{"id":{"repo_id":"mississippi","oai_identifier":"oai:egrove.olemiss.edu:etd-2113"},"canonical_url":"https://search.dev.ndltd.org/etd/mississippi/oai:egrove.olemiss.edu:etd-2113","repository":{"repo_id":"mississippi","name":"University of Mississippi","base_url":"https://egrove.olemiss.edu/do/oai/"},"display":{"title":"Biomolecular Folding Rates As Understood From Single-Reaction-Coordinate Langevin Dynamics And Kramers’ Theory","abstract":"Langevin dynamics was used to model the folding and unfolding of simple, hairpin-like biomolecules whose ends are attached to laser-trapped beads, as occurs in optical tweezers experiments. The Langevin process was evolved numerically, using parameters motivated by real experimental systems. Folding trajectories were generated and analyzed to extract the folding rate as a function of the force applied to the beads. The observed rate was compared to the analytical predictions of Kramers' theory. Strong discrepancies were noted. The failure of the Kramers' theory was attributed to the slow dynamical response of the beads, which it does not account for. The results of this work highlight the necessity to include in the modeling the experimental systems that mediate force along the length of the biomolecule.","abstract_html":"Langevin dynamics was used to model the folding and unfolding of simple, hairpin-like biomolecules whose ends are attached to laser-trapped beads, as occurs in optical tweezers experiments. The Langevin process was evolved numerically, using parameters motivated by real experimental systems. Folding trajectories were generated and analyzed to extract the folding rate as a function of the force applied to the beads. The observed rate was compared to the analytical predictions of Kramers' theory. Strong discrepancies were noted. The failure of the Kramers' theory was attributed to the slow dynamical response of the beads, which it does not account for. The results of this work highlight the necessity to include in the modeling the experimental systems that mediate force along the length of the biomolecule.","abstract_has_math":false,"creators":["Kabir, Md Adnan"],"institution":null,"degree_name":"M.S. in Physics","degree_level":"Thesis","degree_discipline":"Physics and Astronomy","degree_department":null,"school":null,"contributors":["Kevin Beach","Cecille Labuda","Luca Bombelli"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2015,"date_issued":"2015-01-01T08:00:00Z","date_published":"2015-01-01T08:00:00Z","updated_at":"2026-07-24T03:06:21Z","subjects":["Biomolecular","Kramers'","Langevin Dynamics","Protein","Physics"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://egrove.olemiss.edu/etd/1114","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Kevin Beach","Cecille Labuda","Luca Bombelli"]},{"key":"dc:creator","label":"Author","values":["Kabir, Md Adnan"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2019-06-20T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Physics and Astronomy"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S. in Physics"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Biomolecular","Kramers'","Langevin Dynamics","Protein","Physics"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://egrove.olemiss.edu/etd/1114"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Langevin dynamics was used to model the folding and unfolding of simple, hairpin-like biomolecules whose ends are attached to laser-trapped beads, as occurs in optical tweezers experiments. The Langevin process was evolved numerically, using parameters motivated by real experimental systems. Folding trajectories were generated and analyzed to extract the folding rate as a function of the force applied to the beads. The observed rate was compared to the analytical predictions of Kramers' theory. Strong discrepancies were noted. The failure of the Kramers' theory was attributed to the slow dynamical response of the beads, which it does not account for. The results of this work highlight the necessity to include in the modeling the experimental systems that mediate force along the length of the biomolecule."]},{"key":"dc:title","label":"Title","values":["Biomolecular Folding Rates As Understood From Single-Reaction-Coordinate Langevin Dynamics And Kramers’ Theory"]}]}],"canonical_facts":{"dc:contributor":["Kevin Beach","Cecille Labuda","Luca Bombelli"],"dc:creator":["Kabir, Md Adnan"],"dc:date.available":["2019-06-20T07:00:00Z"],"dc:description.abstract":["Langevin dynamics was used to model the folding and unfolding of simple, hairpin-like biomolecules whose ends are attached to laser-trapped beads, as occurs in optical tweezers experiments. The Langevin process was evolved numerically, using parameters motivated by real experimental systems. Folding trajectories were generated and analyzed to extract the folding rate as a function of the force applied to the beads. The observed rate was compared to the analytical predictions of Kramers' theory. Strong discrepancies were noted. The failure of the Kramers' theory was attributed to the slow dynamical response of the beads, which it does not account for. The results of this work highlight the necessity to include in the modeling the experimental systems that mediate force along the length of the biomolecule."],"dc:identifier":["https://egrove.olemiss.edu/etd/1114"],"dc:subject":["Biomolecular","Kramers'","Langevin Dynamics","Protein","Physics"],"dc:title":["Biomolecular Folding Rates As Understood From Single-Reaction-Coordinate Langevin Dynamics And Kramers’ Theory"],"thesis:degree_discipline":["Physics and Astronomy"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S. in Physics"]},"updated_at":"2026-07-24T03:06:21Z"}