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65
Complex systems models: engineering simulations
- Eleventh International Conference on the Simulation and Synthesis of Living Systems
, 2008
"... As part of research towards the CoSMoS unified infrastructure for modelling and simulating complex systems, we review uses of definitional and descriptive models in natural science and computing, and existing integrated platforms. From these, we identify requirements for engineering models of comple ..."
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Cited by 10 (8 self)
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As part of research towards the CoSMoS unified infrastructure for modelling and simulating complex systems, we review uses of definitional and descriptive models in natural science and computing, and existing integrated platforms. From these, we identify requirements for engineering models of complex systems, and consider how some of the requirements could be met, using state-of-the-art model management and a mobile, process-oriented computing paradigm.
An interdisciplinary perspective on artificial immune systems
- Evolutionary Intelligence
"... Immune Systems (AIS) in a broader context of interdisciplinary research. We review AIS based on an established conceptual framework that encapsulates mathematical and computational modelling of immunology, abstraction and then development of engineered systems. We argue that Artificial Immune System ..."
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Cited by 8 (1 self)
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Immune Systems (AIS) in a broader context of interdisciplinary research. We review AIS based on an established conceptual framework that encapsulates mathematical and computational modelling of immunology, abstraction and then development of engineered systems. We argue that Artificial Immune Systems are much more than engineered systems inspired by the immune system and that there is a great deal for both immunology and engineering to learn from each other through working in an interdisciplinary manner. Keywords artificial immune systems, immunological modelling, mathematical modelling, computational modelling, applications of artificial immune systems, immune inspired computing, immunocomputing, computational immunology 1
The κ-lattice: Decidability boundaries for qualitative analysis in biological languages
, 2009
"... The κ-calculus is a formalism for modelling molecular biology where molecules are terms with internal state and sites, bonds are represented by shared names labelling sites, and reactions are represented by rewriting rules. Depending on the shape of the rewriting rules, a lattice of dialects of κ c ..."
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Cited by 8 (7 self)
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The κ-calculus is a formalism for modelling molecular biology where molecules are terms with internal state and sites, bonds are represented by shared names labelling sites, and reactions are represented by rewriting rules. Depending on the shape of the rewriting rules, a lattice of dialects of κ can be obtained. We analyze the expressive power of some of these dialects by focusing on the thin boundary between decidability and undecidability for problems like reachability and coverability. This analysis may be used, for instance, for excluding the genesis of dangerous substances.
Biochemical reaction rules with constraints
- OF LECTURE NOTES IN COMPUTER SCIENCE
, 2011
"... We propose React(C), an expressive programming language for stochastic modeling and simulation in systems biology that is based on biochemical reactions with constraints. We prove that React(C) can express the stochastic pi-calculus, in contrast to previous rule-based programming languages, and fur ..."
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Cited by 7 (3 self)
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We propose React(C), an expressive programming language for stochastic modeling and simulation in systems biology that is based on biochemical reactions with constraints. We prove that React(C) can express the stochastic pi-calculus, in contrast to previous rule-based programming languages, and further illustrate the high expressiveness of React(C). We present a stochastic simulator for React(C) independently of the choice of the constraint language C. Our simulator decides for a given reaction rule whether it can be applied to the current biochemical solution. We show that this decision problem is NP-complete for arbitrary constraint systems C and that it can be solved in polynomial time for rules of bounded arity. In practice, we propose to solve this problem by constraint programming.
A Process Model of Actin Polymerisation
- FBTC 2008
, 2008
"... Actin is the monomeric subunit of actin filaments which form one of the three major cytoskeletal networks in eukaryotic cells. Actin dynamics, be it the polymerisation of actin monomers into filaments or the reverse process, plays a key role in many cellular activities such as cell motility and phag ..."
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Cited by 7 (3 self)
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Actin is the monomeric subunit of actin filaments which form one of the three major cytoskeletal networks in eukaryotic cells. Actin dynamics, be it the polymerisation of actin monomers into filaments or the reverse process, plays a key role in many cellular activities such as cell motility and phagocytosis. There is a growing number of experimental, theoretical and mathematical studies on the components of actin polymerisation and depolymerisation. However, it remains a challenge to develop compositional models of actin dynamics, e.g., by using differential equations. In this paper, we propose compositional process algebra models of actin polymerisation, and present a geometric representation of these models that allows to generate movies reflecting their dynamics.
