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Full-Text Articles in Biomedical Engineering and Bioengineering

Direct Pore‐Level Observation Of Permeability Increase In Two‐Phase Flow By Shaking, Igor A. Beresnev, William Gaul, R. Dennis Vigil Oct 2011

Direct Pore‐Level Observation Of Permeability Increase In Two‐Phase Flow By Shaking, Igor A. Beresnev, William Gaul, R. Dennis Vigil

Chemical and Biological Engineering Publications

Increases in permeability of natural reservoirs and aquifers by passing seismic waves have been well documented. If the physical causes of this phenomenon can be understood, technological applications would be possible for controlling the flow in hydrologic systems or enhancing production from oil reservoirs. The explanation of the dynamically increased mobility of underground fluids must lie at the pore level. The natural fluids can be viewed as two-phase systems, composed of water as the wetting phase and of dispersed non-wetting globules of gas or organic fluids, flowing through tortuous constricted channels. Capillary forces prevent free motion of the suspended non-wetting ...


Thickness Of Residual Wetting Film In Liquid-Liquid Displacement, Igor A. Beresnev, William Gaul, R. Dennis Vigil Aug 2011

Thickness Of Residual Wetting Film In Liquid-Liquid Displacement, Igor A. Beresnev, William Gaul, R. Dennis Vigil

Chemical and Biological Engineering Publications

Core-annular flow is common in nature, representing, for example, how streams of oil, surrounded by water, move in petroleum reservoirs. Oil, typically a nonwetting fluid, tends to occupy the middle (core) part of a channel, while water forms a surrounding wall-wetting film. What is the thickness of the wetting film? A classic theory has been in existence for nearly 50 years offering a solution, although in a controversial manner, for moving gas bubbles. On the other hand, an acceptable, experimentally verified theory for a body of one liquid flowing in another has not been available. Here we develop a hydrodynamic ...


Phylogenetic And Experimental Characterization Of An Acyl-Acp Thioesterase Family Reveals Significant Diversity In Enzymatic Specificity And Activity, Fuyuan Jing, David C. Cantu, Jarmila Tvaruzkova, Jay P. Chipman, Basil J. Nikolau, Marna D. Yandeau-Nelson, Peter J. Reilly Aug 2011

Phylogenetic And Experimental Characterization Of An Acyl-Acp Thioesterase Family Reveals Significant Diversity In Enzymatic Specificity And Activity, Fuyuan Jing, David C. Cantu, Jarmila Tvaruzkova, Jay P. Chipman, Basil J. Nikolau, Marna D. Yandeau-Nelson, Peter J. Reilly

Chemical and Biological Engineering Publications

Background: Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the phosphopantetheine prosthetic group of ACP. This reaction terminates acyl chain elongation of fatty acid biosynthesis, and in plant seeds it is the biochemical determinant of the fatty acid compositions of storage lipids.

Results: To explore acyl-ACP TE diversity and to identify novel acyl ACP-TEs, 31 acyl-ACP TEs from wide-ranging phylogenetic sources were characterized to ascertain their in vivo activities and substrate specificities. These acylACP TEs were chosen by two different approaches: 1) 24 TEs were ...


Forced Instability Of Core-Annular Flow In Capillary Constrictions, Igor A. Beresnev, William Gaul, R. Dennis Vigil Jul 2011

Forced Instability Of Core-Annular Flow In Capillary Constrictions, Igor A. Beresnev, William Gaul, R. Dennis Vigil

Chemical and Biological Engineering Publications

Instability of fluid cylinders and jets, a highly nonlinear hydrodynamic phenomenon, has fascinated researchers for nearly 150 years. A subset of the phenomenon is the core-annular flow, in which a non-wetting core fluid and a surrounding wall-wetting annulus flow through a solid channel. The model, for example, represents the flow of oil in petroleum reservoirs. The flow may be forced to break up when passing through a channel’s constriction. Although it has long been observed that the breakup occurs near the neck of the constriction, the exact conditions for the occurrence of the forced breakup and its dynamic theory ...


