{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/29597"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/29597","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"Java-based modeling of the actin polymerization cycle","abstract":"This thesis project combines work on two aspects· of a project entitled \"A Mechanistic Model of the Actin Cycle\" [ 1,2]. This project uses accumulated biochemical research to write a broad mathematical model that describes the effects of regulatory proteins (profilin, beta-thymosin, cofilin, and capping protein) on the steady-state actin cycle. The model necessitates the simultaneous solving of 90-330 differential equations and 51-171 additional equations. One object of this thesis was to prove that this model could be run on JSim, a modeling architecture developed at the University of Washington, to obtain the same results as McGrath et al calculated using Matlab. The theory behind using JSim was that it would be faster and more accessible, since JSim is Java-based and contains all the necessary software to run on various platforms. This project proved that the equations could be run quickly with JSim. It also highlighted some of the drawbacks of JSim, such as heavy demand on the processor. A second object of this thesis was to provide an independent evaluation of the mathematical model and correct mistakes in the original draft. Several errors were uncovered and the corrected results now appear in the paper submitted to The Biophysical Journal [2].","abstract_html":"This thesis project combines work on two aspects· of a project entitled "A Mechanistic Model of the Actin Cycle" [ 1,2]. This project uses accumulated biochemical research to write a broad mathematical model that describes the effects of regulatory proteins (profilin, beta-thymosin, cofilin, and capping protein) on the steady-state actin cycle. The model necessitates the simultaneous solving of 90-330 differential equations and 51-171 additional equations. One object of this thesis was to prove that this model could be run on JSim, a modeling architecture developed at the University of Washington, to obtain the same results as McGrath et al calculated using Matlab. The theory behind using JSim was that it would be faster and more accessible, since JSim is Java-based and contains all the necessary software to run on various platforms. This project proved that the equations could be run quickly with JSim. It also highlighted some of the drawbacks of JSim, such as heavy demand on the processor. A second object of this thesis was to provide an independent evaluation of the mathematical model and correct mistakes in the original draft. Several errors were uncovered and the corrected results now appear in the paper submitted to The Biophysical Journal [2].","abstract_has_math":false,"creators":["Howell, Catherine, 1980-"],"institution":"Massachusetts Institute of Technology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Dept. of Mechanical Engineering.","school":null,"contributors":[],"advisors":["C. Forbes Dewey, Jr."],"committee_chairs":[],"committee_members":[],"year":2003,"date_issued":"2003","date_published":"2003","updated_at":"2026-07-22T22:22:16Z","subjects":["Mechanical Engineering."],"languages":["eng"],"rights":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."],"rights_urls":["http://dspace.mit.edu/handle/1721.1/7582"],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/1721.1/29597","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["C. Forbes Dewey, Jr."]},{"key":"dc:contributor.department","label":"Department","values":["Massachusetts Institute of Technology. Dept. of Mechanical Engineering."]},{"key":"dc:contributor.other","label":"Dc Contributor Other","values":["Massachusetts Institute of Technology. Dept. of Mechanical Engineering."]},{"key":"dc:creator","label":"Author","values":["Howell, Catherine, 1980-"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2006-03-24T16:06:02Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2006-03-24T16:06:02Z"]},{"key":"dc:date.issued","label":"Date","values":["2003"]},{"key":"dc:publisher","label":"Institution","values":["Massachusetts Institute of Technology"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Mechanical Engineering."]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://dspace.mit.edu/handle/1721.1/7582"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1721.1/29597"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2003.","Includes bibliographical references (leaf 18)."]},{"key":"dc:description.abstract","label":"Abstract","values":["This thesis project combines work on two aspects· of a project entitled \"A Mechanistic Model of the Actin Cycle\" [ 1,2]. This project uses accumulated biochemical research to write a broad mathematical model that describes the effects of regulatory proteins (profilin, beta-thymosin, cofilin, and capping protein) on the steady-state actin cycle. The model necessitates the simultaneous solving of 90-330 differential equations and 51-171 additional equations. One object of this thesis was to prove that this model could be run on JSim, a modeling architecture developed at the University of Washington, to obtain the same results as McGrath et al calculated using Matlab. The theory behind using JSim was that it would be faster and more accessible, since JSim is Java-based and contains all the necessary software to run on various platforms. This project proved that the equations could be run quickly with JSim. It also highlighted some of the drawbacks of JSim, such as heavy demand on the processor. A second object of this thesis was to provide an independent evaluation of the mathematical model and correct mistakes in the original draft. Several errors were uncovered and the corrected results now appear in the paper submitted to The Biophysical Journal [2]."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["S.B."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Java-based modeling of the actin polymerization cycle"]}]}],"canonical_facts":{"dc:contributor.advisor":["C. Forbes Dewey, Jr."],"dc:contributor.department":["Massachusetts Institute of Technology. Dept. of Mechanical Engineering."],"dc:contributor.other":["Massachusetts Institute of Technology. Dept. of Mechanical Engineering."],"dc:creator":["Howell, Catherine, 1980-"],"dc:date.accessioned":["2006-03-24T16:06:02Z"],"dc:date.available":["2006-03-24T16:06:02Z"],"dc:date.issued":["2003"],"dc:description":["Thesis (S.B.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2003.","Includes bibliographical references (leaf 18)."],"dc:description.abstract":["This thesis project combines work on two aspects· of a project entitled \"A Mechanistic Model of the Actin Cycle\" [ 1,2]. This project uses accumulated biochemical research to write a broad mathematical model that describes the effects of regulatory proteins (profilin, beta-thymosin, cofilin, and capping protein) on the steady-state actin cycle. The model necessitates the simultaneous solving of 90-330 differential equations and 51-171 additional equations. One object of this thesis was to prove that this model could be run on JSim, a modeling architecture developed at the University of Washington, to obtain the same results as McGrath et al calculated using Matlab. The theory behind using JSim was that it would be faster and more accessible, since JSim is Java-based and contains all the necessary software to run on various platforms. This project proved that the equations could be run quickly with JSim. It also highlighted some of the drawbacks of JSim, such as heavy demand on the processor. A second object of this thesis was to provide an independent evaluation of the mathematical model and correct mistakes in the original draft. Several errors were uncovered and the corrected results now appear in the paper submitted to The Biophysical Journal [2]."],"dc:description.degree":["S.B."],"dc:format.mimetype":["application/pdf"],"dc:identifier.uri":["http://hdl.handle.net/1721.1/29597"],"dc:language.iso":["eng"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Mechanical Engineering."],"dc:title":["Java-based modeling of the actin polymerization cycle"],"dc:type":["Thesis"]},"updated_at":"2026-07-22T22:22:16Z"}