Biochemical and Biomolecular Engineering Commons^™

Predicting Key Residues Relevant To Hiapp Fibril Stability Using Permuted Residue Minimal Distance Pairs Of Riapp And Hiapp Dimers, Zak Kohler

Williams Honors College, Honors Research Projects

In order to discover the most significant residues involved in hIAPP fibril formation, Replica Exchange Molecular Dynamics (REMD) trajectories of both fibril forming hIAPP dimers and non-fibril-forming rIAPP dimers were analyzed. An import heuristic for this is the minimum distance between the peptides. To gain a greater resolution than the standard center of mass distance or 1-1, 2-2, etc.\ residue distances, every permutation of residue distance between molecules of the dimer was measured ranked. It was found that while the rIAPP had a single favored contact, (26 10), hIAPP appeared to have a network of at least three significant contacts: …

Formation Of Polymer Micro-Tubes, Daniel Peters

Williams Honors College, Honors Research Projects

Abstract

Current demand for organs is greater than the supply of donated organs, which means that a new method of obtaining replacement organs needs to be found. The objective of the research is to evaluate the use of thermo-triggered self-rolling polymer tubes that can be used for scaffolds in tissue engineering. Additionally, the research also includes a method for forming polymer tubes through the removal of a sugar fiber, coated with a thin film of polymer, by dissolving it in deionized water. For the first approach, the effect of the aqueous environment and temperature on a polymer bilayer was observed …

Determining The Critical Micelle Concentration Of Polymer Matrix For Drug Delivery Purposes, Katie Emmert

Williams Honors College, Honors Research Projects

Targeted oral release systems have been a large topic within drug delivery systems. There are several benefits to an oral delivery including patient convenience and lower chance of infection. The colon specifically has been researched as the release media. The colon is an ideal location for a release because the pH is stable with high levels of microorganisms. Like any type of drug delivery research, there are several hurdles to overcome. In order for a drug to be released in the colon, the drug must survive the stomach and be biocompatible. This biocompatibility and pH sensitivity was created using a …

Evaluation Of The Signature Molecular Descriptor With Blosum62 And An All-Atom Description For Use In Sequence Alignment Of Proteins, Lindsay M. Aichinger

Williams Honors College, Honors Research Projects

This Honors Project focused on a few aspects of this topic. The second is comparing the molecular signature kernels to three of the BLOSUM matrices (30, 62, and 90) to test the accuracy of the mathematical model. The kernel matrix was manipulated in order to improve the relationship by focusing on side groups and also by changing how the structure was represented in the matrix by increasing the initial height distance from the central atom (Height 1 and Height 2 included).

There were multiple design constraints for this project. The first was the comparison with the BLOSUM matrices (30, 62, …

Polymer Interactions With Nucleic Acids Under Various Physiological Conditions, Matthew S. Obrzut

Williams Honors College, Honors Research Projects

The goal of this project is to improve our understanding of nucleic acid interactions with cationic polymers with the theory that the polymers could protect the nucleic acids from degradation caused by biological enzymes. We seek to understand what the limitations of the cationic polymers are which, in this case, is mainly polymer-DNA compatibility. This experiment utilized peptide-dextran hybrid polymers with differing functionalizations to condense anionic nucleic acids into nanometer-sized polyplexes. Techniques of dynamic light scattering and zeta-potential were utilized to determine the particle sizes and surface charges of polyplexes.

In this experiment, dextran with a molecular weight of 20 …

New Multiphase Reactor Design Using Electrospun Nanofibers, Victoria Smith

Williams Honors College, Honors Research Projects

No abstract provided.

Effect Of Nitrogen On Properties Of Na2o-Cao-Sro-Zno-Sio2 Glasses, Ahmed Bachar, Cyrille Mercier, Arnaud Tricoteaux, Jean Christophe Hornez, Anne Leriche, Claudine Follet, Bertrand Revel, Stuart Hampshire, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Glasses in the Na₂O-CaO-SrO-ZnO-SiO₂ system have previously been investigated for suitability as a reagent in Al-free glass polyalkenoate cements (GPCs). These materials have many properties that offer potential in orthopedics. However, their applicability has been limited, to date, because of their poor strength. This study was undertaken with the aim of increasing the mechanical properties of a series of these Zn-based GPC glasses by doping with nitrogen to give overall compositions of: 10Na₂O-10CaO-20SrO-20ZnO-(40-3x)SiO₂-xSi₃N₄ (x is the no. of moles of Si₃N₄). The density, glass-transition temperature, hardness, …

Deuterium Enrichment And The Kinetic Isotope Effect During Ruthenium Catalyzed Fischer-Tropsch Synthesis, Jennifer Naumovitz

