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| Main Authors: | , , , |
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| Format: | Preprint |
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2023
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2306.01515 |
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| _version_ | 1866913592502124544 |
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| author | Mirza, Waleed Torres-Sánchez, Alejandro Vilanova, Guillermo Arroyo, Marino |
| author_facet | Mirza, Waleed Torres-Sánchez, Alejandro Vilanova, Guillermo Arroyo, Marino |
| contents | The structure and dynamics of important biological quasi-two-dimensional systems, ranging from cytoskeletal gels to tissues, are controlled by nematic order, flow, defects and activity. Continuum hydrodynamic descriptions combined with numerical simulations have been used to understand such complex systems. The development of thermodynamically consistent theories and numerical methods to model active nemato-hydrodynamics is eased by mathematical formalisms enabling systematic derivations and structured-preserving algorithms. Alternative to classical nonequilibrium thermodynamics and bracket formalisms, here we develop a theoretical and computational framework for active nematics based on Onsager's variational formalism to irreversible thermodynamics, according to which the dynamics result from the minimization of a Rayleighian functional capturing the competition between free-energy release, dissipation and activity. We show that two standard incompressible models of active nemato-hydrodynamics can be framed in the variational formalism, and develop a new compressible model for density-dependent active nemato-hydrodynamics relevant to model actomyosin gels. We show that the variational principle enables a direct and transparent derivation not only of the governing equations, but also of the finite element numerical scheme. We exercise this model in two representative examples of active nemato-hydrodynamics relevant to the actin cytoskeleton during wound healing and to the dynamics of confined colonies of elongated cells. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2306_01515 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Variational formulation of active nematics: theory and simulation Mirza, Waleed Torres-Sánchez, Alejandro Vilanova, Guillermo Arroyo, Marino Biological Physics The structure and dynamics of important biological quasi-two-dimensional systems, ranging from cytoskeletal gels to tissues, are controlled by nematic order, flow, defects and activity. Continuum hydrodynamic descriptions combined with numerical simulations have been used to understand such complex systems. The development of thermodynamically consistent theories and numerical methods to model active nemato-hydrodynamics is eased by mathematical formalisms enabling systematic derivations and structured-preserving algorithms. Alternative to classical nonequilibrium thermodynamics and bracket formalisms, here we develop a theoretical and computational framework for active nematics based on Onsager's variational formalism to irreversible thermodynamics, according to which the dynamics result from the minimization of a Rayleighian functional capturing the competition between free-energy release, dissipation and activity. We show that two standard incompressible models of active nemato-hydrodynamics can be framed in the variational formalism, and develop a new compressible model for density-dependent active nemato-hydrodynamics relevant to model actomyosin gels. We show that the variational principle enables a direct and transparent derivation not only of the governing equations, but also of the finite element numerical scheme. We exercise this model in two representative examples of active nemato-hydrodynamics relevant to the actin cytoskeleton during wound healing and to the dynamics of confined colonies of elongated cells. |
| title | Variational formulation of active nematics: theory and simulation |
| topic | Biological Physics |
| url | https://arxiv.org/abs/2306.01515 |