Biochemical and Biomolecular Engineering Commons^™

A New Interpretation Of The √7×√7 R19.1° Structure For P Adsorbed On A Ni(111) Surface, Elizabeth Barrow, Grant S. Seuser, Hiroko Ariga-Miwa, Donna A. Chen, Jochen A. Lauterbach, Kiyotaka Asakura

Faculty Publications

We have studied P adsorption on Ni(111), a system which shows complex adsorbate structures. We determined the phase diagram of the surface P adsorbed on Ni(111). At low coverage, amorphous P was observed. At temperatures between 373 and 673 K and coverages above 0.1 monolayer, we found a √7×√7 R19.1° structure, but above 673 K, other complex structures were created. These structures seemed to correlate with each other and we reinterpret a √7×√7 R19.1° structure of P adsorbed on Ni(111) based on the similarities of these surface structures. The new rectangular structure for the √7×√7 19.1° is discussed in relation …

A New Interpretation Of The √7×√7 R19.1° Structure For P Adsorbed On A Ni(111) Surface, Elizabeth Barrow, Grant S. Seuser, Hiroko Ariga-Miwa, Donna A. Chen, Jochen A. Lauterbach, Kiyotaka Asakura

Faculty Publications

We have studied P adsorption on Ni(111), a system which shows complex adsorbate structures. We determined the phase diagram of the surface P adsorbed on Ni(111). At low coverage, amorphous P was observed. At temperatures between 373 and 673 K and coverages above 0.1 monolayer, we found a √7×√7 R19.1° structure, but above 673 K, other complex structures were created. These structures seemed to correlate with each other and we reinterpret a √7×√7 R19.1° structure of P adsorbed on Ni(111) based on the similarities of these surface structures. The new rectangular structure for the √7×√7 19.1° is discussed in relation …

Development Of A Comsol Microdialysis Model, Towards Creation Of Microdialysis On A Chip With Improved Geometries And Recovery, Patrick Pysz

Graduate Theses and Dissertations

Microdialysis (µD) sampling is a diffusion-limited sampling method that has been widely used in different biomedical fields for greater than 35 years. Device calibration for in vivo studies is difficult for current non-steady state analytes of interest correlated with both inflammatory response and microbial signaling molecules (QS); which exist in low ng/mL to pg/mL with molecular weights over a wide range of 170 Da to 70 kDa. The primary performance metric, relative recovery (RR), relating the collected sample to the extracellular space concentration varies from 10% to 60% per analyte even under controlled bench-top conditions. Innovations in microdialysis device design …

Bioluminescence Resonance Energy Transfer (Bret) - Based Nanostructured Biosensor For Detection Of Glucose, Eugene Hwang

Electronic Thesis and Dissertation Repository

Bioluminescence resonance energy transfer (BRET) is a distance dependent, non-radiative energy transfer, which uses a bioluminescent protein to excite an acceptor through resonance energy transfer. In this thesis, BRET technology is incorporated into a sensor comprised of a recombinant protein and quantum dots. The recombinant protein, which includes the bioluminescent protein, Renilla luciferase (Rluc), is used as the donor molecule and cadmium tellurium quantum dots as the acceptor molecules. Separating the donor-acceptor pair is a recombinant protein, glucose binding protein, which changes conformation upon binding glucose and brings the pair closer together, thus allowing BRET to occur. Optimization of the …

In-Situ Extraction And Impregnation Of Black Walnut Husk Into Polyethylene Film Using Supercritical Carbon Dioxide With An Ethanol Modifier, Johnathon Wenzel, Veronica Moorman, Lihua Wang, Cheryl S. Samaniego, Michelle Ammerman, Isaiah Spencer-Williams, Mitchell Hall

Chemical Engineering Publications

Walnuts are commonly cultivated for their kernel, which is a rich source of antioxidant phenolic compounds. The husk likewise contains antioxidant and antimicrobial compounds, but is typically discarded without further processing. Antioxidant compounds are useful in creating active packaging films, but typically decompose at melt extrusion temperatures in polymer processing. Due to carbon dioxide's low critical point and ability to swell polymer films, supercritical carbon dioxide may be used to impregnate phenolic compounds into polymers. For this study, a novel technique is used to simultaneously produce walnut husk extracts and impregnate the extract into polymer films in the same batch …

Gradient Precipitation Of Recombinant Proteins Contained In Silkworm Larvae (Bombyx Mori) With Ammonium Sulphate, Abdurhakhmanov Jaloliddin, Sasmakov Sobirdjan, Khasanov Shuhrat, Ashirov Оybek

CHEMISTRY AND CHEMICAL ENGINEERING

We investigated the protein extract of silkworm larvae. For the first time, an extract containing proteins from silkworm larvae, obtained by fractional precipitation using ammonium sulfate, was studied. As a result of experiment is established, that solutions of ammonium sulfate with a concentration from 20% to 65% are optimal for the sedimentation of protein molecules with a mass in the range of 25 and 45 kDa. Optimal results of the study proposed to use in the process of purification of recombinant proteins.

