scholarly journals Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs

2017 ◽  
Vol 8 (1) ◽  
pp. 20170026 ◽  
Author(s):  
B. de Bono ◽  
S. Safaei ◽  
P. Grenon ◽  
P. Hunter
Keyword(s):  
Bond Graph ◽  
Bond Graphs ◽  
Acid Base ◽  
Distinct Process ◽  
Biophysical Processes ◽  
Biological Structures

We introduce, and provide examples of, the application of the bond graph formalism to explicitly represent biophysical processes between and within modular biological compartments in ApiNATOMY. In particular, we focus on modelling scenarios from acid–base physiology to link distinct process modalities as bond graphs over an ApiNATOMY circuit of multiscale compartments. The embedding of bond graphs onto ApiNATOMY compartments provides a semantically and mathematically explicit basis for the coherent representation, integration and visualisation of multiscale physiology processes together with the compartmental topology of those biological structures that convey these processes.

Bond Graph Sign Conventions

1975 ◽  
Vol 97 (2) ◽  
pp. 184-188 ◽  
Author(s):  
A. S. Perelson
Keyword(s):  
Graph Model ◽  
Bond Graph ◽  
Equivalence Classes ◽  
Parameter System ◽  
Bond Graphs ◽  
Lumped Parameter ◽  
Oriented Object

The lack of arbitrariness in the choice of bond graph sign conventions is established. It is shown that an unoriented bond graph may have no unique meaning and that with certain choices of orientation a bond graph may not correspond to any lumped parameter system constructed from the same set of elements. Network interpretations of these two facts are given. Defining a bond graph as an oriented object leads to the consideration of equivalence classes of oriented bond graphs which represent the same system. It is also shown that only changes in the orientation of bonds connecting 0-junctions and 1-junctions can lead to changes in the observable properties of a bond graph model.

scholarly journals Analysing and simulating energy-based models in biology using BondGraphTools

2021 ◽  
Author(s):  
Peter Cudmore ◽  
Michael Pan ◽  
Peter J. Gawthrop ◽  
Edmund J. Crampin
Keyword(s):  
Systems Biology ◽  
Mathematical Models ◽  
Bond Graph ◽  
Experimental Measurements ◽  
Bond Graphs ◽  
Graph Models ◽  
Conservation Of Energy ◽  
Conservation Of Mass ◽  
Physical Systems ◽  
Complex Interactions

AbstractLike all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry frequently neglect the conservation of energy, leading to unrealistic behaviour. Energy-based models that are consistent with conservation of mass, charge and energy have the potential to aid the understanding of complex interactions between biological components, and are becoming easier to develop with recent advances in experimental measurements and databases. In this paper, we motivate the use of bond graphs (a modelling tool from engineering) for energy-based modelling and introduce, BondGraphTools, a Python library for constructing and analysing bond graph models. We use examples from biochemistry to illustrate how BondGraphTools can be used to automate model construction in systems biology while maintaining consistency with the laws of physics.

Some Key Issues in Using Bond Graphs and Genetic Programming for Mechatronic System Design

2001 ◽  
Author(s):  
R. C. Rosenberg ◽  
E. D. Goodman ◽  
Kisung Seo
Keyword(s):  
Genetic Programming ◽  
System Design ◽  
Design Space ◽  
Bond Graph ◽  
Mechatronic System ◽  
Bond Graphs ◽  
Mechatronic Systems ◽  
Energy Behavior ◽  
Key Issues ◽  
Bond Graph Modeling

Abstract Mechatronic system design differs from design of single-domain systems, such as electronic circuits, mechanisms, and fluid power systems, in part because of the need to integrate the several distinct domain characteristics in predicting system behavior. The goal of our work is to develop an automated procedure that can explore mechatronic design space in a topologically open-ended manner, yet still find appropriate configurations efficiently enough to be useful. Our approach combines bond graphs for model representation with genetic programming for generating suitable design candidates as a means of exploring the design space. Bond graphs allow us to capture the common energy behavior underlying the several physical domains of mechatronic systems in a uniform notation. Genetic programming is an effective way to generate design candidates in an open-ended, but statistically structured, manner. Our initial goal is to identify the key issues in merging the bond graph modeling tool with genetic programming for searching. The first design problem we chose is that of finding a model that has a specified set of eigenvalues. The problem can be studied using a restricted set of bond graph elements to represent suitable topologies. We present the initial results of our studies and identify key issues in advancing the approach toward becoming an effective and efficient open-ended design tool for mechatronic systems.

