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Title: Multiscale modeling and computation of nano-electronic transistors and transmembrane proton channels
Creator: Chen, Duan
Date: 2010
Collection: Electronic Theses & Dissertations
Description: The miniaturization of nano-scale electronic transistors, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. In biology, proton dynamics and transport across membrane proteins are of paramount importance to the normal function of living cells. Similar physical characteristics are behind the two subjects, and model...
Show moreThe miniaturization of nano-scale electronic transistors, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. In biology, proton dynamics and transport across membrane proteins are of paramount importance to the normal function of living cells. Similar physical characteristics are behind the two subjects, and model simulations share common mathematical interests/challenges. In this thesis work, multiscale and multiphysical models are proposed to study the mechanisms of nanotransistors and proton transport in transmembrane at the atomic level.For nano-electronic transistors, we introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential. This framework enables us to put microscopic and macroscopic descriptions on an equal footing at nano-scale. Additionally, this model includes layered structures and random doping effect of nano-transistors.For transmembrane proton channels, we describe proton dynamics quantum mechanically via a density functional approach while implicitly treat numerous solvent molecules as a dielectric continuum. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered in atomic details. We formulate a total free energy functional to include kinetic and potential energies of protons, as well as electrostatic energy of all other ions on an equal footing.For both nano-transistors and proton channels systems, the variational principle is employed to derive nonlinear governing equations. The Poisson-Kohn-Sham equations are derived for nano-transistors while the generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained for proton channels. Related numerical challenges in simulations are addressed: the matched interface and boundary (MIB) method, the Dirichlet-to-Neumann mapping (DNM) technique, and the Krylov subspace and preconditioner theory are introduced to improve the computational efficiency of the Poisson-type equation. The quantum transport theory is employed to solve the Kohn-Sham equation. The Gummel iteration and relaxation technique are utilized for overall self-consistent iterations.Finally, applications are considered and model validations are verified by realistic nano-transistors and transmembrane proteins. Two distinct device congurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our three dimensionalnumerical simulations. For these devices, the current uctuation and voltage threshold lowering effect induced by discrete dopants are explored. For proton transport, a realistic channel protein, the Gramicidin A (GA) is used to demonstrate the performance of the proposed proton channel model and validate the efficiency of the proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. Proton channel conductances are studied over a number of applied voltages and reference concentrations. Comparisons with experimental data are utilized to verify our model predictions.
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Title: Nanorobotic end-effectors : design, fabrication, and in situ characterization
Creator: Fan, Zheng (Of Michigan State University)
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Nano-robotic end-effectors have promising applications for nano-fabrication, nano-manufacturing, nano-optics, nano-medical, and nano-sensing; however, low performances of the conventional end-effectors have prevented the widespread utilization of them in various fields. There are two major difficulties in developing the end-effectors: their nano-fabrication and their advanced characterization in the nanoscale. Here we introduce six types of end-effectors: the nanotube fountain pen (NFP), the...
Show moreNano-robotic end-effectors have promising applications for nano-fabrication, nano-manufacturing, nano-optics, nano-medical, and nano-sensing; however, low performances of the conventional end-effectors have prevented the widespread utilization of them in various fields. There are two major difficulties in developing the end-effectors: their nano-fabrication and their advanced characterization in the nanoscale. Here we introduce six types of end-effectors: the nanotube fountain pen (NFP), the super-fine nanoprobe, the metal-filled carbon nanotube (m@CNT)-based sphere-on-pillar (SOP) nanoantennas, the tunneling nanosensor, and the nanowire-based memristor. The investigations on the NFP are focused on nano-fluidics and nano-fabrications. The NFP could direct write metallic "inks" and fabricating complex metal nanostructures from 0D to 3D with a position servo control, which is critically important to future large-scale, high-throughput nanodevice production. With the help of NFP, we could fabricate the end-effectors such as super-fine nanoprobe and m@CNT-based SOP nanoantennas. Those end-effectors are able to detect local flaws or characterize the electrical/mechanical properties of the nanostructure. Moreover, using electron-energy-loss-spectroscopy (EELS) technique during the operation of the SOP optical antenna opens a new basis for the application of nano-robotic end-effectors. The technique allows advanced characterization of the physical changes, such as carrier diffusion, that are directly responsible for the device's properties. As the device was coupled with characterization techniques of scanning-trasmission-electron-microscopy (STEM), the development of tunneling nanosensor advances this field of science into quantum world. Furthermore, the combined STEM-EELS technique plays an important role in our understanding of the memristive switching performance in the nanowire-based memristor. The developments of those nano-robotic end-effectors expend the study abilities in investigating the in situ nanotechnology, providing efficient ways in in situ nanostructure fabrication and the advanced characterization of the nanomaterials.
