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Full-Text Articles in Biomedical Engineering and Bioengineering

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

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 Nov 2010

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 ...


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

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 ...


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

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 ...


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 May 2010

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 ...


Sensing Polymer/Dna Polyplex Dissociation Using Quantum Dot Fluorophores, Bingqi Zhang, Yanjie Zhang, Surya K. Mallapragada, Aaron R. Clapp Jan 2010

Sensing Polymer/Dna Polyplex Dissociation Using Quantum Dot Fluorophores, Bingqi Zhang, Yanjie Zhang, Surya K. Mallapragada, Aaron R. Clapp

Chemical and Biological Engineering Publications

We characterized the dissociation of polymer/DNA polyplexes designed for gene delivery using water-soluble quantum dots (QDs). A pH-responsive pentablock copolymer was designed to form stable complexes with plasmid DNA via tertiary amine segments. Dissociation of the polyplex was induced using chloroquine where the efficiency of this process was sensed through changes in QD fluorescence. We found that increasing concentrations of pentablock copolymer and DNA led to quenching of QD fluorescence, while chloroquine alone had no measurable effect. The mechanism of quenching was elucidated by modeling the process as the combination of static and dynamic quenching from the pentablock copolymer ...


Utilizing Protein-Lean Coproducts From Corn Containing Recombinant Pharmaceutical Proteins For Ethanol Production, Ilankovan Paraman, Lorena Beatriz Moeller, M. Paul Scott, Kan Wang, Charles E. Glatz, Lawrence A. Johnson Jan 2010

Utilizing Protein-Lean Coproducts From Corn Containing Recombinant Pharmaceutical Proteins For Ethanol Production, Ilankovan Paraman, Lorena Beatriz Moeller, M. Paul Scott, Kan Wang, Charles E. Glatz, Lawrence A. Johnson

Chemical and Biological Engineering Publications

Protein-lean fractions of corn (maize) containing recombinant (r) pharmaceutical proteins were evaluated as a potential feedstock to produce fuel ethanol. The levels of residual r-proteins in the coproduct, distillers dry grains with solubles (DDGS), were determined. Transgenic corn lines containing recombinant green fluorescence protein (r-GFP) and a recombinant subunit vaccine of Escherichia coli enterotoxin (r-LTB), primarily expressed in endosperm, and another two corn lines containing recombinant human collagen (r-CIα1) andr-GFP, primarily expressed in germ, were used as model systems. The kernels were either ground and used for fermentation or dry fractionated to recover germ-rich ...


Metabolic Analysis Of Wild-Type Escherichia Coli And A Pyruvate Dehydrogenase Complex (Pdhc)-Deficient Derivative Reveals The Role Of Pdhc In The Fermentative Metabolism Of Glucose, Abhishek Murarka, James M. Clomburg, Sean Moran, Jacqueline V. Shanks, Ramon Gonzalez Jan 2010

Metabolic Analysis Of Wild-Type Escherichia Coli And A Pyruvate Dehydrogenase Complex (Pdhc)-Deficient Derivative Reveals The Role Of Pdhc In The Fermentative Metabolism Of Glucose, Abhishek Murarka, James M. Clomburg, Sean Moran, Jacqueline V. Shanks, Ramon Gonzalez

Chemical and Biological Engineering Publications

Pyruvate is located at a metabolic junction of assimilatory and dissimilatory pathways and represents a switch point between respiratory and fermentative metabolism. In Escherichia coli, the pyruvate dehydrogenase complex (PDHC) and pyruvate formate-lyase are considered the primary routes of pyruvate conversion to acetyl-CoA for aerobic respiration and anaerobic fermentation, respectively. During glucose fermentation, the in vivo activity of PDHC has been reported as either very low or undetectable, and the role of this enzyme remains unknown. In this study, a comprehensive characterization of wild-type E. coli MG1655 and a PDHC-deficient derivative (Pdh) led to the identification of the role of ...


Combined Electrochemical Surface Plasmon Resonance For Angle Spread Imaging Of Multielement Electrode Arrays, Andrew C. Hillier, Chang Hoon Choi Jan 2010

Combined Electrochemical Surface Plasmon Resonance For Angle Spread Imaging Of Multielement Electrode Arrays, Andrew C. Hillier, Chang Hoon Choi

Chemical and Biological Engineering Publications

A surface plasmon resonance imaging system combined with a multielement electrode array is described. An optical system with shaping optics is used to direct a wedge of light onto a gold-coated sample. The reflected light is detected in the form of an angle-spread image of the surface, with one direction denoting a variable incident angle and the other showing a span of locations along one lateral direction of the sample surface. At the proper incident angle, the angle-spread image shows the complete surface plasmon resonance curve over a span of locations on the surface. This imaging system is combined with ...


