{"id":{"repo_id":"uno","oai_identifier":"oai:scholarworks.uno.edu:td-1242"},"canonical_url":"https://search.dev.ndltd.org/etd/uno/oai:scholarworks.uno.edu:td-1242","repository":{"repo_id":"uno","name":"University of New Orleans","base_url":"https://scholarworks.uno.edu/do/oai/"},"display":{"title":"A Multi-Dimensional Width-Bounded Geometric Separator and its Applications to Protein Folding","abstract":"We used a divide-and-conquer algorithm to recursively solve the two-dimensional problem of protein folding of an HP sequence with the maximum number of H-H contacts. We derived both lower and upper bounds for the algorithmic complexity by using the newly introduced concept of multi-directional width-bounded geometric separator. We proved that for a grid graph G with n grid points P, there exists a balanced separator A subseteq P$ such that A has less than or equal to 1.02074 sqrt{n} points, and G-A has two disconnected subgraphs with less than or equal to {2over 3}n nodes on each subgraph. We also derive a 0.7555sqrt {n} lower bound for our balanced separator. Based on our multidirectional width-bounded geometric separator, we found that there is an O(n^{5.563sqrt{n}}) time algorithm for the 2D protein folding problem in the HP model. We also extended the upper bound results to rectangular and triangular lattices.","abstract_html":"We used a divide-and-conquer algorithm to recursively solve the two-dimensional problem of protein folding of an HP sequence with the maximum number of H-H contacts. We derived both lower and upper bounds for the algorithmic complexity by using the newly introduced concept of multi-directional width-bounded geometric separator. We proved that for a grid graph G with n grid points P, there exists a balanced separator A subseteq P$ such that A has less than or equal to 1.02074 sqrt{n} points, and G-A has two disconnected subgraphs with less than or equal to {2over 3}n nodes on each subgraph. We also derive a 0.7555sqrt {n} lower bound for our balanced separator. Based on our multidirectional width-bounded geometric separator, we found that there is an O(n^{5.563sqrt{n}}) time algorithm for the 2D protein folding problem in the HP model. We also extended the upper bound results to rectangular and triangular lattices.","abstract_has_math":false,"creators":["Oprisan, Sorinel"],"institution":null,"degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Computer Science","degree_department":null,"school":null,"contributors":["Fu, Bin","DePano, Adlai","Chen, Yixin"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2005,"date_issued":"2005-05-20T07:00:00Z","date_published":"2005-05-20T07:00:00Z","updated_at":"2026-07-24T05:28:10Z","subjects":["Planar graphs","Divide and conquer","HP model","Algorithmic complexity","Grid graphs"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://scholarworks.uno.edu/td/238","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Fu, Bin","DePano, Adlai","Chen, Yixin"]},{"key":"dc:creator","label":"Author","values":["Oprisan, Sorinel"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"thesis:degree_discipline","label":"Discipline","values":["Computer Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Planar graphs","Divide and conquer","HP model","Algorithmic complexity","Grid graphs"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://scholarworks.uno.edu/td/238"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["We used a divide-and-conquer algorithm to recursively solve the two-dimensional problem of protein folding of an HP sequence with the maximum number of H-H contacts. We derived both lower and upper bounds for the algorithmic complexity by using the newly introduced concept of multi-directional width-bounded geometric separator. We proved that for a grid graph G with n grid points P, there exists a balanced separator A subseteq P$ such that A has less than or equal to 1.02074 sqrt{n} points, and G-A has two disconnected subgraphs with less than or equal to {2over 3}n nodes on each subgraph. We also derive a 0.7555sqrt {n} lower bound for our balanced separator. Based on our multidirectional width-bounded geometric separator, we found that there is an O(n^{5.563sqrt{n}}) time algorithm for the 2D protein folding problem in the HP model. We also extended the upper bound results to rectangular and triangular lattices."]},{"key":"dc:title","label":"Title","values":["A Multi-Dimensional Width-Bounded Geometric Separator and its Applications to Protein Folding"]}]}],"canonical_facts":{"dc:contributor":["Fu, Bin","DePano, Adlai","Chen, Yixin"],"dc:creator":["Oprisan, Sorinel"],"dc:description.abstract":["We used a divide-and-conquer algorithm to recursively solve the two-dimensional problem of protein folding of an HP sequence with the maximum number of H-H contacts. We derived both lower and upper bounds for the algorithmic complexity by using the newly introduced concept of multi-directional width-bounded geometric separator. We proved that for a grid graph G with n grid points P, there exists a balanced separator A subseteq P$ such that A has less than or equal to 1.02074 sqrt{n} points, and G-A has two disconnected subgraphs with less than or equal to {2over 3}n nodes on each subgraph. We also derive a 0.7555sqrt {n} lower bound for our balanced separator. Based on our multidirectional width-bounded geometric separator, we found that there is an O(n^{5.563sqrt{n}}) time algorithm for the 2D protein folding problem in the HP model. We also extended the upper bound results to rectangular and triangular lattices."],"dc:identifier":["https://scholarworks.uno.edu/td/238"],"dc:subject":["Planar graphs","Divide and conquer","HP model","Algorithmic complexity","Grid graphs"],"dc:title":["A Multi-Dimensional Width-Bounded Geometric Separator and its Applications to Protein Folding"],"thesis:degree_discipline":["Computer Science"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."]},"updated_at":"2026-07-24T05:28:10Z"}