Engineering Science and Materials Commons^™

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

Mechanical Characterization And Modeling Of Rat Myocardia Under The Influence Of Epirubicin, Abdallah Mahmoud Alkhaiyat

Theses and Dissertations

Cancer remains a predominant health challenge that is responsible for a significant portion of global morbidity and mortality. Epirubicin (EPI), a chemotherapeutic anti-cancer drug, has shown remarkable efficacy in combating various malignancies. However, it is known to have undesirable side effects on the heart, collectively referred to as cardiotoxicity. This research investigates the adverse effects of chemotherapy on cardiac contractility through an in vitro examination of the mechanics of healthy and infarcted animal heart tissues. Electrically stimulated slices of rat ventricular tissue were tested using an isometric force measurement tissue bath. The tissue slices were subjected to uniaxial stretching, allowing …

Swarm Of One: Self-Organization In Multicellular Robots, Trevor Riley Smith

Graduate Theses, Dissertations, and Problem Reports (ETD)

Designing robots traditionally relies on centralized, top-down methods that constrain adaptability and resiliency, producing systems optimized for specific tasks. However, such systems often fail in complex environments, such as extraterrestrial, disaster, or natural settings, where designers cannot foresee every scenario a robot may encounter. Achieving autonomy in these contexts requires robots that are resilient and capable of adapting to the unknown. Multicellular organisms exhibit this adaptability through self-organization, where complex structures and behaviors emerge from local interactions among their cells. Such organisms can be viewed simultaneously as a single entity and a swarm of cooperating cells, i.e., a Swarm-of-One.

This …

Automation And Habitat Development For A Space Based Marine Life Environment, Logan Trimmer, Alexander Hang

Harrisburg University Other Works

This project was a cross-collaboration between the Environmental Sciences and Advanced Manufacturing and Robotics programs for the company Monolith Space.

The goal of this project was to design an autonomous system to be able to track qualities of water in an aquaculture system designed to be sent to space.

Entropic Forces Near Fluctuating Surfaces, Rubayet Hassan

Dissertations

Nanoscale structures are inherently dynamic due to persistent thermal fluctuations. Even in solid materials, these random deformations, driven by ambient thermal energy, can become significant when their characteristic scale approaches that of the structure itself and strongly influence their overall mechanical behavior. Examples of such structures include crystalline membranes, appearing in diverse forms such as nanotubes, nanoribbons, and kirigami/origami structures. Similarly, biological nanostructures, including lipid membranes, microtubules, actin filaments, and DNA, exhibit extreme flexibility and responsiveness due to their low bending rigidity. Numerous physiological processes are intrinsically linked to these thermal fluctuations, including exocytosis and endocytosis, membrane fusion, pore formation, …

Multi-Domain Machine Learning For Biological Classification: Mallard Classification And Protein Function Prediction, Tolulope Samuel Adeyina

Open Access Theses & Dissertations

Multi-domain machine learning applications have revolutionized how we understand and predict complex biological phenomena. This dissertation presents novel computational methodologies addressing two critical problems: mallard classification using single-nucleotide polymorphisms (SNPs), and protein function prediction via interpretable topic-aware peptide embeddings. The research focuses on distinguishing mallard populations through SNP data, which are inherently characterized by ultra-high dimensionality. The research uses advanced feature-selection and dimensionality-reduction strategies alongside machine learning classification algorithms to identify minimal, yet highly predictive SNP sets crucial for accurate breed differentiation. This framework demonstrates robust performance with optimal computational efficiency, significantly aiding conservation and breed management efforts. Furthermore, the …

Design And Optimization Of Aquaculture Gear: Development Of A Cage-Integrated Reeling Mechanism For Oyster Farming, Felicity Bryant

Honors Theses

This project encompasses the design, fabrication, and testing of a cage-integrated reeling system aimed at reducing the physical labor required in oyster aquaculture at Bama Bay Oyster Farm, the last operational oyster farm in Mobile Bay. The proposed system includes two primary components: lightweight, modular oyster cages and a dual-winch reeling device for automated retrieval. Three cage prototypes—rectangular, oval, and hexagonal—were evaluated for structural performance and fabrication feasibility. The oval design was ultimately excluded due to practical fabrication limitations. The rectangular and hexagonal designs were fabricated using recycled materials and tested under the most extreme environmental conditions derived from years …

Treating Ground Water For Agricultural And Individual Consumption, Gabby Miller, Bronson Scott, Michael Clawson

Biomedical Engineering

This project, conducted in collaboration with Cal Poly seniors and Da Vinci High School students, aims to develop a solar-powered groundwater purification system. This system is designed to provide clean water for agricultural use and individual consumption, addressing the growing concerns of groundwater contamination and accessibility needs. The final prototype integrates a gravity filtration system combined with chemical purification, utilizing aluminum sulfate and chlorine to remove particulates, bacteria, and organic compounds.

