{"id":{"repo_id":"anu","oai_identifier":"oai:openresearch-repository.anu.edu.au:1885/47286"},"canonical_url":"https://search.dev.ndltd.org/etd/anu/oai:openresearch-repository.anu.edu.au:1885/47286","repository":{"repo_id":"anu","name":"Australian National University","base_url":"https://openresearch-repository.anu.edu.au/server/oai/request"},"display":{"title":"Computer Simulation of Biological Ion Channels","abstract":"This thesis describes a project in which algorithms are developed for the rapid and accurate solution of Poisson's equation in the presence of a dielectric boundary and multiple point charges. These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily shaped boundaries, but is too slow to perform Brownian dynamics. An analytical solution is derived, which is faster and more accurate, but only works for a toroidal boundary. Finally, a method is developed of pre-calculating solutions to Poisson's equation and storing them in tables. The solution for a particular configuration of ions in the channel can then be assembled by interpolation from the tables and application of the principle of superposition. This algorithm combines the flexibility of the iterative method with greater speed even than the analytical method, and is fast enough that channel conductance can be predicted. The results of simulations for a model single-ion channel, based on the acetylcholine receptor channel, show that the narrow pore through the low dielectric strength medium of the protein creates an energy barrier which restricts the permeation of ions. They further show that this barrier can be removed by dipoles in the neck of the channel, but that the barrier is not removed by shielding by counter-ions. The results of simulations for a model multi-ion channel, based on a bacterial potassium channel, show that the model channel has conductance characteristics similar to those of real potassium channels. Ions appear to move through the model multi-ion channel via rapid transitions between a series of semi-stable states. This observation suggests a possible physical basis for the reaction rate theory of channel conductance, and opens up an avenue for future research.","abstract_html":"This thesis describes a project in which algorithms are developed for the rapid and accurate solution of Poisson's equation in the presence of a dielectric boundary and multiple point charges. These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily shaped boundaries, but is too slow to perform Brownian dynamics. An analytical solution is derived, which is faster and more accurate, but only works for a toroidal boundary. Finally, a method is developed of pre-calculating solutions to Poisson's equation and storing them in tables. The solution for a particular configuration of ions in the channel can then be assembled by interpolation from the tables and application of the principle of superposition. This algorithm combines the flexibility of the iterative method with greater speed even than the analytical method, and is fast enough that channel conductance can be predicted. The results of simulations for a model single-ion channel, based on the acetylcholine receptor channel, show that the narrow pore through the low dielectric strength medium of the protein creates an energy barrier which restricts the permeation of ions. They further show that this barrier can be removed by dipoles in the neck of the channel, but that the barrier is not removed by shielding by counter-ions. The results of simulations for a model multi-ion channel, based on a bacterial potassium channel, show that the model channel has conductance characteristics similar to those of real potassium channels. Ions appear to move through the model multi-ion channel via rapid transitions between a series of semi-stable states. This observation suggests a possible physical basis for the reaction rate theory of channel conductance, and opens up an avenue for future research.","abstract_has_math":false,"creators":["Hoyles, Matthew"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":1999,"date_issued":"1999","date_published":"1999","updated_at":"2026-07-24T00:54:51Z","subjects":["computer simulation","ion channels","conductance theories","electrostatics","Brownian dynamics","single-ion channel","multi-ion channel","Poisson's equation","dielectric boundary","potassium channel"],"languages":["en"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.other","label":"Dc Identifier Other","values":["b20525011"],"render_values":[{"text":"b20525011","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/1885/47286","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["Hoyles, Matthew"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2008-07-08T06:09:05Z","2011-01-04T02:39:04Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2008-07-08T06:09:05Z","2011-01-04T02:39:04Z"]},{"key":"dc:date.issued","label":"Date","values":["1999"]},{"key":"dc:type","label":"Dc Type","values":["Thesis (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["computer simulation","ion channels","conductance theories","electrostatics","Brownian