Development And Characterisation Of High Surface Energy Microstructured Sol-Gel Coatings For Sensing Applications, Emma Machugh

Doctoral

This study investigates the development of high surface energy photoreactive organic inorganic hybrid sol-gel coatings for the microstructuration of high-resolution microfluidic platforms and optofluidic biosensor platforms by standard photolithography processes. To achieve this, the first step of our work consisted of identifying the fundamental physico chemical processes governing the structuration and surface properties of hybrid organic inorganic sol-gel coatings. For this purpose, a reference material based on the combination of an organosilane (3-Methacryloxypropytrimethoxysilane, MAPTMS) and a transition metal (zirconium propoxide, ZPO), was firstly developed and characterised. It was highlighted that chemical, physical and combined physical and chemical processes can be …

A Review Of Materials For Managing Bone Loss In Revision Total Knee Arthroplasty, Romina Shafaghi, Omar Rodriguez, Emil H. Schemitsch, Paul Zalzal, Stephen D. Waldman, Marcello Papini, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

In 2014–2015, 61,421 total knee arthroplasties (TKAs) were performed in Canada; an increase of about 20% over 2000–2001. Revision total knee arthroplasties (rTKAs) accounted for 6.8% of TKAs performed between 2014 and 2015, and this is estimated to grow another 12% by 2025. rTKAs are typically more complicated than primary TKAs due to the significant loss of femoral and tibial bone stock. The escalating demand and limitations associated with total knee arthroplasty and their revision drives the development of novel treatments. A variety of materials have been utilized to facilitate regeneration of healthy bone around the site of a knee …

Selection Of Optimal Conditions For The Cultivation Of Insect Cells For Use In Biotechnology, Khasanоv Shuhrat, Sasmakоv Sobir, Abdurakhmanоv Jaloliddin, Ashirоv Оybek

CHEMISTRY AND CHEMICAL ENGINEERING

The article discusses use of the insect cell cultures for biotechnological purposes. Optimal conditions for the cultiva-tion of Spodoptera exigua and Lymantria dispar cell lines were selected.

Development Of A Method Of Oriented Immobilization Of Lipases On A Solid Carrier, Ziyavitdinov Jamolitdin Fazlitdinovich, Inogamov Utkir Kudratillayevich, Berdiev Nodir Sharifovich, Ishimov Uchkun Jomuradovich

CHEMISTRY AND CHEMICAL ENGINEERING

The methods of oriented immobilization of lipases on a solid carrier - Silochrome C-80 have been developed. The resulting sorbents were tested in the process of obtaining biodiesel from cotton oil. It was shown that immobilized lipase on Silochrome C-80 with NH2 group has the highest transetrification ability and stability, while in sorbents with the enzyme immobilized with -COOH and -SH groups this value was 87 and 53%, respectively. Biocatalysis using an affinity sorbent of immobilized lipase with the –NH2 group has a high operational stability, which, after 240 hours of operation, retains more than 50%, and after 480 hours, …

Bioremediation Of Refinery Desalter Effluent Using Debaryomyces Hansenii And Parachlorella Kessleri, Leila Azimian

Electronic Thesis and Dissertation Repository

Crude oil desalting operations produce an effluent stream which is challenging to treat due to its salt, heavy metal and hydrocarbon content. Consequently, desalter effluent (DE) is usually diluted into other effluent streams and sent to conventional wastewater treatment plants which may lead to upsets the plant operation.

