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. Optical tweezers / trapping deals with extremely small objects so how do you know its working? There seems to be a lot that could be wrong / off.
3. None.
4. The concept is difficult for me to wrap my head around yet there are tremendous application.
0 Knew: Basic setup of optical tweezers and their ability to trap particles.
ReplyDelete1 Learned: the specific design considerations and equations used to analyze data
2 Pressing: How do optical tweezers monitor movement of particles in the axial direction? (direction of laser beam)
3 Presentation: Lasers and Optical Forces
4 Thoughts: Still confused as to how light can exert force. Is it the bead that functions as the diode in this case?
Look at the Wikipedia page again - first paragraph of General Description. The particles being trapped react to the electric field produced by the photons in the waist of the beam - the electrical equivalent of a magnet attracting a piece of "soft" (not magnetized)iron. The resulting electric dipole moment induced in the particle reacts with the gradient of the electric field to push the particle towards the axis. (Note that a uniform field attracts net charge, but the particles have no net charge. But a gradient can attract a dipole - so the electric field in the laser beam creates the dipole moment, and the gradient in the electric field produces the lateral force. Neat trick). There is also downward pressure by the photons themselves.
ReplyDeleteDavid Wooten
ReplyDeleteSysBio13 Asgn_6E_Class_06_Article_13_2013_09_10
0. Knew: Some basics of optical traps and feedback control
1. Learned: About holographic optical traps... cool!
2. Pressing ?: ---
3. Presentation: ---
4. Thoughts: I'm still trying to bring things together in my mind. Looking forward to a good class discussion.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_6E_Class_06_Article_13_2013_09_10
0. Knew: Not much, except what was in the earlier material.
1. Learned: Issue of detecting the position of what is trapped. More on isolation of sound, air motion, etc. Optical torque.
2. Pressing: The ultrasound signal is modulating the laser signal. Is anyone listening to (transducing) the reflected ultrasound signal? Or the transmitted or refracted signal?
3. Presentation: Principles of ultrasound
4. A trapped particle - with the spring constant model - should have a fixed resonant frequency. Can this not be measured?
But the stiffness should vary in all three dimensions, or at least be different for axial vs. radial ... Thus it would different resonance in different axes (like Dr. Wikswo on his swing).
0. Knew: Basics of optical tweezing
ReplyDelete1. Learned: Commercial systems are available. Position detection techniques.
2. Pressing ?: Does inducing a dipole moment in the particle manipulated affect its structure (e.g. proteins that fold based on charged and uncharged domains)?
3. Presentation: Acousto-optic deflectors; Piezoelectric stage technology
4: Thoughts: The piezoelectric stage technology required for trapping is incredible (positional uncertainty of 1 nm). This stage could be used in 3D printing of organs and capillaries.
0. Knew: Basics of instrumentation and manipulation of optical tweezers.
ReplyDelete1. Learned: Gradient force dependent on polarizability of the molecule and optical intensity gradient, steep gradients required, optical trapping and position detection based on scattered light, the article introduced obstacles and solutions encountered in using optical tweezers.
2. Pressing: Where’s the lower limit on positioning quantification, is there a region where movements are so small they can’t be differentiated from random light-molecule collisions?
3. Presentation: The paper mentioned the potential gains by combining optical trapping and single molecule fluorescence, since 2004 what progress has been seen in that field?
4. Thoughts: Going through the article reinforced some of the topics previously discussed, I thought he text accompanying the figure describing transcription was especially enlightening.
SysBio13 Asgn_6E_Class_06_Article_13_2013_09_10
ReplyDelete0. Knew: Basics on optical tweezers ability to trap particles.
1. Learned: More on instrumentation, design, and measurements of optical tweezers
2. Questions: When would you move the stage versus the bead itself to align the object of interest in the trap?
3. Presentation: ---
4. Thoughts: I think I have the main idea, but the more complicated portions on collecting data and calibrating I am still working to grasp.
Typically one grabs a bead to which the molecule is attached.
ReplyDeleteBlog harvested.
ReplyDeleteJPW