Demonstrating the Generation of Bond Graphs From 3D Assemblies

2020 ◽  
Author(s):  
Corey J. Alicchio ◽  
Justin S. Vitiello ◽  
Pradeep Radhakrishnan
Keyword(s):  
Bond Graph ◽  
Dynamic Responses ◽  
Bond Graphs ◽  
Mechatronic Systems ◽  
3D Cad ◽  
Related Information ◽  
Grammar Rules ◽  
Gear Trains ◽  
System Graph ◽  
Future Work

Abstract The bond graph method provides a generic and simple way to compute differential equations and dynamic responses for complex mechatronic systems. This paper will illustrate the process of automatically generating bond graphs from 3D CAD assemblies of gear-trains. Using appropriate CAD application programming interfaces (APIs), information on parts and mates within an existing assembly is extracted. The extracted information is stored as an identity graph, which also stores all geometry and mass related information of every part. Grammar rules are then used to transform the identity graph to a system graph, which is then converted to bond graph using an existing bond graph generation program. The paper will discuss the process, challenges and planned future work.

Open Systems Formulation and Gaining Insight Using Lagrangian Bond Graphs

2000 ◽  
Author(s):  
Robin C. Redfield
Keyword(s):  
System Dynamics ◽  
Open Systems ◽  
Classical Method ◽  
System Modeling ◽  
Bond Graph ◽  
Small Scale ◽  
Bond Graphs ◽  
Model Modification ◽  
System Equations ◽  
Insight Into

Abstract Models of a small-scale water rocket are developed as an example of open system modeling by both the bond graph approach and a more classical method. One goal of the development is to determine the benefits of the bond graph approach into affording insight into the system dynamics. Both modeling approaches yield equivalent differential equations as they should, while the bond graph approach yields significantly more insight into the system dynamics. If a modeling goal is to simply find the system equations and predict behavior, the classical approach may be more expeditious. If insight and ease of model modification are desired, the bond graph technique is probably the better choice. But then you have to learn it!

scholarly journals Bond graph modelling of the cardiac action potential: implications for drift and non-unique steady states

2018 ◽  
Vol 474 (2214) ◽  
pp. 20180106 ◽  
Author(s):  
Michael Pan ◽  
Peter J. Gawthrop ◽  
Kenneth Tran ◽  
Joseph Cursons ◽  
Edmund J. Crampin
Keyword(s):  
Action Potential ◽  
Conservation Laws ◽  
Cardiac Electrophysiology ◽  
Bond Graph ◽  
Steady States ◽  
Cardiac Action Potential ◽  
Bond Graphs ◽  
Charge Conservation ◽  
Cardiac Action ◽  
Wide Range

Mathematical models of cardiac action potentials have become increasingly important in the study of heart disease and pharmacology, but concerns linger over their robustness during long periods of simulation, in particular due to issues such as model drift and non-unique steady states. Previous studies have linked these to violation of conservation laws, but only explored those issues with respect to charge conservation in specific models. Here, we propose a general and systematic method of identifying conservation laws hidden in models of cardiac electrophysiology by using bond graphs, and develop a bond graph model of the cardiac action potential to study long-term behaviour. Bond graphs provide an explicit energy-based framework for modelling physical systems, which makes them well suited for examining conservation within electrophysiological models. We find that the charge conservation laws derived in previous studies are examples of the more general concept of a ‘conserved moiety’. Conserved moieties explain model drift and non-unique steady states, generalizing the results from previous studies. The bond graph approach provides a rigorous method to check for drift and non-unique steady states in a wide range of cardiac action potential models, and can be extended to examine behaviours of other excitable systems.

Vector Bond Graphs Applied to One-Dimensional Distributed Systems

1975 ◽  
Vol 97 (1) ◽  
pp. 75-82 ◽  
Author(s):  
L. S. Bonderson
Keyword(s):  
Distributed Systems ◽  
Bond Graph ◽  
Bond Graphs ◽  
One Dimensional ◽  
Lumped Models ◽  
Multiple Power

Vector bond graph notation and conventions are presented which simplify the task of representing the multiple power bonds, transformations and junction structures of multiport systems. These ideas are shown to be particularly convenient in the reticulation of represntative microelements for a class of one-dimensional multipower distributed systems. The microelements are an aid in understanding the dynamics of distributed systems and may be used to construct approximate lumped models.