dynamics","single-ion channel","multi-ion channel","Poisson's equation","dielectric boundary","potassium channel"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en"]},{"key":"dc:rights.uri","label":"Rights URI","values":["The Australian National University"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.other","label":"Dc Identifier Other","values":["b20525011"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1885/47286"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["This thesis describes a project in which algorithms are developed for the rapid and accurate solution of Poisson's equation in the presence of a dielectric boundary and multiple point charges. These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily shaped boundaries, but is too slow to perform Brownian dynamics. An analytical solution is derived, which is faster and more accurate, but only works for a toroidal boundary. Finally, a method is developed of pre-calculating solutions to Poisson's equation and storing them in tables. The solution for a particular configuration of ions in the channel can then be assembled by interpolation from the tables and application of the principle of superposition. This algorithm combines the flexibility of the iterative method with greater speed even than the analytical method, and is fast enough that channel conductance can be predicted. The results of simulations for a model single-ion channel, based on the acetylcholine receptor channel, show that the narrow pore through the low dielectric strength medium of the protein creates an energy barrier which restricts the permeation of ions. They further show that this barrier can be removed by dipoles in the neck of the channel, but that the barrier is not removed by shielding by counter-ions. The results of simulations for a model multi-ion channel, based on a bacterial potassium channel, show that the model channel has conductance characteristics similar to those of real potassium channels. Ions appear to move through the model multi-ion channel via rapid transitions between a series of semi-stable states. This observation suggests a possible physical basis for the reaction rate theory of channel conductance, and opens up an avenue for future research."]},{"key":"dc:title","label":"Title","values":["Computer Simulation of Biological Ion Channels"]}]}],"canonical_facts":{"dc:creator":["Hoyles, Matthew"],"dc:date.accessioned":["2008-07-08T06:09:05Z","2011-01-04T02:39:04Z"],"dc:date.available":["2008-07-08T06:09:05Z","2011-01-04T02:39:04Z"],"dc:date.issued":["1999"],"dc:description.abstract":["This thesis describes a project in which algorithms are developed for the rapid and accurate solution of Poisson's equation in the presence of a dielectric boundary and multiple point charges. These algorithms are then used to perform Brownian dynamics simulations on realistic models of biological ion channels. An iterative method of solution, in which the dielectric boundary is tiled with variable sized surface charge sectors, provides the flexibility to deal with arbitrarily shaped boundaries, but is too slow to perform Brownian dynamics. An analytical solution is derived, which is faster and more accurate, but only works for a toroidal boundary. Finally, a method is developed of pre-calculating solutions to Poisson's equation and storing them in tables. The solution for a particular configuration of ions in the channel can then be assembled by interpolation from the tables and application of the principle of superposition. This algorithm combines the flexibility of the iterative method with greater speed even than the analytical method, and is fast enough that channel conductance can be predicted. The results of simulations for a model single-ion channel, based on the acetylcholine receptor channel, show that the narrow pore through the low dielectric strength medium of the protein creates an energy barrier which restricts the permeation of ions. They further show that this barrier can be removed by dipoles in the neck of the channel, but that the barrier is not removed by shielding by counter-ions. The results of simulations for a model multi-ion channel, based on a bacterial potassium channel, show that the model channel has conductance characteristics similar to those of real potassium channels. Ions appear to move through the model multi-ion channel via rapid transitions between a series of semi-stable states. This observation suggests a possible physical basis for the reaction rate theory of channel conductance, and opens up an avenue for future research."],"dc:identifier.other":["b20525011"],"dc:identifier.uri":["http://hdl.handle.net/1885/47286"],"dc:language.iso":["en"],"dc:rights.uri":["The Australian National University"],"dc:subject":["computer simulation","ion channels","conductance theories","electrostatics","Brownian dynamics","single-ion channel","multi-ion channel","Poisson's equation","dielectric boundary","potassium channel"],"dc:title":["Computer Simulation of Biological Ion Channels"],"dc:type":["Thesis (PhD)"]},"updated_at":"2026-07-24T00:54:51Z"}