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1,232 full-text articles. Page 32 of 35.

Molecular Dynamics Simulation Of Fractal Aggregate Diffusion, Gaurav Pranami, Monica H. Lamm, R. Dennis Vigil 2010 Iowa State University

Molecular Dynamics Simulation Of Fractal Aggregate Diffusion, Gaurav Pranami, Monica H. Lamm, R. Dennis Vigil

R. Dennis Vigil

The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D), but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the ...


Molecular Dynamics Simulation Of Fractal Aggregate Diffusion, Gaurav Pranami, Monica H. Lamm, R. Dennis Vigil 2010 Iowa State University

Molecular Dynamics Simulation Of Fractal Aggregate Diffusion, Gaurav Pranami, Monica H. Lamm, R. Dennis Vigil

Chemical and Biological Engineering Publications

The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)] comprised of Np spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D), but these can be corrected by carrying out simulations using different simulation box sizes. Specifically, the diffusion coefficient is inversely proportional to the length of a cubic simulation box, and the constant of proportionality appears to be independent of the ...


Thyme: A Database For Thioester-Active Enzymes, David C. Cantu, Yingfei Chen, Matthew L. Lemons, Peter J. Reilly 2010 Iowa State University

Thyme: A Database For Thioester-Active Enzymes, David C. Cantu, Yingfei Chen, Matthew L. Lemons, Peter J. Reilly

Chemical and Biological Engineering Publications

The ThYme (Thioester-active enzYme;http://www.enzyme.cbirc.iastate.edu) database has been constructed to bring together amino acid sequences and 3D (tertiary) structures of all the enzymes constituting the fatty acid synthesis and polyketide synthesis cycles. These enzymes are active on thioester-containing substrates, specifically those that are parts of the acyl-CoA synthase, acyl-CoA carboxylase, acyl transferase, ketoacyl synthase, ketoacyl reductase, hydroxyacyl dehydratase, enoyl reductase and thioesterase enzyme groups. These groups have been classified into families, members of which are similar in sequences, tertiary structures and catalytic mechanisms, implying common protein ancestry. ThYme is continually updated as sequences and tertiary ...


Removal Of Low Density Sediments By Vegetative Filters, Brent M. Hall 2010 University of Nebraska-Lincoln

Removal Of Low Density Sediments By Vegetative Filters, Brent M. Hall

Biological Systems Engineering--Dissertations, Theses, and Student Research

The use of vegetative filter strips (VFS) is a longstanding best management practice for the removal of sediment and other pollutants from overland flow. Many attempts have been made to model the effectiveness of a VFS based upon soil, vegetation, and sediment properties, and also upon flow conditions, but little work has been done to investigate the reliability of the existing models when considering sediments, such as microbial pathogens, that have a lower density than the mineral sediments used for development of the models. The objectives of this study were to: 1) quantify the ability of a VFS to remove ...


Mechanism Of Xylobiose Hydrolysis By Gh43 Β-Xylosidase, Ian J. Barker, Luis Petersen, Peter J. Reilly 2010 Iowa State University

Mechanism Of Xylobiose Hydrolysis By Gh43 Β-Xylosidase, Ian J. Barker, Luis Petersen, Peter J. Reilly

Chemical and Biological Engineering Publications

Glycoside hydrolases cleave the glycosidic linkage between two carbohydrate moieties. They are among the most efficient enzymes currently known. β-Xylosidases from glycoside hydrolase family 43 hydrolyze the nonreducing ends of xylooligomers using an inverting mechanism. Although the general mechanism and catalytic amino acid residues of β-xylosidases are known, the nature of the reaction’s transition state and the conformations adopted by the glycon xylopyranosyl ring along the reaction pathway are still elusive. In this work, the xylobiose hydrolysis reaction catalyzed by XynB3, a β-xylosidase produced byGeobacillus stearothermophilus T-6, was explicitly modeled using first-principles quantum mechanics/molecular mechanics Car−Parrinello ...