In this study, a novel microbial approach was applied which investigated DE treatment using halotolerant yeast Debaryomyces hansenii (LAF-3 10 U) or the environmentally robust micro-algae Parachlorella kessleri strain CPCC 266. The effect of these two different approaches on both synthetic and actual DE was investigated in both batch and/or continuous mode. …

The Effect Of Tantalum Incorporation On The Physical And Chemical Properties Of Ternary Silicon–Calcium–Phosphorous Mesoporous Bioactive Glasses, Andrew Mendonca, Md Saidur Rahman, Adel Alhalawani, Omar Rodriguez, Reid C. Gallant, Heyu Ni, Owen M. Clarkin, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Synthesis and characterization of the first mesoporous bioactive glasses (MBGs) containing tantalum are reported here, along with their potential application as hemostats. Silica MBGs were synthesized using with the molar composition of (80-x)% Si, 15% Ca, 5% P, and x% Ta. It was found that incorporation of >1 mol % Ta into the MBGs changes their physical and chemical properties. Increasing Ta content from 0 to 10 mol % causes a decrease in the surface area and pore volume of ~20 and ~35%, respectively. This is due to the increase in nonbridging oxygens and mismatch of thermal expansion coefficient which …

Immobilization Of The Influenza A M2 Transmembrane Peptide In Virus Envelope−Mimetic Lipid Membranes: A Solid-State Nmr Investigation, Wenbin Luo, Sarah D. Cady, Mei Hong

Sarah Cady

The dynamic and structural properties of membrane proteins are intimately affected by the lipid bilayer. One property of membrane proteins is uniaxial rotational diffusion, which depends on the membrane viscosity and thickness. This rotational diffusion is readily manifested in solid-state NMR spectra as characteristic line shapes and temperature-dependent line narrowing or broadening. We show here that this whole-body uniaxial diffusion is suppressed in lipid bilayers mimicking the composition of eukaryotic cell membranes, which are rich in cholesterol and sphingomyelin. We demonstrate this membrane-induced immobilization on the transmembrane peptide of the influenza A M2 (AM2-TM) proton channel protein. At physiological temperature, …

Sequencing Heparan Sulfate Using Hilic Lc-Netd-Ms/Ms, Jiandong Wu, Juan Wei, Pradeep Chopra, Geert Jan Boons, Cheng Lin, Joseph Zaia

Chemical and Biochemical Engineering Faculty Research & Creative Works

Heparan Sulfate (HS) Mediates a Wide Range of Protein Binding Interactions Key to Normal and Pathological Physiology. Though Liquid Chromatography Coupled with Mass Spectrometry (LC-MS) based Disaccharide Composition Analysis is Able to Profile Changes in HS Composition, the Heterogeneity of Modifications and the Labile Sulfate Group Present Major Challenges for Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) Sequencing of the HS Oligosaccharides that Represent Protein Binding Determinants. Here, We Report Online LC-MS/MS Sequencing of HS Oligosaccharides using Hydrophilic Interaction Liquid Chromatography (HILIC) and Negative Electron Transfer Dissociation (NETD). a Series of Synthetic HS Oligosaccharides Varying in Chain Length (Tetramers and Hexamers), …

Evaluation Of Biohydrogen Production From Co-Fermentation Of Carbohydrates And Proteins, Emmanuel Andrew Tepari Jr,

Electronic Thesis and Dissertation Repository

The aim of this study was to examine volatile fatty acid (VFA) production from a proteinaceous substrate, bovine serum albumin (BSA) for a pH range of 5 – 9, and to further assess its impact on hydrogen production in a co-fermentation process using starch and BSA at different ratios. The established optimum conditions for VFA production from BSA were an initial pH of 8, incubation time of 3 days and an operating temperature of 37 ℃. Using these fermentation conditions, the stoichiometric reactions that describe the anaerobic degradation of BSA were investigated. A methodology that describes organic acid production from …

Measurement Of Adhesion Of Sternal Wires To A Novel Bioactive Glass-Based Adhesive, Varinder Pal Singh Sidhu, Mark R. Towler, Marcello Papini

Chemical and Biochemical Engineering Faculty Research & Creative Works

Stainless steel wires are the standard method for sternal closure because of their strength and rigidity, the simplicity of the process, and the short healing time that results from their application. Despite this, problems still exist with sternal stability due to micromotion between the two halves of the dissected and wired sternum. Recently, a novel glass-based adhesive was developed which, in cadaveric trials and in conjunction with wiring, was shown to restrict this micromotion. However, in order to avoid complications during resternotomy, the adhesive should adhere only to the bone and not the sternal wire. In this study, sternal wires …

Renal Specific Rnai Delivery By Fibrillar Nanoparticle Excipients, Sam Wong

Dissertations, Theses, and Capstone Projects

RNA interference (RNAi) is a powerful tool to manipulate the phenotype of an organism by silencing the expression of specific genes and is viewed as a highly promising platform for treating undruggable targets and disorders where small molecule drugs and antibodies would fail. However, development of RNAi based therapies has faced major barriers including cellular and tissue-specific uptake of the Small Interfering RNA (siRNA). Utilizing different nanoparticles as RNAi excipients, cellular uptake and gene silencing potency can be greatly improved. The research in Dr. McDevitt groups has fibrillar carbon nanotubes (CNT) as carriers for siRNA for gene silencing in vitro …

