Single‐Molecule Unzipping Force Analysis of HU–DNA Complexes

The genome of bacteria is organized and compacted by the action of nucleoid‐associated proteins. These proteins are often present in tens of thousands of copies and bind with low specificity along the genome. DNA‐bound proteins thus potentially act as roadblocks to the progression of machinery that moves along the DNA. In this study, we have investigated the effect of histone‐like protein from strain U93 (HU), one of the key proteins involved in shaping the bacterial nucleoid, on DNA helix stability by mechanically unzipping single dsDNA molecules. Our study demonstrates that individually bound HU proteins have no observable effect on DNA helix stability, whereas HU proteins bound side‐by‐side within filaments increase DNA helix stability. As the stabilizing effect is small compared to the power of DNA‐based motor enzymes, our results suggest that HU alone does not provide substantial hindrance to the motor's progression in vivo.     

Characterizing Weave Geometry in Textile Ceramic Composites Using Digital Image Correlation

Techniques for characterizing tow architectures and defects in woven ceramic composites are required for generating high‐fidelity geometric models and subsequently probing effects of defects on composite performance. Although X‐ray computed tomography (CT) has been shown to provide the requisite information with potentially sub‐μm resolution, the technique is inherently limited to probing only small volumes: on the order of a few unit cells of typical weaves. Here, we present an assessment of the efficacy of a complementary 2D technique, based on surface topography mapping via 3‐D (three‐dimensional) digital image correlation (DIC), with potential for ascertaining long‐range features in weaves and defects that cannot be gleaned from CT imaging alone. Upon comparing surfaces reconstructed from CT and DIC data, we find that DIC is capable of resolving surface heights with a root mean square(RMS) error of ~10 μm (about twice the CT voxel size, 4.4 μm) and a spatial resolution of ~20 μm over areas of several cm². Achieving this level of resolution requires use of sufficiently small speckles (~50 μm) and small subset size (~300 μm) relative to the characteristic tow dimensions (~1 mm). The error is somewhat higher (about 20 μm) in areas where surface discontinuities or rapid changes in topography exist (e.g., at tow boundaries).     

Weak identification in the ESTAR model and a new model

Determining good parameter estimates in (exponential smooth transition autoregressive) models is known to be difficult. We show that the phenomena of getting strongly biased estimators is a consequence of the so‐called identification problem, the problem of properly distinguishing the transition function in relation to extreme parameter combinations. This happens in particular for either very small or very large values of the error term variance. Furthermore, we introduce a new alternative model – the TSTAR model – which has similar properties as the ESTAR model but reduces the effects of the identification problem. We also derive a linearity and a unit root test for this model.     

Characterization of Thiol‐Ene Crosslinked PEG Hydrogels

The properties of synthetic hydrogels can be tuned to address the needs of many tissue‐culture applications. This work characterizes the swelling and mechanical properties of thiol‐ene crosslinked PEG hydrogels made with varying prepolymer formulations, demonstrating that hydrogels with a compressive modulus exceeding 600 kPa can be formed. The amount of peptide incorporated into the hydrogel is shown to be proportional to the amount of peptide in the prepolymer solution. Cell attachment and spreading on the surface of the peptide‐functionalized hydrogels is demonstrated. Additionally, a method for bonding distinct layers of cured hydrogels is used to create a microfluidic channel.

     

Surface-Induced Interphases During Curing Processes Between Bi- and Pentafunctional Components: Reactive Coarse-Grained Molecular Dynamics Simulations

The present reactive molecular dynamics (RMD) simulations discuss the formation of interphase regions in cured polymer adhesives. The latter are obtained from the curing of reactive liquid mixtures composed of pentafunctional linkers and bifunctional monomers in contact with idealized surfaces. The present reactive scheme mimics the one of epoxies with amine linkers, i.e., processes investigated experimentally by Possart and co-workers. Generic RMD simulations are performed in a coarse-grained (CG) resolution to evaluate basic principles in curing characterized by preferential interactions. The creation of linker-rich domains is promoted by preferential surface-linker as well as linker-linker interactions in the reactive mixtures. The dimension of the interphase both in the starting mixture and the cured network depends on these preferential interactions which lead to a retardation of the curing velocity. This retardation behavior is mapped by conversion curves as a function of the number of reactive steps and by the spatially resolved profiles of the connected linkers. Although derived by generic potentials, the simulated reduction of the curing velocity is in agreement with experimental results in epoxies. The chosen interactions also imply a smaller number of linker bonds in the interphase than in the bulk region. The present RMD approach offers insight into key parameters of curing processes under the influence of preferential surface interactions coupled to selective attractions in the liquid starting mixture.     