Deletion Of The Cel48s Cellulase From Clostridium Thermocellum, Daniel G. Olson, Shital A. Tripathi, Richard J. Giannone, Jonathan Lo, Nicky C. Caiazza, David A. Hogsett, Robert L. Hettich, Adam M. Guss, Genia Dubrovsky, Lee R. Lynd 2010 Dartmouth College

Deletion Of The Cel48s Cellulase From Clostridium Thermocellum, Daniel G. Olson, Shital A. Tripathi, Richard J. Giannone, Jonathan Lo, Nicky C. Caiazza, David A. Hogsett, Robert L. Hettich, Adam M. Guss, Genia Dubrovsky, Lee R. Lynd

Dartmouth Scholarship

Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cellulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, S(S), and S8), the most abundant cellulosome subunit, was undertaken to gain insight into its role in enzymatic and microbial cellulose solubilization. Cultures of the Cel48S deletion mutant (S mutant) were able to completely solubilize 10 g/L crystalline cellulose. The cellulose hydrolysis rate of the S mutant strain was 60% lower than the parent strain, with the S mutant strain also exhibiting a 40% reduction in cell yield. The ...


Selective Biochlorination Of Hydroxyquinolines By A Flavin-Dependent Halogenase, Fuchao Xu, Amanda Merkley, Dayu Yu, Jixun Zhan 2010 Utah State University

Selective Biochlorination Of Hydroxyquinolines By A Flavin-Dependent Halogenase, Fuchao Xu, Amanda Merkley, Dayu Yu, Jixun Zhan

Biological Engineering Faculty Publications

Rdc2 is a flavin-dependent halogenase from Pochonia chlamydosporia. Through the introduction of a His6-tag to both the N- and C-termini, the isolation yield of Rdc2 from Escherichia coli using Ni-NTA affinity chromatography was increased by three-fold. In vitro reaction of Rdc2 and a flavin reductase (Fre) with seven different hydroxyquinolines revealed that 3-hydroxyquinoline (3), 5-hydroxyquinoline (5), 6-hydroxyquinoline (6), and 7-hydroxyquinoline (7) can be specifically halogenated. These products were prepared by incubating the corresponding substrates with IPTG-induced E. coli BL21(DE3)/Rdc2. They were respectively characterized as 3-hydroxy-4-chloroquinoline (3a), 5-hydroxy-6-chloroquinoline (5a), 5-chloro-6-hydroxyquinoline (6a), and 7-hydroxy-8-chloroquinoline (7a) by NMR and ...


Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. McCool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza 2010 Mascoma Corporation

Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

We report development of a genetic system for making targeted gene knockouts in Clostridium thermocellum, a thermophilic anaerobic bacterium that rapidly solubilizes cellulose. A toxic uracil analog, 5-fluoroorotic acid (5-FOA), was used to select for deletion of the pyrF gene. The ΔpyrF strain is a uracil auxotroph that could be restored to a prototroph via ectopic expression of pyrF from a plasmid, providing a positive genetic selection. Furthermore, 5-FOA was used to select against plasmid-expressed pyrF, creating a negative selection for plasmid loss. This technology was used to delete a gene involved in organic acid production, namely pta, which encodes ...


The Other Gulf Oil Crisis - In Southwest Asia, Adam Liska 2010 University of Nebraska-Lincoln

The Other Gulf Oil Crisis - In Southwest Asia, Adam Liska

Biological Systems Engineering: Papers and Publications

The oil spill in the Gulf of Mexico is a rude reminder of the risks inherent in an economy dependent upon petroleum. But there's a quieter crisis in the other gulf - the Persian Gulf - that should call Americans' attention to the even more severe consequences of relying upon imported oil. The costs of using the military to protect the transport of oil from the most turbulent part of the world should convince our country's policymakers to increase investments in researching and developing affordable, American-made clean-burning alternative fuels. But, first, we have to understand the real causes, costs and ...


Evaluation Of Ethanol And Water Introduction Via Fumigation On Efficiency And Emissions Of A Compression Ignition Engine Using An Atomization Technique, Grant S. Janousek 2010 University of Nebraska at Lincoln

Evaluation Of Ethanol And Water Introduction Via Fumigation On Efficiency And Emissions Of A Compression Ignition Engine Using An Atomization Technique, Grant S. Janousek

Biological Systems Engineering--Dissertations, Theses, and Student Research

Performance of a diesel engine, equipped for ethanol and water fumigation, was studied. The method implemented allowed for non-destructive introduction of liquids in advance of the turbocharger. Engine torque, speed, emission components, diesel and ethanol fuel rates were recorded and analyzed for each mixture of inputs. Based on the results of the study, thermal efficiency was not significantly different from the baseline diesel performance when using several ethanol and water mixtures. On the other hand, ethanol fumigation caused a significant reduction in NOx emissions and an increase in HC and CO emissions. No significant changes in CO2 or O2 occurred.


