相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。A semantics, energy-based approach to automate biomodel composition
Niloofar Shahidi et al.
PLOS ONE (2022)
Analysing and simulating energy-based models in biology using BondGraphTools
Peter Cudmore et al.
EUROPEAN PHYSICAL JOURNAL E (2021)
Modular assembly of dynamic models in systems biology
Michael Pan et al.
PLOS COMPUTATIONAL BIOLOGY (2021)
Energy-Based Modeling of the Feedback Control of Biomolecular Systems With Cyclic Flow Modulation
Peter J. Gawthrop
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2021)
Hierarchical semantic composition of biosimulation models using bond graphs
Niloofar Shahidi et al.
PLOS COMPUTATIONAL BIOLOGY (2021)
Theory and Implementation of Coupled Port-Hamiltonian Continuum and Lumped Parameter Models
Finbar J. Argus et al.
JOURNAL OF ELASTICITY (2021)
Network Thermodynamical Modeling of Bioelectrical Systems: A Bond Graph Approach
Peter J. Gawthrop et al.
BIOELECTRICITY (2021)
Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data
Peter J. Gawthrop et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2021)
Physically-plausible modelling of biomolecular systems: A simplified, energy-based model of the mitochondrial electron transport chain
Peter J. Gawthrop et al.
JOURNAL OF THEORETICAL BIOLOGY (2020)
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
Derek N. Macklin et al.
SCIENCE (2020)
A thermodynamic framework for modelling membrane transporters
Michael Pan et al.
JOURNAL OF THEORETICAL BIOLOGY (2019)
An energetic reformulation of kinetic rate laws enables scalable parameter estimation for biochemical networks
John C. Mason et al.
JOURNAL OF THEORETICAL BIOLOGY (2019)
Computing Biomolecular System Steady-States
Peter Gawthrop
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2018)
Bond graph modelling of the cardiac action potential: implications for drift and non-unique steady states
Michael Pan et al.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2018)
Bond Graph Representation of Chemical Reaction Networks
Peter Gawthrop et al.
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2018)
Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction
Peter J. Gawthrop
IEEE TRANSACTIONS ON NANOBIOSCIENCE (2017)
Bond graph modelling of chemoelectrical energy transduction
Peter J. Gawthrop et al.
IET SYSTEMS BIOLOGY (2017)
Energy-based analysis of biomolecular pathways
Peter J. Gawthrop et al.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2017)
A network dynamics approach to chemical reaction networks
A. J. van der Schaft et al.
INTERNATIONAL JOURNAL OF CONTROL (2016)
Modular bond-graph modelling and analysis of biomolecular systems
Peter J. Gawthrop et al.
IET SYSTEMS BIOLOGY (2016)
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
Junyoung O. Park et al.
NATURE CHEMICAL BIOLOGY (2016)
The Virtual Physiological Human The physiome project aims to develop reproducible, multiscale models for clinical practice
Peter Hunter
IEEE PULSE (2016)
Complex and detailed balancing of chemical reaction networks revisited
Arjan van der Schaft et al.
JOURNAL OF MATHEMATICAL CHEMISTRY (2015)
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases
Maxwell L. Neal et al.
PLOS ONE (2015)
Hierarchical bond graph modelling of biochemical networks
Peter J. Gawthrop et al.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2015)
Irreversible thermodynamics of open chemical networks. I. Emergent cycles and broken conservation laws
Matteo Polettini et al.
JOURNAL OF CHEMICAL PHYSICS (2014)
Energy-based analysis of biochemical cycles using bond graphs
Peter J. Gawthrop et al.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES (2014)
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems
Maxwell L. Neal et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
Early bioenergetic evolution
Filipa L. Sousa et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2013)
ON THE MATHEMATICAL STRUCTURE OF BALANCED CHEMICAL REACTION NETWORKS GOVERNED BY MASS ACTION KINETICS
Arjan van der Schaft et al.
SIAM JOURNAL ON APPLIED MATHEMATICS (2013)
A Whole-Cell Computational Model Predicts Phenotype from Genotype
Jonathan R. Karr et al.
CELL (2012)
Chemiosmotic coupling in oxidative and photosynthetic phosphorylation
Peter Mitchell
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2011)
The Physiome Model Repository 2
Tommy Yu et al.
BIOINFORMATICS (2011)
Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology
Daniel L. Cook et al.
PLOS ONE (2011)
Modeling formalisms in Systems Biology
Daniel Machado et al.
AMB EXPRESS (2011)
Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models
Neema Jamshidi et al.
BIOPHYSICAL JOURNAL (2010)
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
Chen Li et al.
BMC SYSTEMS BIOLOGY (2010)
Systems Biology: An Approach
P. Kohl et al.
CLINICAL PHARMACOLOGY & THERAPEUTICS (2010)
Parameter Balancing in Kinetic Models of Cell Metabolism
Timo Lubitz et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
The energetics of genome complexity
Nick Lane et al.
NATURE (2010)
A Thermodynamic Model of the Cardiac Sarcoplasmic/Endoplasmic Ca2+ (SERCA) Pump
Kenneth Tran et al.
BIOPHYSICAL JOURNAL (2009)
A Tutorial on Chemical Reaction Network Dynamics
David Angeli
EUROPEAN JOURNAL OF CONTROL (2009)
The Cardiac Physiome: perspectives for the future
James Bassingthwaighte et al.
EXPERIMENTAL PHYSIOLOGY (2009)
Bond graph for dynamic modelling in chemical engineering
F. Couenne et al.
CHEMICAL ENGINEERING AND PROCESSING-PROCESS INTENSIFICATION (2008)
The Behavioral Approach to open and interconnected systems
Jan C. Willems
IEEE CONTROL SYSTEMS MAGAZINE (2007)
Bond-graph modeling
Peter J. Gawthrop et al.
IEEE CONTROL SYSTEMS MAGAZINE (2007)
Bond graph modelling for chemical reactors
F Couenne et al.
MATHEMATICAL AND COMPUTER MODELLING OF DYNAMICAL SYSTEMS (2006)
Sensitivity bond graphs
PJ Gawthrop
JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS (2000)