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Title: On designing biological nanoscale organization
Creator: Young, Eric J.
Date: 2019
Collection: Electronic Theses & Dissertations
Description: "Life at the nanoscale creates a dazzling array machines and structures. Studying these nanoscale creations often requires inter-disciplinary efforts of scientists, along with the support of other personnel. This thesis serves to communicate some personal insights and data captured in studying nanoscale organization of biologically-driven components, as part of such a team. The first chapter addresses spatiotemporal organization of material inside cells, with a focus on scaffolding-type...
Show more"Life at the nanoscale creates a dazzling array machines and structures. Studying these nanoscale creations often requires inter-disciplinary efforts of scientists, along with the support of other personnel. This thesis serves to communicate some personal insights and data captured in studying nanoscale organization of biologically-driven components, as part of such a team. The first chapter addresses spatiotemporal organization of material inside cells, with a focus on scaffolding-type strategies. The second chapter offers a literature perspective on constructing scaffolds with a structurally-characterized protein-domain. The third chapter surveyed functionality of an in vivo designer nanoscaffolding system. The fourth chapter, alongside the appendix materials, forms a collection of future-steps and comments on projects I have encountered while working on my thesis project."--Page ii.
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Title: Physical properties and transformations of low-dimensional systems
Creator: Liu, Dan (Graduate of Michigan State University)
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Evolving from the macroscopic scale to the nanometer scale, inparticular by reducing the dimensionality, fundamental properties(such as electronic and mechanical properties) of certain systemsexhibit dramatic changes, which not only give rise to a wide rangeof emergent phenomena, but also boost technology developmentincluding nanoelectronics, optoelectronics and catalysis. In thisthesis, I utilized combined techniques including densityfunctional theory (DFT), molecular dynamic simulations (MD...
Show moreEvolving from the macroscopic scale to the nanometer scale, inparticular by reducing the dimensionality, fundamental properties(such as electronic and mechanical properties) of certain systemsexhibit dramatic changes, which not only give rise to a wide rangeof emergent phenomena, but also boost technology developmentincluding nanoelectronics, optoelectronics and catalysis. In thisthesis, I utilized combined techniques including densityfunctional theory (DFT), molecular dynamic simulations (MD),continuum elasticity approach, and the tight-binding model toconduct a systematic study on low-dimensional nanostructuresregarding their electronic and mechanical properties as well asunderlying microscopic transformation mechanisms between differentstructural allotropes.First, I briefly introduce the motivation and background of thisthesis. Then, in Chapter 2, I describe the computationaltechniques, mainly the DFT approach, on which most of my thesis isbased.In Chapters 3 and 4, I apply the continuum elasticity method tostudy the phonon spectrum of two-dimensional (2D) andone-dimensional (1D) systems. My results highlight advantages ofthe continuum elasticity approach especially for the flexuralacoustic phonon modes close to the $\Gamma$ point, which areotherwise extremely hard to converge in atomistic calculationsthat use very large supercell sizes.From Chapter 5 to Chapter 7, I focus on allotropes of groupIII, V and VI elements and study boththeir stability and microscopic transformation mechanisms from oneallotrope to another. First, I predicted a stable phosphorus coilstructure, which may form by reconstruction of red phosphorous,and which was synthesized by filling a carbon nanotube withsublimed red phosphorus. Second, I proposed two stable 2Dallotropes of Se and Te. I also suggested and evaluated apromising fabrication approach starting from natural 1D structuresof these elements. After considering low-dimensional chargeneutral systems, I changed my focus to study the effect of netcharge on the equilibrium structure. Considering a heterostructureof alternating electron donor layers an monolayers of boron, Ihave identified previously unknown stable 2D boron allotropes thatmay change their structure under different levels of chargetransfer.From Chapter 8 to Chapter 10, I focus mainly on carbon-basednanomaterials and their properties. In Chapter 8, I proposed a wayto enhance the density of states at the Fermi level in dopedC60 crystals in order to increase their superconductingcritical temperature to room temperature. In Chapter 9, I haveinvestigated a shear instability twisted bilayer graphene usingthe tight binding model. This system is susceptible to very smallstructural changes, since it becomes superconducting in a verynarrow range of twist angles near the 'magic angle'. In Chapter10, I introduced the cause of an unusual negative Poisson ratioand a shape-memory behavior in porous graphene with anartificially designed pattern.In Chapter 11, I finally present general conclusions of my PhDThesis.