Enhanced Anthocyanin Extraction From Red Cabbage Using Pulsed Electric Field Processing, Tanya K. Gachovska, David A. Cassada, Jeyamkondan Subbiah, Milford Hanna, Harshavardhan Thippareddi, Daniel D. Snow 2010 University of Nebraska-Lincoln

Enhanced Anthocyanin Extraction From Red Cabbage Using Pulsed Electric Field Processing, Tanya K. Gachovska, David A. Cassada, Jeyamkondan Subbiah, Milford Hanna, Harshavardhan Thippareddi, Daniel D. Snow

Biological Systems Engineering: Papers and Publications

This study was conducted to evaluate the effect of pulsed electric field (PEF) treatment on anthocyanin extraction from red cabbage using water as a solvent. Mashed cabbage was placed in a batch treatment chamber and subjected to PEF (2.5 kV/cm electric field strength; 15 μs pulse width and 50 pulses, specific energy 15.63 J/g). Extracted anthocyanin concentrations (16 to 889 μg/mL) were determined using HPLC. Heat and light stabilities of the control and PEF-treated samples, having approximately the same initial concentrations, were studied. PEF treatments enhanced total anthocyanin extraction in water from red cabbage by ...


Securing Foreign Oil: A Case For Including Military Operations In The Climate Change Impact Of Fuels, Adam J. Liska, Richard K. Perrin 2010 University of Nebraska-Lincoln

Securing Foreign Oil: A Case For Including Military Operations In The Climate Change Impact Of Fuels, Adam J. Liska, Richard K. Perrin

Biological Systems Engineering: Papers and Publications

Military operations are major industrial activities that use massive amounts of fuel and materials that significantly contribute to climate change. In this article, we assert that military activity to protect international oil trade is a direct production component for importing foreign oil— as necessary for imports as are pipelines and supertankers—and therefore the greenhouse gas (GHG) emissions from that military activity are relevant to U.S. fuel policies related to climate change. Military security for protection of global maritime petroleum distribution is part of the acquisition process, but in addition, recent Middle Eastern wars may also be related to ...


Three-Dimensional Atom Probe Tomography Of Oxide, Anion, And Alkanethiolate Coatings On Gold, Yi Zhang, Andrew C. Hillier 2010 Iowa State University

Three-Dimensional Atom Probe Tomography Of Oxide, Anion, And Alkanethiolate Coatings On Gold, Yi Zhang, Andrew C. Hillier

Chemical and Biological Engineering Publications

We have used three-dimensional atom probe tomography to analyze several nanometer-thick and monomolecular films on gold surfaces. High-purity gold wire was etched by electropolishing to create a sharp tip suitable for field evaporation with a radius of curvature of layer, primarily consisting of water and atmospheric gases, was observed on a fresh tip. This sample exhibited crystalline lattice spacings consistent with the interlayer spacing of {200} lattice planes of bulk gold. A thin oxide layer was created on the gold surface via plasma oxidation, and the thickness and composition of this layer was measured. Clear evidence of a nanometer-thick oxide ...


Ultrasound Transient Shear Wave Elasticity Imaging For Tendon Tissue, Pengfei Song 2010 University of Nebraska at Lincoln

Ultrasound Transient Shear Wave Elasticity Imaging For Tendon Tissue, Pengfei Song

Biological Systems Engineering--Dissertations, Theses, and Student Research

Degeneration of tendon tissue is a common cause of tendon dysfunction with the symptoms of repeated episodes of pain and palpable increase of tendon thickness. Tendon mechanical properties are directly related to its physiological composition and the structural organization of the interior collagen fibers which could be altered by tendon degeneration due to overuse or injury. Thus, measuring mechanical properties of tendon tissue may represent a quantitative measurement of pain, reduced function, and tissue health. Ultrasound elasticity imaging has been developed in the last two decades and has proved to be a promising tool for tissue elasticity imaging. To date ...


Cell Culture Method And Apparatus For Mechanically Stimulating Cells, Seth W. Donahue 2010 Michigan Technological University

Cell Culture Method And Apparatus For Mechanically Stimulating Cells, Seth W. Donahue

Michigan Tech Patents

A cell culture assembly and a method for culturing cells that provide mechanical stimulation to cells. The cell culture assembly can include a flow chamber positioned in a fluid path and a support comprising cells positioned within the flow chamber to expose the cells to the fluid path. The cell culture assembly can further include a means for producing a steady flow of fluid in the fluid path, and a means for producing an oscillatory flow of fluid in the fluid path simultaneously with producing the steady flow of fluid in the fluid path to mechanically stimulate the cells. The ...


