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Nonlinear Dynamics of Nanoscale Systems


Hodas, Nathan Oken (2011) Nonlinear Dynamics of Nanoscale Systems. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/8CK3-8F45.


This work builds theoretical tools to better understand nanoscale systems, and it ex- plores experimental techniques to probe nanoscale dynamics using nonlinear optical microscopy. In both the theory and experiment, this work harnesses nonlinearity to explore new boundaries in the ongoing attempts to understand the amazing world that is much smaller than we can see. In particular, the first part of this work proves the upper-bounds on the number and quality of oscillations when the sys- tem in question is homogeneously driven and has discrete states, a common way of describing nanoscale motors and chemical systems, although it has application to networked systems in general. The consequences of this limit are explored in the context of chemical clocks and limit cycles. This leads to the analysis of sponta- neous oscillations in GFPmut2, where we postulate that the oscillations must be due to coordinated rearrangement of the beta-barrel. Next, we utilize nonlinear optics to probe the constituent structures of zebrafish muscle. By comparing experimental observations with computational models, we show how second harmonic generation differs from fluorescence for confocal imaging. We use the wavelength dependence of the second harmonic generation conversion efficiency to extract information about the microscopic organization of muscle fibers, using the coherent nature of second ix harmonic generation as an analytical probe. Finally, existing experiments have used a related technique, sum-frequency generation, to directly probe the dynamics of free OH bonds at the water-vapor boundary. Using molecular dynamic simulations of the water surface and by designating surface-sensitive free OH bonds on the water surface, many aspects of the sum-frequency generation measurements were calcu- lated and compared with those inferred from experiment. The method utilizes results available from independent IR and Raman experiments to obtain some of the needed quantities, rather than calculating them ab initio. The results provide insight into the microscopic dynamics at the air-water interface and have useful application in the field of on-water catalysis.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:nonlinear optics, shg, sfg, GFP, oscillations, zebrafish, master equation
Degree Grantor:California Institute of Technology
Division:Physics, Mathematics and Astronomy
Major Option:Physics
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Fraser, Scott E. (co-advisor)
  • Marcus, Rudolph A. (co-advisor)
Thesis Committee:
  • Politzer, Hugh David (chair)
  • Marcus, Rudolph A.
  • Fraser, Scott E.
  • Atwater, Harry Albert
Defense Date:6 May 2011
Record Number:CaltechTHESIS:05202011-154531397
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:6413
Deposited By: Nathan Hodas
Deposited On:27 May 2011 21:05
Last Modified:09 Oct 2019 17:09

Thesis Files

PDF (Complete Thesis) - Final Version
Creative Commons Attribution.

PDF (Front Matter and Ch1 Introduction) - Final Version
Creative Commons Attribution No Derivatives.

PDF (Ch2 Oscillations on Networks) - Final Version
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PDF (Ch3 Endogenous Second Harmonic Generation in Zebrafish) - Final Version
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PDF (Ch4 Theory of Second Harmonic Generation from Zebrafish Muscle) - Final Version
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PDF (Ch5 Microscopic Structure and Dynamics of Air/Water Interface by Computer Simulations and Comparison with Sum-Frequency Generation Experiments) - Final Version
Creative Commons Attribution.

PDF (Bibliography) - Final Version
Creative Commons Public Domain Dedication.


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