Integration of the Control Software for the Electromagnetic and Permanent Magnet Tweezers Público
Miller, Sam (Spring 2021)
Published
Abstract
Magnetic tweezers are single-molecule instruments that are often used to impart forces and torques on DNA molecules. They typically have a pair of permanent magnets attached to a motor that can be vertically translated and rotated to adjust the magnitude and orientation of the magnetic field, respectively. Then, DNA molecules are chemically attached to the microscope stage and a paramagnetic bead, which translates a magnetic force from the magnetic field onto the molecule. An objective captures images of the samples and computer software uses diffraction pattern analysis to determine the position, magnetic force, and tether length of the DNA molecule. The electromagnetic tweezers developed by the Finzi-Dunlap lab improve upon the existing technology by generating a magnetic field with current-carrying wires. Although this set-up offers numerous advantages over traditional magnetic tweezers, the program that drives the electromagnetic tweezers existed independently of the permanent magnet program. As a result, users of the electromagnetic tweezers were required to launch and engage with two separate, non-communicative programs. In order to solve this problem, I introduced a new “Axis-type” class that mimicked the behavior of the existing classes that represented the motors in the permanent magnet program. The ElectromagnetAxis class wraps all of the functionality required to set the current values that map to the strength and orientation of the resulting magnetic field. Additionally, this class collects all of the relevant data from the electromagnetic tweezers program into a single place. As such, ElectromagnetAxis objects allow the electromagnet program to access the particle-tracking and data-processing components of the permanent magnet program. The result is a single, unified program that launches and closes simultaneously, allows for the manipulation of the magnetic field through the design introduced with the electromagnetic tweezers program, and tracks beads and processes data through the software from the permanent magnetic tweezers program. Finally, the unified software shows deference for the tenets of the object-oriented programming paradigm through increased encapsulation of methods and properties. Therefore, users of the Finzi-Dunlap lab’s electromagnetic tweezers only need to operate a single program to investigate the effects of magnetic forces and torques on DNA molecules.
Table of Contents
Transcription and Supercoiling. 1
Magnetic Tweezers. 3
Electromagnetic Tweezers. 7
Hardware. 7
Software. 9
Problem and Rationale. 11
Simultaneous Launching and Closing of the Two Programs. 13
Development of the Current Object. 15
Adding Speed Parameters. 20
Integration of Simple measurements. 22
Force Extension. 23
Chapeau Curve. 25
Object Oriented Design. 26
Robustness. 26
Conclusion. 28
References. 31
Appendix A – Bead Simulation. 32
Appendix B – Relevant Code. 34
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