Waterloo

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<center><font size="6">[[Image:UWLogo.jpg]] University of Waterloo iGEM Team </font></center>
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<center> [[Image:UW_iGEMLogoHeader.png | 935px]] </center>
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<br>
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== Our Team ==
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{| style="border-spacing:0px; border-width:thin; border-color:black; border-style:solid"
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The UW iGEM team is a very interdisciplinary group. Our team members span the three faculties of Science, Mathematics and Engineering and include the programs of Biology, Biomedical Sciences, Computer Science, Bioinformatics, Computer Engineering, Electrical Engineering, Chemical Engineering, and Mathematical Physics at undergraduate and graduate levels. Even our professor advisors are cross-appointed to two other faculties. Our diverse backgrounds bring together a wide range of skills and ideas to the iGEM project. iGEM is giving us the opportunity to apply the skills learned in our lectures and labs to real life applications in molecular biology and biotechnology.
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| style="font-size:x-large; font-weight:bold; border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; font-size:x-large; font-weight:bold; padding:5px; background-color:#FBCC30" | Our Team
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| style="padding:5px" | [[Image:Group photo mimi1.JPG|470px|left|thumb|Undergraduate Members]]  [[Image:UW_Advisors.jpg|407px|center|thumb|Faculty and Graduate Advisors]]
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| style="padding:5px" | The UW iGEM team is a very interdisciplinary group. Our team members span three faculties: Science, Mathematics, and Engineering, and represent a wide range of undergraduate programs: Biology, Biomedical Sciences, Biochemistry, Computer Science, Bioinformatics, Computer Engineering, Electrical Engineering, Chemical Engineering, Systems Design Engineering, and Mathematical Physics.
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==Abstract==
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Drawing on our diverse backgrounds, we bring a wide range of skills and modes of creative thinking to our iGEM project. The iGEM competition is providing us with an opportunity to become more familiar with the emerging field of synthetic biology in an engaging and fun atmosphere. In addition to gaining experience in the design, construction, and analysis of genetic circuits, we are also meeting the challenge of bringing together a large, diverse group toward a common goal.
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==Background==
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  Binary Addition
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Half Adder
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DNA as Logic Gates
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==Project Details==
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  |}
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  Inputs (stimuli and the genes used to detect them)
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Output (observable change and what it represents)
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Gene Diagram
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==Testing/Results==
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Mathematical Model
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Measurements
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==Extensions==
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{| style="border-spacing:0px; border-width:thin; border-color:black; border-style:solid; width:100%"
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  Full Adder
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| colspan="4" style="border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; font-size:x-large; font-weight:bold; padding:5px; background-color:#FBCC30" | Our Project
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|-
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| colspan="4" style="padding:5px; font-size:large" | Abstract
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| colspan="2" style="vertical-align:top; border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; padding:5px" | The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome.
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==Acknowledgements== (Sponsor logos)
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Half adders are used as building blocks for full adders, which perform calculations similar to long addition but in binary. They are also an essential component in a device called the Arithmetic Logic Unit (ALU), a fundamental building block for the central processing unit in a modern computer. ALUs perform simple and complex operations such as bitwise logical operations and mathematical operations.
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The constructs for the half adder were built in parallel as well as the testing constructs. A future extension to this project would be to create a full adder. More information on each stage of the project is available below.
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| colspan="2" style="border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; padding:5px; vertical-align:middle" | [[Image:Design schematic.jpg|thumb|center|475px|Schematic Design of the Biological Half-Adder]]