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Title: Polyelectrolyte multilayer coatings for conductive nanomaterials patterning and anti-wrinkling applications
Creator: Hendricks, Troy Richard
Date: 2008
Collection: Electronic Theses & Dissertations

Title: Robust control of systems with piecewise linear hysteresis
Creator: Edardar, Mohamed Mohamed
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Hysteresis nonlinearity is found in many control system applications such as piezo-actuated nanopositioners. The positioner is represented as a linear system preceded by hysteresis. This hysteresis nonlinearity is usually modeled by operators in order to simulate their effects in the closed-loop system or to use their inverse to compensate for their effects. In order to reduce the hysteresis effect, an approximate inverse operator is used as a feedforward compensator. The first part of our...
Show moreHysteresis nonlinearity is found in many control system applications such as piezo-actuated nanopositioners. The positioner is represented as a linear system preceded by hysteresis. This hysteresis nonlinearity is usually modeled by operators in order to simulate their effects in the closed-loop system or to use their inverse to compensate for their effects. In order to reduce the hysteresis effect, an approximate inverse operator is used as a feedforward compensator. The first part of our work considers driving an upper bound on the inversion error using the hysteresis model. This bound is a function of the input references, which is much less conservative than constant bounds. It is used in designing the closed-loop control systems. The second part is to design feedback controller to achieve the desired performance. Three different methods are used throughout this work and a comparison between them is also provided. First, we use the conventional proportional Integral (PI) control method, which is extensively used in commercial applications. However, in our method we add a feedforward component which improves the performance appreciably. Second, a sliding-mode-control (SMC) scheme is used because it is one of the very powerful nonlinear robust control methods. Other schemes like high gain feedback and Lyapunov redesign have close results to SMC and hence it is not included in this work. The third control is H∞ control. It is a robust linear control method, which deals with uncertainty in the system in an optimal control structure. Unlike the PI controller, the H∞ controller uses the features of the linear plant in the design which allows to accomplish more than the simple PI controller. Mainly, it can shape the closed-loop transfer function of the system to achieve the design objectives. Including the operators in the closed-loop system, makes it hard to obtain explicit solutions of the dynamics using conventional methods. We exploit two features of piezoelectric actuators to provide a complete solution of the tracking error. First, the hysteresis is approximated by a piece-wise linear operator. Second, the linear plant has a large bandwidth which allows using singular perturbation techniques to put the system in a time-scale structure. We show that the slope of a hysteresis loop segment plays an important role in determining the error size. Our analysis also shows how error is affected by increasing the frequency of the reference input. We verify that the accumulation of the error, which is propagating from segment to another is bounded and derive its limit. We provide a comparison between simulation and the analytic expressions of the tracking error at different frequencies. Experimental results are also presented to show the effectiveness of our controllers compared with other techniques.
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Title: Segmented nano-force sensor
Creator: Dharuman, Gautham
Date: 2013
Collection: Electronic Theses & Dissertations
Description: Nanoscale force sensors are finding widespread applications in atomic and biological force sensing where forces involved range from zeptonewtons to several nanonewtons. Different methods of nanoscale force sensing based on optical, electrical or purely mechanical schemes have been reported. However, each technique is limited by factors such as large size, low resolution, slow response, force range and alignment issues. In this research, a new device structure which could overcome the above...
