Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy

In this work, we will make an energetic and structural characterization of three-dimensional linear chains generated from a simple self-avoiding random walk process in a finite time, without boundary conditions, without the need to explore all possible configurations. From the analysis of the energy...

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Autores:
Avellaneda B, David R.
R. González, Ramón E.
Ariza-Colpas, Paola
Morales-Ortega, Roberto Cesar
Collazos-Morales, Carlos Andrés
Tipo de recurso:
Article of journal
Fecha de publicación:
2021
Institución:
Corporación Universidad de la Costa
Repositorio:
REDICUC - Repositorio CUC
Idioma:
eng
OAI Identifier:
oai:repositorio.cuc.edu.co:11323/8818
Acceso en línea:
https://hdl.handle.net/11323/8818
https://doi.org/10.1007/978-3-030-86653-2_13
https://repositorio.cuc.edu.co/
Palabra clave:
Self-avoiding random walk
Linear chains
Interaction energy
Bending energy
Moment of inertia
Radius of gyration
Asphericity
Prolate structure
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openAccess
License
Attribution-NonCommercial-NoDerivatives 4.0 International
id RCUC2_e4077d95176927d41de8197af2013e00
oai_identifier_str oai:repositorio.cuc.edu.co:11323/8818
network_acronym_str RCUC2
network_name_str REDICUC - Repositorio CUC
repository_id_str
dc.title.spa.fl_str_mv Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
title Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
spellingShingle Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
Self-avoiding random walk
Linear chains
Interaction energy
Bending energy
Moment of inertia
Radius of gyration
Asphericity
Prolate structure
title_short Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
title_full Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
title_fullStr Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
title_full_unstemmed Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
title_sort Structural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and Anisotropy
dc.creator.fl_str_mv Avellaneda B, David R.
R. González, Ramón E.
Ariza-Colpas, Paola
Morales-Ortega, Roberto Cesar
Collazos-Morales, Carlos Andrés
dc.contributor.author.spa.fl_str_mv Avellaneda B, David R.
R. González, Ramón E.
Ariza-Colpas, Paola
Morales-Ortega, Roberto Cesar
Collazos-Morales, Carlos Andrés
dc.subject.spa.fl_str_mv Self-avoiding random walk
Linear chains
Interaction energy
Bending energy
Moment of inertia
Radius of gyration
Asphericity
Prolate structure
topic Self-avoiding random walk
Linear chains
Interaction energy
Bending energy
Moment of inertia
Radius of gyration
Asphericity
Prolate structure
description In this work, we will make an energetic and structural characterization of three-dimensional linear chains generated from a simple self-avoiding random walk process in a finite time, without boundary conditions, without the need to explore all possible configurations. From the analysis of the energy balance between the terms of interaction and bending (or correlation), it is shown that the chains, during their growth process, initially tend to form clusters, leading to an increase in their interaction and bending energies. Larger chains tend to “escape” from the cluster when they reach a number of “steps” N>∼1040 , resulting in a decrease in their interaction energy, however, maintaining the same behavior as flexion energy or correlation. This behavior of the bending term in the energy allows distinguishing chains with the same interaction energy that present different structures. As a complement to the energy analysis, we carry out a study based on the moments of inertia of the chains and their radius of gyration. The results show that the formation of clusters separated by “tails” leads to a final “prolate” structure for this type of chain, the same structure evident in real polymeric linear chains in a good solvent.
publishDate 2021
dc.date.accessioned.none.fl_str_mv 2021-10-29T13:54:18Z
dc.date.available.none.fl_str_mv 2021-10-29T13:54:18Z
dc.date.issued.none.fl_str_mv 2021
dc.type.spa.fl_str_mv Artículo de revista
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dc.identifier.uri.spa.fl_str_mv https://hdl.handle.net/11323/8818
dc.identifier.doi.spa.fl_str_mv https://doi.org/10.1007/978-3-030-86653-2_13
dc.identifier.instname.spa.fl_str_mv Corporación Universidad de la Costa
dc.identifier.reponame.spa.fl_str_mv REDICUC - Repositorio CUC
dc.identifier.repourl.spa.fl_str_mv https://repositorio.cuc.edu.co/
url https://hdl.handle.net/11323/8818
https://doi.org/10.1007/978-3-030-86653-2_13
https://repositorio.cuc.edu.co/