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| style="width:25%; border-right-width:thin; border-right-color:black; border-right-style:solid; font-size:large; text-align:left; padding:5px; background-color:#FBCC30" | [[Project | Project Design]] || style="width:25%; border-right-width:thin; border-right-color:black; border-right-style:solid; font-size:large; text-align:left; padding:5px; background-color:#FBCC30"  | [[Modelling | Mathematical Modelling]] || style="width:25%; border-right-width:thin; border-right-color:black; border-right-style:solid; font-size:large; text-align:left; padding:5px; background-color:#FBCC30" | [[Construction_and_Testing | Construction and Testing]] || style="width:25%; font-size:large; text-align:left; padding:5px; background-color:#FBCC30" | [[Future_Work | Future Work]]
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|-
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| style="vertical-align:top; border-right-width:thin; border-right-color:black; border-right-style:solid; padding:5px" |
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* Binary addition and boolean logic
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* Half-adder vs. full-adder designs
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* Biological half-adder implementation
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| style="vertical-align:top; border-right-width:thin; border-right-color:black; border-right-style:solid; padding:5px" |
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* Modelling the gene regulatory network
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* Simulation results
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| style="vertical-align:top; border-right-width:thin; border-right-color:black; border-right-style:solid; padding:5px" |
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* Strategy for half-adder construction
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* Testing constructs for device
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* Test execution plan
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* Submitted parts
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| style="vertical-align:top; padding:5px" |
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* Explanation of a full adder
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* Gene design for full adder
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* Implementation plan
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|}
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<br clear="all">
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{| style="border-spacing:0px; border-width:thin; border-color:black; border-style:solid; width:100%; text-align:center"
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|-
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| style="font-size:x-large; font-weight:bold; font-size:x-large; font-weight:bold; padding:5px; background-color:#FBCC30; border-bottom-width:thin; border-bottom-color:black; border-bottom-style:solid; text-align:left" colspan="15" | Acknowledgements
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| colspan="3" | [[Image:Fsf_logo.gif|150px]] || colspan="3" | [[Image:MEF_logo.gif|150px]] || colspan="3" | [[Image:SFF_Logo.gif|150px]] || colspan="3" | [[Image:WEEFLogo.jpg|150px]] || colspan="3" | [[Image:WatSEF_Logo.jpg|150px]]
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|-
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| colspan="3" | [http://www.science.uwaterloo.ca/fsf/index.html Faculty of Science Foundation ] || colspan="3" | [http://www.student.math.uwaterloo.ca/~mefcom/ Mathematics Endowment Fund ] || colspan="3" | [http://www.eng.uwaterloo.ca/~sff/ Sir Sanford Fleming Foundation] || colspan="3" | [http://www.weef.uwaterloo.ca/ Waterloo Engineering Endowment Fund] || colspan="3" | [http://www.science.uwaterloo.ca/~watsef/mainpage.html Waterloo Science Endowment Fund]
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|-
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| colspan="15" | &nbsp;
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|-
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| colspan="5" | [[Image:UW_EngFacLogo.PNG |150px]] || colspan="5" | [[Image:UW_SciFacLogo.PNG|150px]] || colspan="5" | [[Image:UW_MathFacLogo.PNG|150px]]
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| colspan="5" | [http://www.engineering.uwaterloo.ca University of Waterloo Faculty of Engineering] || colspan="5" | [http://www.science.uwaterloo.ca University of Waterloo Faculty of Science] || colspan="5" | [http://www.math.uwaterloo.ca University of Waterloo Faculty of Mathematics]
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| colspan="15" | &nbsp;
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| colspan="5" style="padding:5px" | [[Image:UW_Waterloocrest.PNG | 150px]] || colspan="10" style="text-align:left; padding:5px" | We would like to thank the following people for their support and guidance:
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* Dr. Trevor Charles
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* Dr. Barbara Moffatt
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* Dr. Joshua Neufeld
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|}
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== Our Design ==
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'''1. A Biological Full Adder'''
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  [[Waterloo | Home ]] | [[Project | Project]] | [[Modelling | Mathematical Modelling]] | [[Construction_and_Testing | Construction and Testing]] | [[Future_Work | Future Work]]  
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</center>
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Our project is a light and chemical controlled full adder meant to reproduce a circuit element called a full-adder within a biological system. In the electronic version, signals come in in binary as values of 0 or 1 which correspond to 0 V or 5 V respectively. For the biological version, we make 0 represent basal expression of a protein and 1 represent full expression of a protein. The 0 value does not to need to be 0 as much as there needs to be a noticeable difference between 0 and 1. A simple half-adder takes in two bits and adds them. The possibilities are as follows:
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[[Image:000.jpg]]
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The value 10 in binary represents 2. The adder can be seen as having two outputs: a sum and a carry. The carry being the number that would be carried into the next column when adding by hand (Figure 1). For example, the sum of 101 + 001 is 110. The problem is in the second column. It needs to add the values in the second column and the carry from the first column (Figure 2). To fix this problem, we need a full adder. In addition to our inputs A and B, it will take a carry in Ci. The behavior of a full adder can be seen in figure 3.
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''Figure 1: Half Adder Truth Table''
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[[Image:111.jpg]]
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''Figure 2: Long Addition of 101 + 001''
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[[Image:222.jpg]]
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''Figure 3: Full Adder Truth Table''
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[[Image:333.jpg]]
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Once we have a full adder, we can chain them to add any number of bits. This is called a ripple carry adder (Figure 4). However the project will not be a ripple carry adder. Only one full-adder unit will be produced.
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''Figure 4: Block Diagram of a Ripple Carry Adder''
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[[Image:444.jpg]]
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'''2. Implementation of the Adder'''
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The current design designates the three inputs A, B, and Ci as red light, tetracycline, and lactose respectively. Ideally, one of these (preferably lactose) will be replaced by blue light. The outputs Co and S will be expressed using red fluorescent and green
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fluorescent protein. The development of the design (Figure 5) best explains how it functions.
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''Figure 5: Project Gene Design''
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[[Image:555.jpg]]
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If none of the promotors are active, nothing happens. This gives us 0 + 0 + 0 = 0 for free. The carry is on when at least two inputs are active. In digital logic, this is an AND gate. The quorum-sensing systems work much like AND gate. Only when both LuR and LuxI are present will anything under the control of Plux be expressed. To accomplish this, LuxI will be put under the control of A and LuxR under the control of B. Only if A and B are active will genes under Plux be transcribed. The three quorum-sensing system Lux, Las, and Cin, cover the combinations A and B, A and Ci, and, B and C. If we make any single input produce GFP, that will make S = 1 in the cases where 1 + 0 + 0, but this will be incorrect in the cases where 1 + 1 + 0. If the input is 1 + 1 + 0, the sum should be repressed. This can be done using the cI repressor. All of the AND gates will produce cI which will stop GFP production if two or more inputs are active. This will produce correct output in all but one case: 1 + 1 + 1. GFP will be repressed because all of the AND gates will be producing cI. To fix this, GFP will be added to the A and B gene after the terminator. Using ’s antitermination system under the control of Ci, GFP will be produced when A and B and Ci are active. This set of genes should match the output shown in figure 3.
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'''3. Photo-Active Blue'''
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CURRENTLY IN PROGRESS
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=== The Inputs ===
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We have chosen to use light as an input for the reasons that it does not require altering the media, it can be turned on and off rapidly, and it has extremely high resolution and accuracy. We will be using one light input in the form of red light and two chemical inputs. The red light will be detected by the previously used Cph1/EnvZ fusion protein ([http://partsregistry.org/Part:BBa_I15010 BBa_I15010]). 
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The chemical inputs to be used are currently being determined. We are considering using a lacIq strain to reduce leakiness of the lac promoter. A RecA strain will be used throughout construction in order to avoid recombination amongst repeated regions; a RecA+ will be necessary for transductions. The F plasmid is a promising final vector, since it holds large amounts of DNA and has a relatively low copy number leading to less leakiness.
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Bacterial two-hybrid systems exist and so we are researching those for a potential final AND gate. The lambda N protein is involved in antitermination, which may prove useful for the final AND gate as well although its antitermination effect is processive, which would be problematic. Supposedly Q protein, also from lambda, is similar but recognizes a special site at which it will allow termination, but more research on its functionality needs to be conducted.
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== Supporters ==
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We would like to thank:
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[http://www.science.uwaterloo.ca Faculty of Science] — [http://www.math.uwaterloo.ca Faculty of Math] — [http://www.engineering.uwaterloo.ca Faculty of Engineering]
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[http://www.weef.uwaterloo.ca Waterloo Engineering Endowment Fund] — [http://www.mef.uwaterloo.ca Mathematics Endowment Fund]
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Latest revision as of 04:02, 27 October 2007