Online Theses and Dissertations

Fischer Tropsch Synthesis is a highly researched field that is still widely debated today. Research in this field could lead to many different advances, such as alternative fuel sources, explanations of abiogenic hydrocarbons and the formation of organic matter in the solar nebula. Analysis of this synthesis was carried out with a ruthenium catalyst at controlled temperatures and pressures. Two types of experiments were performed: H2/D2 switching and competitive methods. The products showed that the hydrocarbon production rate was slightly increased when syngas was switched to D2/CO. Also, the H/D ratios of the hydrocarbons produced by the FT reaction using …

Effects Of De-Polymerization Of Cellulose In Producing Sugar From Cellulosic Biomass At Low-Temperature, Lin Ling Wu

Online Theses and Dissertations

Lignocellulosic biomass is an abundant, renewable and environmentally friendly raw materials that can be converted into biofuels as an efficient alternative energy source. Sugar production is one of the key steps in converting biomass to fuels and chemicals. In order to enhance the accessibility of lignocellulosic biomass to catalytic enzyme, microorganism, and other types of catalysis during bioprocessing, the pre-treatment of lignocellulosic biomass is needed. To depolymerize the lignocellulosic materials, a 7% NaOH/12% urea solution was used. Selection of enzyme from Novozyme was performed, as a result, NS22074, a Cellulase complex was used throughout the research. Under the same reaction …

Integrated Nanoscale Imaging And Spatial Recognition Of Biomolecules On Surfaces, Congzhou Wang

Theses and Dissertations

Biomolecules on cell surfaces play critical roles in diverse biological and physiological processes. However, conventional bulk scale techniques are unable to clarify the density and distribution of specific biomolecules in situ on single, living cell surfaces at the micro or nanoscale. In this work, a single cell analysis technique based on Atomic Force Microscopy (AFM) is developed to spatially identify biomolecules and characterize nanomechanical properties on single cell surfaces. The unique advantage of these AFM-based techniques lies in the ability to operate in situ (in a non-destructive fashion) and in real time, under physiological conditions or controlled micro-environments.

First, AFM-based …

Polysaccharide-Based Shear Thinning Hydrogels For Three-Dimensional Cell Culture, Vasudha Surampudi

Theses and Dissertations

The recreation of the complicated tissue microenvironment is essential to reduce the gap between in vitro and in vivo research. Polysaccharide-based hydrogels form excellent scaffolds to allow for three-dimensional cell culture owing to the favorable properties such as capability to absorb large amount of water when immersed in biological fluids, ability to form “smart hydrogels” by being shear-thinning and thixotropic, and eliciting minimum immunological response from the host. In this study, the biodegradable shear-thinning polysaccharide, gellan-gum based hydrogel was investigated for the conditions and concentrations in which it can be applied for the adhesion, propagation and assembly of different mammalian …

Biomolecule Localization And Surface Engineering Within Size Tunable Nanoporous Silica Particles, Daniel M. Schlipf

Theses and Dissertations--Chemical and Materials Engineering

Mesoporous silica materials are versatile platforms for biological catalysis, isolation of small molecules for detection and separation applications. The design of mesoporous silica supports for tailored protein and biomolecule interactions has been limited by the techniques to demonstrate biomolecule location and functionality as a function of pore size. This work examines the interaction of proteins and lipid bilayers with engineered porous silica surfaces using spherical silica particles with tunable pore diameters (3 – 12 nm) in the range relevant to biomolecule uptake in the pores, and large particle sizes (5 - 15 µm) amenable to microscopy imaging

The differentiation of …

Design And Synthesis Of Sigma-1 Probe For Positron Emission Tomography (Pet) Imaging, May Ly

Honors Theses

Sigma-1 receptor radioligands have the potential to detect and monitor various neurological diseases. Because sigma-1 receptors are believed to be associated with numerous psychiatric conditions and neurodegenerative diseases, radioligands for sigma-1 receptors have the potential to serve as novel diagnostic tools and may be useful in assessing treatment effectiveness. A benzothiazolone 18F-labeled sigma-1 receptor ligand, CM304, has demonstrated promise as a specific positron emission tomography radiotracer for visualizing sigma-1 receptors in living subjects. Based on CM304, backup molecules were created to improve the overall drug profile, including half- life and bioavailability.

