{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/132723"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/132723","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Bridging molecular and systems scales in membrane biology","abstract":"Membrane proteins serve a variety of roles which include mediating transport, serving as a trigger for cellular response, and catalyzing bioenergetic reactions. This body of work uses computational methods to study different aspects of membrane biology. The first two studies presented in my thesis use approaches based in molecular simulation, to study the influence of protein-lipid (Chapter 3) and protein-protein interactions (Chapter 4) on molecular diffusion in photosynthetic processes. The next two studies are focused on using non-equilibrium MD methods such as steered molecular dynamics (SMD), coupled with umbrella sampling (US), and Alchemical Free-Energy Perturbation (Alchemical FEP) to study how the structural changes associated with point mutations affect mechanical aspects of conformational change in channels, such as hERG (Chapter 5), and the ability of growth factors to bind and activate growth factor receptors, such as VEGFR-2 (Chapter 6). The last chapter showcases the application of different computational methods, which integrates molecular simulation and metabolic modeling in the development of a whole-cell model for the photosynthetic bacteria \\textit{Procholorococcus marinus} MED4.","abstract_html":"Membrane proteins serve a variety of roles which include mediating transport, serving as a trigger for cellular response, and catalyzing bioenergetic reactions. This body of work uses computational methods to study different aspects of membrane biology. The first two studies presented in my thesis use approaches based in molecular simulation, to study the influence of protein-lipid (Chapter 3) and protein-protein interactions (Chapter 4) on molecular diffusion in photosynthetic processes. The next two studies are focused on using non-equilibrium MD methods such as steered molecular dynamics (SMD), coupled with umbrella sampling (US), and Alchemical Free-Energy Perturbation (Alchemical FEP) to study how the structural changes associated with point mutations affect mechanical aspects of conformational change in channels, such as hERG (Chapter 5), and the ability of growth factors to bind and activate growth factor receptors, such as VEGFR-2 (Chapter 6). The last chapter showcases the application of different computational methods, which integrates molecular simulation and metabolic modeling in the development of a whole-cell model for the photosynthetic bacteria \\textit{Procholorococcus marinus} MED4.","abstract_has_math":false,"creators":["Chan, Aaron"],"institution":"University of Illinois Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics & Quant Biology","degree_department":null,"school":null,"contributors":["Tajkhorshid, Emad","Luthey-Schulten, Zaida","Gruebele, Martin","Pogorelov, Taras"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-12","date_published":"2025-12","updated_at":"2026-07-22T22:25:07Z","subjects":["computational biology","membrane biology","molecular simulation"],"languages":["en"],"rights":["Copyright 2025 Aaron Chan"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/132723","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Tajkhorshid, Emad","Luthey-Schulten, Zaida","Gruebele, Martin","Pogorelov, Taras"]},{"key":"dc:creator","label":"Author","values":["Chan, Aaron"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-12","2025-08-12"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics & Quant Biology"]},{"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 Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["computational biology","membrane biology","molecular simulation"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Aaron Chan"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/132723"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Membrane proteins serve a variety of roles which include mediating transport, serving as a trigger for cellular response, and catalyzing bioenergetic reactions. This body of work uses computational methods to study different aspects of membrane biology. The first two studies presented in my thesis use approaches based in molecular simulation, to study the influence of protein-lipid (Chapter 3) and protein-protein interactions (Chapter 4) on molecular diffusion in photosynthetic processes. The next two studies are focused on using non-equilibrium MD methods such as steered molecular dynamics (SMD), coupled with umbrella sampling (US), and Alchemical Free-Energy Perturbation (Alchemical FEP) to study how the structural changes associated with point mutations affect mechanical aspects of conformational change in channels, such as hERG (Chapter 5), and the ability of growth factors to bind and activate growth factor receptors, such as VEGFR-2 (Chapter 6). The last chapter showcases the application of different computational methods, which integrates molecular simulation and metabolic modeling in the development of a whole-cell model for the photosynthetic bacteria \\textit{Procholorococcus marinus} MED4.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-12-01","The student, Aaron Chan, accepted the attached license on 2025-08-01 at 15:19.","The student, Aaron Chan, submitted this Dissertation for approval on 2025-08-01 at 16:10.","This Dissertation was approved for publication on 2025-08-12 at 09:48.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22745 on 2026-02-19 at 20:07:50"]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Bridging molecular and systems scales in membrane biology"]}]}],"canonical_facts":{"dc:contributor":["Tajkhorshid, Emad","Luthey-Schulten, Zaida","Gruebele, Martin","Pogorelov, Taras"],"dc:creator":["Chan, Aaron"],"dc:date":["2025-12","2025-08-12"],"dc:description":["Membrane proteins serve a variety of roles which include mediating transport, serving as a trigger for cellular response, and catalyzing bioenergetic reactions. This body of work uses computational methods to study different aspects of membrane biology. The first two studies presented in my thesis use approaches based in molecular simulation, to study the influence of protein-lipid (Chapter 3) and protein-protein interactions (Chapter 4) on molecular diffusion in photosynthetic processes. The next two studies are focused on using non-equilibrium MD methods such as steered molecular dynamics (SMD), coupled with umbrella sampling (US), and Alchemical Free-Energy Perturbation (Alchemical FEP) to study how the structural changes associated with point mutations affect mechanical aspects of conformational change in channels, such as hERG (Chapter 5), and the ability of growth factors to bind and activate growth factor receptors, such as VEGFR-2 (Chapter 6). The last chapter showcases the application of different computational methods, which integrates molecular simulation and metabolic modeling in the development of a whole-cell model for the photosynthetic bacteria \\textit{Procholorococcus marinus} MED4.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-12-01","The student, Aaron Chan, accepted the attached license on 2025-08-01 at 15:19.","The student, Aaron Chan, submitted this Dissertation for approval on 2025-08-01 at 16:10.","This Dissertation was approved for publication on 2025-08-12 at 09:48.","DSpace SAF Submission Ingestion Package generated from Vireo submission #22745 on 2026-02-19 at 20:07:50"],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/132723"],"dc:language":["en"],"dc:rights":["Copyright 2025 Aaron Chan"],"dc:subject":["computational biology","membrane biology","molecular simulation"],"dc:title":["Bridging molecular and systems scales in membrane biology"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Biophysics & Quant Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:07Z"}