Engineering Commons^™

Regularized Fourier Ptychographic Microscopy, Shiqi Xu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Quantitative phase image (QPI) is a popular microscopy technique for studying cell morphology. Recently, Fourier ptychographic microscopy (FPM) has emerged as a low-cost computational microscopy technique for forming high-resolution wide-field QPI images by taking multiple images from different illumination angles. However, the applicability of FPM to dynamic imaging is limited by its high data requirement. In this thesis, we propose new methods for highly compressive FPM imaging using a data-adaptive sparse coding and an online plug-and-play (PnP) method with non-local priors based on the fast iterative shrinkage/threshold algorithm (FISTA). We validate the proposed method on both simulated and experimental data …

Feature Extraction Form Ct Scan Of Plant Root, Chunyuan Li

All Computer Science and Engineering Research

Roots are vital for plant by absorbing water and nutrients and providing anchorage from beneath the soil. These roles are closely related to the roots’ architecture, which describes the geometry of individual roots and their branching structure. We proposed a pipeline to efficiently annotate root architecture. My contribution focus on building an interactive tool to visual and annotate root architecture. Besides, we come up with heuristics to automate the annotation process.

Computational Geometry Teaching Tool, Yujie Zhou, Tao Ju

All Computer Science and Engineering Research

When students are taking Computational Geometry course which covers many geometry algorithms, most of them are difficult to follow because these algorithms are very abstract even if authors draw pictures to illustrate. In order to help students to get a better understanding of these algorithms, we decide to design Computational Geometry Teaching Tool. This tool is a web application that covers 8 geometry algorithms : Graham Scan, Quick Hull, Line Segment Intersection, Dual, Line Arrangement, Voronoi Diagram, Incremental Delaunay Triangulation and Kd Tree. First, this tool is developed by using JavaScript so that users don't need to install any software …

Long-Term, Super-Resolution Imaging Of Amyloid Structures Using Transient Amyloid Binding Microscopy, Tianben Ding, Kevin Spehar, Jan Bieschke, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Amyloid fibrils and tangles are signatures of Alzheimer disease, but nanometer-sized aggregation intermediates are hypothesized to be the structures most toxic to neurons. The structures of these oligomers are too small to be resolved by conventional light microscopy. We have developed a simple and versatile method, called transient amyloid binding (TAB), to image amyloid structures with nanoscale resolution using amyloidophilic dyes, such as Thioflavin T, without the need for covalent labeling or immunostaining of the amyloid protein. Transient binding of ThT molecules to amyloid structures over time generates photon bursts that are used to localize single fluorophores with nanometer precision. …

Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Various methods exist for measuring molecular orientation, thereby providing insight into biochemical activities at nanoscale. Since fluorescence intensity and not electric field is detected, these methods are limited to measuring even-order moments of molecular orientation. However, any measurement noise, for example photon shot noise, will result in nonzero measurements of any of these even-order moments, thereby causing rotationally-free molecules to appear to be partially constrained. Here, we build a model to quantify measurement errors in rotational mobility. Our theoretical framework enables scientists to choose the optimal single-molecule orientation measurement technique for any desired measurement accuracy and photon budget.

Numerical Simulations Of Flow Past A Triangular Airfoil And In A Sweeping Jet Actuator Using Different Turbulence Models, Han Yang

McKelvey School of Engineering Graduate Student Theses & Dissertations

The goal of this research is to perform 2D turbulent flow simulations to predict the flow past a triangular airfoil used for a Mars air vehicle and in a sweeping jet actuator used for active flow control. Simulations are performed using the commercial CFD software ANSYS Fluent.