The research phase involved an extensive review of groundwater contamination issues, existing filtration technologies, and market analysis. Key design constraints included cost-effectiveness, ease of maintenance, and minimal energy consumption, …

Realization Of Water Tidal Datum Levels From Observed Sea Level Data In Damietta Harbor, Egypt, Mohamed M. Helmy, Amr N. Shokry, Mohamed M. Youssef, Ahmed M. Khedr

Mansoura Engineering Journal

Sea level is an essential oceanographic parameter in hydrographic surveying that is always necessary for the realization of Chart Datum (CD). The International Hydrographic Organization (IHO) defines sea levels as those expected to occur under typical meteorological conditions, regardless of any possible combination of astronomical conditions. The current research focuses on analysing the observed sea level in Damietta Harbor, using two sets of sea-level records obtained from two sensors: a pressure sensor and a radar sensor. These records were collected from a tide gauge station located at Damietta Harbor from July 1, 2019, to March 2, 2020. Furthermore, harmonic analysis …

3d Printed Microfluidic Fabrication Methodology, Characterization, Mechanical Design, And Applications In Electrostatic Artificial Muscles And Benthic Microbial Fuel Cells, Terak B. Hornik

Master's Theses

The fabrication of microfluidic devices often requires specialized methods. The development of these methods requires careful characterization and understanding of the processes involved. Using primarily PolyJet 3D printing technology, microfluidics offers a wide scope of applications such as microfluidic benthic microbial fuel cells (MBMFCs) and electrostatic artificial muscles. MBMFCs benefit from the confinement of the microbes resulting in close proximity between the electrode and the organisms. Using a modular design called the Sponge, assembly and upscaling is possible. Electrostatic artificial muscles benefit from a microfluidic approach due to the non-linearity of electrostatic attraction creating disproportionate benefits when miniaturized. When designed …

New York City’S Rising Sea Level And Coastal Erosion: Approaches To Resiliency, Ryder D. Isidro

Student Theses 2015-Present

No abstract provided.

Investigation On The Effects Of Biofouling On The Boundary Layer, Adam N. Bacon

LSU New Orleans Theses and Dissertations

This study is an investigation of the effect of biofouling on the boundary layer of a flat plate and a NACA 4-digit series foil. Three identical hydrofoils made of resin were placed in the Gulf of Mexico at Grand Isle, Louisiana, and observed and analyzed by marine biologists at the University of New Orleans for their species composition. The resulting biofouling that grew was primarily made up of barnacles and bryozoans. The foils were submerged in an open channel flume at zero incidence and subjected to a series of experiments whose arc-length Reynolds numbers ranged from approximately 13000 to 32000. …

Design And Application Of Smart Systems To Address Analytical Problems, Lucas B. Ayres

All Dissertations

This dissertation is a multidisciplinary effort that integrates low-cost analytical instrumentation, redox chemistry, and artificial intelligence to overcome existing limitations in the fields of wearable sensing technology, Deep Eutectic Solvents (DES), and antioxidant chemistry. The overall goal behind each implemented strategy is to enhance the accuracy, efficiency, and accessibility of analytical processes and technologies. A general overview of the thesis, along with the research outcomes is included in Chapter One. The theoretical framework of this dissertation is presented in Chapter Two. Chapter Three describes the development of a wearable platform (sensor and instrumentation) to rapidly detect (~20 minutes) S. aureus …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Moisture Effects On Visible Near-Infrared And Mid-Infrared Soil Spectra And Strategies To Mitigate The Impact For Predictive Modeling, Francis Hettige Chamika Anuradha Silva

Theses and Dissertations

Instrumental disparities and soil moisture are two of the key limitations in implementing spectroscopic techniques in the field. This study sought to address these challenges through two objectives. The first objective was to assess Visible-near infrared (VisNIR) and mid-infrared (MIR) spectroscopic approaches and explore the feasibility of transferring calibration models between laboratory and portable spectrometers. The second objective addressed the challenge of soil moisture and its impact on spectra. The portable spectrometers demonstrated comparable performance to their laboratory-based counterparts in both regions. Spiking with extra-weight, was the most effective calibration transfer method eliminating disparities between instruments. The samples were rewetted …

Nanoscale Modeling Of Membrane Systems Under Mechanical Deformation In Traumatic Brain Injury Using Molecular Dynamics, Anh Thi Ngoc Vo

Theses and Dissertations

Neuronal membrane disruption and mechanoporation are nanoscale damage mechanisms that critically affect brain cell viability during traumatic brain injury (TBI). These nanoscale cellular impairments are elusive in experiments and necessitate in silico approaches such as molecular dynamics (MD) simulations. Implementing MD, this research aims to investigate the effects of different key factors related to membrane deformation and damage, including force field resolutions, lipid compositions, and loading conditions.