Development Towards A Protocol To Test For The Creation Of A “Diabetic” Environment In A Blood Vessel Mimic, Kaitlyn Kirk, development towards a protocol to test for the creation of a “diabetic” environment in a blood vessel mimic 2010 California Polytechnic State University, San Luis Obispo

Development Towards A Protocol To Test For The Creation Of A “Diabetic” Environment In A Blood Vessel Mimic, Kaitlyn Kirk, Development Towards A Protocol To Test For The Creation Of A “Diabetic” Environment In A Blood Vessel Mimic

Biomedical Engineering

Diabetes mellitus affects a huge proportion of people; about 6% of the population in the US had diabetes in 2007 (16). Diabetes promotes dyslipidemia, an imbalance in the circulating levels of lipids and lipoproteins, and diabetes is one of the leading risk factors for coronary artery and peripheral vascular diseases (11, 51, 52). There are two types of diabetes; type 1 diabetes accounts for about 10% of diagnosed cases and type 2 accounts for about 90% (11). Diabetic patients react differently to stents and there is a great need to enhance the treatment. The goal of this project was, and ...


Antenna Development For Radio Frequency Hyperthermia Applications, Sergio Curto 2010 Technological University Dublin

Antenna Development For Radio Frequency Hyperthermia Applications, Sergio Curto

Doctoral

This thesis deals with the design steps, development and validation of an applicator for radio frequency hyperthermia cancer therapy. An applicator design to enhance targeted energy coupling is a key enabler for preferential temperature increments in tumour regions. A single-element, near-field approach requires a miniaturised solution, that addresses ergonomic needs and is tolerant to patient anatomy. The antenna war-field rriodality and the high-dielectric patient loading introduce significant analytical and computational resource challenges. The antenna input impedance has to be sufficiently insensitive to in-band resonant cletuning and the fields in the tissue can he targeted to selected areas in the patient ...


The Gel Documentation System: A Cornerstone To The Implementation Of The Introduction To Biotechnology And Introduction To Bioinformatics Cross-Disciplinary Course Series, Marcy Kelly, Gregory Lampard, Constance Knapp 2010 Dyson College of Arts and Sciences, Pace University

The Gel Documentation System: A Cornerstone To The Implementation Of The Introduction To Biotechnology And Introduction To Bioinformatics Cross-Disciplinary Course Series, Marcy Kelly, Gregory Lampard, Constance Knapp

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.


Molecular Mechanism Of The Glycosylation Step Catalyzed By Golgi Α-Mannosidase Ii: A Qm/Mm Metadynamics Investigation, Luis Petersen, Albert Ardèvol, Carme Rovira, Peter J. Reilly 2010 Iowa State University

Molecular Mechanism Of The Glycosylation Step Catalyzed By Golgi Α-Mannosidase Ii: A Qm/Mm Metadynamics Investigation, Luis Petersen, Albert Ardèvol, Carme Rovira, Peter J. Reilly

Chemical and Biological Engineering Publications

Golgi α-mannosidase II (GMII), a member of glycoside hydrolase family 38, cleaves two mannosyl residues from GlcNAcMan5GlcNAc2 as part of the N-linked glycosylation pathway. To elucidate the molecular and electronic details of the reaction mechanism, in particular the conformation of the substrate at the transition state, we performed quantum mechanics/molecular mechanics metadynamics simulations of the glycosylation reaction catalyzed by GMII. The calculated free energy of activation for mannosyl glycosylation (23 kcal/mol) agrees very well with experiments, as does the conformation of the glycon mannosyl ring in the product of the glycosylation reaction (the covalent intermediate ...


Liquid Crystalline Elastomers: Effects Of Substrate Anisotropy On Cell Behavior, Christine DePompeo 2010 Syracuse University

Liquid Crystalline Elastomers: Effects Of Substrate Anisotropy On Cell Behavior, Christine Depompeo

Syracuse University Honors Program Capstone Projects

One of the major challenges in tissue engineering today is inducing organization at the cellular level in vitro. Most biological tissues exhibit anisotropic behavior. They perform differently and have different mechanical properties in different directions. This environment is difficult to mimic with traditional cell culturing methods. The development of anisotropic cell substrates may have the potential to encourage the organization required at the cellular level to induce in vitro tissue formation, an exciting prospect for the advancement of the field of tissue engineering.

It is well known that liquid crystalline elastomers (LCEs) are highly organized polymers with temperature-dependent properties. Previous ...


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