{"id":{"repo_id":"cagliari","oai_identifier":"oai:iris.unica.it:11584/266556"},"canonical_url":"https://search.dev.ndltd.org/etd/cagliari/oai:iris.unica.it:11584/266556","repository":{"repo_id":"cagliari","name":"Università di Cagliari","base_url":"https://iris.unica.it/oai/request"},"display":{"title":"Modelling in chimica computazionale: ottimizzazione di codici MD ed applicazioni allo studio di sistemi ad elevata carica","abstract":"M.DynaMix is a modular general purpose Molecular Dynamics code for simulations of arbitrary mixtures of either rigid or flexible molecules. For its features and capabilities, M.DynaMix is diffused in a large simulation community and it is worth to keep it efficient and updated. With this goal in mind, a major revision of the package has been performed, leading to a version where several enhancements have been added: two efficient grid-based algorithm for long range interactions, SPME and ENUF, are now available; besides, a version of the code runnable on multi graphics boards has been produced. With the new features, the program exhibits a remarkable increase of computational efficiency and an improvement in global performance. The new version of M.DynaMix has been applied for studying some selected high charged particle system: DNA oligomers and ionic liquids. For oligomers, interactions between DNA and counterions has been investigated, searching for sequence dependent features. For ionic liquids, we focused on 1-decyl-3-methil-imidazolium chloride, to find a proper Force Field parameter set for its description. In both cases, the problem of validation of MD simulations has been treated, testing a new technique based upon the determination of quadrupolar decay parameters, for direct comparison between simulation and experiments.","abstract_html":"M.DynaMix is a modular general purpose Molecular Dynamics code for simulations of arbitrary mixtures of either rigid or flexible molecules. For its features and capabilities, M.DynaMix is diffused in a large simulation community and it is worth to keep it efficient and updated. With this goal in mind, a major revision of the package has been performed, leading to a version where several enhancements have been added: two efficient grid-based algorithm for long range interactions, SPME and ENUF, are now available; besides, a version of the code runnable on multi graphics boards has been produced. With the new features, the program exhibits a remarkable increase of computational efficiency and an improvement in global performance. The new version of M.DynaMix has been applied for studying some selected high charged particle system: DNA oligomers and ionic liquids. For oligomers, interactions between DNA and counterions has been investigated, searching for sequence dependent features. For ionic liquids, we focused on 1-decyl-3-methil-imidazolium chloride, to find a proper Force Field parameter set for its description. In both cases, the problem of validation of MD simulations has been treated, testing a new technique based upon the determination of quadrupolar decay parameters, for direct comparison between simulation and experiments.","abstract_has_math":false,"creators":["PORCU, MASSIMILIANO"],"institution":"Università degli Studi di Cagliari","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-03-13","date_published":"2015-03-13","updated_at":"2026-07-24T01:30:12Z","subjects":["DNA","GPU","Ionic liquids","Molecular Dynamic","NMR","Settore CHIM/02 - Chimica Fisica"],"languages":["ita"],"rights":["info:eu-repo/semantics/openAccess","license:Non specificato"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/11584/266556","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["PORCU, MASSIMILIANO"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2015-03-13"]},{"key":"dc:publisher","label":"Institution","values":["Università degli Studi di Cagliari"]},{"key":"dc:relation","label":"Dc Relation","values":["numberofpages:152"]},{"key":"dc:type","label":"Dc Type","values":["info:eu-repo/semantics/doctoralThesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["DNA","GPU","Ionic liquids","Molecular Dynamic","NMR","Settore CHIM/02 - Chimica Fisica"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["ita"]},{"key":"dc:rights","label":"Dc Rights","values":["info:eu-repo/semantics/openAccess","license:Non specificato"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/11584/266556"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["M.DynaMix is a modular general purpose Molecular Dynamics code for simulations of arbitrary mixtures of either rigid or flexible molecules. For its features and capabilities, M.DynaMix is diffused in a large simulation community and it is worth to keep it efficient and updated. With this goal in mind, a major revision of the package has been performed, leading to a version where several enhancements have been added: two efficient grid-based algorithm for long range interactions, SPME and ENUF, are now available; besides, a version of the code runnable on multi graphics boards has been produced. With the new features, the program exhibits a remarkable increase of computational efficiency and an improvement in global performance. The new version of M.DynaMix has been applied for studying some selected high charged particle system: DNA oligomers and ionic liquids. For oligomers, interactions between DNA and counterions has been investigated, searching for sequence dependent features. For ionic liquids, we focused on 1-decyl-3-methil-imidazolium chloride, to find a proper Force Field parameter set for its description. In both cases, the problem of validation of MD simulations has been treated, testing a new technique based upon the determination of quadrupolar decay parameters, for direct comparison between simulation and experiments."]},{"key":"dc:title","label":"Title","values":["Modelling in chimica computazionale: ottimizzazione di codici MD ed applicazioni allo studio di sistemi ad elevata carica"]}]}],"canonical_facts":{"dc:creator":["PORCU, MASSIMILIANO"],"dc:date":["2015-03-13"],"dc:description":["M.DynaMix is a modular general purpose Molecular Dynamics code for simulations of arbitrary mixtures of either rigid or flexible molecules. For its features and capabilities, M.DynaMix is diffused in a large simulation community and it is worth to keep it efficient and updated. With this goal in mind, a major revision of the package has been performed, leading to a version where several enhancements have been added: two efficient grid-based algorithm for long range interactions, SPME and ENUF, are now available; besides, a version of the code runnable on multi graphics boards has been produced. With the new features, the program exhibits a remarkable increase of computational efficiency and an improvement in global performance. The new version of M.DynaMix has been applied for studying some selected high charged particle system: DNA oligomers and ionic liquids. For oligomers, interactions between DNA and counterions has been investigated, searching for sequence dependent features. For ionic liquids, we focused on 1-decyl-3-methil-imidazolium chloride, to find a proper Force Field parameter set for its description. In both cases, the problem of validation of MD simulations has been treated, testing a new technique based upon the determination of quadrupolar decay parameters, for direct comparison between simulation and experiments."],"dc:identifier":["http://hdl.handle.net/11584/266556"],"dc:language":["ita"],"dc:publisher":["Università degli Studi di Cagliari"],"dc:relation":["numberofpages:152"],"dc:rights":["info:eu-repo/semantics/openAccess","license:Non specificato"],"dc:subject":["DNA","GPU","Ionic liquids","Molecular Dynamic","NMR","Settore CHIM/02 - Chimica Fisica"],"dc:title":["Modelling in chimica computazionale: ottimizzazione di codici MD ed applicazioni allo studio di sistemi ad elevata carica"],"dc:type":["info:eu-repo/semantics/doctoralThesis"]},"updated_at":"2026-07-24T01:30:12Z"}