identifier_str_mv Corporación Universidad de la Costa
REDICUC - Repositorio CUC
dc.language.iso.none.fl_str_mv eng
language eng
dc.relation.references.spa.fl_str_mv Flory, P.J.: Principles of Polymer Chemistry. Cornell University Press, Ithaca (1953)
Flory, P.J.: The configuration of real polymer chains. J. Chem. Phys. 17(3), 303–310 (1949)
Madras, N., Sokal, A.: The pivot algorithm: a highly efficient Monte Carlo method for self-avoiding walk. J. Stat. Phys. 50(1–2), 109–186 (1988)
Slade, G.: Self-avoiding walks. Math. Intell. 16(1), 29–35 (1994). https://doi.org/10.1007/BF03026612
Figueirêdo, P.H., Moret, M.A., Coutinho, S., Nogueira, J.: The role of stochasticity on compactness of the native state of protein peptide backbone. J. Chem. Phys. 133, 08512 (2010)
Boglia, R.A., Tiana, G., Provasi, D.: Simple models of the protein folding and of non-conventional drug design. J. Phys. Condens. Matter 16(6), 111 (2004)
Tang, C.: Simple models of the protein folding problem. Phys. A Stat. Mech. Appl. 288(1), 31–48 (2000)
Grosberg, A.Y., Khokhlov, A.R.: Statistical Physics of Macromolecules. AIP Press, New York (1994)
Rubinstein, M., Colby, R.H.: Polymer Physics. Oxford University Press, New York (2003)
Teraoka, I.: Polymer Solutions: An Introduction to Physical Properties. Wiley Inter-science, New York (2002)
Hsu, H.P., Paul, W., Binder, K.: Standard definitions of persistence length do not describe the local “intrinsic” stiffness of real polymers. Macromolecules 43(6), 3094–3102 (2010)
Landau, L.D., Lifshitz, E.M.: Theory of Elasticity. Elsevier Sciences, New York (1986)
Schöbl, S., Sturm, S., Janke, W., Kroy, K.: Persistence-length renormalization of polymers in a crowded environment of hard disks. Phys. Rev. Lett. 113(23), 238302 (2014)
Amit, D.J., Parisi, G., Paliti, L.: Asymptotic behavior of the “true” self-avoiding walk. Phys. Rev. B 27(3), 1635–1645 (1983)
Solc, K.: Shape of random-flight chain. J. Chem. Phys. 55(1), 335–344 (1971)
Rudnick, J., Gaspari, G.: The asphericity of random walks. J. Phys. A: Math. Gen. 30(11), 3867–3882 (1997)
Hadizadeh, S., Linhananta, A., Plotkin, S.S.: Improved measures for the shape of a disordered polymer to test a mean-field theory of collapse. Macromolecules 44(15), 6182–6197 (2011)
Aronovitz, J., Nelson, D.: Universal features of polymer shapes. J. Phys. 47(9), 1445–1456 (1986)
Cannon, J.W., Aronovitz, J.A., Goldbart, P.: Equilibrium distribution of shapes for linear and star macromolecules. J. Phys. I Fr. 1(5), 629–645 (1991)
Alim, K., Frey, E.: Shapes of semi-flexible polymer rings. Phys. Rev. Lett. 99(19), 198102 (2007)
Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., Shakhnovich, E.I.: Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 3(6), 577–587 (1998)
Theiler, J.: Estimating fractal dimension. J. Opt. Soc. Am. A, OSA 7(6), 1055–1073 (1990)
Blavatska, V., Janke, W.: Shape anisotropy of polymers in disordered environment. J. Chem. Phys. 133(18), 184903 (2010)
Rawdon, E.J., et al.: Effect of knotting on the shape of polymers. Macromolecules 41(21), 8281–8287 (2008)
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spelling Avellaneda B, David R.R. González, Ramón E.Ariza-Colpas, PaolaMorales-Ortega, Roberto CesarCollazos-Morales, Carlos Andrés2021-10-29T13:54:18Z2021-10-29T13:54:18Z2021https://hdl.handle.net/11323/8818https://doi.org/10.1007/978-3-030-86653-2_13Corporación Universidad de la CostaREDICUC - Repositorio CUChttps://repositorio.cuc.edu.co/In this work, we will make an energetic and structural characterization of three-dimensional linear chains generated from a simple self-avoiding random walk process in a finite time, without boundary conditions, without the need to explore all possible configurations. From the analysis of the energy balance between the terms of interaction and bending (or correlation), it is shown that the chains, during their growth process, initially tend to form clusters, leading to an increase in their interaction and bending energies. Larger chains tend to “escape” from the cluster when they reach a number of “steps” N>∼1040 , resulting in a decrease in their interaction energy, however, maintaining the same behavior as flexion energy or correlation. This behavior of the bending term in the energy allows distinguishing chains with the same interaction energy that present different structures. As a complement to the energy analysis, we carry out a study based on the moments of inertia of the chains and their radius of gyration. The results show that the formation of clusters separated by “tails” leads to a final “prolate” structure for this type of chain, the same structure evident in real polymeric linear chains in