The thesis consists of two parts. The first part of the thesis deals with the CFD simulations of a triangular airfoil in low-Reynolds-number compressible flow. This airfoil is one of the candidates for propeller blades on a possible future Martian air vehicle design. The aerodynamics and flow physics of the triangular airfoil is …

Modeling Of Cantú Syndrome In Zebrafish, Soma Sekhara Singareddy

McKelvey School of Engineering Graduate Student Theses & Dissertations

Although rare, Cantú syndrome (CS) is a debilitating syndrome without any specific therapy, caused by gain-of-function (GOF) mutations in KCNJ8 and ABCC9 genes that encode ATP-sensitive potassium (KATP) channels. To better understand the link between molecular dysfunction and the complex pathophysiology, animal models that can rigorously mirror human CS are essential. Using ABCC9-mutated zebrafish, which can provide significant advantages over mice as an appropriate vertebrate model, GOF has been demonstrated at a cellular level in the ventricular cardiomyocytes. This also marks the first-known characterization of KATP currents in teleost hearts. In addition, sulfonylurea sensitivities of the channels have been …

Numerical Simulations Of Flow Past A Triangular Airfoil And In A Sweeping Jet Actuator Using Different Turbulence Models, Han Yang

McKelvey School of Engineering Graduate Student Theses & Dissertations

The goal of this research is to perform 2D turbulent flow simulations to predict the flow past a triangular airfoil used for a Mars air vehicle and in a sweeping jet actuator used for active flow control. Simulations are performed using the commercial CFD software ANSYS Fluent.

The thesis consists of two parts. The first part of the thesis deals with the CFD simulations of a triangular airfoil in low-Reynolds-number compressible flow. This airfoil is one of the candidates for propeller blades on a possible future Martian air vehicle design. The aerodynamics and flow physics of the triangular airfoil is …

Electroless Nickel Plating And Spark Plasma Sintering Of Nano Zro2 For Mechanical Property Enhancement, Kunlong Jia

McKelvey School of Engineering Graduate Student Theses & Dissertations

A new approach of combined electroless nickel plating (ENP) and spark plasma sintering (SPS) was used to determine the feasibility of fracture toughness improvement of ZrO2. Nano-grained yttria stabilized zirconia (YSZ) particles of 100nm average diameter were coated with about 1-5 nm of nickel coating by ENP. To reduce nano particle agglomeration throughout the ENP process; vigorous agitation with an ultrasonic horn was used. The coated powder was characterized using Scanning Electron Microscopy (SEM), Energy-dispersive X-ray spectroscopy (EDX) and Transmission electron microscopy (TEM) to study the microstructure and coating characteristics. The coating was identified to be predominantly nickel and of …

Multifunctional Nanocomposites Based On Bacterial Cellulose, Qisheng Jiang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cellulose is biodegradable, renewable, and abundant in nature thus cellulose (or paper)-based products can be inexpensively produced and recycled. Among cellulosic materials, bacterial nanocellulose (BNC) draws a special research attention due to the inherent three-dimensional nanofibrous structure, excellent mechanical flexibility, high purity and well-defined surface chemistry, and cost-efficient, scalable and environment-friendly synthesis. BNC can be biosynthesized by Gluconacetobacter xylinus, which is the most characterized BNC producer among various microorganisms. BNC is composed of highly pure cellulose nanofibrils, produced from well-defined dextrose through biochemical steps and subsequent self-assembling of the secreted cellulose fibrils which has the dimension ranges from 25 to …

Kcnq1/Kcne1 Interaction In The Cardiac Iks Channel And Its Physiological Consequences, Jiajing Xu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Dynamic conformational changes of ion channel proteins during activation gating determine their function as carriers of current. The relationship between these molecular movements and channel function over the physiological timescale of the action potential (AP) has not been fully established due to limitations of existing techniques. We constructed a library of possible cardiac IKs protein conformations and applied a combination of protein segmentation and energy linearization to study this relationship computationally. Simulations reproduced the effects of the beta-subunit (KCNE1) on the alpha-subunit (KCNQ1) dynamics and function, observed in experiments. Mechanistically, KCNE1 increased the probability of “visiting” conducting pore conformations on …

Molecular Basis Of Class Ib Drug Interactions With The Nav Channel Macromolecular Complex: A Route To Personalized Medicine For Cardiac Arrhythmia, Wandi Zhu

McKelvey School of Engineering Graduate Student Theses & Dissertations

The heart rhythm is precisely controlled by the electrical impulse that propagate in the cardiac tissue. In single cardiomyocytes, the electrical activity generated by action potentials (AP). Cardiac NaV channels (NaV1.5) carry a large influx of Na+ that mediates the initiation and propagation of the AP in both atria and ventricles. Disruption of NaV1.5 function by genetic variants or external factors can result in deadly arrhythmias, such as long QT syndrome and Brugada syndrome. Thus, NaV channels are import therapeutic targets. The class I antiarrhythmics are the modulators of the NaV channels. Although they have been used clinically for over …

