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UBC Theses and Dissertations

Deterministic and stochastic modeling of the Min system for cell division : [supplementary material] Jamieson-Lane, Alastair 2019

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33426-ubc_2019_may_jamieson-lane_alastair_Chapter2 Smoldyn_simulations.zip [ 1.3kB ]
33426-ubc_2019_may_jamieson-lane_alastair_Chapter3 Bifurcation_diagram_of_carlquist_model.zip [ 7.65kB ]
33426-ubc_2019_may_jamieson-lane_alastair_Chapter4_Stochastic_Burst_Formation.zip [ 7.85kB ]
33426-README.html [ 724.29kB ]
33426-README.md [ 3.7kB ]
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                             .main-container { max-width: 940px; margin-left: auto; margin-right: auto; } code { color: inherit; background-color: rgba(0, 0, 0, 0.04); } img { max-width:100%; height: auto; } .tabbed-pane { padding-top: 12px; } .html-widget { margin-bottom: 20px; } button.code-folding-btn:focus { outline: none; } summary { display: list-item; } .tabset-dropdown > .nav-tabs { display: inline-table; max-height: 500px; min-height: 44px; overflow-y: auto; background: white; border: 1px solid #ddd; border-radius: 4px; } .tabset-dropdown > .nav-tabs > li.active:before { content: ""; font-family: 'Glyphicons Halflings'; display: inline-block; padding: 10px; border-right: 1px solid #ddd; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before { content: ""; border: none; } .tabset-dropdown > .nav-tabs.nav-tabs-open:before { content: ""; font-family: 'Glyphicons Halflings'; display: inline-block; padding: 10px; border-right: 1px solid #ddd; } .tabset-dropdown > .nav-tabs > li.active { display: block; } .tabset-dropdown > .nav-tabs > li > a, .tabset-dropdown > .nav-tabs > li > a:focus, .tabset-dropdown > .nav-tabs > li > a:hover { border: none; display: inline-block; border-radius: 4px; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { display: block; float: none; } .tabset-dropdown > .nav-tabs > li { display: none; }     Some Programs and scripts used in my thesisThis file contains a number of Matlab and Smoldyn scripts, as used in my PhD thesis. The full thesis is avaliable from the University of British Columbia, Canada. It is named ``Deterministic and Stochastic Modeling of the Min System for Cell Division’’, and is being published in 2019.In order to gain context for what these scripts are, and why they exist, please go and examine the actual thesis.Here I give a BRIEF guide to what the scripts are in each of these files, and how to use them.Chapter 2Chapter 2 of my thesis was associated with examining the occassional mismatch between particle based models of reaction-diffusion systems, and the associated PDE models.In the corresponding folder of this repository, there are a number of smoldyn reaction files. In order to use them, please install smoldyn on your system (http://www.smoldyn.org/download.html), and then open a terminal in the Chapter 2 file type:smoldyn <SIMULATION_NAME_HERE>Chapter 3Chapter 3 of my thesis involved exploring the bifurcation structure of a particular Min model due to William Carlquist. This was primarily done using the continuation package “Coco” for matlab.In order to use the scripts in this file, you will need to have a working copy of matlab, and install the Coco (https://sourceforge.net/projects/cocotools/). Once this is done, you can then run BuildBifurcationCarlquistModel.m followed by DrawBifurcationPlot.m. The first function creates the data for a bifurcation diagram, the second draw things.In order to alter the diagrams, you are best off opening BuildBifurcationCarlquistModel.m and changing either the grid of D and E where you start your bifurcation diagram, and also the h values.The remaining files in the folder are helper scripts.Chapter 4In chapter 4 of my thesis I examined how equations of the form \(u_t=D \Delta u + u^2 +\xi\). The files CartoonBurst.m,CartoonBurst_IC_noise.m and MoriBurst.m are matlab scripts the give simple examples of burst bifurcations. You can run them by opening them in matlab and hitting ‘run’.The script BackForwardSolveAdaptive.m will run the PDE’s required to find the optimal spike for reaching height \(u(0,T)=\)uTarget by time \(T=\)tf, assuming diffusion rate D in m dimensions. If not previously defined, these values default to 10,10, 1 and 1, respectively.The script IterateBFsolve.m can be used to run BackForwardSolveAdaptive.m multipled times, for a collection of parameter values, and is primarily useful if (for example) you wish to leave your computer running overnight, testing the results for multiple set ups.LicenseMIT LicenseCopyright (c) [2018] [Alastair Jamieson-Lane]Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.       

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