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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/22/12464 |
| _version_ | 1797510033978687488 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T05:26:11Z |
| format | Article |
| id | doaj.art-fabaa2b3f9fe44abbd0b1023c8138d28 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T05:26:11Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-fabaa2b3f9fe44abbd0b1023c8138d282023-11-22T23:42:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-11-0122221246410.3390/ijms222212464Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme ConditionsMiguel Herranz0Daniel Martínez-Fernández1Pablo Miguel Ramos2Katerina Foteinopoulou3Nikos Ch. Karayiannis4Manuel Laso5Institute for Optoelectronic Systems and Microtechnology (ISOM) and Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid (UPM), José Gutierrez Abascal 2, 28006 Madrid, SpainInstitute for Optoelectronic Systems and Microtechnology (ISOM) and Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid (UPM), José Gutierrez Abascal 2, 28006 Madrid, SpainInstitute for Optoelectronic Systems and Microtechnology (ISOM) and Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid (UPM), José Gutierrez Abascal 2, 28006 Madrid, SpainInstitute for Optoelectronic Systems and Microtechnology (ISOM) and Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid (UPM), José Gutierrez Abascal 2, 28006 Madrid, SpainInstitute for Optoelectronic Systems and Microtechnology (ISOM) and Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid (UPM), José Gutierrez Abascal 2, 28006 Madrid, SpainInstitute for Optoelectronic Systems and Microtechnology (ISOM) and Escuela Técnica Superior de Ingenieros Industriales (ETSII), Universidad Politécnica de Madrid (UPM), José Gutierrez Abascal 2, 28006 Madrid, SpainWe 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.https://www.mdpi.com/1422-0067/22/22/12464Monte Carloatomistic simulationmolecular simulationhard sphereextreme conditionsconfinement |
| spellingShingle | 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 International Journal of Molecular Sciences Monte Carlo atomistic simulation molecular simulation hard sphere extreme conditions confinement |
| title | 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_short | 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 |
| topic | Monte Carlo atomistic simulation molecular simulation hard sphere extreme conditions confinement |
| url | https://www.mdpi.com/1422-0067/22/22/12464 |
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