Bioengineering Extracellular Matrix Scaffolds For Volumetric Muscle Loss, Kevin Roberts

Graduate Theses and Dissertations

Volumetric muscle loss overwhelms skeletal muscle’s ordinarily capable regenerative machinery, resulting in fibrosis and severe functional deficits which have defied clinical repair strategies. My work spans the design and preclinical evaluation of implants intended to drive the cell community of injured muscle toward a regenerative state, as well as the development of an understanding of the molecular responses of this cell community to biomaterial interventions. I demonstrate a new class of biomaterial by leveraging the productive capacity of sacrificial hollow fiber membrane cell culture; I show specifically that unique threads of whole extracellular matrix can be isolated by solvent degradation …

Bioactive Glass Fiber Fabrication Via A Combination Of Sol-Gel Process With Electro-Spinning Technique, Malvika Nagrath, Adel Alhalawani, Alireza Rahimnejad Yazdi, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

No abstract provided.

Characterization Of Tetrazolium Salts And Formazans Using Computational Chemistry For Radiochromic Dosimetry, Teshome G. Bedada

Electronic Thesis and Dissertation Repository

Computational chemistry is a powerful tool to model different materials and predict their physical and chemical properties. The goal of this thesis was to apply different computational chemistry tools to model the properties of two classes of closely related organic compounds: formazans and tetrazolium salts for ionizing radiation dosimetry in water-based gels, whereby the absorbed dose is registered by optical detection of formazan formation from tetrazolium salts. The structural parameters of phenyl and benzothiazolyl-substituted tetrazolium salts and formazans were computed using the APFD density functional theory (DFT) model and 6-311+G(2d,p) basis set. Conformational searching of stereoisomers (TSCA and TATA structures) …

K-Fit: Parameterizing Kinetic Models Of Metabolism Using Multiple Fluxomic Datasets, Costa Maranas

Biochemical and Molecular Engineering XXI

Kinetic models predict the metabolic flows by directly linking metabolite concentrations and enzyme levels to reaction fluxes. Robust parameterization of organism-level kinetic models that faithfully reproduce the effect of different genetic or environmental perturbations remains an open challenge due to the intractability of existing algorithms. This paper introduces K-FIT, an accelerated kinetic parameterization workflow that leverages a novel decomposition approach to identify steady-state fluxes in response to genetic perturbations followed by a gradient-based update of kinetic parameters until predictions simultaneously agree with the fluxomic data in all perturbed metabolic networks. The applicability of K-FIT to large-scale models is demonstrated by …

The Statistics Of Directed Evolution: From Library Generation To High Throughput Screens, Keith Tyo

Biochemical and Molecular Engineering XXI

Directed evolution has been recognized as a powerful approach to creating enzymes and cells with desirable properties, such as growth on a new substrate, thermotolerance, or even novel reaction mechanisms. The directed evolution approach is to generate diversity through genetic mutations and screen the diversity for mutants that have improved properties compared to the parent. This diversification and screening can be repeated to generate mutants with superior properties.

While the concept is straightforward, the devil is in the details. How should I create diversity (error prone PCR, mutagenic primers, transposons…)? How much diversity do I need (10³, 10 …

Advanced Technologies And Computational Modeling In Continuous Bioprocessing Heather Brooke, Pall Corporation, Usa, Heather Brooke, Edita Botonjic-Sehic

Biochemical and Molecular Engineering XXI

Biotech companies have been emphasizing the implementation and utilization of process analytical technology (PAT) and chemometrics in biomanufacturing. Advanced technologies and computation modeling have contributed significantly in making this capability come to life. Although there are still gaps in the area of advanced analytics for the process, computation modeling has started to contribute towards process characterization, which will lead to real-time process control. PAT and modeling infrastructure can be utilized in integrated continuous bioprocessing to gain better process understating, reduce production cycle time, improve yield, advance efficiency by converting from a batch process into a continuous process, and reduce cost …

Biologicalisation: A Nature-Based Digital Manufacturing Revolution, William Whitford

Biochemical and Molecular Engineering XXI

Industry 4.0 is changing our manufacturing concepts [1]. Biologicalisation is the use of 4.0 principals in concert with biological and bio-inspired materials, chemistries and functions to support an efficient and sustainable manufacturing schema. From product design, to development and manufacturing, biomimetic product designs and bio-integrated manufacturing systems describe this biological transformation of manufacturing [2].

