University of Central Florida STARS Electronic Theses and Dissertations, 2004-2019 2019 Nanoscale Functional Imaging by Tailoring Light-matter Interaction to Explore Organic and Biological Systems Negar Otrooshi University of Central Florida Part of the Physics Commons Find similar works at: https://stars.library.ucf.edu/etd University of Central Florida Libraries http://library.ucf.edu This Doctoral Dissertation (Open Access) is brought to you for free and open access by STARS. It has been accepted for inclusion in Electronic Theses and Dissertations, 2004-2019 by an authorized administrator of STARS. For more information, please contact [email protected]. STARS Citation Otrooshi, Negar, "Nanoscale Functional Imaging by Tailoring Light-matter Interaction to Explore Organic and Biological Systems" (2019). Electronic Theses and Dissertations, 2004-2019. 6695. https://stars.library.ucf.edu/etd/6695 NANOSCALE FUNCTIONAL IMAGING BY TAILORING LIGHT-MATTER INTERACTION TO EXPLORE ORGANIC AND BIOLOGICAL SYSTEMS by NEGAR OTROOSHI B.S. Azad University Tehran Central Branch, 2008 M.Sc. University of Tehran, 2012 M.Sc. University of Central Florida, 2015 A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Physics in the College of Science at University of Central Florida Orlando, Florida Spring Term 2019 Major Professor: Laurene Tetard © 2019 Negar Otrooshi ii ABSTRACT Probing molecular systems with light has been critical to deepen our understanding of life sciences. However, conventional analytical methods fail to resolve small quantities of molecules or the heterogeneity in molecules assembled into complex systems. This bottleneck is mostly attributed to light diffraction limit. In recent years, the successful implementation of new approaches to achieve sub-wavelength chemical speciation with an Atomic Force Microscope (AFM) has paved the way to a deeper understanding of the effect of local composition and structure on the functional properties of a larger scale system. The combination of infrared light, to excite the vibrational modes of a sample, and AFM detection to monitor the resulting local photothermal expansion has emerged as a powerful approach. In this work, we explore new applications of AFM-infrared (IR) to further the understanding of proteins and bacterial cells. We first consider the vibrational modes and secondary structure of proteins. We show that beyond the localized IR fingerprint of the system, light polarization could affect the response of the protein. To investigate this further, we combine the AFM-IR measurements with plasmonic substrates to tune the electromagnetic field. Using plasmonic structures, we map the electromagnetic field confinement using nanomechanical infrared spectroscopy. We detect and quantify, in the near field, the energy transferred to the lattice in the form of thermal expansion resulting from the heat generated. We compare the photothermal expansion patterns in the structures under linearly and circular polarized illumination. The results suggest the formation of hot spots, of great interest for biomolecules detection. Using a model system, poly-L-lysine, we show that the IR spectrum and the vibrational circular dichroism fingerprint of a chiral biological system can be probed at the nanoscale, far beyond the conventional limits of detection. The second iii part of the study focuses on utilizing the capabilities of AFM-IR to investigate bacterial cells and their responses to nanoparticle-based treatments. We highlight the potential of these new capabilities to further dive into the fundamental molecular mechanism of antibacterial activity and of development of drug resistance. We conclude this work by providing a perspective on the impact nanoscale functional imaging and spectroscopy can have on life sciences and beyond. iv To my husband Nima and my parents v ACKNOWLEDGMENTS I would like to thank all those contributed to this achievement. First and foremost, I would like to thank my advisor, Dr. Laurene Tetard for giving me this opportunity to work on my idea and accomplish this work. It was her constant guidance that developed my research project and also helped me grow into the scientist that I am today. I would like to thank my committee members, Dr. Peale, Dr. Tatulian, and Dr. Santra, whose inputs have helped me to stay on track with my research. This work was accomplished in collaboration with several researchers. I would like to thank to Dr. Abraham Vazquez Guardado from the UCF College of Optics (CREOL) for fabricating the cavity-coupled achiral microdisks, and for personal communications on the topic. I would like to thank Dr. Santra and his students Mitsushita and Ali for providing the bacteria and synthesizing the nanoparticles for antibacterial treatments. I would like to thank the University of Central Florida, the Department of Physics and also the Nanoscience Technology Center for providing numerous opportunities to pursue this work. I would like to thank all my teachers and mentors, who have taught me and helped me to get to this level. Lastly, I would like to thank my family, lab members, and friends. I would like to thank my husband, Nima, and my parents who always believe me and support me. I would like to thank all my amazing lab members, specifically Mikhael, Briana, Fernand, Raphael, Chance and Ahmad. Lastly, I would like to thank my friends, who are like my sisters, Javaneh, Haleh, Nahal, Fereshteh, and Mina. vi TABLE OF CONTENTS TABLE OF CONTENTS .............................................................................................................. vii LIST OF FIGURES ........................................................................................................................ x CHAPTER 1 INTRODUCTION .................................................................................................. 20 1.1 Motivation ........................................................................................................................... 20 1.2 Background ......................................................................................................................... 22 1.2.1 Chirality in life science ................................................................................................. 22 1.2.2 Bacteria characterization at nanoscale .......................................................................... 23 1.3 Thesis overview................................................................................................................... 24 CHAPTER 2 CHARACTERIZATION METHODS.................................................................. 26 2.1 Infrared (IR) Spectroscopy ................................................................................................ 26 2.1.1 Michelson Interferometer ............................................................................................. 32 2.2 Polarization of light ............................................................................................................. 35 2.3 Atomic Force Microscopy (AFM) ...................................................................................... 38 2.3.1 The physics behind tip-sample interactions.................................................................. 40 2.4 AFM-IR ............................................................................................................................. 44 2.4.1. AFM-IR theoretical overview ..................................................................................... 48 2.4.2. Cantilever response to the thermal expansion ............................................................. 52 CHAPTER 3 CHIRALITY AT NANOSCALE ......................................................................... 58 3.1 Introduction ...................................................................................................................... 58 vii 3.1.1 Chiral biomolecule overview ...................................................................................... 58 3.1.2 Circular dichroism (CD) spectroscopy ......................................................................... 64 3.1.3 CD spectroscopy limitation ........................................................................................ 68 3.1.4 CD spectroscopy at nanoscale ...................................................................................... 69 3.2 Experimental section ......................................................................................................... 83 3.2.1 Fabrication and sample preparation ............................................................................ 84 3.2.2 Plasmonic structures evaluation ................................................................................ 85 3.2.3 Experimental setup ..................................................................................................... 89 3.3 Results and discussions ....................................................................................................... 95 3.3.1 AFM-IR photothermal expansion of plasmonic structure for linear polarization ...... 95 3.3.2 AFM-IR photothermal expansion of plasmonic structure for circular polarization . 100 3.3.3 Vibrational-CD spectroscopy at nanoscale ................................................................. 102 3.3.4 IR nanopolarimetry of Poly-L Lysine beyond vCD ................................................. 105 3.4 Conclusion ........................................................................................................................