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.
Will Matloff
ReplyDelete9/Novak Oscillators
0. Knew: Negative feedback is an essential component of biochemical oscillators.
1. Learned: The conditions needed for oscillation include nonlinearity of reaction kinetics, enough memory in the negative feedback loop, and proper balancing of timescales of the components in the loop. There are numerous ways to implement these conditions, including taking advantage of structure with compartmentalization.
2. Pressing?: What is the importance of chaotic oscillators?
3. Presentation: Deterministic chaos.
4. Thoughts: The biochemical interactions that lead to oscillations really add a lot of complexity to biology.
Brian Evans
ReplyDelete9/Design Principles of Biochemical Oscillators
0. Knew: The four general requirements for biochemical oscillations.
1. Learned: That an explicit time delay can be substituted by the introduction of intermediate states. As long as the intermediate states have the right balancing of rate constants, then they effectively introduce a time delay into the system.
2. Pressing?: The idea of entrainment is really interesting to me in relevance to the heart. What types of signalling processes result in cellular entrainment (i.e. what type of signalling results in synchronization of the periods of individual biochemical oscillators?) Obviously Gap junctions facilitate entrainment, but are there other, less obvious methods of entrainment?
3. Presentation: Biological Entrainment
4. Thoughts: I thought the comments on dynamic genetic diseases were really interesting: having a gene that is defective in its rate constant but still effective in function can result in pathological oscillatory behavior or even cause the damping of a biochemical oscillator into a steady state, the result depends on the timescale balancing constraints and non-linearity constraints inherent to the system.
Erica Curtis
ReplyDelete9/Design Principals of Biochemical Oscillators
0. Knew - Biochemical oscillators require negative feedback, time delays, and non-linearity.
1. Learned - Oscillations cannot be sustained in a negative-feedback loop with less than three components. Time delay is actually a type of memory due to bistability and the ability to switch between two stable steady states.
2. Pressing Question - Does hysteresis and negative feedback result in an oscillatory mechanism involving memory? I am also not sure that I fully understand the graphs.
3. Presentation - Biological Sources of Nonlinearities
4. Thoughts - I liked the concluding comments on how biochemical oscillations may have evolved and would like to know instances where oscillations were selected for and maladaptive ones.
Ayeeshik Kole
ReplyDelete9/Novak Oscillators
0. Knew: Biological control and oscillatory patterns can be modeled using quantitative models of feedback and time-delays.
1. Learned: Biochemical oscillators require negative feedback, time-delays, nonlinear 'destabilization,' and consumption/production rates must be in the appropriate timescale.
2. Pressing?: What does it mean to have "appropriately balanced" processes? How do you build/use the nonlinearity constraint graphs?
3. Presentation: Oscillator defects and subsequent diseases
4. Thoughts: One the referenced articles mentioned that positive feedback can make a negative-feedback cell-cycle oscillator makes it more robust. I'm curious as to how this works and how they showed that experimentally.
Zach Eagleton
ReplyDelete9/Design Principles of Biochemical Oscillators
0 Knew: Basic reacation kinetics from the previous paper. Many processes in biology are oscillatory.
1 Learned: Biochemical oscillators are all built around some sort of negative feedback loop, and requires sufficient nonlinearity reaction kinetics, cell "memory", and proper timescale balancing.
2 Pressing ?: How does chaotic behavior affect oscillators?
3 Presentation: Cell "memory" mechanisms
4 Thoughts: When you are looking at very complex systems how complex are the oscillatry reaction mechanisms. How many outside factors might effect a motif with multiple components and links.
Lucas Hofmeister
ReplyDelete9/Novak
0. Knew: Feedback, time delay, non-linearity
1. Learned: "Nullcline", "memory is a property of biochemical systems with bistability"
2. Pressing?: What about the resource cost (not just the maximum rate with everything readily available) of degrading/producing mRNA vs. proteins. is it easier to have transient changes in mRNA or Protein
3. Presentation: Mixed mode oscillators
4. thoughts: It seems like the answer to most questions is that you have to maintain the proper balance in all of the characteristics/categories of oscillators...