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Full-Text Articles in Life Sciences

Function And Dissipation In Finite State Automata - From Computing To Intelligence And Back, Natesh Ganesh Oct 2019

Function And Dissipation In Finite State Automata - From Computing To Intelligence And Back, Natesh Ganesh

Doctoral Dissertations

Society has benefited from the technological revolution and the tremendous growth in computing powered by Moore's law. However, we are fast approaching the ultimate physical limits in terms of both device sizes and the associated energy dissipation. It is important to characterize these limits in a physically grounded and implementation-agnostic manner, in order to capture the fundamental energy dissipation costs associated with performing computing operations with classical information in nano-scale quantum systems. It is also necessary to identify and understand the effect of quantum in-distinguishability, noise, and device variability on these dissipation limits. Identifying these parameters is crucial to ...


Walking For Object Transport: An Examination Of The Coordinative Adaptations To Locomotor, Perceptual, And Manual Task Constraints, Avelino Amado Jul 2019

Walking For Object Transport: An Examination Of The Coordinative Adaptations To Locomotor, Perceptual, And Manual Task Constraints, Avelino Amado

Doctoral Dissertations

The goal of this dissertation was to understand how the intrinsic dynamics of gait adapt to support the performance of an ecologically relevant object transport task. A common object transport task is walking with a cup of water. Because the water can move relatively independent of the cup, the cup and water system is classified as a complex object. To model this task participants carried a cup with a wooden lid placed on top. On the lid there was a circular region with the same circumference as the cup and a ball. The object of the task was to keep ...


Integration Of Robotic Perception, Action, And Memory, Li Yang Ku Oct 2018

Integration Of Robotic Perception, Action, And Memory, Li Yang Ku

Doctoral Dissertations

In the book "On Intelligence", Hawkins states that intelligence should be measured by the capacity to memorize and predict patterns. I further suggest that the ability to predict action consequences based on perception and memory is essential for robots to demonstrate intelligent behaviors in unstructured environments. However, traditional approaches generally represent action and perception separately---as computer vision modules that recognize objects and as planners that execute actions based on labels and poses. I propose here a more integrated approach where action and perception are combined in a memory model, in which a sequence of actions can be planned based on ...


Evaluating The Toxicity And Formation Of Halobenzoquinones In Point-Of-Use Chlorinated Drinking Water, Stephanie Hung Oct 2018

Evaluating The Toxicity And Formation Of Halobenzoquinones In Point-Of-Use Chlorinated Drinking Water, Stephanie Hung

Masters Theses

Chlorine has effectively reduced the prevalence of waterborne diseases, however there are secondary consequences to this public health advancement. Disinfection byproducts (DBPs) are chemicals formed when chlorine reacts with natural organic matter (NOM) in water. A new class of DBPs, halobenzoquinones (HBQs), has recently been identified and data suggests it could be potentially carcinogenic and up to 1000 times more toxic than some regulated DBPs. So far, in vitro studies have assessed HBQ toxicity without taking into account its transformation in cell media into potentially less toxic compounds. This study evaluated the toxic effects of one HBQ, 2,6-DCBQ, and ...


Application And Evaluation Of Lighthouse Technology For Precision Motion Capture, Soumitra Sitole Oct 2018

Application And Evaluation Of Lighthouse Technology For Precision Motion Capture, Soumitra Sitole

Masters Theses

This thesis presents the development towards a system that can capture and quantify motion for applications in biomechanical and medical fields demanding precision motion tracking using the lighthouse technology. Commercially known as SteamVR tracking, the lighthouse technology is a motion tracking system developed for virtual reality applications that makes use of patterned infrared light sources to highlight trackers (objects embedded with photodiodes) to obtain their pose or spatial position and orientation. Current motion capture systems such as the camera-based motion capture are expensive and not readily available outside of research labs. This thesis provides a case for low-cost motion capture ...


