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Cited by 31Biomimetic flight and propulsion mechanismsFluid Dynamics Simulations and InteractionsComputer Graphics and Visualization Techniques

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

Open access
Palyanov, Andrey, Khayrulin, Sergey, Larson, Stephen D.·2018·Philosophical Transactions of the Royal Society B: Biological Sciences
DOI 10.1098/rstb.2017.0376PMC PMC6158221
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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’.

AI snapshot

Written from the paper’s full text.

TL;DR

The authors built a three-dimensional particle-based biomechanical model of the *C. elegans* body and body-wall muscle cells using the Sibernetic engine, with an elastic cuticle, internal hydrostatic pressure, and independently activatable muscles. The model reproduces crawling and swimming in gel-like and liquid environments, along with postures such as omega turns, shortening, and two-frequency undulation.

Key findings

  • The model contains 96 independently activatable body-wall muscles, mapped from the real animal’s four muscle quadrants; the real worm has 95 body-wall muscles, and the extra one was retained for symmetry with minimal expected impact.
  • The chosen maximal muscle contraction force was \(2.7 \times 10^{-9}\) N, which the authors report agrees with estimates of *C. elegans* muscle cell force of \((1.4\text{–}9.6) \times 10^{-9}\) N.
  • For swimming and crawling, the simulated frequency–wavelength relationship had a best-fit slope of 0.59 and intercept of 0.48, compared with a previously reported slope of 0.64 and intercept of 0.42.
  • The liquid environment had a viscosity of about 1.4 mPa s and a calculated Reynolds number of 0.05 or less for swimming; the full-resolution liquid used 500 K particles, while a half-resolution version used 81 K particles.

Methods

  • The body model was assembled in Sibernetic, an open-source particle simulation engine using the Predictive Corrective Incompressible Smoothed Particle Hydrodynamics algorithm, with elastic cuticle, contractile muscle fibres, membranes, and internal liquid pressure.
  • Muscle anatomy was mapped from microscopy and WormAtlas data into four longitudinal bundles (VR, VL, DR, DL), with each bundle divided into 24 muscle-cell areas and each simulated cell containing multiple contractile fibres oriented anterior–posteriorly.
  • Crawling was simulated on a gel-like pad made of small elastic cubes arranged in a grid, while swimming was simulated in a liquid-filled box; muscle activation patterns were injected through a computational interface and compared with experimental measurements and videos.

Limitations

  • The paper states that the particle-based approach is more computationally expensive and slower than lower-dimensional dynamical models, harder to iterate and learn, and may produce explanations that take more analysis to understand.
  • The paper states that many mechanical properties of *C. elegans* remain to be simulated, that action potentials are not explicitly represented, and that all fibres within a simulated muscle cell share the same activity level.
  • The text makes evident that validation relies heavily on visual comparison and selected experimental datasets, and that the model does not yet include an electrical neuron–muscle model or sensory input such as mechanosensation; the authors describe these as future work.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1098/rstb.2017.0376

Cites

41 of 42 references verified0 citation errors · 1 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

7 of 22 cited sources checked · 5 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    C. elegans swimming is subject to the counterintuitive properties of low-Reynolds number environments as a result of its small scale.

    “It has been noted that C. elegans swimming is subject to the counterintuitive properties of 'low-Reynolds number environments' as a result of their small scale [20,21].”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [20] 20. Cohen N, Boyle J. 2010 Swimming at low Reynolds number: a beginners guide to undulatory locomotion. Contemp. Phys. 51, 103-123. (doi:10. 1080/00107510903268381) source
    • cites [21] 21. Sznitman J, Purohit PK, Krajacic P, Lamitina T, Arratia PE. 2010 Material properties of Caenorhabditis elegans swimming at low Reynolds number. Biophys. J. 98, 617-626. (doi:10.1016/j. bpj.2009.11.010) source
  • Findingnone given

    The model has 96 independently activable body-wall muscles.

