{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/106166"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/106166","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Understanding long timescale phenomena in atomic systems from accelerated molecular simulation methods","abstract":"Conventional molecular dynamics simulations have been proven instrumental to the understanding of material behaviors. However, the temporal constraints of molecular dynamics simulations have limited attempts to capture long timescale dynamics of material systems, such as phase transitions or dynamics of supercooled liquids. This class of phenomena often requires the crossing by thermal activation of large energy barriers, which represent transition states separating two stable or metastable states of a system. Therefore, we propose two methods to simulate the escape of a system from a metastable state to a transition state, which, when repeated, leads to atomic trajectories of extremely slow or rare phenomena of non-equilibrium matter. The first method, all-atom Metadynamics, is a version of the popular advanced sampling method Metadynamics. By biasing over all atoms rather than collective variables, all-atom Metadynamics samples the potential energy landscape in all-atom dependent variable space. All-atom Metadynamics utility is displayed by studying the nucleation and crystal growth of a model Lennard-Jones Argon system, while also displaying the computational downside of Metadynamics, the scaling over simulation time. Thus, the second method, Varied Steepness Ascent Dynamics (Ascent Dynamics), is introduced as an alternative method with constant computational scaling over simulation time. Ascent Dynamics, based on former surface walking methods, is first verified and validated on several mathematical problems and on vacancy diffusion in a Lennard-Jones system, respectively, followed by application of the method to a two-dimensional polydisperse model liquid. Ascent Dynamics is shown to accurately sample the potential energy landscape without the large computational overhead.","abstract_html":"Conventional molecular dynamics simulations have been proven instrumental to the understanding of material behaviors. However, the temporal constraints of molecular dynamics simulations have limited attempts to capture long timescale dynamics of material systems, such as phase transitions or dynamics of supercooled liquids. This class of phenomena often requires the crossing by thermal activation of large energy barriers, which represent transition states separating two stable or metastable states of a system. Therefore, we propose two methods to simulate the escape of a system from a metastable state to a transition state, which, when repeated, leads to atomic trajectories of extremely slow or rare phenomena of non-equilibrium matter. The first method, all-atom Metadynamics, is a version of the popular advanced sampling method Metadynamics. By biasing over all atoms rather than collective variables, all-atom Metadynamics samples the potential energy landscape in all-atom dependent variable space. All-atom Metadynamics utility is displayed by studying the nucleation and crystal growth of a model Lennard-Jones Argon system, while also displaying the computational downside of Metadynamics, the scaling over simulation time. Thus, the second method, Varied Steepness Ascent Dynamics (Ascent Dynamics), is introduced as an alternative method with constant computational scaling over simulation time. Ascent Dynamics, based on former surface walking methods, is first verified and validated on several mathematical problems and on vacancy diffusion in a Lennard-Jones system, respectively, followed by application of the method to a two-dimensional polydisperse model liquid. Ascent Dynamics is shown to accurately sample the potential energy landscape without the large computational overhead.","abstract_has_math":false,"creators":["Walter, Nathan Peller"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Nuclear, Plasma, Radiolgc Engr","degree_department":null,"school":null,"contributors":["Zhang, Yang","Heuser, Brent","Ruzic, David","Schweizer, Kenneth"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2020,"date_issued":"2020-03-02T21:58:03Z","date_published":"2020-03-02T21:58:03Z","updated_at":"2026-07-22T22:24:45Z","subjects":["Metadynamics, Ascent Dynamics, Advanced Sampling, Molecular Dynamics, Energy Landscape"],"languages":["en"],"rights":["Copyright 2019 Nathan Walter"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/106166","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Zhang, Yang","Heuser, Brent","Ruzic, David","Schweizer, Kenneth"]},{"key":"dc:creator","label":"Author","values":["Walter, Nathan Peller"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2020-03-02T21:58:03Z","2019-10-07","2019-12"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Nuclear, Plasma, Radiolgc Engr"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Metadynamics, Ascent Dynamics, Advanced Sampling, Molecular Dynamics, Energy Landscape"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Nathan Walter"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/106166"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Conventional molecular dynamics simulations have been proven instrumental to the understanding of material behaviors. However, the temporal constraints of molecular dynamics simulations have limited attempts to capture long timescale dynamics of material systems, such as phase transitions or dynamics of supercooled liquids. This class of phenomena often requires the crossing by thermal activation of large energy barriers, which represent transition states separating two stable