation of a simplified patch of epithelial tissue and immune response exhibits distinct patterns of infection dynamics from widespread infection, to recurrence, to clearance. Slower viral internalization and faster immune-cell recruitment slow infection and promote containment. Because antiviral drugs can have side effects and show reduced clinical effectiveness when given later during infection, we studied the effects on progression of treatment potency and time-of-first treatment after infection. In simulations, even a low potency therapy with a drug which reduces the replication rate of viral RNA greatly decreases the total tissue damage and virus burden when given near the beginning of infection. Many combinations of dosage and treatment time lead to stochastic outcomes, with some simulation replicas showing clearance or control (treatment success), while others show rapid infection of all epithelial cells (treatment failure). Thus, while a high potency therapy usually is less effective when given later, treatments at late times are occasionally effective. We illustrate how to extend the platform to model specific virus types (e.g., hepatitis C) and add additional cellular mechanisms (tissue recovery and variable cell susceptibility to infection), using our software modules and publicly-available software repository.

Modeling Progressive Damage Accumulation in Bone Remodeling Explains the Thermodynamic Basis of Bone Resorption by Overloading.

Computational modeling of skeletal tissue seeks to predict the structural adaptation of bone in response to mechanical loading. The theory of continuum damage-repair, a mathematical description of structural adaptation based on principles of damage mechanics, continues to be developed and utilized for the prediction of long-term peri-implant outcomes. Despite its technical soundness, CDR does not account for the accumulation of mechanical damage and irreversible deformation. In this work, a nonlinear mathematical model of independent damage accumulation and plastic deformation is developed in terms of the CDR formulation. The proposed model incorporates empirical correlations from uniaxial experiments. Supporting elements of the model are derived, including damage and yielding criteria, corresponding consistency conditions, and the basic, necessary forms for integration during loading. Positivity of mechanical dissipation due to damage is proved, while strain-based, associative plastic flow and linear hardening describe post-yield behavior. Calibration of model parameters to the empirical correlations from which the model was derived is then accomplished. Results of numerical experiments on a point-wise specimen show that damage and plasticity inhibit bone formation by dissipation of energy available to biological processes, leading to material failure that would otherwise be predicted to experience a net gain of bone.

Unification of aggregate growth models by emergence from cellular and intracellular mechanisms.

Multicellular aggregate growth is regulated by nutrient availability and removal of metabolites, but the specifics of growth dynamics are dependent on cell type and environment. Classical models of growth are based on differential equations. While in some cases these classical models match experimental observations, they can only predict growth of a limited number of cell types and so can only be selectively applied. Currently, no classical model provides a general mathematical representation of growth for any cell type and environment. This discrepancy limits their range of applications, which a general modelling framework can enhance. In this work, a hybrid cellular Potts model is used to explain the discrepancy between classical models as emergent behaviours from the same mathematical system. Intracellular processes are described using probability distributions of local chemical conditions for proliferation and death and simulated. By fitting simulation results to a generalization of the classical models, their emergence is demonstrated. Parameter variations elucidate how aggregate growth may behave like one classical growth model or another. Three classical growth model fits were tested, and emergence of the Gompertz equation was demonstrated. Effects of shape changes are demonstrated, which are significant for final aggregate size and growth rate, and occur stochastically.

A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness: A multiscale model of viral infection in epithelial tissues.

