Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions

We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include...

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Autores principales:	Miguel Herranz, Daniel Martínez-Fernández, Pablo Miguel Ramos, Katerina Foteinopoulou, Nikos Ch. Karayiannis, Manuel Laso
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	Monte Carlo atomistic simulation molecular simulation hard sphere extreme conditions confinement Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/fabaa2b3f9fe44abbd0b1023c8138d28
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spelling	oai:doaj.org-article:fabaa2b3f9fe44abbd0b1023c8138d282021-11-25T17:56:54ZSimu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions10.3390/ijms2222124641422-00671661-6596https://doaj.org/article/fabaa2b3f9fe44abbd0b1023c8138d282021-11-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/22/12464https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions.Miguel HerranzDaniel Martínez-FernándezPablo Miguel RamosKaterina FoteinopoulouNikos Ch. KarayiannisManuel LasoMDPI AGarticleMonte Carloatomistic simulationmolecular simulationhard sphereextreme conditionsconfinementBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 12464, p 12464 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Monte Carlo atomistic simulation molecular simulation hard sphere extreme conditions confinement Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	Monte Carlo atomistic simulation molecular simulation hard sphere extreme conditions confinement Biology (General) QH301-705.5 Chemistry QD1-999 Miguel Herranz Daniel Martínez-Fernández Pablo Miguel Ramos Katerina Foteinopoulou Nikos Ch. Karayiannis Manuel Laso Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
description	We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions.
format	article
author	Miguel Herranz Daniel Martínez-Fernández Pablo Miguel Ramos Katerina Foteinopoulou Nikos Ch. Karayiannis Manuel Laso
author_facet	Miguel Herranz Daniel Martínez-Fernández Pablo Miguel Ramos Katerina Foteinopoulou Nikos Ch. Karayiannis Manuel Laso
author_sort	Miguel Herranz
title	Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
title_short	Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
title_full	Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
title_fullStr	Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
title_full_unstemmed	Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
title_sort	simu-d: a simulator-descriptor suite for polymer-based systems under extreme conditions
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/fabaa2b3f9fe44abbd0b1023c8138d28
work_keys_str_mv	AT miguelherranz simudasimulatordescriptorsuiteforpolymerbasedsystemsunderextremeconditions AT danielmartinezfernandez simudasimulatordescriptorsuiteforpolymerbasedsystemsunderextremeconditions AT pablomiguelramos simudasimulatordescriptorsuiteforpolymerbasedsystemsunderextremeconditions AT katerinafoteinopoulou simudasimulatordescriptorsuiteforpolymerbasedsystemsunderextremeconditions AT nikoschkarayiannis simudasimulatordescriptorsuiteforpolymerbasedsystemsunderextremeconditions AT manuellaso simudasimulatordescriptorsuiteforpolymerbasedsystemsunderextremeconditions
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Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions

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