Michael Pan

Energetic analysis of Na+/K+-ATPase using bond graphs

The paper develops bond graph models of Na+/K+-ATPase to analyze its energetic efficiency, showing 78% efficiency with 66% energy stored in ion gradients under physiological conditions.

fishROI: A specialized workflow for semi-automated muscle morphometry analysis in teleosts

The paper introduces a FIJI2 plugin for semi-automated muscle morphometry analysis in zebrafish, combining cytoplasmic staining and deep learning for accurate quantification and visualization.

A general thermodynamic approach for model reduction of enzyme cycles and electrogenic transporters

This paper introduces a thermodynamic framework for reducing enzyme cycle models while preserving physical constraints, applicable to both hypothetical systems and real data like Na+/K+ ATPase.

Bayesian Parameter Balancing Enables Robust and Consistent Estimation of Kinetic Parameter Uncertainty

The paper introduces a Bayesian parameter balancing framework to estimate kinetic parameter uncertainty with robustness and consistency across studies.

Divergence in skeletal muscle growth by differential spatial hyperplastic patterning in teleost fishes

The paper compares muscle growth dynamics across teleost fish species, identifying spatial hyperplastic patterning and stem cell gene expression as key factors in growth differences.

A mathematical model of metacarpal subchondral bone adaptation, microdamage, and repair in racehorses

This paper develops a mathematical model to simulate bone adaptation, microdamage accumulation, and repair in racehorses, finding that high-speed training causes significant damage and repair rates cannot offset it.

Thermodynamically-consistent, reduced models of gene regulatory networks

This paper develops thermodynamically-consistent, reduced models of gene regulatory networks for scalable agent-based simulations of cell populations.

Energy-based Analysis of Biochemical Oscillators Using Bond Graphs and Linear Control Theory.

The paper combines bond graph modeling with feedback control theory to analyze biochemical oscillators, showing phase margin as a scalar indicator of oscillation presence and structure.

Energy-based Modelling of Single Actin Filament Polymerisation Using Bond Graphs

The paper extends bond graph methodology to model chemomechanical transduction in actin filament polymerisation, showing it matches the Brownian ratchet approach and can model flexibility and compliance.

BondGraphs.jl: Composable energy-based modelling in systems biology

BondGraphs.jl provides a Julia framework for energy-based modelling in systems biology, enforcing thermodynamic constraints through bond graphs.

Sensitivity Analysis of Biochemical Systems Using Bond Graphs

The paper analyzes biochemical system sensitivity using bond graphs, showing parameter sensitivities as bond graph components and applying this to identify essential reactions in the Pentose Phosphate Pathway.

Energy-based Advection Modelling Using Bond Graphs

The paper extends an energy-based bond graph model to include advection, demonstrating its application in pharmacokinetic models and physiological systems.

Network Thermodynamics of Biological Systems: A Bond Graph Approach

This paper summarizes Crampin's group work on applying energy-based bond graph methods to biological systems, focusing on modeling photosynthesis with a new bond graph model.

Analysing and simulating energy-based models in biology using BondGraphTools

This paper introduces BondGraphTools, a Python library for constructing and analysing energy-based models in biochemistry using bond graphs, ensuring consistency with physical laws.

Modular assembly of dynamic models in systems biology

The paper proposes using bond graphs to improve modularity and physical consistency in systems biology models, demonstrating their utility in modelling MAPK cascades and glycolysis.

Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data.

The paper introduces a bond graph methodology to unify stoichiometry, thermodynamics, and kinetics in dynamic biomolecular modelling, demonstrating its application to E. coli.