Mechanisms Of Calcium Phosphate Mineralization On Biological Interfaces And Their Engineering Applications, Doyoon Kim

McKelvey School of Engineering Graduate Student Theses & Dissertations

All living organisms utilize phosphorus (P) as an essential component of their cell membranes, DNA and RNA, and adenosine triphosphate. Bones, in addition to bearing loads, play an important role in balancing P levels in our bodies. In bones, a network of collagen templates and calcium phosphate (CaP) nanocrystals builds hierarchical levels, from nano- to macroscale. Within this architecture, the thermodynamic properties of CaP minerals are influential. Despite the importance of nucleation, growth, and crystallization in collagen structures for tissue development, little kinetic study of these processes has been conducted due to the limited in situ techniques for monitoring these …

Effects Of Secondary Stall And Unsteady Free-Stream On Blade Drag And Pitching Moments, Michael Malick

McKelvey School of Engineering Graduate Student Theses & Dissertations

Dynamic stall is a complex aerodynamic phenomenon occurring in helicopter rotors, limiting the flight envelope and causing control linkage damage and instabilities. The Peters-Modarres semi-empirical dynamic stall model is extended to simulate pitching moment and drag in unsteady freestream and yawed flow, including the effects of secondary stall. The aerodynamics are implemented as a state-space model, suitable for time-marching or aeroelastic analyses. With small modifications to the original stall model, secondary stall effects and unsteady freestream can be simulated without adding additional states. An optimization routine determines sets of parameters that minimize the error between the modeled solution and experimental …

Information-Based Analysis And Control Of Recurrent Linear Networks And Recurrent Networks With Sigmoidal Nonlinearities, Deslin Menolascino

McKelvey School of Engineering Graduate Student Theses & Dissertations

Linear dynamical models have served as an analytically tractable approximation for a variety of natural and engineered systems. Recently, such models have been used to describe high-level diffusive interactions in the activation of complex networks, including those in the brain. In this regard, classical tools from control theory, including controllability analysis, have been used to assay the extent to which such networks might respond to their afferent inputs. However, for natural systems such as brain networks, it is not clear whether advantageous control properties necessarily correspond to useful functionality. That is, are systems that are highly controllable (according to certain …

Decoding Complexity In Metabolic Networks Using Integrated Mechanistic And Machine Learning Approaches, Tolutola Timothy Oyetunde

McKelvey School of Engineering Graduate Student Theses & Dissertations

How can we get living cells to do what we want? What do they actually ‘want’? What ‘rules’ do they observe? How can we better understand and manipulate them? Answers to fundamental research questions like these are critical to overcoming bottlenecks in metabolic engineering and optimizing heterologous pathways for synthetic biology applications. Unfortunately, biological systems are too complex to be completely described by physicochemical modeling alone.

In this research, I developed and applied integrated mechanistic and data-driven frameworks to help uncover the mysteries of cellular regulation and control. These tools provide a computational framework for seeking answers to pertinent biological …

Investigating Cyanobacteria Metabolism And Channeling-Based Regulations Via Isotopic Nonstationary Labeling And Metabolomic Analyses, Mary Helen Abernathy

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cyanobacteria have the potential to be low-cost and sustainable cell factories for bio-products; however, many challenges face cyanobacteria as biorefineries. This dissertation seeks to advance non-model photosynthetic organisms for biotechnology applications by characterizing central carbon metabolism and its regulations. Cyanobacteria phenotypes for bio-production are examined and their intracellular metabolism is quantified. Using isotopic labeling experiments, phenotypic relationships between biomass composition, central carbon fluxes, and metabolite pool sizes are investigated. Metabolic analyses of cyanobacteria led to new investigations of flux regulation mechanisms via protein spatial organizations or metabolite channeling. Metabolite channeling is further explored as a hypothesis to explain enigmatic labeling …

Graphene Oxides In Water: Characterization, Reactivity, And Application, Siyuan An