or metastable states of a system. Therefore, we propose two methods to simulate the escape of a system from a metastable state to a transition state, which, when repeated, leads to atomic trajectories of extremely slow or rare phenomena of non-equilibrium matter. The first method, all-atom Metadynamics, is a version of the popular advanced sampling method Metadynamics. By biasing over all atoms rather than collective variables, all-atom Metadynamics samples the potential energy landscape in all-atom dependent variable space. All-atom Metadynamics utility is displayed by studying the nucleation and crystal growth of a model Lennard-Jones Argon system, while also displaying the computational downside of Metadynamics, the scaling over simulation time. Thus, the second method, Varied Steepness Ascent Dynamics (Ascent Dynamics), is introduced as an alternative method with constant computational scaling over simulation time. Ascent Dynamics, based on former surface walking methods, is first verified and validated on several mathematical problems and on vacancy diffusion in a Lennard-Jones system, respectively, followed by application of the method to a two-dimensional polydisperse model liquid. Ascent Dynamics is shown to accurately sample the potential energy landscape without the large computational overhead.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2020-02-28 without embargo terms","The student, Nathan Walter, accepted the attached license on 2019-10-02 at 15:29.","The student, Nathan Walter, submitted this Dissertation for approval on 2019-10-02 at 15:39.","This Dissertation was approved for publication on 2019-10-07 at 13:27.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14483 on 2020-02-28 at 17:12:32","Made available in DSpace on 2020-03-02T21:58:03Z (GMT). No. of bitstreams: 4 WALTER-DISSERTATION-2019.pdf: 15483762 bytes, checksum: aca7c747b0dc8fd53514e73d73a1ab57 (MD5) 2019 Thesis.zip: 52959199 bytes, checksum: 5711d9dc4b919ba7b208da295046c2e8 (MD5) LICENSE.txt: 4210 bytes, checksum: 20dc2d3403e57d5f501ca443b3af74b1 (MD5) PROQUEST_LICENSE.txt: 4556 bytes, checksum: 88787e9020ad23eb96ef6eeb5b62605d (MD5) Previous issue date: 2019-10-07"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Understanding long timescale phenomena in atomic systems from accelerated molecular simulation methods"]}]}],"canonical_facts":{"dc:contributor":["Zhang, Yang","Heuser, Brent","Ruzic, David","Schweizer, Kenneth"],"dc:creator":["Walter, Nathan Peller"],"dc:date":["2020-03-02T21:58:03Z","2019-10-07","2019-12"],"dc:description":["Conventional molecular dynamics simulations have been proven instrumental to the understanding of material behaviors. However, the temporal constraints of molecular dynamics simulations have limited attempts to capture long timescale dynamics of material systems, such as phase transitions or dynamics of supercooled liquids. This class of phenomena often requires the crossing by thermal activation of large energy barriers, which represent transition states separating two stable or metastable states of a system. Therefore, we propose two methods to simulate the escape of a system from a metastable state to a transition state, which, when repeated, leads to atomic trajectories of extremely slow or rare phenomena of non-equilibrium matter. The first method, all-atom Metadynamics, is a version of the popular advanced sampling method Metadynamics. By biasing over all atoms rather than collective variables, all-atom Metadynamics samples the potential energy landscape in all-atom dependent variable space. All-atom Metadynamics utility is displayed by studying the nucleation and crystal growth of a model Lennard-Jones Argon system, while also displaying the computational downside of Metadynamics, the scaling over simulation time. Thus, the second method, Varied Steepness Ascent Dynamics (Ascent Dynamics), is introduced as an alternative method with constant computational scaling over simulation time. Ascent Dynamics, based on former surface walking methods, is first verified and validated on several mathematical problems and on vacancy diffusion in a Lennard-Jones system, respectively, followed by application of the method to a two-dimensional polydisperse model liquid. Ascent Dynamics is shown to accurately sample the potential energy landscape without the large computational overhead.","Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2020-02-28 without embargo terms","The student, Nathan Walter, accepted the attached license on 2019-10-02 at 15:29.","The student, Nathan Walter, submitted this Dissertation for approval on 2019-10-02 at 15:39.","This Dissertation was approved for publication on 2019-10-07 at 13:27.","DSpace SAF Submission Ingestion Package generated from Vireo submission #14483 on 2020-02-28 at 17:12:32","Made available in DSpace on 2020-03-02T21:58:03Z (GMT). No. of bitstreams: 4 WALTER-DISSERTATION-2019.pdf: 15483762 bytes, checksum: aca7c747b0dc8fd53514e73d73a1ab57 (MD5) 2019 Thesis.zip: 52959199 bytes, checksum: 5711d9dc4b919ba7b208da295046c2e8 (MD5) LICENSE.txt: 4210 bytes, checksum: 20dc2d3403e57d5f501ca443b3af74b1 (MD5) PROQUEST_LICENSE.txt: 4556 bytes, checksum: 88787e9020ad23eb96ef6eeb5b62605d (MD5) Previous issue date: 2019-10-07"],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/106166"],"dc:language":["en"],"dc:rights":["Copyright 2019 Nathan Walter"],"dc:subject":["Metadynamics, Ascent Dynamics, Advanced Sampling, Molecular Dynamics, Energy Landscape"],"dc:title":["Understanding long timescale phenomena in atomic systems from accelerated molecular simulation methods"],"dc:type":["text"],"thesis:degree_discipline":["Nuclear, Plasma, Radiolgc Engr"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:45Z"}