Conversion Of Biorenewable Feedstocks: New Challenges In Heterogeneous Catalysis, Brent H. Shanks Jan 2010

Conversion Of Biorenewable Feedstocks: New Challenges In Heterogeneous Catalysis, Brent H. Shanks

Chemical and Biological Engineering Publications

For biorenewable feedstocks to serve as a significant source of chemicals and/or fuels, the development of new chemical processes as well as biological processes will be required. However, the conversion of biorenewable feedstocks with heterogeneous catalyst-based processes provides new challenges in inorganic catalyst research and development relative to historical work with petrochemical feedstocks. These catalyst and process challenges include the need to convert highly functionalized molecules with high selectivity, to develop stable catalytic liquid-solid interfaces in which the liquid phase is commonly aqueous, to control solvent phase effects and to develop novel reaction systems. While some of these challenges ...


Tracking Chemical Processing Pathways In Combinatorial Polymer Libraries Via Data Mining, Scott Broderick, Joseph R. Nowers, Balaji Narasimhan, Krishna Rajan Jan 2010

Tracking Chemical Processing Pathways In Combinatorial Polymer Libraries Via Data Mining, Scott Broderick, Joseph R. Nowers, Balaji Narasimhan, Krishna Rajan

Chemical and Biological Engineering Publications

Changes in the molecular structure and composition of interpenetrating polymer networks (IPNs) can be used to tailor their properties. While the properties of IPNs are typically different than polymer blends, a clear understanding of the impact of changing polymerization sequence on the physical properties and the corresponding molecular bonding is needed. To address this issue, a data mining approach is used to identify the change with polymerization sequence of tensile and rheological properties of acrylate-epoxy IPNs. The experimental approach used to study the molecular structure is high throughput Fourier transform infrared (FTIR) spectroscopy. Analysis of the FTIR spectra of IPNs ...


Novel, High Throughput Method To Study In Vitro Protein Release From Polymer Nanospheres, L. K. Petersen, C. K. Sackett, Balaji Narasimhan Jan 2010

Novel, High Throughput Method To Study In Vitro Protein Release From Polymer Nanospheres, L. K. Petersen, C. K. Sackett, Balaji Narasimhan

Chemical and Biological Engineering Publications

Controlled delivery of therapeutic protein drugs using biodegradable polymer carriers is a desired characteristic that enables effective, application-specific therapy and treatment. Previous studies have focused on protein delivery from polymers using conventional "one-sample-at-a- time" techniques, which are time-consuming and costly. In addition, many therapeutic proteins are in limited supply and are expensive, so it is desirable to reduce sample size for design and development of delivery devices. We have developed a rapid, high throughput technique based on a highly sensitive fluorescence-based assay to detect and quantify protein released from polyanhydrides while utilizing relatively small amounts of protein (∼40 μg). These ...


Myosin Ii Activity Regulates Vinculin Recruitment To Focal Adhesions Through Fak-Mediated Paxillin Phosphorylation, Ana M. Pasapera, Ian C. Schneider, Erin Rericha, David D. Schlaepfer, Clare M. Waterman Jan 2010

Myosin Ii Activity Regulates Vinculin Recruitment To Focal Adhesions Through Fak-Mediated Paxillin Phosphorylation, Ana M. Pasapera, Ian C. Schneider, Erin Rericha, David D. Schlaepfer, Clare M. Waterman

Chemical and Biological Engineering Publications

Focal adhesions (FAs) are mechanosensitive adhesion and signaling complexes that grow and change composition in response to myosin II-mediated cytoskeletal tension in a process known as FA maturation. To understand tension-mediated FA maturation, we sought to identify proteins that are recruited to FAs in a myosin II-dependent manner and to examine the mechanism for their myosin II-sensitive FA association. We find that FA recruitment of both the cytoskeletal adapter protein vinculin and the tyrosine kinase FA kinase (FAK) are myosin II and extracellular matrix (ECM) stiffness dependent. Myosin II activity promotes FAK/Src-mediated phosphorylation of paxillin on tyrosines 31 and ...


Application Of A Combined Catalyst And Sorbent For Steam Reforming Of Methane, Karl O. Albrecht, Justinus A. Satrio, Brent H. Shanks, Thomas D. Wheelock Jan 2010

Application Of A Combined Catalyst And Sorbent For Steam Reforming Of Methane, Karl O. Albrecht, Justinus A. Satrio, Brent H. Shanks, Thomas D. Wheelock

Chemical and Biological Engineering Publications

The performance of a combined catalyst and sorbent material designed for reforming hydrocarbons was evaluated by reacting methane with steam at different temperatures and pressures in a reactor packed with the material. The combined material was in the form of small spherical pellets comprised of a sorbent core of lime encased in a porous shell made largely of sintered alumina that supported a nickel catalyst. On the basis of previous research, two shell formulations were included in the study. One shell formulation contained a small quantity of CaO for strengthening of the shells, whereas the other contained a similar quantity ...