To examine the impact of force field resolution, MD deformation simulations were conducted on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayer membranes, using all-atom (AA), united-atom (UA), and coarse-grained Martini (CG-M) force fields. The mechanical responses …

Neurocomputing And Interfacing Digital Tasting System: Research, Design, And Evaluation, Amira J. Zaylaa, Ahmad El Hajj

BAU Journal - Science and Technology

The continuous evolution in computing and interfacing has been extended to develop multi-sensory experiences in many domains such as neurological, auditory, vision, and haptic domains. So far, only a few remarkable system approaches have been approved to be serving the taste sensation digitally. Although taste sensation is linked to the brain, there is a lack of optimal neurocomputing digital taste sensation systems. Our study provides a new neurocomputing method to digitally stimulate the sense of taste by electrical stimulation on the human tongue. We aim to link chemical stimulation and electrical stimulation in order to design an electronic interface for …

Soil Respiration Measurements Reveal High Retention Of Organic Carbon From Corn Residue Derived High-Lignin Fermentation Byproduct Enabling Sustainable Lignocellulosic Biofuel Production, Michelle Sun Wang

Dartmouth College Master’s Theses

While 2G biofuel production can utilize non-edible, lignocellulosic feedstocks such as agricultural residues to produce liquid fuel, harvesting crop residues is unsustainable without careful management of the soil underneath. By harvesting a fraction of the crop residues left in the field after harvest, soil health can diminish and critically, the soil organic carbon (SOC) stored in agricultural fields can decrease. Currently, in the most popular 2G process models published, the issue of soil degradation remains unresolved with residue harvest strategies receiving considerable attention in the literature and other SOC management strategies receiving far less. Specifically, the strategy of returning the …

Potential Of Mechanical Grain Dryers In Addressing Exposure Of Rice Farmers To Weather Risks, Hernaiz Malanon, Zenaida Sumalde

The Philippine Agricultural Scientist

Weather risks brought by prolonged rainfall and cloudy days hamper grain drying operations in the Philippines as majority still employ the sun drying method, which limits the opportunity of rice farmers to earn a higher income. While mechanical dryers are considered an important adaptation mechanism to address weather risks, more research needs to be done on their benefits and their disadvantages. This study adapted the Inter-governmental Panel on Climate Change (IPCC) concept which equates hazard, exposure, and vulnerability to quantify risk. Hazard was assessed in terms of the probability of four straight rainy- or cloudy-day occurrences based on a 30-year …

Bbt Acoustic Alternative Top Bracing Cadd Data Set-Norev-2022jun28, Bill Hemphill

STEM Guitar Project’s BBT Acoustic Kit

This electronic document file set consists of an overview presentation (PDF-formatted) file and companion video (MP4) and CADD files (DWG & DXF) for laser cutting the ETSU-developed alternate top bracing designs and marking templates for the STEM Guitar Project’s BBT (OM-sized) standard acoustic guitar kit. The three (3) alternative BBT top bracing designs in this release are
(a) a one-piece base for the standard kit's (Martin-style) bracing,
(b) 277 Ladder-style bracing, and
(c) an X-braced fan-style bracing similar to traditional European or so-called 'classical' acoustic guitars.

The CADD data set for each of the three (3) top bracing designs includes …

Bbt Side Mold Assy, Bill Hemphill

STEM Guitar Project’s BBT Acoustic Kit

This electronic document file set covers the design and fabrication information of the ETSU Guitar Building Project’s BBT (OM-sized) Side Mold Assy for use with the STEM Guitar Project’s standard acoustic guitar kit. The extended 'as built' data set contains an overview file and companion video, the 'parent' CADD drawing, CADD data for laser etching and cutting a drill &/or layout template, CADD drawings in AutoCAD .DWG and .DXF R12 formats of the centerline tool paths for creating the mold assembly pieces on an AXYZ CNC router, and support documentation for CAM applications including router bit specifications, feeds, speed, multi-pass …

Electromechanical Fatigue Properties Of Dielectric Elastomer Stretch Sensors Under Orthopaedic Loading Conditions, Andrea Karen Persons

Theses and Dissertations

Fatigue testing of stretch sensors often focuses on high amplitude, low-cycle fatigue (LCF) behavior; however, when used for orthopaedic, athletic, or ergonomic assessments, stretch sensors are subjected to low amplitude, high-cycle fatigue (HCF) conditions. As an added layer of complexity, the fatigue testing of stretch sensors is not only focused on the life of the material comprising the sensor, but also on the reliability of the signal produced during the extension and relaxation of the sensor. Research into the development of a smart sock that can be used to measure the range of motion (ROM) of the ankle joint during …

Mathematical Model Of The Efficiency Of Investments Aimed In The Implementation Of Water-Saving Technologies