A Quadrature-Based Kinetic Model For Dilute Non-Isothermal Granular Flows, Alberto Passalacqua, Janine E. Galvin, Prakash Vedula, Christine M. Hrenya, Rodney O. Fox Jul 2011

A Quadrature-Based Kinetic Model For Dilute Non-Isothermal Granular Flows, Alberto Passalacqua, Janine E. Galvin, Prakash Vedula, Christine M. Hrenya, Rodney O. Fox

Chemical and Biological Engineering Publications

A moment method with closures based on Gaussian quadrature formulas is proposed to solve the Boltzmann kinetic equation with a hard-sphere collision kernel for mono-dispersed particles. Different orders of accuracy in terms of the moments of the velocity distribution function are considered, accounting for moments up to seventh order. Quadrature-based closures for four different models for inelastic collisionthe Bhatnagar-Gross-Krook, ES-BGK, the Maxwell model for hard-sphere collisions, and the full Boltzmann hard-sphere collision integral-are derived and compared. The approach is validated studying a dilute non-isothermal granular flow of inelastic particles between two stationary Maxwellian walls. Results obtained from the kinetic models ...


Reconstructing Genome-Wide Regulatory Network Of E. Coli Using Transcriptome Data And Predicted Transcription Factor Activities, Yao Fu, Laura R. Jarboe, Julie A. Dickerson Jun 2011

Reconstructing Genome-Wide Regulatory Network Of E. Coli Using Transcriptome Data And Predicted Transcription Factor Activities, Yao Fu, Laura R. Jarboe, Julie A. Dickerson

Chemical and Biological Engineering Publications

Background: Gene regulatory networks play essential roles in living organisms to control growth, keep internal metabolism running and respond to external environmental changes. Understanding the connections and the activity levels of regulators is important for the research of gene regulatory networks. While relevance score based algorithms that reconstruct gene regulatory networks from transcriptome data can infer genome-wide gene regulatory networks, they are unfortunately prone to false positive results. Transcription factor activities (TFAs) quantitatively reflect the ability of the transcription factor to regulate target genes. However, classic relevance score based gene regulatory network reconstruction algorithms use models do not include the ...


Kinetic Characterization Of A Glycoside Hydrolase Family 44 Xyloglucanase/Endoglucanase From Ruminococcus Flavefaciens Fd-1, Christopher D. Warner, Rica M. Go, Carolina García-Salinas, Clark Ford, Peter J. Reilly Jan 2011

Kinetic Characterization Of A Glycoside Hydrolase Family 44 Xyloglucanase/Endoglucanase From Ruminococcus Flavefaciens Fd-1, Christopher D. Warner, Rica M. Go, Carolina García-Salinas, Clark Ford, Peter J. Reilly

Chemical and Biological Engineering Publications

Two forms of Ruminococcus flavefaciens FD-1 endoglucanase B, a member of glycoside hydrolase family 44, one with only a catalytic domain and the other with a catalytic domain and a carbohydrate binding domain (CBM), were produced. Both forms hydrolyzed cellotetraose, cellopentaose, cellohexaose, carboxymethylcellulose (CMC), birchwood and larchwood xylan, xyloglucan, lichenan, and Avicel but not cellobiose, cellotriose, mannan, or pullulan. Addition of the CBM increased catalytic efficiencies on both CMC and birchwood xylan but not on xyloglucan, and it decreased rates of cellopentaose and cellohexaose hydrolysis. Catalytic efficiencies were much higher on xyloglucan than on other polysaccharides. Hydrolysis rates increased with ...


Mannose-Functionalized "Pathogen-Like" Polyanhydride Nanoparticles Target C-Type Lectin Receptors On Dendritic Cells, Brenda Rocio Carrillo-Conde, Eun-Ho Song, Ana Vianey Chavez-Santoscoy, Yashdeep Phanse, Amanda Ellen Ramer-Tait, Nicola L.B. Pohl, Michael J. Wannemuehler, Bryan H. Bellaire, Balaji Narasimhan Jan 2011

Mannose-Functionalized "Pathogen-Like" Polyanhydride Nanoparticles Target C-Type Lectin Receptors On Dendritic Cells, Brenda Rocio Carrillo-Conde, Eun-Ho Song, Ana Vianey Chavez-Santoscoy, Yashdeep Phanse, Amanda Ellen Ramer-Tait, Nicola L.B. Pohl, Michael J. Wannemuehler, Bryan H. Bellaire, Balaji Narasimhan