New Approaches In Engineering Somatic Embryogenesis In Loblolly Pine Suspension Cultures, Elizabeth Morgan Cummings Bende Jul 2018

New Approaches In Engineering Somatic Embryogenesis In Loblolly Pine Suspension Cultures, Elizabeth Morgan Cummings Bende

Doctoral Dissertations

Many industries including agriculture and healthcare require efficient methods for replication of plants with optimal traits. The loblolly pine (Pinus taeda) is a valuable crop in the timber industry, occupying 30 million acres of U.S. land, and breeding efforts aim to produce a crop with ideal phenotypic traits, including superior growth and wood quality. One method to large-scale clonal crop propagation is somatic embryogenesis (SE), the process through which asexual (somatic) plant cells undergo differentiation in vitro, resulting in germination-competent embryos. There are three main stages of growth and development that lead to the production of embryos: 1) aggregated ...


Polymeric Peptide Mimics For Protein Delivery, Coralie Backlund Jul 2018

Polymeric Peptide Mimics For Protein Delivery, Coralie Backlund

Doctoral Dissertations

The plasma membrane is a major obstacle in the development and use of biomacromolecules for intracellular applications. Consequently, proteins with intracellular targets represent an enormous, yet under studied avenue for therapeutics. Extended research has aimed at facilitating intracellular delivery of exogenous proteins using protein transduction domains (PTDs), which allow transport of bioactive molecules into cells. Synthetic polymers, inspired by PTDs, provide a well-controlled platform to vary molecular architecture for structure activity relationship studies. Specifically, this thesis focuses on the use of ring-opening metathesis, a facile and efficient polymerization technique, through which we can vary structural parameters to optimize delivery of ...


Structure-Property Relationships Of Polymer Films And Hydrogels To Control Bacterial Adhesion, Kristopher W. Kolewe Mar 2018

Structure-Property Relationships Of Polymer Films And Hydrogels To Control Bacterial Adhesion, Kristopher W. Kolewe

Doctoral Dissertations

The emergence and spread of antibiotic resistance across microbial species necessitates the need for alternative approaches to mitigate the risk of infection without relying on commercial antibiotics. Biofilm-related infections are a class of notoriously difficult to treat healthcare-associated infections that frequently develop on the surface of implanted medical devices. As biofilm formation is a surface-associated phenomenon, understanding how the intrinsic properties of materials affect bacterial adhesion enables the development of structure-property relationships that can guide the future design of infection-resistant materials. Despite lacking visual, auditory, and olfactory perception, bacteria still manage to sense and attach to surfaces. Previously, it has ...


Microbial Competition In Bioelectrochemical Systems, Varun Srinivasan Nov 2017

Microbial Competition In Bioelectrochemical Systems, Varun Srinivasan

Doctoral Dissertations

Bioelectrochemical systems(BESs)/ microbial fuel fells (MFCs) are a well-studied potential technology for bioremediation and decentralized wastewater treatment. However, progress has been somewhat stalled at the bench-scale. In well controlled experiments electron recovery is high. In natural environments, wastewaters are complex and anode-respiring bacteria can be outcompeted in the presence of competing microorganisms, leading to a loss in electron-recovery and power production. Furthermore, the cathode of the MFC plays a vital role in providing flexibility for treatment options but is an understudied part of MFCs.

Modelling Intracellular Competition in a Denitrifying Biocathode:

One potential MFC configuration uses an organic-oxidizing anode ...


Protein-Nanoparticle Co-Engineering: Self-Assembly, Intracellular Protein Delivery, And Crispr/Cas9-Based Gene Editing, Rubul Mout Nov 2017

Protein-Nanoparticle Co-Engineering: Self-Assembly, Intracellular Protein Delivery, And Crispr/Cas9-Based Gene Editing, Rubul Mout

Doctoral Dissertations

Direct cytoplasmic delivery of gene editing nucleases such CRISPR/Cas9 systems and therapeutic proteins provides enormous opportunities in curing human genetic diseases, and assist research in basic cell biology. One approach to attain such a goal is through engineering nanotechnological tools to mimic naturally existing intra- and extracellular protein delivery/transport systems. Nature builds transport systems for proteins and other biomolecules through evolution-derived sophisticated molecular engineering. Inspired by such natural assemblies, I employed molecular engineering approaches to fabricate self-assembled nanostructures to use as intracellular protein delivery tools. Briefly, proteins and gold nanoparticles were co-engineered to carry complementary electrostatic recognition elements ...


