Related papers: Modular Bond-graph Modelling and Analysis of Biomo…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output.…
Hybrid Bond Graph (HBG) is a Bond Graph-based modelling approach which provides an effective tool not only for dynamic modeling but also for fault detection and isolation (FDI) of switching systems. Bond graph (BG) has been proven useful…
Complex networks play a fundamental role in understanding phenomena from the collective behavior of spins, neural networks, and power grids to the spread of diseases. Topological phenomena in such networks have recently been exploited to…
Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…
The growing complexity of the power grid, driven by increasing share of distributed energy resources and by massive deployment of intelligent internet-connected devices, requires new modelling tools for planning and operation. Physics-based…
In the 20th century, individual technology products like the generator, telephone, and automobile were connected to form many of the large-scale, complex, infrastructure networks we know today: the power grid, the communication…
Models of complex systems often consist of multiple interconnected subsystem/component models that are developed by multi-disciplinary teams of engineers or scientists. To ensure that such interconnected models can be applied for the…
Many complex mechatronic systems consist of multiple interconnected dynamical subsystems, which are designed, developed, analyzed, and manufactured by multiple independent teams. To support such a design approach, a modular model framework…
This paper applies the multibond graph approach for rigid multibody systems to model the dynamics of general spatial mechanisms. The commonly used quick return mechanism which comprises of revolute as well as prismatic joints has been…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
Modularity is a central principle throughout the design process for cyber-physical systems. Modularity reduces complexity and increases reuse of behavior. In this paper we pose and answer the following question: how can we identify…