Tertiary Structure And Characterization Of A Glycoside Hydrolase Family 44 Endoglucanase From Clostridium Acetobutylicum, Christopher D. Warner, Julie A. Hoy, Taran C. Shilling, Michael J. Linnen, Nathaniel D. Ginder, Clark Ford, Richard B. Honzatko, Peter J. Reilly Jan 2010

Tertiary Structure And Characterization Of A Glycoside Hydrolase Family 44 Endoglucanase From Clostridium Acetobutylicum, Christopher D. Warner, Julie A. Hoy, Taran C. Shilling, Michael J. Linnen, Nathaniel D. Ginder, Clark Ford, Richard B. Honzatko, Peter J. Reilly

Chemical and Biological Engineering Publications

A gene encoding a glycoside hydrolase family 44 (GH44) protein from Clostridium acetobutylicum ATCC 824 was synthesized and transformed into Escherichia coli.The previously uncharacterized protein was expressed with a C-terminal His tag and purified by nickel-nitrilotriacetic acid affinity chromatography. Crystallization and X-ray diffraction to a 2.2-Å resolution revealed a triose phosphate isomerase (TIM) barrel-like structure with additional Greek key and β-sandwich folds, similar to other GH44 crystal structures. The enzyme hydrolyzes cellotetraose and larger cellooligosaccharides, yielding an unbalanced product distribution, including some glucose. It attacks carboxymethylcellulose and xylan at approximately the same rates. Its activity on carboxymethylcellulose is ...


Kinetic Modeling Of Nanoprecipitation Using Cfd Coupled With A Population Balance, Janine C. Cheng, Rodney O. Fox Jan 2010

Kinetic Modeling Of Nanoprecipitation Using Cfd Coupled With A Population Balance, Janine C. Cheng, Rodney O. Fox

Chemical and Biological Engineering Publications

A model study has been conducted for Flash Nanoprecipitation (FNP)sa novel approach to produce functional nanoparticles. A population balance equation with the FNP kinetics has been integrated into a computational fluid dynamics (CFD) simulation of a custom-designed microscale multi-inlet vortex reactor (MIVR) to yield conditions comparable to the real experimental settings. In coping with the complicated aggregation model in the CFD code, a new numerical approach, the conditional quadrature method of moments (CQMOM), has been proposed, which is capable of solving the multivariate system efficiently and accurately. It is shown that the FNP process is highly influenced by mixing ...


Quadrature-Based Moment Model For Moderately Dense Polydisperse Gas-Particle Flows, Rodney O. Fox, Prakash Vedula Jan 2010

Quadrature-Based Moment Model For Moderately Dense Polydisperse Gas-Particle Flows, Rodney O. Fox, Prakash Vedula

Chemical and Biological Engineering Publications

A quadrature-based moment model is derived for moderately dense polydisperse gas-particle flows starting from the inelastic Boltzmann-Enskog kinetic equation including terms for particle acceleration (e.g., gravity and fluid drag). The derivation is carried out for the joint number density function, f(t,x,m,u), of particle mass and velocity, and thus, the model can describe the transport of polydisperse particles with size and density differences. The transport equations for the integer moments of the velocity distribution function are derived in exact form for all values of the coefficient of restitution for particle-particle collisions. For particular limiting cases, the ...


Wavelength Tunable Surface Plasmon Resonance-Enhanced Optical Transmission Through A Chirped Diffraction Grating, Wei-Hsun Yeh, Justin Kleingartner, Andrew C. Hillier Jan 2010

Wavelength Tunable Surface Plasmon Resonance-Enhanced Optical Transmission Through A Chirped Diffraction Grating, Wei-Hsun Yeh, Justin Kleingartner, Andrew C. Hillier

Chemical and Biological Engineering Publications

We report the construction and testing of a chirped diffraction grating, which serves as a substrate for surface plasmon-enhanced optical transmission. This grating possesses a spatial variation in both pitch and amplitude along its surface. It was created by plasma oxidation of a curved poly(dimethoxysilane) sheet, which resulted in nonuniform buckling along the polymer surface. A gold-coated replica of this surface elicited an optical response that consisted of a series of narrow, enhanced transmission peaks spread over the visible spectrum. The location and magnitude of these transmission peaks varied along the surface of the grating and coincided with conditions ...