Microbial Dynamics And Design Considerations For Decentralized Microbial Fuel Cell Applications, Cynthia Castro Nov 2017

Microbial Dynamics And Design Considerations For Decentralized Microbial Fuel Cell Applications, Cynthia Castro

Doctoral Dissertations

The purpose of this dissertation was to assess the practicality of using microbial fuel cells (MFCs) as alternative sanitation systems for wastewater treatment and energy recovery, focusing on identifying key design considerations for treating high strength wastewater and managing alternative metabolic pathways.

We evaluated the energetic outputs of a lab-based pilot MFC designed to treat complex organics present in both synthetic feces and municipal wastewater. The pilot MFC produced two energetic products, methane and electricity, when treating two types of complex wastewaters. The energetic products associated with anode respiration and methanogenesis were simultaneously observed and yielded a combined energy ouput ...


Effects Of Malformed Or Absent Valves To Lymphatic Fluid Transport And Lymphedema In Vivo In Mice, Akshay S. Pujari Oct 2017

Effects Of Malformed Or Absent Valves To Lymphatic Fluid Transport And Lymphedema In Vivo In Mice, Akshay S. Pujari

Masters Theses

Lymph is primarily composed of fluid and proteins from the blood circulatory system that drain into the space surrounding cells, interstitial space. From the interstitial space, the fluid enters and circulates in the lymphatic system until it is delivered into the venous system. In contrast to the blood circulatory system, the lymphatic system lacks a central pumping organ dictating the predominant driving pressure and velocity of lymph. Transport of lymph via capillaries, pre-collecting and collecting lymphatic vessels relies on the synergy between pressure gradients, local tissue motion, valves and lymphatic vessel contractility. The direction of lymph transport is regulated by ...


A Magnetic Resonance Compatible Knee Extension Ergometer, Youssef Jaber Jul 2017

A Magnetic Resonance Compatible Knee Extension Ergometer, Youssef Jaber

Masters Theses

The product of this thesis aims to enable the study of the biochemical and physical dynamics of the lower limbs at high levels of muscle tension and fast contraction speeds. This is accomplished in part by a magnetic resonance (MR) compatible ergometer designed to apply a load as a torque of up to 420 Nm acting against knee extension at speeds as high as 4.7 rad/s. The system can also be adapted to apply the load as a force of up to 1200 N acting against full leg extension. The ergometer is designed to enable the use of ...


Vitreous Gel Physics, Svetlana Morozova Jul 2017

Vitreous Gel Physics, Svetlana Morozova

Doctoral Dissertations

The transparent vitreous, which fills the posterior cavity of the eye, is incredibly engineered. The charged polyelectrolyte hyaluronic acid (HA) network swells to maintain the pressure in the eye, while stiff collagen type II bundles help absorb any external mechanical shock. Our investigations have contributed to a few key developments related to the physical properties of the vitreous:

(1) The stiff collagen network that supports the soft gel network is self-assembled from single triple-helix collagen proteins. Electrostatic interactions drive this assembly, such that the size and concentration are optimized at physiological salt concentrations. The width of the assemblies remarkably changes ...


I. The High Strain Rate Response Of Hollow Sphere Steel Foam; Ii. The Dynamic Response Of An American Elm Tree, Ignacio Cetrangolo Mar 2017

I. The High Strain Rate Response Of Hollow Sphere Steel Foam; Ii. The Dynamic Response Of An American Elm Tree, Ignacio Cetrangolo

Masters Theses

PART I

Hollow-sphere (HS) steel foam is a relatively new material whose cellular morphology and material properties qualify it as a metallic foam. This is an innovative foam-like material that exhibits high stiffness paired with low relative densities. Technological advancements in the past few decades have enabled the manufacturing of this material by a sintering process and, as a result, research has begun to accelerate as a multi-school collaboration effort for this particular work. Even though commercialization has been a challenge for metallic foams, it is imperative that researchers continue to prove and promote the advantages of metallic foams despite ...


Methods For Incorporating Ecological Impacts With Climate Uncertainty To Support Robust Flood Management Decision-Making, Caitlin M. Spence Mar 2017

Methods For Incorporating Ecological Impacts With Climate Uncertainty To Support Robust Flood Management Decision-Making, Caitlin M. Spence

Doctoral Dissertations

Modern and historic flood risk management involves accommodating multiple sources of sources of uncertainty and potential impacts across a broad range of interrelated sectors. Sources of uncertainty that affect planning include internal climate variability, anthropogenic changes such as land use and system performance expectations, and more recently changes in climatology that affect the resources supporting the system. Flood management systems potentially impact human settlements within and beyond the systems’ scope of planning, local weather patterns, and associated ecological systems. Federal guidelines across nations have called for greater consideration of uncertainty and impacts of water resources planning projects, but methods for ...