Dynamic Analysis of Flexible Bodies Using Extended Bond Graphs

1994 ◽  
Vol 116 (1) ◽  
pp. 66-72 ◽  
Author(s):  
Chiaming Yen ◽  
Glenn Y. Masada
Keyword(s):  
Reference Frames ◽  
Bond Graph ◽  
Flexible Manipulator ◽  
Bond Graphs ◽  
Inverse Dynamic ◽  
Flexible Bodies ◽  
Rigid Body Dynamic ◽  
Special Cases ◽  
Flexible Multibody ◽  
Body Dynamic

An Extended Bond Graph (EBG) formulation is described for analyzing the dynamics of a flexible multibody system. This work extends the EBG method, which was originally developed for systems with small spatial motion, to rigid and flexible multibody systems exhibiting large overall motions. The development uses modular models for the elements so that complex system models can be derived by coupling these modules. The EBG formulation for moving reference frames is used to derive models of one-link and two-link flexible manipulator systems. This approach has several advantages over the Lagrangian and Newtonian methods, such as its ability to solve the forward and inverse dynamic problems using the same bond graph. Finally, the EBG formulations for cantilever beams and for multi-rigid body dynamic systems are shown to be special cases of the general EGBs for flexible bodies.

Bond-Graph Based Simulation of Thermodynamic Models

2010 ◽  
Vol 132 (6) ◽  
Author(s):  
Forbes T. Brown
Keyword(s):  
Thermodynamic Properties ◽  
Hybrid Systems ◽  
Ad Hoc ◽  
Bond Graph ◽  
The Internet ◽  
Bond Graphs ◽  
Flowing Fluid ◽  
Heat Engines ◽  
Pure Substances ◽  
Compatible Extension

Conventional bond graphs are incompetent to handle thermodynamic systems with flowing fluid and phase change, such as heat engines and refrigeration cycles. Sophisticated bond-graph software for purposes of simulation is widely available for the systems addressable by conventional bond graphs, but heretofore there was no bond-graph software that could simulate the thermodynamic systems of concern. The author has previously published descriptions of a compatible extension to conventional bond graphs, which accommodates these systems through the use of what are known as convection bonds. Simulation of these models required ad hoc writing of the differential equations, however, a difficult task. The present brief announces the availability of software, based on a combination of convection and conventional bond graphs, which considerably expedites the simulation of thermodynamic and hybrid systems. The software is written in MATLAB® and is freely downloadable from the internet. It allows modeling and simulation to be carried out with a minimum knowledge of thermodynamics. Data characterizing the thermodynamic properties of 35 different pure substances and wet air are accessed as needed.

Application of Vector Bond Graphs to the Modeling of a Class of Hand Prostheses

Volume 3 ◽  
2004 ◽  
Author(s):  
Anand Vaz ◽  
Shinichi Hirai
Keyword(s):  
Three Dimensional ◽  
Graph Model ◽  
Systems Design ◽  
Bond Graph ◽  
Bond Graphs ◽  
Prosthetic Joints ◽  
Angular Velocities ◽  
Control Systems Design ◽  
And Control ◽  
Systematic Derivation

Vector bond graphs have been systematically applied to the modeling of prosthesis for a partially impaired hand. The partial impairment considered covers a category of the hand that has lost one or more fingers but retains the ability of its remaining natural fingers. The fingers and their prosthetic extensions are considered as rigid links. Rotation matrices which specify orientation of finger links are obtained from respective angular velocities. String-tube mechanism used to actuate prosthetic joints is modeled with the connection to joint variables of the mechanism. The vector bond graph approach enables the modeling of three dimensional movement of the hand mechanism. An example of a two joint string-tube actuated prosthetic mechanism is presented to describe the construction of the vector bond graph model. Systematic derivation of dynamics from the vector bond graphs is shown. The approach based on vector bond graphs presented here is useful for simulations and control systems design of such biomechanical systems.

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