Please click Additional Files below to see the full abstract.

Conference Program, Christina Chan, Mattheos Koffas, Steffen Schaffer, Rashmi Kshirsagar

Biochemical and Molecular Engineering XXI

No abstract provided.

Beneficial Reuse Of Industrial Co2 Emissions Using A Microalgae Photobioreactor: Waste Heat Utilization Assessment, Daniel T. Mohler, Michael H. Wilson, Zhen Fan, John G. Groppo, Mark Crocker

Center for Applied Energy Research Faculty and Staff Publications

Microalgae are a potential means of recycling CO₂ from industrial point sources. With this in mind, a novel photobioreactor (PBR) was designed and deployed at a coal-fired power plant. To ascertain the feasibility of using waste heat from the power plant to heat algae cultures during cold periods, two heat transfer models were constructed to quantify PBR cooling times. The first, which was based on tabulated data, material properties and the physical orientation of the PBR tubes, yielded a range of heat transfer coefficients of 19–64 W m⁻² K⁻¹ for the PBR at wind speeds of 1–10 …

Carbon Nanotube And Cellulose Nanocrystal Hybrid Films, Mingzhe Jiang, Robert Seney, Paul Charles Bayliss, Christopher L. Kitchens

Publications

The use of cellulose nanocrystals (CNC) in high performance coatings is attractive for micro-scale structures or device fabrication due to the anisotropic geometry, however CNC are insulating materials. Carbon nanotubes (CNT) are also rod-shaped nanomaterials that display high mechanical strength and electrical conductivity. The hydrophobic regions of surface-modified CNC can interact with hydrophobic CNT and aid in association between the two anisotropic nanomaterials. The long-range electrostatic repulsion of CNC plays a role in forming a stable CNT and CNC mixture dispersion in water, which is integral to forming a uniform hybrid film. At concentrations favorable for film formation, the multiwalled …

Ranking And Clustering Of Drosophila Olfactory Receptors Using Mathematical Morphology, Jayanta Kumar Das, Pabitra Pal Choudhury, Neelambuj Chaturvedi, Mohd Tayyab, Sk Sarif Hassan

Journal Articles

This article introduces an alignment-free clustering method in order to cluster all the 66 DORs sequentially diverse protein sequences. Two different methods are discussed: one is utilizing twenty standard amino acids (without grouping) and another one is using chemical grouping of amino acids (with grouping). Two grayscale images (representing two protein sequences by order pair frequency matrices) are compared to find the similarity index using morphology technique. We could achieve the correlation coefficients of 0.9734 and 0.9403 for without and with grouping methods respectively with the ClustalW result in the ND5 dataset, which are much better than some of the …

Modeling The Interplay Between Photosynthesis, Co2 Fixation, And The Quinone Pool In A Purple Non-Sulfur Bacterium, Adil Alsiyabi

Department of Chemical and Biomolecular Engineering: Theses and Student Research

Rhodopseudomonas palustris CGA009 is a purple non-sulfur bacterium (PNSB) that can fix CO₂ and nitrogen or break down organic compounds for its carbon and nitrogen requirements. Light, inorganic, and organic compounds can all be used for its source of energy. Excess electrons produced during its metabolic processes can be exploited to produce hydrogen gas or biodegradable polyesters (polyhydroxybutyrate). A genome-scale metabolic model of the bacterium was reconstructed to study the interactions between photosynthesis, carbon dioxide fixation, and the redox state of the quinone pool. A comparison of model-predicted flux values with published in vivo MFA fluxes resulted in predicted …

Bioproduction Of Adipic Acid Using Engineered Pseudomonas Putida Kt2440 From Lignin-Derived Aromatics, Howard Willett

Department of Chemical and Biomolecular Engineering: Theses and Student Research

Current industrial synthesis of adipic acid is nonrenewable and depends on a carcinogenic starting material, benzene. Biocatalysis with an engineered microorganism could turn a renewable feedstock into a value-added chemical such as adipic acid. Here we engineered P. putida KT2440 to transform lignin-derived aromatics, coumarate and ferulate, into adipic acid. Lignin is a recalcitrant plant biopolymer burned for thermal energy. Conversion of lignin into a value-added chemical will improve the efficiency of lignocellulose processing plants. The best performing engineered KT2440 strain produces 2.52 mM adipate at a 9.5% (mole/mole) yield. This was achieved by the genetic insertion of non-natural biosynthetic …