Show moreNanoscale force sensors are finding widespread applications in atomic and biological force sensing where forces involved range from zeptonewtons to several nanonewtons. Different methods of nanoscale force sensing based on optical, electrical or purely mechanical schemes have been reported. However, each technique is limited by factors such as large size, low resolution, slow response, force range and alignment issues. In this research, a new device structure which could overcome the above mentioned constraints is studied theoretically and experimentally for the possibility of its application in nano-scale force sensing.
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Title: Sensing and actuation of bead-tagged biomaterials on standard CMOS substrates
Creator: Abu-Nimeh, Faisal T.
Date: 2011
Collection: Electronic Theses & Dissertations
Description: Magnetic molecular-level sensing and manipulation are emerging as lab-on-chip platforms. These platforms entail low-cost, low-power, high efficiency, and portable implementations. Biomaterials are usually attached to magnetic beads and used in bio-analysis applications such as sorting, counting, purification, and assembly. Some of the potential applications are 2D biological or artificial tissue assembly at the micro-scale level.Here, we present the design and demonstration of a self...
Show moreMagnetic molecular-level sensing and manipulation are emerging as lab-on-chip platforms. These platforms entail low-cost, low-power, high efficiency, and portable implementations. Biomaterials are usually attached to magnetic beads and used in bio-analysis applications such as sorting, counting, purification, and assembly. Some of the potential applications are 2D biological or artificial tissue assembly at the micro-scale level.Here, we present the design and demonstration of a self-contained device for sensing and manipulating biomaterials tagged with magnetic beads. The core elements of the device consist of all-integrated programmable magnetic coil arrays for pseudo-parallel sensing and actuation, which are capable of maneuvering small (bead-bound) bio-objects individually and larger ones collaboratively. Our design does not require any external magnetic sources. It relies on the magnetic field generated by planar on-chip coil arrays. The coil arrays are selectively and dynamically controlled. Each element, composed of the coil and its logical control circuitry, can detect bio-objects in the order of 1$\mu$m diameter, or manipulate them using eight-level programmable AC or DC magnetic fields. All array sensing and actuation components are shared and multiplexed to reduce the overall imprint. The components are isolated and tuned to work at 900MHz by incorporating high-speed switching (up to 40MHz) for seamless pseudo-parallel execution.In addition, we present a new and unique on-chip biomedical proof-of-concept application. Adopting trends in neuroscience, we employ the magnetic beads to initiate and elongate neuronal axons in vitro on-chip. This application domain will assist in better understanding and studying the process of neuroregeneration, propel future clinical applications, and provide the foundation of techniques needed to wire ``neuronal circuits'' using living cells.
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Title: Sensing and manipulation in a nano-bio environment using atomic force microscopy based robotic system
Creator: Li, Guangyong
Date: 2006
Collection: Electronic Theses & Dissertations

Title: Simulation study of lipid bilayer/nanoparticle interactions
Creator: Musolff, Corey Evan
Date: 2013
Collection: Electronic Theses & Dissertations
Description: A coarse-grained model is used to simulate lipid bilayers (LB) interacting with nanoparticles (NP). Different equilibrium states are observed as the size of the NP is varied along with the interaction strength between the NP and LB. Sufficient attraction causes the NP to become wrapped by the LB. Large NP are able to form pores in the LB. These various outcomes are explained using a continuum theory.The same model is used to simulate pore healing in LB. It is observed that the area of the...
Show moreA coarse-grained model is used to simulate lipid bilayers (LB) interacting with nanoparticles (NP). Different equilibrium states are observed as the size of the NP is varied along with the interaction strength between the NP and LB. Sufficient attraction causes the NP to become wrapped by the LB. Large NP are able to form pores in the LB. These various outcomes are explained using a continuum theory.The same model is used to simulate pore healing in LB. It is observed that the area of the pore decreases linearly with time as explained by Allen-Cahn theory. Bulk properties of the LB can be used to predict the closing time of a pore as well as the amount of charge able to flow through the pore while it is open.
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Title: Structural transitions in nanoscale systems
Creator: Yoon, Mina
Date: 2004
Collection: Electronic Theses & Dissertations

Title: Thermoset polymer-layered silicic acid nanocomposites
Creator: Wang, Zhen
Date: 1997
Collection: Electronic Theses & Dissertations

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