Strength Loss Mechanisms for Adhesive Bonds to Electroplated Zinc and Cold Rolled Steel Substrates Subjected to Moist Environments

Mechanisms of strength toss which affect the durability of epoxy adhesive bonds in moist environments were investigated for electroplated zinc and cold rolled steel substrates. Activation energies for adhesion loss, formation of corrosion product on the substrate surface, and moisture diffusion in the adhesive were determined experimentally. For cold rolled steel substrates, the activation energy for adhesion loss was identical, within experimental error, to the measured activation energy for moisture diffusion in the adhesive. Both of these values were substantially less (=40%) than the activation energy for formation of corrosion product. This confirms the previous results of Gledhill and Kinloch (J. Adhesion 6, 315 (1974)), who attributed strength loss to thermodynamic instability of the adhesive/substrate interface due to the presence of moisture. In contrast, for electroplated zinc substrates, activation energies for adhesion loss and corrosion product formation were essentially equal, and were both significantly higher than that for moisture diffusion. Consequently, it was concluded that corrosion of the electroplated zinc layer was responsible for bond strength loss. Formation of corrosion product in the bond was not, therefore, a post-failure phenomenon as was the case for cold rolled steel.     

FUNGAL-INDUCED REDISTRIBUTION OF KRAFT LIGNIN MOLECULAR WEIGHT BY MULTI-ANGLE LASER LIGHT SCATTERING

Culture broths from Phanerochaete chrysosporium and Trametes cingulata, combined with co-factors such as hydrogen peroxide, dithiothreitol, copper, iron, and manganese ions were examined for the ability to modify lignin structure. High-performance size exclusion chromatography (HP-SEC) coupled to multi-angle laser light scattering (MALLS) detection was used to determine the effect of several white rot fungi, pH values, enzymes, and co-factors on the molecular weight distribution of treated kraft lignin. The analytical procedure tracked changes in molecular weight distribution, radius of gyration, and hydrodynamic radius. Results showed changes in the molecular weight distribution of lignin components when treated with combinations of factors. The induced cultures showed more lignin depolymerization for the specific lignin samples in which they were initially grown. The distribution in the radius of gyration became narrower with time, indicating that molecular conformation changed to a more uniform molecular shape. H₂O₂ and DTT showed the most significant changes in lignin molecular weight distribution.     

Modeling and control of protein crystal shape and size in batch crystallization

In this work, the modeling and control of a batch crystallization process used to produce tetragonal hen egg white lysozyme crystals are studied. Two processes are considered, crystal nucleation and growth. Crystal nucleation rates are obtained from previous experiments. The growth of each crystal progresses via kinetic Monte Carlo simulations comprising of adsorption, desorption, and migration on the (110) and (101) faces. The expressions of the rate equations are similar to Durbin and Feher. To control the nucleation and growth of the protein crystals and produce a crystal population with desired shape and size, a model predictive control (MPC) strategy is implemented. Specifically, the steady‐state growth rates for the (110) and (101) faces are computed and their ratio is expressed in terms of the temperature and protein concentration via a nonlinear algebraic equation. The MPC method is shown to successfully regulate both the crystal size and shape distributions to different set‐point values. © 2013 American Institute of Chemical Engineers AIChE J, 59: 2317–2327, 2013     

Comparison of Predicted and Experimentally Measured Aerosol Deposition Efficiency in BALB/C Mice in a New Nose-Only Exposure System

The use of respiratory tract dosimetry predictions to estimate the desired aerosol exposure concentration required for a specific target deposited dose in animal inhalation studies has been hindered by: (1) a lack of species/strain specific quantitative respiratory tract anatomy; and (2) verification by comparison of calculated and experimentally measured deposited doses. Using recent literature on tracheobronchial and pulmonary respiratory tract anatomy, dosimetry predictions for the Balb/c mouse were compared with deposited doses for 0.5, 1.0, and 2.0 micrometer diameter aerosols in a newly available nose-only exposure system. Spatial and temporal aerosol port to port uniformity of this nose-only exposure system was within ± 10% of the mean. Dosimetry predictions were in agreement with the measured mean deposited doses for the aerosols tested.