Three-dimensional simulation of the Caenorhabditis elegans body and muscle cells in liquid and gel environments for behavioural analysis

To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system–based simulation engine known...

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Published inPhilosophical transactions of the Royal Society of London. Series B. Biological sciences Vol. 373; no. 1758; p. 20170376
Main Authors Palyanov, Andrey, Khayrulin, Sergey, Larson, Stephen D.
Format Journal Article
LanguageEnglish
Published England The Royal Society 10.09.2018
Subjects
Animals
Biomechanical Phenomena
Caenorhabditis elegans - physiology
Computational Biology
Crawling
Hydrodynamics
Hydrostatic Pressure
Locomotion - physiology
Models, Biological
Openworm
Sibernetic
Simulation
Swimming
Caenorhabditis elegans
Sibernetic
swimming
OpenWorm
crawling
simulation
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Abstract To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system–based simulation engine known as Sibernetic, which implements the smoothed particle–hydrodynamics algorithm. The model includes an elastic body-wall cuticle subject to hydrostatic pressure. This cuticle is then driven by body-wall muscle cells that contract and relax, whose positions and shape are mapped from C. elegans anatomy, and determined from light microscopy and electron micrograph data. We show that by using different muscle activation patterns, this model is capable of producing C. elegans-like behaviours, including crawling and swimming locomotion in environments with different viscosities, while fitting multiple additional known biomechanical properties of the animal.  This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
AbstractList To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system-based simulation engine known as Sibernetic, which implements the smoothed particle-hydrodynamics algorithm. The model includes an elastic body-wall cuticle subject to hydrostatic pressure. This cuticle is then driven by body-wall muscle cells that contract and relax, whose positions and shape are mapped from C. elegans anatomy, and determined from light microscopy and electron micrograph data. We show that by using different muscle activation patterns, this model is capable of producing C. elegans-like behaviours, including crawling and swimming locomotion in environments with different viscosities, while fitting multiple additional known biomechanical properties of the animal. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system-based simulation engine known as Sibernetic, which implements the smoothed particle-hydrodynamics algorithm. The model includes an elastic body-wall cuticle subject to hydrostatic pressure. This cuticle is then driven by body-wall muscle cells that contract and relax, whose positions and shape are mapped from C. elegans anatomy, and determined from light microscopy and electron micrograph data. We show that by using different muscle activation patterns, this model is capable of producing C. elegans-like behaviours, including crawling and swimming locomotion in environments with different viscosities, while fitting multiple additional known biomechanical properties of the animal. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.
To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the body based on real anatomical structure. The body model is created with a particle system-based simulation engine known as Sibernetic, which implements the smoothed particle-hydrodynamics algorithm. The model includes an elastic body-wall cuticle subject to hydrostatic pressure. This cuticle is then driven by body-wall muscle cells that contract and relax, whose positions and shape are mapped from anatomy, and determined from light microscopy and electron micrograph data. We show that by using different muscle activation patterns, this model is capable of producing -like behaviours, including crawling and swimming locomotion in environments with different viscosities, while fitting multiple additional known biomechanical properties of the animal. This article is part of a discussion meeting issue 'Connectome to behaviour: modelling at cellular resolution'.
To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system–based simulation engine known as Sibernetic, which implements the smoothed particle–hydrodynamics algorithm. The model includes an elastic body-wall cuticle subject to hydrostatic pressure. This cuticle is then driven by body-wall muscle cells that contract and relax, whose positions and shape are mapped from C. elegans anatomy, and determined from light microscopy and electron micrograph data. We show that by using different muscle activation patterns, this model is capable of producing C. elegans-like behaviours, including crawling and swimming locomotion in environments with different viscosities, while fitting multiple additional known biomechanical properties of the animal.  This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the Caenorhabditis elegans body based on real anatomical structure. The body model is created with a particle system–based simulation engine known as Sibernetic, which implements the smoothed particle–hydrodynamics algorithm. The model includes an elastic body-wall cuticle subject to hydrostatic pressure. This cuticle is then driven by body-wall muscle cells that contract and relax, whose positions and shape are mapped from C. elegans anatomy, and determined from light microscopy and electron micrograph data. We show that by using different muscle activation patterns, this model is capable of producing C. elegans -like behaviours, including crawling and swimming locomotion in environments with different viscosities, while fitting multiple additional known biomechanical properties of the animal.  This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
Author Larson, Stephen D.
Khayrulin, Sergey
Palyanov, Andrey
AuthorAffiliation 1 Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems , Acad. Lavrentiev ave. 6, 630090 Novosibirsk , Russia
2 Laboratory of Structural Bioinformatics and Molecular Modeling, Novosibirsk State University , Pirogova str. 2, 630090 Novosibirsk , Russia
3 OpenWorm Foundation, ℅ Software Freedom Law Center , 1995 Broadway, 17th Fl., New York, NY 10023 , USA
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Issue 1758
Keywords Caenorhabditis elegans
Sibernetic
swimming
OpenWorm
crawling
simulation
Language English
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Notes Discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’ organized and edited by Stephen D. Larson, Padraig Gleeson and André E.X. Brown
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Snippet To better understand how a nervous system controls the movements of an organism, we have created a three-dimensional computational biomechanical model of the...
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SubjectTerms Animals
Biomechanical Phenomena
Caenorhabditis elegans - physiology
Computational Biology
Crawling
Hydrodynamics
Hydrostatic Pressure
Locomotion - physiology
Models, Biological
Openworm
Sibernetic
Simulation
Swimming
Title Three-dimensional simulation of the Caenorhabditis elegans body and muscle cells in liquid and gel environments for behavioural analysis
URI https://royalsocietypublishing.org/doi/full/10.1098/rstb.2017.0376
https://www.ncbi.nlm.nih.gov/pubmed/30201840
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