Chemical and Biological Engineering Publications

Targeting pathogen recognition receptors on dendritic cells (DCs) offers the advantage of triggering specific signaling pathways to induce a tailored and robust immune response. In this work, we describe a novel approach to targeted antigen delivery by decorating the surface of polyanhydride nanoparticles with specific carbohydrates to provide "pathogen-like" properties that ensure nanoparticles engage C-type lectin receptors on DCs. The surface of polyanhydride nanoparticles was functionalized by covalent linkage of dimannose and lactose residues using an amine-carboxylic acid coupling reaction. Coculture of functionalized nanoparticles with bone marrow-derived DCs significantly increased cell surface expression of MHC II, the T cell costimulatory ...


Diffraction-Based Tracking Of Surface Plasmon Resonance Enhanced Transmission Through A Gold-Coated Grating, Wei-Hsun Yeh, Joseph W. Petefish, Andrew C. Hillier Jan 2011

Diffraction-Based Tracking Of Surface Plasmon Resonance Enhanced Transmission Through A Gold-Coated Grating, Wei-Hsun Yeh, Joseph W. Petefish, Andrew C. Hillier

Chemical and Biological Engineering Publications

Surface plasmon resonance enhanced transmission through metal-coated nanostructures represents a highly sensitive yet simple method for quantitative measurement of surface processes and is particularly useful in the development of thin film and adsorption sensors. Diffraction-induced surface plasmon excitation can produce enhanced transmission at select regions of the visible spectrum, and wavelength shifts associated with these transmission peaks can be used to track adsorption processes and film formation. In this report, we describe a simple optical microscope-based method for monitoring the first-order diffracted peaks associated with enhanced transmission through a gold-coated diffraction grating. A Bertrand lens is used to focus the ...


Steam Reforming Of Bio-Oil Fractions: Effect Of Composition And Stability, Pedro J, Ortiz-Toral, Justinus A. Satrio, Robert C. Brown, Brent H. Shanks Jan 2011

Steam Reforming Of Bio-Oil Fractions: Effect Of Composition And Stability, Pedro J, Ortiz-Toral, Justinus A. Satrio, Robert C. Brown, Brent H. Shanks

Chemical and Biological Engineering Publications

The efficacy of steam reforming of the aqueous species in bio-oils produced from the fast pyrolysis of biomass is examined. A fractionating condenser system was used to collect a set of fractions of fast pyrolysis liquids with different chemical characteristics. The water-soluble components from the different fractions were steam-reformed using a nickel-based commercial catalyst in a fixed-bed reactor system. When reforming at 500 °C, an overall positive effect in hydrogen yields was observed for the fractions with higher concentrations of lower molecular-weight oxygenates, such as acetic acid and acetol, while the heavier compounds, such as the carbohydrates, showed an ...


A Multi-Gaussian Quadrature Method Of Moments For Simulating High Stokes Number Turbulent Two-Phase Flows, Aymeric Vie, Christophe Chalons, Rodney O. Fox, Frederique Laurent, Marc Massot Jan 2011

A Multi-Gaussian Quadrature Method Of Moments For Simulating High Stokes Number Turbulent Two-Phase Flows, Aymeric Vie, Christophe Chalons, Rodney O. Fox, Frederique Laurent, Marc Massot

Chemical and Biological Engineering Publications

With the great increase in computational resources, Large Eddy Simulation (LES) of industrial configurations is now an efficient and tractable tool. Numerous applications involve a liquid or solid disperse phase carried by a gaseous flow field (eg, fuel injection in automotive or aeronautical engines, fluidized beds, and alumina particles in rocket boosters). To simulate this kind of flow, one may resort to a Number Density Function (NDF), which satisfies a kinetic equation.