Thiol-Ene Chemistry As An Enabler Of New Polymer Structures And Architectures, Joel M. Sarapas Mar 2017

Thiol-Ene Chemistry As An Enabler Of New Polymer Structures And Architectures, Joel M. Sarapas

Doctoral Dissertations

This dissertation focuses on two distinct projects: the synthesis and design of novel cell penetrating peptides mimics (CPPMs), and the implementation of the thiol-ene click reaction to generate new polymer architectures and chemistries. Guanidinium-rich CPPMs were generated through both ROMP and RAFT polymerizations, allowing for a comparison to be made across polymer backbone chemistries with respect to both siRNA and protein cellular internalization. A particularly effective methacrylate derived block copolymer was able to deliver siRNA to nearly an entire Jurkat T cell population.

The thiol-ene reaction was implemented initially within the context of improving material design for solid polymer electrolytes ...


Total Organic Iodine Quantification And Occurrence In Drinking Water, And Toxicity Assessment Of Iodinated Disinfection By-Products, Rassil El Sayess Mar 2017

Total Organic Iodine Quantification And Occurrence In Drinking Water, And Toxicity Assessment Of Iodinated Disinfection By-Products, Rassil El Sayess

Doctoral Dissertations

The focus of this work has been placed is on iodinated DBPs (I-DBPs), measured using total organic iodine (TOI), a surrogate measure of iodinated organics. This is due to the growing toxicity literature that places I-DBPs among the most toxic of all DBPs. To measure TOI in water, a new method was developed. This method combines adsorption, combustion, and trapping of combustion products, with an offline inductively coupled plasma/mass spectrometer (ICP-MS) for iodide detection. Three factors were varied across two levels each in order to optimize the method. The chosen method used a sample pH of less than 1 ...


Biopolymer Electrospun Nanofiber Mats To Inactivate And Remove Bacteria, Katrina Ann Rieger Nov 2016

Biopolymer Electrospun Nanofiber Mats To Inactivate And Remove Bacteria, Katrina Ann Rieger

Doctoral Dissertations

The persistence of antibiotic resistance in bacterial pathogens remains a primary concern for immunocompromised and critically-ill hospital patients. Hospital associated infections can be deadly and reduce the successes of medical advancements, such as, cancer therapies and medical implants. Thus, it is imperative to develop materials that can (i) deliver new antibiotics with accuracy, as well as (ii) uptake pathogenic microbes. In this work, we will demonstrate that electrospun nanofiber mats offer a promising platform for both of these objectives because of their high surface-to-volume ratio, interconnected high porosity, gas permeability, and ability to contour to virtually any surface. To provide ...


Label-Free And Aptamer-Based Surface Enhanced Raman Spectroscopy For Detection Of Food Contaminants, Shintaro Pang Nov 2016

Label-Free And Aptamer-Based Surface Enhanced Raman Spectroscopy For Detection Of Food Contaminants, Shintaro Pang

Doctoral Dissertations

The development of analytical methods to detect food contaminants is a critical step for improving food safety. Surface enhanced Raman spectroscopy (SERS) is an emerging detection technology that has the potential to rapidly, accurately and sensitively detect a wide variety of food contaminants. However, SERS detection becomes a challenge in real complex matrix, such as food, since non-specific matrix signals have the potential to drown out target associated Raman peaks. In this dissertation, we focused on the development and application of label-free, aptamer-based SERS in order to improve the accuracy and specificity of target contaminant detection in food. To accomplish ...