Sulfated Zirconia Modified Sba-15 Catalysts For Cellobiose Hydrolysis, Volkan Degirmenci, Deniz Uner, Basak Cinlar, Brent H. Shanks, Aysen Yilmaz, Rutget A. Van Santen, Emiel J. M. Hensen Jan 2010

Sulfated Zirconia Modified Sba-15 Catalysts For Cellobiose Hydrolysis, Volkan Degirmenci, Deniz Uner, Basak Cinlar, Brent H. Shanks, Aysen Yilmaz, Rutget A. Van Santen, Emiel J. M. Hensen

Chemical and Biological Engineering Publications

Zirconia modified SBA-15 becomes a very active catalyst for the selective hydrolysis of cellobiose to glucose after sulfation. Spectroscopic investigations indicate the presence of Brønsted acid sites with similar properties to those present in conventional sulfated zirconia. Indications are found that the sulfate groups attached to zirconia interact with silanol groups of SBA-15. The catalytic activity in cellobiose hydrolysis correlates well with results for temperature-programmed decomposition of i-propylamine for a range of sulfated ZrO2/SBA-15 catalysts. A glucose yield of 60% during cellobiose hydrolysis at a reaction time of 90 min at 160° C is obtained.


Metabolic Engineering For Production Of Biorenewable Fuels And Chemicals: Contributions Of Synthetic Biology, Laura R. Jarboe, Xueli Zhang, Xuan Wang, Jonathan C. Moore, K. T. Shanmugam, Lonnie O. Ingram Jan 2010

Metabolic Engineering For Production Of Biorenewable Fuels And Chemicals: Contributions Of Synthetic Biology, Laura R. Jarboe, Xueli Zhang, Xuan Wang, Jonathan C. Moore, K. T. Shanmugam, Lonnie O. Ingram

Chemical and Biological Engineering Publications

Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemicalbased production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use ...


An Extended Data Mining Method For Identifying Differentially Expressed Assay-Specific Signatures In Functional Genomic Studies, Derrick K. Rollins Sr., Ai-Ling Teh Jan 2010

An Extended Data Mining Method For Identifying Differentially Expressed Assay-Specific Signatures In Functional Genomic Studies, Derrick K. Rollins Sr., Ai-Ling Teh

Chemical and Biological Engineering Publications

Background: Microarray data sets provide relative expression levels for thousands of genes for a small number, in comparison, of different experimental conditions called assays. Data mining techniques are used to extract specific information of genes as they relate to the assays. The multivariate statistical technique of principal component analysis (PCA) has proven useful in providing effective data mining methods. This article extends the PCA approach of Rollins et al. to the development of ranking genes of microarray data sets that express most differently between two biologically different grouping of assays. This method is evaluated on real and simulated data and ...


Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 3. Reaction Rate Constant Calculations, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox Jan 2010

Theoretical Study Of The Pyrolysis Of Methyltrichlorosilane In The Gas Phase. 3. Reaction Rate Constant Calculations, Yingbin Ge, Mark S. Gordon, Francine Battaglia, Rodney O. Fox

Chemical and Biological Engineering Publications

The rate constants for the gas-phase reactions in the silicon carbide chemical vapor deposition of methyltrichlorosilane (Ge, Y. B.; Gordon, M. S.; Battaglia, F.; Fox, R. O. J. Phys. Chem. A 2007, 111, 1462.) were calculated. Transition state theory was applied to the reactions with a well-defined transition state; canonical variational transition state theory was applied to the barrierless reactions by finding the generalized transition state with the maximum Gibbs free energy along the reaction path. Geometry optimizations were carried out with second-order perturbation theory (MP2) and the cc-pVDZ basis set. The partition functions were calculated within the harmonic oscillator ...


Multiscale Modeling Of Tio2 Nanoparticle Production In Flame Reactors: Effect Of Chemical Mechanism, Maulik Mehta, Yonduck Sung, Venkatramanan Raman, Rodney O. Fox Jan 2010

Multiscale Modeling Of Tio2 Nanoparticle Production In Flame Reactors: Effect Of Chemical Mechanism, Maulik Mehta, Yonduck Sung, Venkatramanan Raman, Rodney O. Fox

Chemical and Biological Engineering Publications

For titanium dioxide (TiO2) nanoparticles manufactured in flame reactors, the precursor is injected into a pre-existing flame, exposing it to a high-temperature gas phase, leading to nucleation and particle growth. Predictive modeling of this chemical process requires simultaneous development of detailed chemical mechanisms describing gas-phase combustion and particle evolution, as well as advanced computational tools for describing the turbulent flow field and its interactions with the chemical processes. Here, a multiscale computational tool for flame-based TiO2 nanoparticle synthesis is developed and a flamelet model representing detailed chemistry for particle nucleation is proposed. The effect of different chemical mechanisms ...