Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework.
Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool i...
| Published in: | BioMed Research International Vol. 2015; pp. 1 - 13 |
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| Main Authors: | , , , , , |
| Format: | equations & formulas research tables/charts Journal Article |
| Published: |
Wiley-Blackwell
3/22/2015
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| Online Access: | View this record in EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=109273745&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 109273745 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 3/22/2015 vid: 2015 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 109273745 109273745 109273745 10.1155/2015/769471 109273745 ppf: 1 ppct: 12 formats: fmt: @attributes: type: P tig: atl: Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework. aug: au: Pérez-Rodríguez, Gael Pérez-Pérez, Martín Glez-Peña, Daniel Fdez-Riverola, Florentino Azevedo, Nuno F. Lourenço, Anália affil: Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Campus Universitario As Lagoas s/n, 32004 Ourense, Spain sug: subj: Cell Physiology Models, Biological Biochemical Instruments Evaluation Intracellular Signaling Peptides and Proteins Conceptual Framework Behavior Kinetics Biochemistry Descriptive Statistics Data Analysis Software Odds Ratio Confidence Intervals Funding Source ab: Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly. pubtype: Academic Journal doctype: equations & formulas research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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