    “96 independently activable body-wall muscles”
    Quote in the paperSubstantial claim
    • Rests on an assumption: C. elegans has 95 body-wall muscles arranged in four quadrants, each rhomboid-shaped and appearing as staggered pairs.
  • Findingown data

    In measurements of velocity versus force, the simulated muscle tissue shows a characteristic nonlinear relationship that is well known in muscle physiology.

    “In measurements of velocity versus force, we found a characteristic nonlinear relationship that is well known in muscle physiology (e.g.[23]).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [23] 23. Gordon AM, Huxley AF, Julian FJ. 1966 The variation in isometric tension with sarcomere length in vertebrate muscle fibers. J. Physiol. 184, 170-192. source
  • Findingreasoning

    The model can reproduce idiosyncratic behaviour such as two-frequency undulation.

    “The model can also reproduce idiosyncratic behaviour such as two-frequency undulation”
    Quote in the paperSubstantial claim
  • Findingown data

    The model can reproduce postures observed in the real worm, such as omega turns and shortening.

    “the ability to reproduce postures observed in the real worm, such as omega turns and shortening”
    • Also stated in: § (b) Reproducing basic movements · plain
      “Basic behaviours such as assuming an omega-turn posture, rstb.royalsocietypublishing.org Phil.Trans.R. Soc.B 373: 20170376 shortening (figure 4) and reproducing two-frequency undulation (figure 6) were reproduced.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: C. elegans has a well-known omega-turn posture where it contracts muscles on one side only.
    • Rests on an assumption: Strains of C. elegans that have muscle cells with greater than average contraction often have the 'shortening' phenotype.
  • Classified as probably not a substantial claim. 23
  • May combine two claims. 13
  • The quote only partly states this claim. 1

  • Classified as probably not a substantial claim.

    Premisecitation

    Fouad et al. demonstrated that C. elegans is capable of producing different undulatory frequencies in different parts of its body.

    “Fouad et al. [29] demonstrated, through optogenetic inactivation of neck muscles among other methods, that C. elegans is capable of producing different undulatory frequencies in different parts of its body”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [29] 29. Fouad AD, Teng S, Mark JR et al. 2018 Distributed rhythm generators underlie Caenorhabditis elegans forward locomotion. eLife 7, e29913. (doi:10.7554/ eLife.29913) source

  • May combine two claims.

    Findingown data

    In measurements of force versus length, the simulated muscle results are consistent with the model of [24] and include additional noise introduced by the particle-based approach.

    “In measurements of force versus length, we compared our results to the model of [24] to demonstrate both the consistency to this previously reported model, but also the additional noise introduced by our particle-based approach.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [24] 24. Boyle JH, Berri S, Cohen N. 2012 Gait modulation in C. elegans: an integrated neuromechanical model. Front. Comput. Neurosci. 6, 10. (doi:10.3389/fncom. 2012.00010) source

  • May combine two claims.

    Findingown data

    Frequency and wavelength measurements from Sibernetic experiments for swimming and crawling have a best fit line with slope 0.59 and intercept 0.48, comparable to [28] slope 0.64 and intercept 0.42.

    “with the best fit line having a slope of 0.59 and an intercept of 0.48 ( [28] slope: 0.64, intercept 0.42).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [28] 28. Boyle JH, Berri S, Tassieri M, Hope IA, Cohen N. 2011 Gait modulation in C. elegans: it's not a choice, it's a reflex! Front. Behav. Neurosci. 5, 10. (doi:10.3389/fnbeh.2011.00010) source

      The Figure 1A caption in the section on patterns of body bending shows a frequency–wavelength relation with a best linear fit, so the comparison has a basis in the cited paper. Our copy does not give the attributed slope of 0.64 or intercept of 0.42; the citing paper’s 0.59 and 0.48 describe its own fit. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Biophysical measurements of the C. elegans worm body are some of the most comprehensive for any animal in the field of biology.