Engineering Ethanologenic Escherichia Coli For Levoglucosan Utilization, Donovan S. Layton, Avanthi Ajjarapu, Dong Won Choi, Laura R. Jarboe Jan 2011

Engineering Ethanologenic Escherichia Coli For Levoglucosan Utilization, Donovan S. Layton, Avanthi Ajjarapu, Dong Won Choi, Laura R. Jarboe

Chemical and Biological Engineering Publications

Levoglucosan is a major product of biomass pyrolysis. While this pyrolyzed biomass, also known as bio-oil, contains sugars that are an attractive fermentation substrate, commonly-used biocatalysts, such as Escherichia coli, lack the ability to metabolize this anhydrosugar. It has previously been shown that recombinant expression of the levoglucosan kinase enzyme enables use of levoglucosan as carbon and energy source. Here, ethanologenic E. coli KO11 was engineered for levoglucosan utilization by recombinant expression of levoglucosan kinase from Lipomyces starkeyi. Our engineering strategy uses a codon-optimized gene that has been chromosomally integrated within the pyruvate to ethanol (PET) operon and does not ...


Identifying Factors Controlling Protein Release From Combinatorial Biomaterial Libraries Via Hybrid Data Mining Methods, Xue Li, Latrisha K. Petersen, Scott Broderick, Balaji Narasimhan, Krishna Rajan Jan 2011

Identifying Factors Controlling Protein Release From Combinatorial Biomaterial Libraries Via Hybrid Data Mining Methods, Xue Li, Latrisha K. Petersen, Scott Broderick, Balaji Narasimhan, Krishna Rajan

Chemical and Biological Engineering Publications

Polyanhydrides are a class of degradable biomaterials that have shown much promise for applications in drug and vaccine delivery. Their properties can be tailored for controlled drug release, drug/protein stability, and immune regulation (adjuvant effect). Identifying the relationship between the molecular structures of the polymers and the drug release kinetics profiles would help understand the release mechanism and aid in the accurate prediction of drug release and the rational design of polymer-based drug carrier systems. The molecular structure descriptors that had the most impact on the release kinetics were identified using a prediction/optimization data mining approach. Using this ...


An Algorithm For Optimally Fitting A Wiener Model, Lucas P. Beverlin, Derrick K. Rollins Sr., Nisarg Vyas, David Andre Jan 2011

An Algorithm For Optimally Fitting A Wiener Model, Lucas P. Beverlin, Derrick K. Rollins Sr., Nisarg Vyas, David Andre

Chemical and Biological Engineering Publications

The purpose of this work is to present a new methodology for fitting Wiener networks to datasets with a large number of variables. Wiener networks have the ability to model a wide range of data types, and their structures can yield parameters with phenomenological meaning. There are several challenges to fitting such a model: model stiffness, the nonlinear nature of a Wiener network, possible overfitting, and the large number of parameters inherent with large input sets. This work describes a methodology to overcome these challenges by using several iterative algorithms under supervised learning and fitting subsets of the parameters at ...


Hybrid Thermochemical Processing: Fermentation Of Pyrolysis-Derived Bio-Oil, Laura R. Jarboe, Zhiyou Wen, Dong Won Choi, Robert C. Brown Jan 2011

Hybrid Thermochemical Processing: Fermentation Of Pyrolysis-Derived Bio-Oil, Laura R. Jarboe, Zhiyou Wen, Dong Won Choi, Robert C. Brown

Chemical and Biological Engineering Publications

Thermochemical processing of biomass by fast pyrolysis provides a nonenzymatic route for depolymerization of biomass into sugars that can be used for the biological production of fuels and chemicals. Fermentative utilization of this bio-oil faces two formidable challenges. First is the fact that most bio-oil-associated sugars are present in the anhydrous form. Metabolic engineering has enabled utilization of the main anhydrosugar, levoglucosan, in workhorse biocatalysts. The second challenge is the fact that bio-oil is rich in microbial inhibitors. Collection of bio-oil in distinct fractions, detoxification of bio-oil prior to fermentation, and increased robustness of the biocatalyst have all proven effective ...


