## Research Articles

The PBPK model of FcRn-mediated recycling of large molecules was developed and studied by deWitte et al. (2023) to characterize and predict Immunoglobulin G (IgG) disposition in plasma and tissues. This study investigated the large-molecule model in PK-Sim and its applicability to molecules with FcRn binding affinity in plasma.

The PBPK model of FcRn-mediated recycling of large molecules was developed and studied by deWitte et al. (2023) to characterize and predict Immunoglobulin G (IgG) disposition in plasma and tissues. This study investigated the large-molecule model in PK-Sim and its applicability to molecules with FcRn binding affinity in plasma.

An effort at reducing the Tong et al. (2011) model into a smaller number of equations for computational efficiency – the 'reduced' Tong model – aims at reproducing the overall behaviour without excessive detail.

An effort at reducing the Tong et al. (2011) model into a smaller number of equations for computational efficiency – the 'reduced' Tong model – aims at reproducing the overall behaviour without excessive detail.

We describe here our implementation of a renal epithelial model as published in Noroozbabaee et al. (2022). The flexible and modular model we presented in Noroozbabaee et al. (2022) can be adapted to specific configurations of epithelial transport.

We describe here our implementation of a renal epithelial model as published in Noroozbabaee et al. (2022). The flexible and modular model we presented in Noroozbabaee et al. (2022) can be adapted to specific configurations of epithelial transport.

The system of equations and figures presented in Imtiaz *et al.* (2002) are verified and reproduced in the current curation paper.

The system of equations and figures presented in Imtiaz *et al.* (2002) are verified and reproduced in the current curation paper.

Afshar *et al.* (2021) generated a computational model of non-isotonic glucose uptake by small intestinal epithelial cells. The model incorporates apical uptake via SGLT1 and GLUT2, basolateral efflux into the blood via GLUT2 and cellular volume changes in response to non-isotonic conditions.

Afshar *et al.* (2021) generated a computational model of non-isotonic glucose uptake by small intestinal epithelial cells. The model incorporates apical uptake via SGLT1 and GLUT2, basolateral efflux into the blood via GLUT2 and cellular volume changes in response to non-isotonic conditions.

Lees-Green *et al.* (2014) describes a biophysical computational model of anoctamin 1 calcium-activated chloride channels. The system of equations and simulation results are verified and reproduced.

Lees-Green *et al.* (2014) describes a biophysical computational model of anoctamin 1 calcium-activated chloride channels. The system of equations and simulation results are verified and reproduced.

The mechanistic model of neurovascular coupling was developed and studied by Sten *et al.* (2020). This model describes and predicts the arteriolar dilation data of mice under various stimulations while anaesthetised and awake. We reconstructed the model in CellML, using a modular approach for each neuronal pathway, and successfully reproduced the original experiments.

The mechanistic model of neurovascular coupling was developed and studied by Sten *et al.* (2020). This model describes and predicts the arteriolar dilation data of mice under various stimulations while anaesthetised and awake. We reconstructed the model in CellML, using a modular approach for each neuronal pathway, and successfully reproduced the original experiments.

The muscle spindle model presented in Maltenfort & Burke (2003) calculates muscle spindle primary afferent feedback depending on the muscle fibre stretch and fusimotor drive.

The muscle spindle model presented in Maltenfort & Burke (2003) calculates muscle spindle primary afferent feedback depending on the muscle fibre stretch and fusimotor drive.

The model incorporates processes of intracellular Ca²⁺ concentration control, myosin light chain (MLC) phosphorylation and stress production.

The model incorporates processes of intracellular Ca²⁺ concentration control, myosin light chain (MLC) phosphorylation and stress production.

The system of equations and figures presented in Saucerman *et al.*, 2003 are verified and reproduced in this paper’s curation effort.

The system of equations and figures presented in Saucerman *et al.*, 2003 are verified and reproduced in this paper’s curation effort.

The Poh *et al.* (2012) paper describes the first biophysically based computational model of human jejunal smooth muscle cell (hJSMC) electrophysiology. The ionic currents are described by either a traditional Hodgkin-Huxley (HH) formalism or a deterministic multi-state Markov (MM) formalism.

The Poh *et al.* (2012) paper describes the first biophysically based computational model of human jejunal smooth muscle cell (hJSMC) electrophysiology. The ionic currents are described by either a traditional Hodgkin-Huxley (HH) formalism or a deterministic multi-state Markov (MM) formalism.

*et al.*2017 model of the human sinus node action potential

The sinoatrial node (SAN) is the natural pacemaker of the mammalian heart. It has been the subject of several mathematical studies, aimed at reproducing its electrical response under normal sinus rhythms, as well as under various conditions.

The sinoatrial node (SAN) is the natural pacemaker of the mammalian heart. It has been the subject of several mathematical studies, aimed at reproducing its electrical response under normal sinus rhythms, as well as under various conditions.

An implemented model of glucose absorption in the enterocyte, as previously published by Afshar *et al.* (2019).

An implemented model of glucose absorption in the enterocyte, as previously published by Afshar *et al.* (2019).

A multi-scale model computational model of myocardial energetics—oxidative ATP synthesis, ATP hydrolysis, and phosphate metabolite kinetics—and myocardial mechanics used to analyze data from a rat model of cardiac decompensation and failure.

A multi-scale model computational model of myocardial energetics—oxidative ATP synthesis, ATP hydrolysis, and phosphate metabolite kinetics—and myocardial mechanics used to analyze data from a rat model of cardiac decompensation and failure.

We reproduce muscle cramp, as well as its prevention and reversal, by investigating muscle contraction and cramp, in which calcium regulatory networks are involved, using the extended model in comparison with the original model.

We reproduce muscle cramp, as well as its prevention and reversal, by investigating muscle contraction and cramp, in which calcium regulatory networks are involved, using the extended model in comparison with the original model.

*et al.*(2007) model of skeletal muscle: equations, coding and stability

We describe a major development of the Shorten *et al.* (2007) model of skeletal muscle electrophysiology, biochemistry and mechanics.

We describe a major development of the Shorten *et al.* (2007) model of skeletal muscle electrophysiology, biochemistry and mechanics.

^{+}/K

^{+}ATPase: An updated, thermodynamically consistent model

The Na⁺/K⁺ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na⁺ and K⁺ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na⁺/K⁺ ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately there was no archived code associated with the original manuscript.

The Na⁺/K⁺ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na⁺ and K⁺ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na⁺/K⁺ ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately there was no archived code associated with the original manuscript.

The classic Boron & De Weer (1976) paper provided the first evidence of active regulation of pH in cells by an energy-dependent acid-base transporter. This Physiome paper seeks to make that model, and the experimental conditions under which it was developed, available in a reproducible and well-documented form, along with a software implementation that makes the model easy to use and understand.

The classic Boron & De Weer (1976) paper provided the first evidence of active regulation of pH in cells by an energy-dependent acid-base transporter. This Physiome paper seeks to make that model, and the experimental conditions under which it was developed, available in a reproducible and well-documented form, along with a software implementation that makes the model easy to use and understand.

The primary paper Safaei et al. (2018) proposed an anatomically detailed model of the human cerebral circulation that runs faster than real-time on a desktop computer and is designed for use in clinical settings when the speed of response is important.

The primary paper Safaei et al. (2018) proposed an anatomically detailed model of the human cerebral circulation that runs faster than real-time on a desktop computer and is designed for use in clinical settings when the speed of response is important.