    “Biophysical measurements of the C. elegans worm body are some of the most comprehensive for any animal in the field of biology.”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [8] 8. Butler VJ, Branicky R, Yemini E, Liewald JF, Gottschalk A, Kerr RA, Chklovskii DB, Schafer WR. 2015 A consistent muscle activation strategy underlies crawling and swimming in Caenorhabditis elegans. J. R. Soc. Interface 12, 20140963. (doi:10. 1098/rsif.2014.0963) source

      The Results section ('Development of a whole-worm tracking and calcium imaging system'; page unavailable) reports measurements of C. elegans body curvature and muscle activity along the worm. It does not compare the comprehensiveness of biophysical measurements of C. elegans with those of other animals, so the claim's ranking is unsupported. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [11] 11. Backholm M, Ryu WS, Dalnoki-Veress K. 2013 Viscoelastic properties of the nematode Caenorhabditis elegans, a self-similar, shear- thinning worm. Proc. Natl Acad. Sci USA 110, 4528 -4533. (doi:10.1073/pnas.1219965110) source
    • cites [13] 13. Johari S, Nock V, Alkaisi MM, Wang W. 2013 On-chip analysis of C. elegans muscular forces and locomotion patterns in microstructured environments. Lab Chip. 13, 1699-1707. (doi: 10.1039/c3lc41403e) source

  • May combine two claims.

    Premisecitation

    At low-Reynolds number, inertial forces are far outweighed by viscous forces, making the progress of a swimming undulatory animal stop immediately when it stops moving.

    “The key difference is that inertial forces at low-Reynolds number are far outweighed by viscous forces, making the progress of a swimming undulatory animal stop immediately when it stops moving.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [20] 20. Cohen N, Boyle J. 2010 Swimming at low Reynolds number: a beginners guide to undulatory locomotion. Contemp. Phys. 51, 103-123. (doi:10. 1080/00107510903268381) source
    • cites [21] 21. Sznitman J, Purohit PK, Krajacic P, Lamitina T, Arratia PE. 2010 Material properties of Caenorhabditis elegans swimming at low Reynolds number. Biophys. J. 98, 617-626. (doi:10.1016/j. bpj.2009.11.010) source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Swimming behaviour in C. elegans has been well studied biomechanically.

    “It has been well studied biomechanically [25].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [25] 25. Fang-Yen C, Wyart M, Xie J, Kawai R, Kodger T et al. 2010 Biomechanical analysis of gait adaptation in the nematode Caenorhabditis elegans. Proc. Natl Acad. Sci USA 107, 20 323-20 328. (doi:10.1073/ pnas.1003016107) source

  • May combine two claims.

    Findingown data

    The model can simulate swimming and crawling within a single scene, as well as crawling forwards followed by a reverse.

    “an ability of simulating swimming and crawling within the single scene was demonstrated, 6 as well as crawling forwards followed by a reverse.7”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    The model is fully open-source and available for inspection and use by the broader scientific community.

    “It is also fully open-source, available for inspection and use by the broader scientific community.”
    Quote in the paperNot a substantial claim

  • The quote only partly states this claim.

    Findingown data

    When equal activation force is sent to all muscles between the tail and the head, the model reduces its length and increases its width in a characteristic shortening manner observed in the real organism.

    “we observed the worm reducing its length and increasing its width in a characteristic manner observed in the real organism.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Strains of C. elegans that have muscle cells with greater than average contraction often have the 'shortening' phenotype.

  • Classified as probably not a substantial claim.

    Findingown data

    The model assumes an omega-turn posture after the dorsal muscles on the right and left sides are caused to contract.

    “Figure 4a demonstrates the final posture assumed by the body model after this contraction took place.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: C. elegans has a well-known omega-turn posture where it contracts muscles on one side only.

  • May combine two claims.

    Findingown data

    In the additional in silico experiment, soon after the simulation starts and the worm starts moving, the worm descends so that its body is positioned halfway between the surface of the liquid and the bottom of the environment and continues swimming at this position.

