Biomechanical Information Transfer: Maximum Caliber, λ Genome Ejection Dynamics, and the Formation of Otoliths in Zebrafish

Author: Wu, David Dah-wei

Year: 2010

Degree: Dissertation (Ph.D.)

Advisors: Fraser, Scott E.; Phillips, Robert B.

Committee Members: Pierce, Niles A.; Wang, Zhen-Gang; Brady, John F.; Fraser, Scott E.; Phillips, Robert B.

Option: Bioengineering

DOI: 10.7907/X454-MV52

Abstract

Biology is inherently a non-equilibrium process - constantly battling or co-opting the entropic enemy in order to achieve its sine qua non: growth, development, and reproduction. Involved in these processes is the formation of temporal and spatial order from disorder, and the transfer of information in genomic content but also in the form of physical principles.

First, I will describe a different way to analyze dynamics called Maximum Caliber, a model-free application of the Principle of Maximum Entropy to trajectories or processes, based purely on information theorya. We apply Maximum Caliber to analyze particles diffusing on a dual-minima energy landscape and attempt to describe and predict the probability distribution of trajectories. Next, I will discuss our efforts in analyzing the literal transfer of information from one organism to the next: specifically, how phage lambda's DNA gets inside Escherichia coli. The use of counterions as a parameter to tune the force of in vitro ejections is clarified before performing suggestive in vivo injection experiments. Last, the process of building and shaping the otolith of the zebrafish (the accelerometer and hearing organ) is analyzed, with the conclusion that it is possible to generate said organ through purely physical mechanisms, suggesting that biological information transfer is not exclusively genetic.

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