UW iGEMLogoHeader.png


Our Team
Undergraduate Members
Faculty and Graduate Advisors
The UW iGEM team is a very interdisciplinary group. Our team members span three faculties: Science, Mathematics, and Engineering, and represent a wide range of undergraduate programs: Biology, Biomedical Sciences, Biochemistry, Computer Science, Bioinformatics, Computer Engineering, Electrical Engineering, Chemical Engineering, Systems Design Engineering, and Mathematical Physics.

Drawing on our diverse backgrounds, we bring a wide range of skills and modes of creative thinking to our iGEM project. The iGEM competition is providing us with an opportunity to become more familiar with the emerging field of synthetic biology in an engaging and fun atmosphere. In addition to gaining experience in the design, construction, and analysis of genetic circuits, we are also meeting the challenge of bringing together a large, diverse group toward a common goal.


Our Project
Abstract
The goal of this project is to design a basic device for computing. Our idea was to reproduce a circuit element called a half adder with DNA, which takes in two 1-bit inputs, adds them, and outputs a sum and a carry. Our device responds to two inputs: red light and the chemical tetracycline. The input sensors control a set of genetic switches in order to carry out the computation and fluoresces green, red, or neither, depending on the outcome.

Half adders are used as building blocks for full adders, which perform calculations similar to long addition but in binary. They are also an essential component in a device called the Arithmetic Logic Unit (ALU), a fundamental building block for the central processing unit in a modern computer. ALUs perform simple and complex operations such as bitwise logical operations and mathematical operations.

The constructs for the half adder were built in parallel as well as the testing constructs. A future extension to this project would be to create a full adder. More information on each stage of the project is available below.

Schematic Design of the Biological Half-Adder
Project Design Mathematical Modelling Construction and Testing Future Work
  • Binary addition and boolean logic
  • Half-adder vs. full-adder designs
  • Biological half-adder implementation
  • Modelling the gene regulatory network
  • Simulation results
  • Strategy for half-adder construction
  • Testing constructs for device
  • Test execution plan
  • Submitted parts
  • Explanation of a full adder
  • Gene design for full adder
  • Implementation plan


Acknowledgements
Fsf logo.gif MEF logo.gif SFF Logo.gif WEEFLogo.jpg WatSEF Logo.jpg
[http://www.science.uwaterloo.ca/fsf/index.html Faculty of Science Foundation ] [http://www.student.math.uwaterloo.ca/~mefcom/ Mathematics Endowment Fund ] [http://www.eng.uwaterloo.ca/~sff/ Sir Sanford Fleming Foundation] [http://www.weef.uwaterloo.ca/ Waterloo Engineering Endowment Fund] [http://www.science.uwaterloo.ca/~watsef/mainpage.html Waterloo Science Endowment Fund]
 
UW EngFacLogo.PNG UW SciFacLogo.PNG UW MathFacLogo.PNG
[http://www.engineering.uwaterloo.ca University of Waterloo Faculty of Engineering] [http://www.science.uwaterloo.ca University of Waterloo Faculty of Science] [http://www.math.uwaterloo.ca University of Waterloo Faculty of Mathematics]
 
UW Waterloocrest.PNG We would like to thank the following people for their support and guidance:
  • Dr. Trevor Charles
  • Dr. Barbara Moffatt
  • Dr. Joshua Neufeld 


  Home  |  Project |  Mathematical Modelling |  Construction and Testing |  Future Work
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