Energy Intensity And Environmental Impact Metrics Of The Back-End Separation Of Ethylene Plant By Thermodynamic Analysis, Mahdi H. Alhajji, Yaşar Demirel

Department of Chemical and Biomolecular Engineering: Faculty Publications

This study presents metrics of energy intensity and environmental impact of the back-end separation of ethylene plant consisting three interacting distillation columns by thermodynamic analysis. The objective is to explore the scope of reducing the energy for utilities and CO₂ emissions. Thermodynamic analysis is carried out using the column targeting tool (CTT) to address the sustainability metrics of ‘Energy Intensity.’ CTT is based on the ‘Practical Near-Minimum Thermodynamic Condition’ representing a close to practical reversible column operation. Environmental impact metrics are estimated from the carbon tracking options. The carbon tracking are estimated by the CO₂ emission data source …

Processing And Mechanical Testing Of Strontium-Substituted Hydroxyapatite/Glass Composites, Chokchai Yatongchai, Mark R. Towler, Anthony W. Wren

Chemical and Biochemical Engineering Faculty Research & Creative Works

Sr-HA/Glass composites were produced. Phase composition of composites was evaluated. Their physical and mechanical properties were determined. Sintered composites mainly consisted of Sr-HA/β-TCP, or β-TCP/Ca₂ZnSi₂O₇. The composites had porosity up to 4 times those of undoped Sr-HA. Compared to undoped Sr-HA, the Sr-HA/Glass composites had lower biaxial flexural strength and hardness. The Weibull modulus for the composites ranged from 2.77 to 18.74.

Photobioreactor Design For Improved Energy Efficiency Of Microalgae Production, Alexander Burns

Master's Theses

ABSTRACT

Photobioreactor Design for Improved Energy Efficiency of Microalgae Production

Alexander Burns

The objective of this research was to investigate a new photobioreactor (PBR) design for microalgae production that retains the typical advantages of existing tubular PBRs while reducing power consumption by providing simultaneous culture circulation and gas exchange with airlift alone and no centrifugal recirculating pump. Traditional tubular PBR designs feature a compressed air supply and a centrifugal pump for culture circulation and gas exchange. Circulation and gas exchange in a closed-system PBR is necessary to keep the algae suspended and to provide sufficient mass transfer (mainly for the …

Photonic Crystal-Based Flow Cytometry, Justin William Stewart

USF Tampa Graduate Theses and Dissertations

Photonic crystals serve as powerful building blocks for the development of lab-on-chip devices. Currently they are used for a wide range of miniaturized optical components such as extremely compact waveguides to refractive-index based optical sensors. Here we propose a new technique for analyzing and characterizing cells through the design of a micro-flow cytometer using photonic crystals. While lab scale flow cytometers have been critical to many developments in cellular biology they are not portable, difficult to use and relatively expensive. By making a miniature sensor capable of replicating the same functionality as the large scale units with photonic crystals, we …

Investigating The Stability Of Eliposomes At Elevated Temperatures, Ghaleb A. Husseini, William G. Pitt, Marjan Javadi

Faculty Publications

eLiposomes encapsulate a perfluorocarbon nanoemulsion droplet inside a liposome. Ultrasound is then used as a trigger mechanism to vaporize the perfluorocarbon, break the liposome, and release the desired drug to the tumor tissue. The purpose of this research is to show that eLiposomes synthesized using perfluoropentane are stable above the normal boiling point of the perfluoropentane and at body temperature and thus has potential for use in vivo. Experiments involving the release of fluorescent calcein molecules were performed on eLiposomes to measure the release of calcein at various temperatures in the absence of ultrasound. Results showed that eLiposomes are stable …

Method And Apparatus For Surface Chemical Functionalization Of Powders And Nanoparticles, Mary Gilliam, Susan Farhat, Graham Garner, Michael Magyar

Chemical Engineering Patents

A method and apparatus is provided for the modification of the surface chemistry of solid nano- and micro-particles in order to tailor the properties and functions of these particles. The method generally involves the generation of an atmospheric plasma glow discharge and energetic species that undergo chemical reaction with the surface of the primary particles. The process includes the generation of energetic species to initiate reaction, optional delivery of a precursor fluid, optional delivery of chemical species for grafting, and delivery of separated and de-agglomerated particles into the plasma discharge exiting the plasma generation chamber.

An Economic Analysis Of Small-Scale Biodiesel Production: Implementation Of Ethyl Ester Production In A Job Shop Setting, Scott Haase, Benjamin Craig

Journal of Undergraduate Research at Minnesota State University, Mankato

Biodiesel is becoming a demanded consumer automotive alternative fuel used in diesel vehicles today. An emerging trend is toward small-scale biodiesel production performed by the final consumer. A limited source of commercially available production systems exists and has resulted in many systems being designed and built by the user. Preliminary research conducted by the authors has shown biodiesel to be the least-cost alternative to petroleum diesel after as few as 8 months of system use. This study examines the economic viability of building and producing biodiesel using a small-scale production system versus buying consumer petroleum diesel. During production, measurements were …