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Title:	Coupled oscillators: protein and acoustics
Author:	McFarlane, Angelique N.
View Online:	njit-etd2022-049 (ix, 29 pages ~ 2.5 MB pdf)
Department:	Department of Physics
Degree:	Master of Science
Program:	Materials Science and Engineering
Document Type:	Thesis
Advisory Committee:	Prodan, Camelia (Committee chair) Ahn, Ken Keunhyuk (Committee member) Shakib, Farnaz A. (Committee member)
Date:	2022-08
Keywords:	Microtubules Topological insulators SSH model Acoustics Protein Resonators
Availability:	Unrestricted
Abstract:	This work encompassed three different vibrational energy transfer studies of coupled resonators (metal, topological, and microtubule comparison) inspired by the lattices of microtubules from regular and cancerous cells. COMSOL Multiphysics 5.4 was utilized to design the experiment. The simulation starts with an acoustic pressure study to examine the vibrational modes present in coupled cylinders, representing α-, β-tubulin heterodimers. The Metal Study consisted of 3 models (monomer, dimer, and trimer) to choose the correct height (40 mm) and mode (Mode 1) for study. The Topological Study was run to predict and understand how the lattice structure changes over a parametric sweep (Qian et al. [7]). This study includes a Su-Schrieffer-Heeger Model for prediction, then a Model inspired by the microtubule protofilament. Finally, a new proposed method is given to simulate a microtubule. Study 3 has 2 models, both with a two-dimensional lattice, but the second with two distinct domains to emulate the 80 % - 20 % healthy/cancerous regions within a cancerous microtubule. The spectrums from each model is inspired by the microtubule-associated proteins (MAPs) bound to the tubulin dimers, in Region 1, then unbinding in Region 2. The Cancerous Model shows less energy held within the lattice as compared to the Microtubule Model. Future work could involve changing the coupling strengths and distances to conform to schematics from Mart´inez et al. [5] and Deniz et al. [4].