Simulations of tissue-specific effects of 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 to rapid advances in understanding of infection mechanisms, and parallel development of components by multiple groups. We present an open-source platform for multiscale spatiotemporal simulation of an epithelial tissue, viral infection, cellular immune response and tissue damage, specifically designed to be modular and extensible to support continuous updating and parallel development. The base simulation of a simplified patch of epithelial tissue and immune response exhibits distinct patterns of infection dynamics from widespread infection, to recurrence, to clearance. Slower viral internalization and faster immune-cell recruitment slow infection and promote containment. Because antiviral drugs can have side effects and show reduced clinical effectiveness when given later during infection, we studied the effects on progression of treatment potency and time-of-first treatment after infection. In simulations, even a low potency therapy with a drug which reduces the replication rate of viral RNA greatly decreases the total tissue damage and virus burden when given near the beginning of infection. Many combinations of dosage and treatment time lead to stochastic outcomes, with some simulation replicas showing clearance or control (treatment success), while others show rapid infection of all epithelial cells (treatment failure). Thus, while a high potency therapy usually is less effective when given later, treatments at late times are occasionally effective. We illustrate how to extend the platform to model specific virus types (e.g., hepatitis C) and add additional cellular mechanisms (tissue recovery and variable cell susceptibility to infection), using our software modules and publicly-available software repository.

Computational fluid dynamic analysis of bioprinted self-supporting perfused tissue models.

Natural tissues are incorporated with vasculature, which is further integrated with 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 tissues being developed into clinical implants, research models, and pharmaceutical testing platforms should similarly exhibit perfused tissue-like structures, we generated a generalizable biofabrication method resulting in self-supporting perfused (SSuPer) tissue constructs incorporated with perfusible microchannels and integrated with the modular FABRICA perfusion bioreactor. As proof of concept, we perfused an MLO-A5 osteoblast-based SSuPer tissue in the FABRICA. Although our resulting SSuPer tissue replicated vascularization and perfusion observed in situ, supported its own weight, and stained positively for mineral using Von Kossa staining, our in vitro results indicated that computational fluid dynamics (CFD) should be used to drive future construct design and flow application before further tissue biofabrication and perfusion. We built a CFD model of the SSuPer tissue integrated in the FABRICA and analyzed flow characteristics (net force, pressure distribution, shear stress, and oxygen distribution) through five SSuPer tissue microchannel patterns in two flow directions and at increasing flow rates. Important flow parameters include flow direction, fully developed flow, and tissue microchannel diameters matched and aligned with bioreactor flow channels. We observed that the SSuPer tissue platform is capable of providing direct perfusion to tissue constructs and proper culture conditions (oxygenation, with controllable shear and flow rates), indicating that our approach can be used to biofabricate tissue representing primary tissues and that we can model the system in silico.

A heuristic computational model of basic cellular processes and oxygenation during spheroid-dependent biofabrication.

An emerging approach in biofabrication is the creation of 3D tissue constructs through scaffold-free, cell spheroid-only methods. The basic mechanism in this technology is spheroid fusion, which is driven by the minimization of energy, the same biophysical mechanism that governs spheroid formation. However, other factors such as oxygen and metabolite accessibility within spheroids impact on spheroid properties and their ability to form larger-scale structures. The goal of our work is to develop a simulation platform eventually capable of predicting the conditions that minimize metabolism-related cell loss within spheroids. To describe the behavior and dynamic properties of the cells in response to their neighbors and to transient nutrient concentration fields, we developed a hybrid discrete-continuous heuristic model, combining a cellular Potts-type approach with field equations applied to a randomly populated spheroid cross-section of prescribed cell-type constituency. This model allows for the description of: (i) cellular adhesiveness and motility; (ii) interactions with concentration fields, including diffusivity and oxygen consumption; and (iii) concentration-dependent, stochastic cell dynamics, driven by metabolite-dependent cell death. Our model readily captured the basic steps of spheroid-based biofabrication (as specifically dedicated to scaffold-free bioprinting), including intra-spheroid cell sorting (both in 2D and 3D implementations), spheroid defect closure, and inter-spheroid fusion. Moreover, we found that when hypoxia occurring at the core of the spheroid was set to trigger cell death, this was amplified upon spheroid fusion, but could be mitigated by external oxygen supplementation. In conclusion, optimization and further development of scaffold-free bioprinting techniques could benefit from our computational model which is able to simultaneously account for both cellular dynamics and metabolism in constructs obtained by scaffold-free biofabrication.