Irrigation and Melioration

In Uzbekistan, research work is being carried out aimed at improving the economic mechanisms for the introduction of water-saving technologies for irrigating agricultural crops. At the same time, the issues related to the analysis of the effectiveness of the use of water-saving technologies when irrigating cotton, the development of mathematical methods for assessing the effectiveness of investments, as well as their introduction into practice have not been sufficiently studied. This article provides a mathematical model of the efficiency of investments aimed at introducing water-saving technologies. The results of a numerical experiment of a mathematical model show that the introduction of …

Efficient Use Of Water Resources In The Basins Of Small Rivers, F. Gapparov, M.F. Gafforova

Irrigation and Melioration

The article provides a recommendation for the efficient use of water resources in the basins of small foothill rivers. The research was carried out on the example of the Govasay river basin located in the northern part of the Fergana Valley. The efficiency factor of the canal has been determined and a technical assessment has been given for the management of water resources in the river basin; the efficiency of the canal is 65-75%. A program for the operational management of water resources in The Govasay river basin and a GIS map of water consumers in the Govasay river basin …

Model Of Groundwater Level Control Using Horizontal Drainage, A. Arifjanov, M. Otaxonov, Z. Abdulkhaev

Irrigation and Melioration

The article describes the main factors affecting the rise in the level of groundwater in the city of Fergana and ways to eliminate them. Currently, in order to reduce the negative impact of rising groundwater levels on the environment, crops, buildings and structures, as well as underground utilities, it is proposed to design horizontal drainage in urban areas and a mathematical model has been developed for changing the groundwater level. For this, long-term data from observation wells were analyzed and the hydraulic parameters of horizontal drainage were selected taking into account the hydrogeology of the area. Taking into account the …

Results Of Proximate Analysis Of Energy Use Of Municipal Solid Waste, N.N. Abduganiev

Irrigation and Melioration

In the modern industrialized world, various raw materials are processed and used for human consumption. While some of the raw materials are converted into the desired product, the rest is thrown into the environment as waste. It is known that solid waste is a type of biomass that is formed in the course of human life. The article presents the results of a preliminary analysis of studies on the use of solid waste energy in the Urta-Chirchik district of the Tashkent region. Sorting results showed that the total volume of municipal solid waste in the district consists mainly of wood …

Shredding Of Cotton Stalks Under The Action Of Toothpicks In A Combined Unit, B. Khudayarov, U. Kuziev, B. Sarimsakov, М. Kholbutaev

Irrigation and Melioration

The article presents materials devoted to the justification of the parameters of the crown-wheel of the combined aggreagate. The technological process of work and the design of the working part, which is crushed by crushing cotton stalks, without breaking them, laying them on the movement of the unit, has been substantiated and developed. The optimal parameters of the crown-wheel and the tooth are determined by solving the regression equations that determine the optimal values of the vertical load on the teeth and its working quality. The results of theoretical and experimental research show that the amount of crushing of cotton …

Influence Of Electrophysical Methods On The Processes Of Root Formation Of Grapes, N.M. Markayev

Irrigation and Melioration

The article describes the possibilities of electrophysical processing before planting cuttings during vegetative cultivation of grape seedlings. The processes of root formation in cuttings using the electrophysical method in the article Acceleration of the process of root formation in cuttings of black raisins, treated at 71 V/m and an electric field strength of 15 hours, and an increase in the viability, quality, growth and survival of rooted seedlings up to 16.67-34% Presented the results of experiments on the increase and methods of electrotechnological processing of grape cuttings. The result of the study is the analysis and results of the processes …

Conditions, Criteria And Principles For Creating An Agri-Cultural Land Market In Uzbekistan, A.R. Nurnazarov

Irrigation and Melioration

The article analyzes the prerequisites for creating a market for agricultural land in the Republic of Uzbekistan, special attention is paid to land reform, land degradation (reduction of the bonitet score from 60 in 1991 to 50 or more at present, pasture degradation by 20-30%) and increase in economic from their use, the role of land rent in payments for land. 6 basic principles for creating a land market have been established and systematized, the relationship between X-rays and water in the irrigated farming zone, the role of the market in increasing the efficiency and effectiveness of the use of …

Economic Assessment Of The Effect Of Family Income On Students' Disciplines, Sh.A. Muratov

Irrigation and Melioration

The importance of higher education in scientific research, its role in poverty reduction and population growth has been studied theoretically. Also, when using the data of social surveys conducted by 538 respondents (students) studying in higher education institutions, they were awarded the Order of the logistics regulator in the economic assessment of the factors influencing the rate of mastery of disciplines. Factors influencing the acquisition of subjects by students: the main income of the family comes from non-farm (69,9 %), sex (52,2 %), studying at a higher education institution on a state grant (108,8 %), the student's course of study …