McKelvey School of Engineering Graduate Student Theses & Dissertations

Recently discovered, graphene and graphene oxide materials have drawn considerable research attention due to outstanding and novel properties, which underpin wide material potential for a number of advanced applications including supercapacitors, solar cells, sensors, catalysts, semiconductors, sorbents, and membranes, among others. Graphene oxides (GO), which are considered as a family of oxidized graphene materials (derivatives), is a key precursor to the synthesis of free-standing graphene via oxidation-exfoliation-reduction pathways. GO properties depend on the synthesis routes/conditions (i.e. derivatization), including partially maintaining graphene (i.e. sp2) properties. Further, oxygen-containing functionalities (epoxy, hydroxyl, carbonyl, and carboxyl groups) render GO hydrophilic – and correspondingly stability …

Basis Vector Model Method For Proton Stopping Power Estimation Using Dual-Energy Computed Tomography, Shuangyue Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Accurate estimation of the proton stopping power ratio (SPR) is important for treatment planning and dose prediction for proton beam therapy. The state-of-the-art clinical practice for estimating patient-specific SPR distributions is the stoichiometric calibration method using single-energy computed tomography (SECT) images, which in principle may introduce large intrinsic uncertainties into estimation results. One major factor that limits the performance of SECT-based methods is the Hounsfield unit (HU) degeneracy in the presence of tissue composition variations. Dual-energy computed tomography (DECT) has shown the potential of reducing uncertainties in proton SPR prediction via scanning the patient with two different source energy spectra. …

Effects Of Secondary Stall And Unsteady Free-Stream On Blade Drag And Pitching Moments, Michael Malick

McKelvey School of Engineering Graduate Student Theses & Dissertations

Dynamic stall is a complex aerodynamic phenomenon occurring in helicopter rotors, limiting the flight envelope and causing control linkage damage and instabilities. The Peters-Modarres semi-empirical dynamic stall model is extended to simulate pitching moment and drag in unsteady freestream and yawed flow, including the effects of secondary stall. The aerodynamics are implemented as a state-space model, suitable for time-marching or aeroelastic analyses. With small modifications to the original stall model, secondary stall effects and unsteady freestream can be simulated without adding additional states. An optimization routine determines sets of parameters that minimize the error between the modeled solution and experimental …

Towards Engineering Advanced Nanomaterials: Elucidating Fundamental Particle Behavior In Water And Critical Sorption Dynamics, Changwoo Kim

McKelvey School of Engineering Graduate Student Theses & Dissertations

As advanced nanomaterials, inorganic-organic nano composites have received great interest as potential platform (nano) structures for sensor, catalyst, sorbent, and environmental applications. Here, my Ph.D. research has focused on the design, synthesis, and characterization of advanced water-stable engineered metal-oxide nanoparticles functionalized by organic frames for environmental applications. For the environmental applications, I have evaluated particleoptimized sorption processes for the remediation and separation of arsenic, chromium, and uranium under environmentally relevant conditions. More specifically, I have explored the critical role of organic coating on sorption mechanisms and performances using engineered iron oxide -based, manganese oxide -based, and manganese ferrite -based (core) …

Multifunctional Nanocomposites Based On Bacterial Cellulose, Qisheng Jiang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cellulose is biodegradable, renewable, and abundant in nature thus cellulose (or paper)-based products can be inexpensively produced and recycled. Among cellulosic materials, bacterial nanocellulose (BNC) draws a special research attention due to the inherent three-dimensional nanofibrous structure, excellent mechanical flexibility, high purity and well-defined surface chemistry, and cost-efficient, scalable and environment-friendly synthesis. BNC can be biosynthesized by Gluconacetobacter xylinus, which is the most characterized BNC producer among various microorganisms. BNC is composed of highly pure cellulose nanofibrils, produced from well-defined dextrose through biochemical steps and subsequent self-assembling of the secreted cellulose fibrils which has the dimension ranges from 25 to …