GPA — Tool for rapid analysis of very large scale PEPA models
- In Proceedings of the 26th UK Performance Engineering Workshop (UKPEW 2010
, 2010
"... (GPA) that allows fast analysis of large scale models described in the stochastic process algebra PEPA. GPA employs the techniques for approximations of transient moments in PEPA models with ordinary differential equations (ODEs), which allow analysis of systems with state spaces far beyond the limi ..."
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Cited by 5 (2 self)
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(GPA) that allows fast analysis of large scale models described in the stochastic process algebra PEPA. GPA employs the techniques for approximations of transient moments in PEPA models with ordinary differential equations (ODEs), which allow analysis of systems with state spaces far beyond the limits of standard techniques. These moments provide useful information about the evolution of the model over time. Additionally, GPA implements a recently developed extension for moments of accumulated rewards, giving access to measures representing important factors in performance modeling such as energy consumption. GPA is also able to use these moments to calculate bounds on various passage time probabilities as well as completion times of the accumulated rewards. We describe the features of GPA in detail and briefly mention some design issues. We also present a technique that GPA implements for analysing more complex PEPA models with a higher degree of accuracy. I.
Bioscape: A modeling and simulation language for bacteria-materials interactions
- In the proceedings of 3 rd International Workshop on Interactions between Computer Science and Biology (CS2Bio
, 2012
"... Abstract—We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need of individual-based, continuous motion, and continuous sp ..."
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Cited by 4 (2 self)
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Abstract—We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need of individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials- associated bacterial infections. The novel aspects of BioScape include syntactic primitives to declare the scope in space where species can move, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from BioScape to 3π and prove its soundness with respect to the operational semantics. Statement: We define a programming language for the modeling and stochastic simulation of bacteria-materials interactions. Existing modeling languages lack the combination of features needed to successfully capture such scenarios: concurrent, 3D, combining stochastic and non-stochastic semantics, being able to define boundaries, diffusion rates and shapes, and agent-based. We validate our language by defining a translation into a well established predecessor, and show the the soundness of the translation with respect to the operational semantics. I.
Immuno-engineering
"... Abstract In this position paper, we outline a vision for a new type of engineering: immuno-engineering, that can be used for the development of biologically grounded and theoretically understood Artificial Immune Systems (AIS). We argue that, like many bio-inspired paradigms, AIS have drifted somewh ..."
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Cited by 4 (0 self)
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Abstract In this position paper, we outline a vision for a new type of engineering: immuno-engineering, that can be used for the development of biologically grounded and theoretically understood Artificial Immune Systems (AIS). We argue that, like many bio-inspired paradigms, AIS have drifted somewhat away from the source of inspiration. We also argue that through an interdisciplinary approach, it is possible to exploit the underlying biology for computation in a way that, as yet, has not been achieved. Immuno-engineering will not only allow for the potential development of more powerful AIS, but allow for feed back to biology from computation. 1
A Process Model of Rho GTP-binding Proteins
, 2007
"... Rho GTP-binding proteins play a key role as molecular switches in many cellular activities. In response to extracellular stimuli and with the help from regulators (GEF, GAP, Effector, GDI), these proteins serve as switches that interact with their environment in a complex manner. Based on the struct ..."
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Rho GTP-binding proteins play a key role as molecular switches in many cellular activities. In response to extracellular stimuli and with the help from regulators (GEF, GAP, Effector, GDI), these proteins serve as switches that interact with their environment in a complex manner. Based on the structure of a published ordinary differential equations (ODE) model, we first present a generic process model for the Rho GTP-binding proteins, and compare it with the ODE model. We then extend the basic model to include the behaviour of the GDIs and explore the parameter space for the extended model with respect to biological data from the literature. We discuss the challenges this extension brings and the directions of further research.
Rule-based modeling of transcriptional attenuation at the tryptophan operon
- International Winter Simulation Conference
, 2009
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