Investigate The Interactions Between Silver Nanoparticles And Spinach Leaf By Surface Enhanced Raman Spectroscopic Mapping, Zhiyun Zhang Nov 2016

Investigate The Interactions Between Silver Nanoparticles And Spinach Leaf By Surface Enhanced Raman Spectroscopic Mapping, Zhiyun Zhang

Masters Theses

Owing to their increasing application and potential toxicity, engineered nanoparticles (ENPs) have been considered as a potential agricultural contaminant that may pose unknown risk to human beings. However, many techniques require invasive and complicated sample preparation procedures to detect and characterize engineered nanomaterials in complex matrices. In the first part of this thesis, we present a non-destructive and label-free approach based on surface enhanced Raman spectroscopic (SERS) mapping technique to qualitatively detect and characterize gold nanoparticles (AuNPs), on and in spinach leaves in situ. We were able to detect the clearly enhanced signals from AuNPs at 15 to 125 nm ...


Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins Jul 2016

Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins

Doctoral Dissertations

Van der Waals (vdW) interactions influence a variety of mesoscale phenomena, such as surface adhesion, friction, and colloid stability, and play increasingly important roles as science seeks to design systems on increasingly smaller length scales. Using the full Lifshitz continuum formulation, this thesis investigates the effects of system materials, shapes, and configurations and presents open-source software to accurately calculate vdW interactions.

In the Lifshitz formulation, the microscopic composition of a material is represented by its bulk dielectric response. Small changes in a dielectric response can result in substantial variations in the strength of vdW interactions. However, the relationship between these ...


Synthesis And Applications Of Non-Migratory Metal Chelating Active Packaging, Maxine J. Roman Jul 2016

Synthesis And Applications Of Non-Migratory Metal Chelating Active Packaging, Maxine J. Roman

Doctoral Dissertations

Many packaged foods use synthetic chelators (e.g. ethylenediaminetetraacetic acid, EDTA) to inhibit metal promoted oxidation and/or microbial growth that may cause food spoilage. Consumer demand for foods without synthetic additives has prompted growing interest in alternative preservation methods. Our research group has previously developed non-migratory metal chelating active packaging materials by surface immobilization of polymeric chelators and demonstrated their ability to inhibit lipid oxidation in model food emulsions. The work presented in this dissertation investigates the synthesis, performance stability, and practical application of metal chelating surface modifications to optimize design of non-migratory metal chelating active packaging materials.

Metal ...


Enzyme Stabilization In Hierarchical Biocatalytic Food Packaging And Processing Materials, Dana Erin Wong Jul 2016

Enzyme Stabilization In Hierarchical Biocatalytic Food Packaging And Processing Materials, Dana Erin Wong

Doctoral Dissertations

The partnership of biocatalysts and solid support materials provides many opportunities for bioactive packaging and bioprocessing aids beneficial to the agricultural and food industries. Biocatalysis, or reactions modulated by enzymes, allows bioactive materials to assist in bringing a substrate to product. Enzymes are proteins which catalyze reactions by lowering the activation energy required to drive the production of a desired product. Enzymes are commonly utilized in food processing as catalysts with specificity in order to enhance product quality through the production of beneficial food components, and to break down undesirable components that may be harmful or may decrease product quality ...


Bioengineered Platforms To Study Carcinoma Cell Response To Drug Treatment, Thuy V. Nguyen Jul 2016

Bioengineered Platforms To Study Carcinoma Cell Response To Drug Treatment, Thuy V. Nguyen

Doctoral Dissertations

The tumor extracellular matrix (ECM) plays an important role in facilitating tumor growth and mediating tumor cells' resistance to drugs. However, during drug development, potential chemotherapeutics are screened in plastic plates, which lack relevant ECM physicochemical cues. In order to improve drug development process, this dissertation includes the development of relevant 2D and 3D biomaterial systems that can be used to study carcinoma cell response to drug treatment.

A novel poly(ethylene glycol)-phosphorylcholine (PEG-PC) high-throughput biomaterial platform was developed to study how the ECM mechanochemical properties affect cancer cells' response to drug. The PEG-PC biomaterial is optically transparent, has ...


Promoting Extracellular Matrix Crosslinking In Synthetic Hydrogels, Marcos M. Manganare Nov 2015

Promoting Extracellular Matrix Crosslinking In Synthetic Hydrogels, Marcos M. Manganare

Masters Theses

The extracellular matrix (ECM) provides mechanical and biochemical support to tissues and cells. It is crucial for cell attachment, differentiation, and migration, as well as for ailment-associated processes such as angiogenesis, metastases and cancer development. An approach to study these phenomena is through emulation of the ECM by synthetic gels constructed of natural polymers, such as collagen and fibronectin, or simple but tunable materials such as poly(ethylene glycol) (PEG) crosslinked with short peptide sequences susceptible to digestion by metalloproteases and cell-binding domains. Our lab uses PEG gels to study cell behavior in three dimensions (3D). Although this system fosters ...