Nanopower Analog Frontends For Cyber-Physical Systems, Kenji Aono

McKelvey School of Engineering Graduate Student Theses & Dissertations

In a world that is increasingly dominated by advances made in digital systems, this work will explore the exploiting of naturally occurring physical phenomena to pave the way towards a self-powered sensor for Cyber-Physical Systems (CPS). In general, a sensor frontend can be broken up into a handful of basic stages: transduction, filtering, energy conversion, measurement, and interfacing. One analog artifact that was investigated for filtering was the physical phenomenon of hysteresis induced in current-mode biquads driven near or at their saturation limit. Known as jump resonance, this analog construct facilitates a higher quality factor to be brought about without …

Biosensing By “Growing” Antennas And Error-Correcting Codes, Mingquan Yuan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Food-borne disease outbreaks not only cause numerous fatalities every year but also contribute to significant economic losses. While end-to-end supply chain monitoring can be one of the keys to preventing these outbreaks, screening every food product in the supply chain is not feasible considering the sheer volume and prohibitive test costs. Fortunately, two converging economic trends promise to make this end-to-end supply chain monitoring possible. The first trend is that passive radio-frequency identification (RFID) tags and quick response (QR) codes are now widely accepted for food packaging. The second trend is that smartphones are now equipped with the capability to …

Acetylation Profiles Of Histone And Non-Histone Proteins In Breast Cancer, Alla Karpova

McKelvey School of Engineering Graduate Student Theses & Dissertations

This study evaluates the impact of protein acetylation on breast cancer gene expression and the regulation of metabolism. Acetylation is the second abundant post-translational modification after phosphorylation, regulating protein activity and function. The alterations in acetylation of both histone and non-histone proteins is known to be related to many human diseases, including cancer. Acetylation and deacetylation of histones is closely associated with the regulation of gene expression, while acetylation of non-histone proteins may have a broad effect on major cellular processes, such as proliferation, metabolism, cell cycle and apoptosis, imbalanced regulation of which is essential for cancer development. Therefore, it’s …

Numerical Simulation And Optimization Of Blalock-Taussig Shunt, Thomas Hess, Ramesh K. Agarwal

McKelvey School of Engineering Graduate Student Theses & Dissertations

The goal of this study is to create an optimized Blalock-Taussig shunt used to temporarily repair pulmonary vascular blockages allowing a child time to grow so a more permanent surgical repair of the heart and vasculature can be performed. Blalock-Taussig or BT shunts are a surgical procedure performed on infants suffering from cyanosis or “Blue Baby Syndrome.” A BT shunt is an artificial vessel placed between the right ventricle and the pulmonary artery to increase blood flow in the lung and blood oxygen saturation levels. In a study of 96 patients with currently in use modified BT shunts, 32 patients …

Pick And Place Bot: Asme Design Challenge, Steven Mumford, Josh Clark, Stephan Meyer

Mechanical Engineering Design Project Class

Design a bot that meets the standards of and is able to compete in the 2019 ASME Design Challenge.

Group B: Polar Coordinate Whiteboard Writer, Dylan Wu, Zexin Han, Keon Kim, Jiahao Wei

Mechanical Engineering Design Project Class

From the initial funding of $250.00, our group attempted to make a polar coordinate whiteboard writer that was to be used in educational settings. Market for polar coordinate whiteboard writer is a blue ocean. Having a successful prototype will allow us to find a niche place in a market that shares border with the global education market.

Group V: Color Mixer, Kate Baskin, Mark Livshin, Andy Johnston

Mechanical Engineering Design Project Class

This project was an exercise in product design, modeling, and prototyping. The result of this process was a partially functional prototype which successfully met two of the three design goals.

Group L: T-Shirt2 Cutter, Sophie Anderson, Avery German, Taylor Tuleja

Mechanical Engineering Design Project Class

The T-shirt square cutter was commissioned by fashion design professor at Washington University, Dr. Mary RuppertStroescu who has developed a method of turning T-shirts that might have otherwise been thrown away into a unique, woven fabric. Dr. Ruppert-Stroescu cuts T-shirts into either strips or squares that she then quilts together, she uses this fabric to make one-of-a-kind clothes, bags, and rugs. Though she is proficient at weaving the fabric scraps together, cutting the Tshirts was a very time-consuming process – it takes her at least 20 minutes to cut a T-shirt into squares by hand. Our team was tasked with …