scholarly journals Energy-based analysis of biochemical cycles using bond graphs

2014 ◽  
Vol 470 (2171) ◽  
pp. 20140459 ◽  
Author(s):  
Peter J. Gawthrop ◽  
Edmund J. Crampin
Keyword(s):  
Chemical Potential ◽  
Simulation Models ◽  
Bond Graph ◽  
Biochemical Networks ◽  
Engineering Systems ◽  
Bond Graphs ◽  
Secure Foundation ◽  
Biochemical Systems ◽  
Gibb’S Free Energy

Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks.

Reflections on Engineering Systems and Bond Graphs

1993 ◽  
Vol 115 (2B) ◽  
pp. 242-251 ◽  
Author(s):  
R. C. Rosenberg
Keyword(s):  
Mechanical Engineer ◽  
Problem Solving ◽  
Large Scale ◽  
Bond Graph ◽  
Engineering System ◽  
Engineering Systems ◽  
Bond Graphs ◽  
Modern Engineering ◽  
Versatile Tool ◽  
Systems Simulation

An important aspect of modern engineering systems is their great diversity. Often they include interactions among different physical domains, contain control subsystems, and are large-scale and complex. The bond graph is a powerful and versatile tool that can help the engineer to design modern engineering systems. Three issues are explored from a bond graph perspective: modeling of engineering systems, simulation of their behavior, and teaching about engineering systems. It is the author’s observation that bond graph methodology is one of the most useful engineering system techniques available and belongs in the problem-solving tool kit of every mechanical engineer. This paper develops a rationale for this viewpoint both for readers familiar with bond graph methods and for readers to whom they are new.

Towards Automated Evaluation of Vehicle Dynamics in System-Level Designs

2012 ◽  
Author(s):  
Zsolt Lattmann ◽  
Adam Nagel ◽  
Jason Scott ◽  
Kevin Smyth ◽  
Chris vanBuskirk ◽  
...  
Keyword(s):  
Design Space Exploration ◽  
Design Space ◽  
Test Bench ◽  
Simulation Models ◽  
Mobility Model ◽  
System Level ◽  
Bond Graphs ◽  
Automated Evaluation ◽  
Design Alternatives ◽  
Automatic Composition

We describe the use of the Cyber-Physical Modeling Language (CyPhyML) to support trade studies and integration activities in system-level vehicle designs. CyPhyML captures parameterized component behavior using acausal models (i.e. hybrid bond graphs and Modelica) to enable automatic composition and synthesis of simulation models for significant vehicle subsystems. Generated simulations allow us to compare performance between different design alternatives. System behavior and evaluation are specified independently from specifications for design-space alternatives. Test bench models in CyPhyML are given in terms of generic assemblies over the entire design space, so performance can be evaluated for any selected design instance once automated design space exploration is complete. Generated Simulink models are also integrated into a mobility model for interactive 3-D simulation.

Noncommutative scalar field in de Sitter space–time and pair creation process

2021 ◽  
Vol 36 (02) ◽  
pp. 2150011
Author(s):  
Nabil Mehdaoui ◽  
Lamine Khodja ◽  
Salah Haouat
Keyword(s):  
Scalar Field ◽  
Chemical Potential ◽  
De Sitter Space ◽  
Space Time ◽  
Pair Creation ◽  
De Sitter ◽  
Creation Process ◽  
Scalar Particles ◽  
Constant Electromagnetic Field

In this work, we address the process of pair creation of scalar particles in [Formula: see text] de Sitter space–time in presence of a constant electromagnetic field by applying the noncommutativity on the scalar field up to first-order in [Formula: see text]. We calculate the density of particles created in the vacuum by the mean of the Bogoliubov transformations. In contrast to a previous result, we show that noncommutativity contributes to the pair creation process. We find that the noncommutativity plays the same role of chemical potential and gives an important interest for studies at high energies.

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.

Role of Trace Nonmetals in Biochemical Systems

2020 ◽  
pp. 231-242
Author(s):  
Pabitra Krishna Bhattacharya ◽  
Prakash B. Samnani
Keyword(s):  
Biochemical Systems

scholarly journals Modular Dynamic Biomolecular Modelling: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data

2021 ◽  
Author(s):  
Peter J. Gawthrop ◽  
Michael Pan ◽  
Edmund J. Crampin
Keyword(s):  
Dynamic Models ◽  
System Development ◽  
Kinetic Modelling ◽  
Simulation Models ◽  
Bond Graph ◽  
Model Parameters ◽  
Biomolecular Systems ◽  
Genome Wide ◽  
Estimation Of Model Parameters ◽  
Genome Scale

AbstractRenewed interest in dynamic simulation models of biomolecular systems has arisen from advances in genome-wide measurement and applications of such models in biotechnology and synthetic biology. In particular, genome-scale models of cellular metabolism beyond the steady state are required in order to represent transient and dynamic regulatory properties of the system. Development of such whole-cell models requires new modelling approaches. Here we propose the energy-based bond graph methodology, which integrates stoichiometric models with thermo-dynamic principles and kinetic modelling. We demonstrate how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems. The approach is illustrated using a well-established stoichiometric model of E. coli and published experimental data.

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.

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.

scholarly journals Knowledge machines

2018 ◽  
Vol 33 ◽  
Author(s):  
Paul Smart
Keyword(s):  
Intelligent Systems ◽  
Ad Hoc ◽  
Knowledge Engineering ◽  
Theory And Practice ◽  
Philosophical Study ◽  
Engineering Systems ◽  
Web Based ◽  
Knowledge Based ◽  
Data Formats

AbstractThe World Wide Web has had a notable impact on a variety of epistemically relevant activities, many of which lie at the heart of the discipline of knowledge engineering. Systems like Wikipedia, for example, have altered our views regarding the acquisition of knowledge, while citizen science systems such as Galaxy Zoo have arguably transformed our approach to knowledge discovery. Other Web-based systems have highlighted the ways in which the human social environment can be used to support the development of intelligent systems, either by contributing to the provision of epistemic resources or by helping to shape the profile of machine learning. In the present paper, such systems are referred to asknowledge machines. In addition to providing an overview of the knowledge machine concept, the present paper reviews a number of issues that are associated with the scientific and philosophical study of knowledge machines. These include the potential impact of knowledge machines for the theory and practice of knowledge engineering, the role of social participation in the realization of knowledge-based processes, and the role of standardized, semantically enriched data formats in supporting thead hocassembly of special-purpose knowledge systems and knowledge processing pipelines.

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