1. Senior Design Group 12 Identifying Behavioral Patterns of Living Microorganisms Using Microfluidic Systems Team Members: Jon Sunderland, Justin Mai, Kyle Petersen, Prateek Bhatnagar, Umair Ilyas Project Advisor: Santosh Pandey Co-Advisor: Umesh Vadya Graduate Student Advisors: Archana Parashar, John Carr

2. Outline Project Plan Goals Problems Solutions Design System Design Detailed Design Implementation Prototype Project Closure Project Success Questions & Answers

3. Why? Parasitic nematodes are harmful for the environment Understanding the behavior of nematodes in order to prevent their negative effects http://www.divergence.com/ma_crop_protection.php Why C. elegans? C. elegans is a transparent nematode whose genome has been mapped completely

4. Problems How to get useful work out of microorganisms Finding response of C. elegans to different taxes Finding effective ways of mixing immiscible and miscible chemicals at a micro level Producing results from data coming out of the tracking software

5. Solutions/Project Goals Identify, characterize, and understand behavioral patterns of microorganisms by designing and fabricating microfluidic chips Design liquid diffusion biomotors Create data analysis GUI

6. Concept Sketch Concept: Use taxes to develop biomotors Electrotaxis: response to electric fields Magnetotaxis: response to magnetic fields Geotaxis: response to gravitational fields

7. Functional Requirements Determine and quantify the effects of magnetic fields (magnetotaxis) on C. elegans Design and test useful biomotor applications Produce work C. elegans sort themselves Develop procedures to perform these experiments

8. Functional Requirements Create an apparatus that is necessary but unavailable Holders with specific dimensions, magnetic properties or optical properties Design microfluidic chip layout Obtain accurate experimental data Ethical research, which includes quality of research, ethical conduct, proper acknowledgements

9. Non-Functional Requirements

10. Intuitive data analysis Easy-to-use universal design Robust for adding additional plots Significantly reduced plotting times

11. Fabrication of Microfluidic Chips Soft Lithography Process: Master Mold Fabrication Polymer Molding

12. Market & Literature Previous taxes studied include electrotaxis, phototaxis, chemotaxis, phonotaxis, and some geotaxis Magnetotaxis has not been fully understood

13. Market & Literature C. elegans genotypes well studied, phenotypes not so much C. elegans cheap, easy to store, simple, and transparent Knowledge of previous research is important Our research needs to be new and useful Figure: C.elegans in microfluidic channel

14. Resource & Cost Estimate

15. Project Schedule (Gantt Chart)

16. Potential Risks and Mitigation Strategies All risks that can be foreseen can be avoided through proper procedure in the lab. There are few chemicals that are dangerous and if those are properly stored then no one is in danger of exposure. Proper procedure was determined so that all participants were aware of the risks. One can seriously injure oneself while working with extremely strong magnets. Magnets should be handled properly

17. System Design

18. Functional Decomposition Project flow highlights biomotor design Using multiple taxes

19. Technology Platforms Software Microscope imaging software – Q-Imaging & Q-Capture Pro Worm tracking – Worm Tracker V2.1.3 & Analyzer Matlab Hardware Microscopes integrated with cameras Strong permanent magnets of varying strengths (magnetotaxis) Custom designed magnet holders Misc. equipment include glass slides, forceps, masks, chip designs etc.

20. Magnetotaxis Experiment Design Main goal, to eliminate bias in C. elegans’ behavior Stage 1: Chip Design

21. Magnetotaxis Experiment Design Understand relation of field and behavior 6 data points Stage 2: Determine Effect of Field Strength

22. Magnetotaxis Experiment Design Prefer North? Prefer North to South? Stage 3: Determine Effect of Field Polarity

23. Magnetotaxis Experiment Design Experiment: Reverse polarity, observe response rate Stage 4: Determine Amount of Control Jon Please add two most relevent result graphs on magnetotaxis

24. Magnetotaxis Experiment Design Experiment: Reverse polarity, observe response rate Stage 4: Determine Amount of Control Jon Please add two most relevent result graphs on magnetotaxis

25. What are Biomotors Molecular Motors/Molecular walking machines

26. Biomotor Design Stage 1: Developing Ideas for biomotor uses Key objective is to find how C. elegans can be used as biomotors Integrate the taxis results into biomotor design

27. Biomotor Design Stage 2: Designing Microfluidic Chips for the Specific Application Stage 3: Testing Chip Design Stage 4: Optimization of the Biomotor Figure : Fluid Flow/Diffusion Biomotor Design

28. Implementation Two prototype biomotor designs tested for mixing of drugs First design with straight channel was successful

29. Design Tradeoffs Design modification had to be done to the second design Increasing the width of the main channel Decreasing the side angles to 30 ° as opposed to 45°

30. Software Implementation

31. Data Analysis & Results

33. Project Success and Future Work Team was able to demonstrate a workable biomotor design which was the end goal of the project Additionally the team came up with eight biomotor designs which can be tested by future teams working on same or similar projects

34. Questions & Answers