Mimicking The Arterial Microenvironment With Peg-Pc To Investigate The Roles Of Physicochemical Stimuli In Smc Phenotype And Behavior, William G. Herrick Aug 2015

Mimicking The Arterial Microenvironment With Peg-Pc To Investigate The Roles Of Physicochemical Stimuli In Smc Phenotype And Behavior, William G. Herrick

Doctoral Dissertations

The goal of this dissertation was to parse the roles of physical, mechanical and chemical cues in the phenotype plasticity of smooth muscle cells (SMCs) in atherosclerosis. We first developed and characterized a novel synthetic hydrogel with desirable traits for studying mechanotransduction in vitro. This hydrogel, PEG-PC, is a co-polymer of poly(ethylene glycol) and phosphorylcholine with an incredible range of Young’s moduli (~1 kPa - 9 MPa) that enables reproduction of nearly any tissue stiffness, exceptional optical and anti-fouling properties, and support for covalent attachment of extracellular matrix (ECM) proteins. To our knowledge, this combination of mechanical range, low ...


Thermo-Responsive Poly(N-Isopropylacrylamide) And Its Critical Solution Temperature Type Behavior In Presence Of Hydrophilic Ionic Liquids, Purnendu K. Nayak Mar 2015

Thermo-Responsive Poly(N-Isopropylacrylamide) And Its Critical Solution Temperature Type Behavior In Presence Of Hydrophilic Ionic Liquids, Purnendu K. Nayak

Masters Theses

Thermo-responsive homopolymer poly(N-isopropylacrylamide), is a widely studied and used polymer. Our recent observations on thermal behavior of aqueous solutions of this polymer requires a short overview of existing results in order to understand the formation of different phases, both stable and unstable with the addition of hydrophilic Ionic liquids (ILs) 1-Butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), 1-Butyl-3-methylimidazolium acetate ([BMIM][OAc]) and 1-Butyl-3-methylimidazolium thiocyanate ([BMIM][SCN]) to the system. PNIPAM is soluble in cold water due to its inter- and intramolecular hydrogen bonding but phase separates upon heating at T > 32 , which is its lower critical solution temperature (LCST). PNIPAM exists ...


Experimental And Modeling Studies On The Formulation Of Stable Lipid Nanoparticle Dispersions, Yihui Yang Mar 2015

Experimental And Modeling Studies On The Formulation Of Stable Lipid Nanoparticle Dispersions, Yihui Yang

Doctoral Dissertations

This thesis presents both experimental and modeling studies on the formulation of stable lipid nanoparticle dispersions. A population balance equation (PBE) model was developed for prediction of the average polymorph content and aggregate size distribution to better understand the undesirable SLN aggregation behavior. Experimental and modeling studies showed that the polymorphic transformation was the rate determining step for my system, SLNs with smaller initial size distributions aggregated more rapidly, and aggregates contained particles with both alpha and beta crystals. Next the effect of different liquid carrier oils on the crystallization and aggregation behavior of tristearin NLC dispersions was investigated. I ...


Cell Adhesion Biophysics On Dynamic Polymer Constructs, Andreas Kourouklis Mar 2015

Cell Adhesion Biophysics On Dynamic Polymer Constructs, Andreas Kourouklis

Doctoral Dissertations

The biophysical characteristics of cell adhesion from single protein to cell length scales have primarily been studied using purely elastic substrates. However, natural extracellular matrix (ECM) is viscoelastic and contains mobile components. In this work, we combined chemistry and cell biology tools to design and characterize laterally mobile viscoelastic polymer films that promote receptor-specific cell adhesion. Moreover, we used amphiphilic block copolymers that are end-labeled with RGD peptide ligands to allow for integrin-mediated cell adhesion. The addition of a trace hydrophobic homopolymer in the supported bilayer block-copolymer films is used to tune the lateral mobility of the films. NIH 3T3 ...