    “Soon after the simulation starts and the worm starts moving, the worm descends so that its body is positioned halfway between the surface of the liquid and the bottom of the environment and continues swimming at this position”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Findingnone given

    The particle system simulation is more computationally expensive than two-dimensional dynamical systems, and therefore runs more slowly on the same hardware.

    “One is that the particle system simulation is more computationally expensive than two-dimensional dynamical systems, and therefore run more slowly on the same hardware.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Cohen & Ranner offer a novel method for calculating a rigid 2D or 3D cylindrical shell for a worm.

    “Cohen & Ranner [32] offer a novel method for calculating a rigid 2D or 3D cylindrical shell for a worm”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [32] 32. Cohen N, Ranner T. 2017 A new computational method for a model of C. elegans biomechanics: insights into elasticity and locomotion performance. arXiv:1702.04988 [ physics.bio-ph] source

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    The additional nonlinearities in the model add additional biological realism to the model implemented in Sibernetic.

    “we believe that these additional nonlinearities add additional biological realism to the model we have implemented in Sibernetic.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    In the simulated agar environment, the worm creates forward motion by forming a groove, and forces parallel to the worm create forward motion as the cuticle interacts with the formed groove.

    “In the case of simulating agar, the force enables the worm to create forward motion by forming a groove.As the groove forms, forces that are in parallel with the worm create forward motion as the cuticle interacts with the formed groove.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Agar is a gel-like elastic matter (a polymerized state of 2-5% agar solution) that is quite deformable, as evidenced by a worm crawling over its plane surface leaving a groove in it.

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    The additional nonlinearities create additional challenges for a control system to deal with, which in turn creates a higher standard for the output of a neuronal system to meet to be comparable to the real animal.

    “As a result, it creates additional challenges for a control system to deal with, which in turn creates a higher standard for the output of a neuronal system to meet to be comparable to the real animal.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    In Sibernetic, updates to incorporate additional anatomical features are simply a matter of adding or modifying the appropriate relationships between key particles within the volume of our model.

    “In Sibernetic, these updates are simply a matter of adding or modifying the appropriate relationships between key particles within the volume of our model.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    Using an SPH-based approach, increasing the resolution of material (liquid, elastic etc.) is a simpler and more automated process.

    “Using an SPH-based approach, increasing the resolution of material (liquid, elastic etc.) is a simpler and more automated process.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    Here we have the ability to also simulate gentle touch or harsh touch on any point along the 3D surface area of the worm's cuticle.

    “While some recent 2D models have incorporated proprioception [35], this has been captured purely as a matter of the posture of the worm's body, whereas here we have the ability to also simulate gentle touch or harsh touch on any point along the 3D surface area of the worm's cuticle.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationreasoning

    The model allows exploration of how different patterns of muscle activation affect behaviour, which in turn allows users to explore how different patterns of nervous system activity affect behaviour.

    “In turn, we can explore the space of possibilities of how different patterns of muscle activation affect behaviour, which in turn allows users of this model to explore the space of possibilities of how different patterns of nervous system activity affect behaviour.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    From basic components, multiple kinds of tissue can be constructed from different lattice configurations.

    “From basic components, multiple kinds of tissue can be constructed from different lattice configurations.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    The PCISPH approach enables both fluid and soft bodies to be simulated and to interact, in contrast with a rigid-body approach.

    “Additionally, in contrast with a rigid-body approach, it enables both fluid and soft bodies to be simulated and to interact.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    For the first time, this enables an approach to generate new hypotheses with greater biological specificity about the internal state of the C. elegans neurons and body-wall muscles relative to its body posture and the forces acting on it.

    “For the first time, this enables an approach to generate new hypotheses with greater biological specificity about the internal state of the C. elegans neurons and body-wall muscles relative to its body posture and the forces acting on it.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    Real muscles in C. elegans change their shape when they contract, which in turn affects the shape of the body they are inside.

