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Created page with "{{PHYS434-2012}} *Welcome *Details and expectations **We will schedule a 2-hour office hour/supplementary instruction sections **Very mathematical course, but we will create ..."

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{{PHYS434-2012}}

*Welcome
*Details and expectations
**We will schedule a 2-hour office hour/supplementary instruction sections
**Very mathematical course, but we will create an infrastructure for you to succeed
**Starting end of October, we will be devoting about one class every two weeks to students presenting journal papers. I will provide you with a list of papers to choose from by mid-September.
**Homeworks will be due by end of the day on Fridays.
*The main questions to be asked in the whole course (not necessarily in this order):
**'''How well, in objective terms, do various biological systems transduce available sensory information?'''
**'''What stays in the way of their performance?'''
**'''Which strategies can be used by the systems to improve the quality of processing?'''
*Intro to ''E. coli'' chemosensing
**''E. coli'' is small -- natural measuring stick. See ''Sizing up E coli'' section in ''Physical Biology of the Cell'' -- see below.
**Can have as few as one or even less of molecules of a chemoattractant in a volume the size of ''E. coli''. 1 nM concentration is about 1 molecule per ''E. coli'' volume
**Still, even with these concentrations, ''E. coli'' can follow chemoattractants (Adler 1975, Budrene and Berg, 1991, 1995)
**The flagella and the run/tumble strategy of ''E. coli'' motion. See movies at http://www.rowland.harvard.edu/labs/bacteria/movies_ecoli.html
**The reason the bacterium does runs is to outrun diffusion: the ability to measure the concentration of a chemical around oneself is limited in accuracy by <math>\delta C/C \sim 1/\sqrt{CaDt}</math>, where <math> C</math> is the concentration, <math> a</math> is the ''linear'' size of the detecting cell, <math> D</math> is the diffusion coefficient, and <math>t</math> is the observation time.
**The ''E. coli'' behavioral strategy is fully dictated by the physical structure of the world it leaves in: small size that limits total number of molecules in the cell volume, diffusion that takes molecules to and away from the cell and prevents the bacterium from keeping moving in a straight line, and the need to go to greener pastures.
**The basic structure of the ''E. coli'' chemotaxis signaling pathway. See http://www.rowland.harvard.edu/labs/bacteria/projects_fret.html
*Intro to neural computation
**Neurons communicate with spikes (see Dayan and Abbott, 2005)
**Spikes occur at random times, and it takes only a handful of spikes for a system to make a decision (Rieke et al, 1999)
*Intro to decision making processes
**Behavioral changes in rodents happen on the time scales of only very few observations (Gallistel et al, 2001)
*'''Main point to carry out: Biological signal processing is not deterministic''', hence we will spend the next lectures on some basic probabilistic concepts

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Physics 434, 2012: Lecture 1 - Revision history

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nemenman>Ilya: Created page with "{{PHYS434-2012}} *Welcome *Details and expectations **We will schedule a 2-hour office hour/supplementary instruction sections **Very mathematical course, but we will create ..."

nemenman>Ilya: Created page with "{{PHYS434-2012}} Welcome Details and expectations We will schedule a 2-hour office hour/supplementary instruction sections Very mathematical course, but we will create ..."