1,720,962 research outputs found
Combining game theory and graph theory to model interactions between cells in the tumor microenvironment
No full textMathematical concepts of graph theory and game theory both influence models of biological systems. We combine these two approaches to understand how game-like interactions influence the cellular topology of a planar tissue. We review the literature on the role of cell to cell interactions in tumourigenesis and survey the mathematical approaches that have been used to simulate such cell-cell interactions. We present how this game-graph approach can be used to simulate epithelial tissue growth and how it can foster our understanding of the role of cell-cell communication in the early stages of cancer development. We present computational models that we use to test how cooperating and non-cooperating cells build planar tissues and compare the simulated tissue topologies with literature data. We further discuss how such system could be used to model microenviromental communications between cancer cells and the surrounding tissue
Membrane Systems with Peripheral Proteins: Transport and Evolution
Full text linkTransport of substances and communication between compartments are fundamental biological processes, often mediated by the presence of opportune and complementary proteins attached to the surfaces of membranes. Within compartments, substances are acted upon by local biochemical rules. Inspired by this behaviour we present a model based on membrane systems, with objects attached to the sides of the membranes and floating objects that can move between the regions of the system. Moreover, in each region there are evolution rules that rewrite the transported objects, mimicking chemical reactions. We first analyse the system, showing that interesting qualitative properties can be decided (like reachability of configurations) and then present a simulator based on a stochastic version of the introduced model and show how it can be used to simulate relevant quantitative biological processes. This is a preliminary version of a paper that was published in Proceedings of MeCBIC06, Electronic Notes in Theoretical Computer Science, 171:2, 37-53, 2007. The original version can be found at http://www.elsevier.com/wps/find/journaldescription.cws_home/681021/description#descriptio
Decision problems in membrane systems with peripheral proteins, transport and evolution
Full text linkTransport of substances and communication between compartments are fundamental biological processes, often mediated by the presence of complementary proteins attached to the surfaces of membranes. Within compartments, substances are acted upon by local biochemical rules. Inspired by this behaviour we present a model based on Membrane Systems, with objects attached to the sides of the membranes and floating objects that can be moved between the regions of the system. Moreover, in each region there are evolution rules that rewrite the transported objects, mimicking chemical reactions.We investigate qualitative properties, like configuration reachability, in relation to the use of cooperative or non-cooperative evolution and transport rules and in the contexts of free- and maximal-parallel evolution
Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins
Full text linkMembrane systems were introduced as models of computation inspired by the structure and functioning of biological cells. Recently, membrane systems have also been shown to be suitable to model cellular processes. We introduce a new model called Membrane Systems with Peripheral and Integral Proteins. The model has compartments enclosed by membranes, floating objects, objects associated to the internal and external surfaces of the membranes and also objects integral to the membranes. The floating objects can be processed within the compartments and can interact with the objects associated to the membranes. The model can be used to represent cellular processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we model a circadian clock and the G-protein cycle in yeast saccharomyces cerevisiae and present a quantitative analysis using an implemented simulator. This is a preliminary version of a paper that was published in Proceedings of the International Conference on Computational Methods in Systems Biology, CMSB06, Lecture Notes in Bioinformatics, 4210:108-126, 2006. The original publication is available at www.springerlink.co
A Logical Characterization of Robustness, Mutants and Species in Colonies of Agents
Full text linkWe study a modeling framework and computational paradigm called Colonies of Syn- chronizing Agents (CSAs), which abstracts intracellular and intercellular mechanisms of biological tissues. The model is based on a multiset of agents (cells) in a com- mon environment. Each agent has a local contents, stored in the form of a multiset of atomic objects, updated by multiset rewriting rules which may act on individual agents (intracellular action) or synchronize the contents of pairs of agents (intercellu-lar action). In this paper we investigate dynamic properties of CSAs, by means of temporal logic, and we give a logical characterization of some notions inspired by evolutionary biology such as robustness, mutants and species. We reveal the relation that exists between the concept of robustness for CSAs and the bisimulation relation on colonies. We also present some decidability results for particular cases of robustness. Preprint of an article submitted for consideration in International Journal of Foundations of Computer Science ©2008 copyright World Scientific Publishing Company [http://www.worldscinet.com/ijfcs/ijfcs.shtml
A multiset-based model of synchronizing agents: Computability and robustness
Full text linkWe introduce a modelling framework and computational paradigm called Colonies of Synchronizing Agents (CSAs) inspired by the intracellular and intercellular mechanisms in biological tissues. The model is based on a multiset of agents in a common environment. Each agent has a local state stored in the form of a multiset of atomic objects, which is updated by global multiset rewriting rules either independently or synchronously with another agent. We first define the model then study its computational power, considering trade-offs between internal rewriting (intracellular mechanisms) and synchronization between agents (intercellular mechanisms). We also investigate dynamic properties of CSAs, including behavioural robustness (ability to generate a core behaviour despite agent loss or rule failure) and safety of synchronization (ability of an agent to synchronize with some other agent whenever needed)
Cellular interaction network dynamics during homeostasis and cancer formation
No full textThe construction of a network of cell-to-cell contacts networks makes it possible to objectively characterize the patterns and the spatial organisation of tissues. Such networks are highly dynamic depending on the
changes of the tissue architecture caused by cell division, death and migration. Local competitive and cooperative cell to cell interactions influence the choice cells make. We present a dynamical network model
that can be used to explore the dynamics of a two dimensional tissue architecture in presence of cell to cell interactions. Various forms of experimentally observed types of interactions can be abstracted using game theory. We discuss a model of cooperative and non-cooperative cell-cell communication that can capture the interplay between cellular competition and tissue dynamics. We conclude with an outlook on the possible uses of this approach in modelling tumorigenesis and tissue homeostasi
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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