    “For example, real muscles in C. elegans will change their shape when they contract [19], which in turn affects the shape of the body they are inside (e.g.figure 4b).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [19] 19. Gao S, Zhen M. 2011 Action potentials drive body wall muscle contractions in Caenorhabditis elegans. Proc. Natl Acad. Sci USA 108, 2557 -2562. (doi:10. 1073/pnas.1012346108) source

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).

    Interpretationnone given

    A much more accurate mapping of microscopy data surrounding the anatomy of the muscle cells can be incorporated.

    “A much more accurate mapping of microscopy data surrounding the anatomy of the muscle cells can be incorporated.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing). May combine two claims.

    Interpretationnone given

    The higher complexity means that it takes more time to iterate the model and it is more complicated to learn how it works.

    “Additionally, the higher complexity means that it takes more time to iterate the model and it is more complicated to learn how it works.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    This provides a foundation to seek dynamical principles that hold within the complex biophysical interactions between the activity of the cells of the nervous system, muscular system and outside environment of a living organism.

    “This provides a foundation to seek dynamical principles that hold within the complex biophysical interactions between the activity of the cells of the nervous system, muscular system and outside environment of a living organism.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    There is a significant literature on the biophysical properties of the body of C. elegans, estimating parameters such as stiffness based on muscle tension versus hydrostatic pressure on the cuticle or the Young's modulus of the worm's shell.

    “There is a significant literature on the biophysical properties of the body of C. elegans, estimating parameters such as stiffness based on muscle tension versus hydrostatic pressure on the cuticle [33] or the Young's modulus of the worm's shell [11], and many others that demonstrate results from experiments with the physical 3D body of C. elegans.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [33] 33. Petzold BC, Park SJ, Ponce P, Roozeboom C et al. 2011 Caenorhabditis elegans body mechanics are regulated by body wall muscle tone. Biophys. J. 100, 1977-1985. (doi:10.1016/j.bpj. 2011.02.035) source
    • cites [11] 11. Backholm M, Ryu WS, Dalnoki-Veress K. 2013 Viscoelastic properties of the nematode Caenorhabditis elegans, a self-similar, shear- thinning worm. Proc. Natl Acad. Sci USA 110, 4528 -4533. (doi:10.1073/pnas.1219965110) source

  • May combine two claims.

    Interpretationreasoning

    Its musculature is therefore capable of producing motion in all three directions, especially its neck muscles.

    “Its musculature is therefore capable of producing motion in all three directions, especially its neck muscles.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: In nature, C. elegans lives and behaves not in a two-dimensional flat land but burrows through soil in three dimensions.

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    Our approach provides the ability to use corresponding points of the simulated C. elegans body for providing input data for the sensory system, especially mechanosensory.

    “Our approach provides the ability to use corresponding points of the simulated C. elegans body for providing input data for the sensory system, especially mechanosensory.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    A three-dimensional body enables three-dimensional range of motion.

    “A three-dimensional body enables three-dimensional range of motion.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationreasoning

    Because the particles draw a direct analogy to tissue that has mass and takes up 3D space, we can continue incorporating additional anatomical features of C. elegans within the same simulation framework.

    “Because the particles draw a direct analogy to tissue that has mass and takes up 3D space, we can continue incorporating additional anatomical features of C. elegans within the same simulation framework.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    These observations can only be fully reconciled with each other and integrated together via a modelling system in which the biomechanical experiments conducted on C. elegans bodies can be conducted on the model and compared.

    “These observations can only be fully reconciled with each other and integrated together via a modelling system in which the biomechanical experiments conducted on C. elegans bodies can be conducted on the model and compared.”
    Quote in the paperNot a substantial claim
33 of 33

  • The paper relies on this without support.

    C. elegans has 95 body-wall muscles arranged in four quadrants, each rhomboid-shaped and appearing as staggered pairs.

    “In C. elegans, 95 body-wall muscles are arranged in four quadrants as one observes the worm's body in cross section.Each muscle is rhomboid-shaped, and appears as staggered pairs.”

  • The paper relies on this without support.

