The Systems Biology of COVID-19 and the SARS-CoV-2 virus. The class will build a foundation that includes the emergence of complexity, simple biological subsystems, their reductionist and equivalent toy and organ-chip models, and the measurements required to specify model architecture and parameters. Applications to biology, physiology, medicine, chemical and biological defense, pharmacology, drug discovery, and toxicology. UGrad: PHYS 240 01 and BME 290B; Grad: PHYS 326 and BME 395C.
0. I had never heard of optical tweezers until a couple of days ago so knew very little.
ReplyDelete1. All of it.
2. I am sure there are some but still trying to understand the concept.
3. None.
4. Having not see or dealt with optical tweezers the concept seems more theoretical than real.
SysBio13 Asgn_6D_Class_06_Article_12_2013_09_10
ReplyDelete0. Knew: Very basic idea of optical traps.
1. Learned: Position clamp vs. force clamps. Instrumentation setup and basic techniques. Use in studying kinesin.
2. Question: What is the purpose of the bead? Why can you not just trap the kinesin protein?
3. Presentation: ---
4. Thoughts: Seems like the concentrations of ATP changing the speed of stepping could also be affecting the step size. Similarly, could the various stiffness be doing the same thing? How do you know if you have the correct conditions such that you are measuring its natural movement?
0 Knew: basic function of optical tweezers and force measurement
ReplyDelete1 Learned: The concept of position and force clamps to measure the movement of kinesins and forces exerted by them
2 Pressing: Is there a direct balance of the forces (exerted by laser and kinesin)? if so, how is there relative movement of the kinesin?
3 Presentation: Lasers and Optics
4 Thoughts: I am interested to see how we apply this to our discussion of systems biology.
1. a. Optical tweezers can be used as position clamp and force clamp.
ReplyDeleteb. The fig 2 and fig 4, 5 are extremely helpful to understand the principles behind laser tweezers and how one could using knobs such as beam positon, laser intensity and stiffness to build feedback loop to both monitor position and measure corresponding force.
2. why the optical tweezers reach the resolution of nanometers when the tracked particle is about 10um?
David Wooten
ReplyDeleteSysBio13 Asgn_6D_Class_06_Article_12_2013_09_10
0. Knew: The basic concept of optical traps
1. Learned: Considerations like stiffness, compliance, and roughly how they get dealt with using feedback control ("Finesse the Problem Altogether!")
2. Pressing ?: Can this be used in vivo? Or at least on-a-chip?
3.
4. Thoughts: This has been a lot to take in. I'm looking forward to learning about it with more clarity in class.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_6D_Class_06_Article_12_2013_09_10
0. Knew: Some vague principles of the physics behind this.
1. Learned: Need for soundproofing and blocking air currents etc.
2. Pressing: How does the Heisenberg Uncertainty Principle apply here?
3. Presentation: Basics of laser instrumentation.
4. Thoughts: The laser is being modulated with an acoustic signal. The signal is transferred to whatever the laser strikes. One can use a super-sensitive microphone (e.g., from Bruel & Kjaer http://www.bksv.com/) to LISTEN to what is going on, i.e., how the sound is being modulated. (This principle was used in an anesthetic agent gas monitor.) If you had a microphone that was sensitive ENOUGH, you would be able to really, truly HEAR the steps of kinesin (from changes in the force).
0. Knew: Basic principles of optical tweezing.
ReplyDelete1. Learned:Balance of scattering force and gradient force. Wavelengths of 800 - 1100 nm are used to minimize damage to biological specimens.
2. Pressing ?: I know the scattering and gradient forces cancel (net force = 0) but does this put any stress on the trapped object? (Is the cell or molecule being stretched while at rest?)
3. Optics of laser manipulation
4. There could be problems if the forces on the trapped object stretch the object while it is supposed to be at rest (net force = 0). This could also be valuable experimentally to determine effects of stretching.
0. Knew: -
ReplyDelete1. Learned: Use of different methods for finding force acting on particle or the displacement of the particle by a controlled force. Bead ‘handle’ displacements can be correlated to kinesin motor action. Through a variety of mechanisms the mechanical dynamics of a molecule can be elucidated and subsequently coupled with the known structure of said molecule to better describe its function.
2. Pressing: Even at a low attenuation coefficient some energy is absorbed by the molecule in question, so does that reduce the viability of gathered data if trapping kinesin directly? Does this strong-arm scientists into using the handle method?
3. Presentation: Going through the thought process of choosing which method/tweezer setup gives best results without being overly cumbersome.
4. Thoughts: going over the merits and setbacks of each technique was interesting, realizing the versatility of optical tweezers.
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