a good solvent.Avellaneda B, David R.R. González, Ramón E.Ariza-Colpas, PaolaMorales-Ortega, Roberto CesarCollazos-Morales, Carlos Andrésapplication/pdfengAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2International Conference on Computational Science and Its Applicationshttps://link.springer.com/chapter/10.1007/978-3-030-86653-2_13Self-avoiding random walkLinear chainsInteraction energyBending energyMoment of inertiaRadius of gyrationAsphericityProlate structureStructural Characterization of Linear Three-Dimensional Random Chains: Energetic Behaviour and AnisotropyArtículo de revistahttp://purl.org/coar/resource_type/c_6501http://purl.org/coar/resource_type/c_2df8fbb1Textinfo:eu-repo/semantics/articlehttp://purl.org/redcol/resource_type/ARTinfo:eu-repo/semantics/acceptedVersionFlory, P.J.: Principles of Polymer Chemistry. Cornell University Press, Ithaca (1953)Flory, P.J.: The configuration of real polymer chains. J. Chem. Phys. 17(3), 303–310 (1949)Madras, N., Sokal, A.: The pivot algorithm: a highly efficient Monte Carlo method for self-avoiding walk. J. Stat. Phys. 50(1–2), 109–186 (1988)Slade, G.: Self-avoiding walks. Math. Intell. 16(1), 29–35 (1994). https://doi.org/10.1007/BF03026612Figueirêdo, P.H., Moret, M.A., Coutinho, S., Nogueira, J.: The role of stochasticity on compactness of the native state of protein peptide backbone. J. Chem. Phys. 133, 08512 (2010)Boglia, R.A., Tiana, G., Provasi, D.: Simple models of the protein folding and of non-conventional drug design. J. Phys. Condens. Matter 16(6), 111 (2004)Tang, C.: Simple models of the protein folding problem. Phys. A Stat. Mech. Appl. 288(1), 31–48 (2000)Grosberg, A.Y., Khokhlov, A.R.: Statistical Physics of Macromolecules. AIP Press, New York (1994)Rubinstein, M., Colby, R.H.: Polymer Physics. Oxford University Press, New York (2003)Teraoka, I.: Polymer Solutions: An Introduction to Physical Properties. Wiley Inter-science, New York (2002)Hsu, H.P., Paul, W., Binder, K.: Standard definitions of persistence length do not describe the local “intrinsic” stiffness of real polymers. Macromolecules 43(6), 3094–3102 (2010)Landau, L.D., Lifshitz, E.M.: Theory of Elasticity. Elsevier Sciences, New York (1986)Schöbl, S., Sturm, S., Janke, W., Kroy, K.: Persistence-length renormalization of polymers in a crowded environment of hard disks. Phys. Rev. Lett. 113(23), 238302 (2014)Amit, D.J., Parisi, G., Paliti, L.: Asymptotic behavior of the “true” self-avoiding walk. Phys. Rev. B 27(3), 1635–1645 (1983)Solc, K.: Shape of random-flight chain. J. Chem. Phys. 55(1), 335–344 (1971)Rudnick, J., Gaspari, G.: The asphericity of random walks. J. Phys. A: Math. Gen. 30(11), 3867–3882 (1997)Hadizadeh, S., Linhananta, A., Plotkin, S.S.: Improved measures for the shape of a disordered polymer to test a mean-field theory of collapse. Macromolecules 44(15), 6182–6197 (2011)Aronovitz, J., Nelson, D.: Universal features of polymer shapes. J. Phys. 47(9), 1445–1456 (1986)Cannon, J.W., Aronovitz, J.A., Goldbart, P.: Equilibrium distribution of shapes for linear and star macromolecules. J. Phys. I Fr. 1(5), 629–645 (1991)Alim, K., Frey, E.: Shapes of semi-flexible polymer rings. Phys. Rev. Lett. 99(19), 198102 (2007)Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., Shakhnovich, E.I.: Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 3(6), 577–587 (1998)Theiler, J.: Estimating fractal dimension. J. Opt. Soc. Am. A, OSA 7(6), 1055–1073 (1990)Blavatska, V., Janke, W.: Shape anisotropy of polymers in disordered environment. J. Chem. Phys. 133(18), 184903 (2010)Rawdon, E.J., et al.: Effect of knotting on the shape of polymers. Macromolecules 41(21), 8281–8287 (2008)PublicationORIGINALStructural Characterization of Linear Three.pdfStructural Characterization of Linear Three.pdfapplication/pdf135081https://repositorio.cuc.edu.co/bitstreams/35670cb2-cfed-46c6-938c-0df780a1e51f/downloadfd435c4ab8ca3bf869f665e21f50cd0fMD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8805https://repositorio.cuc.edu.co/bitstreams/5553a774-712b-4870-aeee-d7a9da3598d6/download4460e5956bc1d1639be9ae6146a50347MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-83196https://repositorio.cuc.edu.co/bitstreams/d753ae3e-f42a-4e36-9065-a2124273e841/downloade30e9215131d99561d40d6b0abbe9badMD53THUMBNAILStructural Characterization of Linear Three.pdf.jpgStructural Characterization of Linear Three.pdf.jpgimage/jpeg45364https://repositorio.cuc.edu.co/bitstreams/b2c46972-3281-4360-8f89-47161a79312c/download84cf038ca269725f748da933ad68795eMD54TEXTStructural Characterization of Linear Three.pdf.txtStructural Characterization 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