    C. elegans has a well-known omega-turn posture where it contracts muscles on one side only.

    “Caenorhabditis elegans has a well-known omega-turn posture where it contracts muscles on one side only.”

  • The paper relies on this without support.

    Strains of C. elegans that have muscle cells with greater than average contraction often have the 'shortening' phenotype.

    “Strains of C. elegans that have muscle cells with greater than average contraction often have the 'shortening' phenotype.”

  • The paper relies on this without support.

    C. elegans is capable of swimming through water and other low viscosity environments, using a significantly different gait than it uses during crawling.

    “Caenorhabditis elegans is capable of swimming through water and other low viscosity environments, using a significantly different gait than it uses during crawling.”

  • The paper relies on this without support.

    Agar is a gel-like elastic matter (a polymerized state of 2-5% agar solution) that is quite deformable, as evidenced by a worm crawling over its plane surface leaving a groove in it.

    “'Agar' is a gel-like elastic matter (a polymerized state of 2 -5% agar solution), which is quite deformable as evidenced by the way a worm crawling over its plane surface leaves a groove in it.”

  • The paper relies on this without support.

    The natural habitat of the worm is soil, and in a laboratory it usually lives in agar plates.

    “The natural habitat of the worm is soil, and in a laboratory it usually lives in agar plates.”

  • The paper relies on this without support.

    In nature, C. elegans lives and behaves not in a two-dimensional flat land but burrows through soil in three dimensions.

    “In nature, C. elegans lives and behaves not in a two-dimensional flat land but burrows through soil in three dimensions.”

  • The paper relies on this without support.

    As the worm swims, the surface of the liquid it is swimming in completely encases it.

    “As the worm swims, the surface of the liquid it is swimming in completely encases it.”

  • The paper relies on this without support.

    As the worm moves through liquid, differential pressure on one side of the worm increases relative to the other side.

    “As it moves through that liquid, differential pressure on one side of the worm increases relative to the other side.”
9 of 9

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Authors
Palyanov, A., Khayrulin, S., & Larson, S. D.
Affiliations
  • Novosibirsk State University (RU)
  • OpenWorm Foundation, ℅ Software Freedom Law Center, 1995 Broadway, 17th Fl., New York, NY 10023, USA
Corresponding author
Palyanov, Andrey
ORCID
Venue
Philosophical Transactions of the Royal Society B: Biological Sciences
Publisher
The Royal Society
Published
2018-09-10
Volume
373
Issue
1758
Pages
20170376
ISSN
  • 0962-8436 (ISSN-L)
  • 1471-2970
DOI
10.1098/rstb.2017.0376
PMC
PMC6158221
OpenAlex
W2891826237
Cited by
31
References
39
Citations by year
2025: 3 · 2024: 4 · 2023: 6 · 2022: 3 · 2021: 4 · 2020: 1 · 2019: 3 · 2018: 7
FWCI
3.05
Type
journal article
Language
en
Open access
Licence
royalsociety.org/journals/ethics-policies/data-sharing-mining/ (tdm)
Locations
  • Philosophical Transactions of the Royal Society B Biological Sciences (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Russian Ministry of Science and Education under 5-100 Excellence Programme
  • Russian Foundation for Basic Research grant (18-07-00903)
Topics
  • Physical Sciences › Engineering › Aerospace Engineering › Biomimetic flight and propulsion mechanisms
  • Physical Sciences › Engineering › Computational Mechanics › Fluid Dynamics Simulations and Interactions
  • Physical Sciences › Computer Science › Computer Graphics and Computer-Aided Design › Computer Graphics and Visualization Techniques
Keywords
Caenorhabditis elegans, three-dimensional biomechanical model, smoothed particle hydrodynamics, body wall muscle, hydrostatic pressure, crawling locomotion, swimming locomotion, viscosity, muscle activation patterns, behavioral simulation
MeSH terms
Animals, Biomechanical Phenomena, Hydrostatic Pressure, Locomotion, Models, Biological, Caenorhabditis elegans, Computational Biology, Hydrodynamics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-10.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-10.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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