Research Articles

Retrospective
Reproducibility study to simulate a chain of collapsible contracting lymphangions with progressive valve closure
Article thumbnail
Jun 17, 2024

This paper presents a reproduced computational model of lymphatic collecting vessels. The model was originally introduced by Bertram et al. (2011), and comprises a series of contractile segments, known as lymphangions, interconnected by secondary lymphatic valves. The model focused on elucidating the pumping behavior of contracting lymphangions and deriving pump-characteristic curves, by incorporating pressure-dependent valve resistance, passive elasticity, and active contraction terms in multiple lymphangions connected in series.

Original Research
Reproducibility Study on a PBPK Model of FcRn-Mediated Recycling for Large Molecules
Article thumbnail
Feb 12, 2024

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.

Original Research
Steady-state Approximations for Hodgkin-Huxley Cell Models: Towards Multi-scale Models of Uterine Smooth Muscle
Article thumbnail
Dec 4, 2023

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.

Original Research
Reproducibility study of the modular and reusable model of epithelial transport in the proximal convoluted tubule
Article thumbnail
May 27, 2023

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.

Original Research
A theoretical model of slow wave regulation using voltage-dependent synthesis of inositol 1, 4, 5-trisphosphate
Article thumbnail
Jan 20, 2023

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

Original Research
Reproducibility Study of Computational Modelling of Glucose Uptake by SGLT1 and GLUT2 in the Enterocyte
Article thumbnail
Jan 19, 2023

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.

Original Research
Reproducibility Study for a Computational Model of the Neurovascular Coupling Unit
Article thumbnail
Jan 11, 2023

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.

Original Research
Computational modeling of anoctamin 1 calcium-activated chloride channels as pacemaker channels in interstitial cells of Cajal
Article thumbnail
Jan 11, 2023

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.

Retrospective
Spindle Model Responsive to Mixed Fusimotor Inputs: an updated version of the Maltenfort and Burke (2003) model
Article thumbnail
Jan 27, 2022

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

Original Research
Mathematical model of excitation-contraction in a uterine smooth muscle cell
Article thumbnail
Oct 27, 2021

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

Original Research
A kinetic model of β-adrenergic control in cardiac myocytes
Article thumbnail
Sep 23, 2021

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

Original Research
A Quantitative Model of Human Jejunal Smooth Muscle Cell Electrophysiology
Article thumbnail
Sep 9, 2021

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.

Original Research
Reproducibility study of the Fabbri et al. 2017 model of the human sinus node action potential
Article thumbnail
Sep 1, 2021

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.

Original Research
Computational Modelling of Glucose Uptake in the Enterocyte
Article thumbnail
Oct 1, 2020

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

Original Research
Computational Modeling of Coupled Energetics and Mechanics in the Rat Ventricular Myocardium
Article thumbnail
Sep 15, 2020

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.

Retrospective
Incorporation of sarcolemmal calcium transporters into the Shorten et al. (2007) model of skeletal muscle: equations, coding and stability
Article thumbnail
Aug 28, 2020

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

Letter
Model of skeletal muscle cramp and its reversal
Article thumbnail
Aug 28, 2020

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.

review
The Boron & De Weer Model of Intracellular pH Regulation
Article thumbnail
Aug 27, 2020

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.

Retrospective
The cardiac Na+/K+ ATPase: An updated, thermodynamically consistent model
Article thumbnail
Aug 27, 2020

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.

Original Research
Bond Graph Model of Cerebral Circulation: Toward Clinically Feasible Systemic Blood Flow Simulations
Article thumbnail
Aug 26, 2020

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.

Funding and support by:
International Union of Physiological SciencesAuckland Bioengineering InstituteDigital ScienceVPH Institute