Chemical Organization Theory Applied to Virus Dynamics (Theorie chemischer Organisationen angewendet auf Infektionsmodelle)

Matsumaru, Naoki; Centler, Florian; Fenizio, Pietro Speroni di; Dittrich, Peter

doi:10.1524/itit.2006.48.3.154

Cited by 10 publications

(6 citation statements)

References 15 publications

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“…systems in which new species appear and stay over a longer period. So far, COT was applied successfully in various areas like chemical computing ( Matsumaru et al , 2007 ), social systems ( Dittrich and Winter, 2005 ), evolutionary game theory ( Veloz et al , 2014 ), HIV dynamics ( Matsumaru et al , 2006 ) or checking systems biology models for inconsistencies ( Kaleta et al , 2009 ). The theoretical results are based on the continuous dynamics and include the observation that in every fixed point there is a chemical organization ( Dittrich and di Fenizio, 2007 ; Peter and Dittrich, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Effects of small particle numbers on long-term behaviour in discrete biochemical systems

et al. 2014

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Motivation: The functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state.Results: We provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism.Availability and implementation: http://www.biosys.uni-jena.de/Services.html.Contact: bashar.ibrahim@uni-jena.de or dittrich@minet.uni-jena.deSupplementary information: Supplementary data are available at Bioinformatics online.

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Section: Introductionmentioning

confidence: 99%

Effects of small particle numbers on long-term behaviour in discrete biochemical systems

et al. 2014

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“…Most obviously, COT has been used to simulate networks of chemical reactions, with a focus on the emergence of stable systems. The first examples were models of virus dynamics [51] and the chemistry of a planetary atmosphere [52]. The initial inspiration for the development of COT was to model how such chemical networks could develop the degree of autonomy that we associate with simple living systems [53].…”

Section: Concrete Applicationsmentioning

confidence: 99%

Chemical Organization Theory as a General Modeling Framework for Self-Sustaining Systems

Heylighen,

Beigi,

Veloz

2024

Systems

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This paper summarizes and reviews Chemical Organization Theory (COT), a formalism for the analysis of complex, self-organizing systems across multiple disciplines. Its elements are resources and reactions. A reaction maps a set of resources onto another set, thus representing an elementary process that transforms resources into new resources. Reaction networks self-organize into invariant subnetworks, called ‘organizations’, which are attractors of their dynamics. These are characterized by closure (no new resources are added) and self-maintenance (no existing resources are lost). Thus, they provide a simple model of autopoiesis: the organization persistently recreates its own components. The resilience of organizations in the face of perturbations depends on properties such as the size of their basin of attraction and the redundancy of their reaction pathways. Application domains of COT include the origin of life, systems biology, cognition, ecology, Gaia theory, sustainability, consciousness, and social systems.

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“…COT has been advanced in many fronts, including applications in chemical systems of diverse nature [ 27 , 28 ], computer-science-related applications [ 29 , 30 ] and for modeling ecological systems [ 15 , 31 , 32 ]. Theoretically, the relation between organizations and dynamical attractors has been extended to more complicated cases, such as limit cycles and heterocyclic orbits [ 24 , 25 , 26 ], and to cases where the reaction network structure is able to change [ 22 , 33 ].…”

Section: Reaction Network and Chemical Organizationsmentioning

confidence: 99%

Modelling Worldviews as Stable Metabolisms

Veloz

Maldonado

2022

Entropy

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The emergence and evolution of worldviews is a complex phenomenon that requires strong and rigorous scientific attention in our hyperconnected world. On the one hand, cognitive theories have proposed reasonable frameworks but have not reached general modeling frameworks where predictions can be tested. On the other hand, machine-learning-based applications perform extremely well at predicting outcomes of worldviews, but they rely on a set of optimized weights in a neural network that does not comply to a well-founded cognitive framework. In this article, we propose a formal approach used to investigate the establishment of and change in worldviews by recalling that the realm of ideas, where opinions, perspectives and worldviews are shaped, resemble, in many ways, a metabolic system. We propose a general modelization of worldviews based on reaction networks, and a specific starting model based on species representing belief attitudes and species representing belief change triggers. These two kinds of species combine and modify their structures through the reactions. We show that chemical organization theory combined with dynamical simulations can illustrate various interesting features of how worldviews emerge, are maintained and change. In particular, worldviews correspond to chemical organizations, meaning closed and self-producing structures, which are generally maintained by feedback loops occurring within the beliefs and triggers in the organization. We also show how, by inducing the external input of belief change triggers, it is possible to change from one worldview to another, in an irreversible way. We illustrate our approach with a simple example reflecting the formation of an opinion and a belief attitude about a theme, and, next, show a more complex scenario containing opinions and belief attitudes about two possible themes.

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Chemical Organization Theory Applied to Virus Dynamics (Theorie chemischer Organisationen angewendet auf Infektionsmodelle)

Cited by 10 publications

References 15 publications

Effects of small particle numbers on long-term behaviour in discrete biochemical systems

Effects of small particle numbers on long-term behaviour in discrete biochemical systems

Chemical Organization Theory as a General Modeling Framework for Self-Sustaining Systems

Modelling Worldviews as Stable Metabolisms

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