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Single molecule optical absorption by STM and a new algorithm for solving dynamics on a free energy surface

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Title: Single molecule optical absorption by STM and a new algorithm for solving dynamics on a free energy surface
Author(s): Scott, Gregory E.
Director of Research: Gruebele, Martin H.
Doctoral Committee Chair(s): Gruebele, Martin H.
Doctoral Committee Member(s): Lyding, Joseph W.; Johnson, Harley T.; McDonald, J. Douglas
Department / Program: Chemistry
Discipline: Chemistry
Degree Granting Institution: University of Illinois at Urbana-Champaign
Degree: Ph.D.
Genre: Dissertation
Subject(s): single-molecule scanning tunneling microscopy optical absorption free energy surfaces Smoluchowski equation
Abstract: The combination of the high spatial resolution of the scanning tunneling microscope (STM) and the spectral resolution of a laser provides a powerful tool for probing the local optical and electronic properties of materials. Optical absorption detected by STM offers direct imaging of molecular absorption well below the diffraction limit that hampers traditional spectroscopic methods. This technique is used to optically differentiate carbon nanotubes within nanometers of each other and, further, to resolve local variations in absorption within a single carbon nanotube. Provided from this is direct imaging of the spatial distribution of exciton generation from an optical absorption event. The interactions between light and single molecules are shown to be highly wavelength dependent and are very sensitive to the local electronic environment. Relating experimental thermodynamic and kinetic data to the dynamics on free energy surfaces can be cumbersome for all but the most trivial of cases. Many models have been developed to explain a variety of phenomena, but few methods are appropriate for cases with low kinetic barriers. Those methods that do fit free energy surfaces with low barriers are typically computationally expensive in multiple dimensions. A new method is presented for solving dynamics on free energy surfaces based on the Smoluchowski diffusion equation. Computational cost is saved by reducing the complexity of the surface through the use of a singular value decomposition basis set. Fitting is performed with a parallelized genetic algorithm. Free energy surfaces are fitted in up to 2-dimensions for the α3D and PTB1:4W proteins. The algorithm is further used to create test data for a new method for finding thermodynamic data from kinetic experiments when thermodynamic experiments are insufficient for probing the stability of proteins.
Issue Date: 2011-05-25
URI: http://hdl.handle.net/2142/24422
Rights Information: Copyright 2011 Gregory E. Scott
Date Available in IDEALS: 2011-05-25
2013-05-26
Date Deposited: 2011-05
 

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