Design Of A Protective Single-Dose Intranasal Nanoparticle-Based Vaccine Platform For Respiratory Infectious Diseases, Bret Daniel Ulery, Devender Kumar, Amanda Ellen Ramer-Tait, Dennis W. Metzger, Michael J. Wannemuehler, Balaji Narasimhan Jan 2011

Design Of A Protective Single-Dose Intranasal Nanoparticle-Based Vaccine Platform For Respiratory Infectious Diseases, Bret Daniel Ulery, Devender Kumar, Amanda Ellen Ramer-Tait, Dennis W. Metzger, Michael J. Wannemuehler, Balaji Narasimhan

Chemical and Biological Engineering Publications

Despite the successes provided by vaccination, many challenges still exist with respect to controlling new and re-emerging infectious diseases. Innovative vaccine platforms composed of adaptable adjuvants able to appropriately modulate immune responses, induce long-lived immunity in a single dose, and deliver immunogens in a safe and stable manner via multiple routes of administration are needed. This work describes the development of a novel biodegradable polyanhydride nanoparticle-based vaccine platform administered as a single intranasal dose that induced long-lived protective immunity against respiratory disease caused by Yesinia pestis, the causative agent of pneumonic plague. Relative to the responses induced by the recombinant ...


Rational Design Of Pathogen-Mimicking Amphiphilic Materials As Nanoadjuvants, Bret Daniel Ulery, Latrisha K. Petersen, Yashdeep Phanse, Chang Sun Kong, Scott Broderick, Devender Kumar, Amanda Ellen Ramer-Tait, Brenda Rocio Carrillo-Conde, Krishna Rajan, Michael J. Wannemuehler, Bryan H. Bellaire, Dennis W. Metzger, Balaji Narasimhan Jan 2011

Rational Design Of Pathogen-Mimicking Amphiphilic Materials As Nanoadjuvants, Bret Daniel Ulery, Latrisha K. Petersen, Yashdeep Phanse, Chang Sun Kong, Scott Broderick, Devender Kumar, Amanda Ellen Ramer-Tait, Brenda Rocio Carrillo-Conde, Krishna Rajan, Michael J. Wannemuehler, Bryan H. Bellaire, Dennis W. Metzger, Balaji Narasimhan

Chemical and Biological Engineering Publications

An opportunity exists today for cross-cutting research utilizing advances in materials science, immunology, microbial pathogenesis, and computational analysis to effectively design the next generation of adjuvants and vaccines. This study integrates these advances into a bottom-up approach for the molecular design of nanoadjuvants capable of mimicking the immune response induced by a natural infection but without the toxic side effects. Biodegradable amphiphilic polyanhydrides possess the unique ability to mimic pathogens and pathogen associated molecular patterns with respect to persisting within and activating immune cells, respectively. The molecular properties responsible for the pathogen-mimicking abilities of these materials have been identified. The ...


Confocal Imaging Of Laminar And Turbulent Mixing In A Microscale Multi-Inlet Vortex Nanoprecipitation Reactor, Yanxiang Shi, Rodney O. Fox, Michael G. Olsen Jan 2011

Confocal Imaging Of Laminar And Turbulent Mixing In A Microscale Multi-Inlet Vortex Nanoprecipitation Reactor, Yanxiang Shi, Rodney O. Fox, Michael G. Olsen

Chemical and Biological Engineering Publications

Mass production of functional nanoparticles may be realized through flash nanoprecipiation in microscale reactors such as the multi-inlet vortex reactor (MIVR). A comprehensive understanding of mixing in the MIVR is required for process control and reactor design. Mixing in the MIVR is studied using a technique coupling laser induced fluorescence with confocal laser scanning microscopy. It is shown to provide meaningful qualitative and statistical data of the scalar field for analysis and comparison with numerical simulations. Data were collected for four flow rates, showing that mixing is incomplete even at the highest flow rate.


Improving The Stability Of A Cao-Based Sorbent For Co 2 By Thermal Pretreatment, Dursun Can Ozcan, Brent H. Shanks, Thomas D. Wheelock Jan 2011

Improving The Stability Of A Cao-Based Sorbent For Co 2 By Thermal Pretreatment, Dursun Can Ozcan, Brent H. Shanks, Thomas D. Wheelock

Chemical and Biological Engineering Publications

Although the reversible absorption of CO 2 by CaO at high temperature has been proposed as a promising method for capturing and removing CO 2 from hot gas streams produced by the combustion of fossil fuels and other industrial processes, the activity of the sorbent has invariably declined when applied over many cycles of CO 2 absorption and desorption. The objective of the present investigation was to extend the life cycle performance of the absorbent through improved thermal pretreatment as the absorbent was prepared from limestone, dolomite, calcium acetate, or plaster of Paris. The first three materials were converted to ...