Modeling force-induced bio-polymer unfolding

We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N = 55 using exact enumeration techniques. We analyze in detail the differences between the constant force and constant distance ensembles for large but finite N. At low temperatures, and in the constant force ensemble, the force–extension curve shows multiple plateaus (intermediate states), in contrast with the abrupt transition to an extended state prevailing in the N → ∞ limit. In the constant distance ensemble, the same curve provides a unified response to pulling and compressing forces, and agrees qualitatively with recent experimental results. We identify a cross-over length, proportional to N, below which the critical force of unfolding decreases with temperature, while above, it increases with temperature. Finally, the force–extension curve for stiff chains exhibits “saw-tooth” like behavior, as observed in protein unfolding experiments.     

Synthesis of substituted 2-cyanoarylboronic esters

The synthesis of substituted 2-cyanoarylboronic esters is described via lithiation/in situ trapping of the corresponding methoxy-, trifluoromethyl-, fluoro-, chloro-, and bromobenzonitriles. The crude arylboronic esters were obtained in high yields and purities and with good regioselectivities.     

Tuning quadratic nonlinear photonic crystal fibers for zero group-velocity mismatch

We consider an index-guiding silica photonic crystal fiber with a triangular hole pattern and a periodically poled quadratic nonlinearity. By tuning the pitch and the relative hole size, second-harmonic generation with zero group-velocity mismatch is found for any fundamental wavelength above 780 nm. The nonlinear strength is optimized when the fundamental has maximum confinement in the core. The conversion bandwidth allows for femtosecond-pulse conversion, and 4%-180%W(-1)cm(-2) relative efficiencies were found.     

Reversible formation of a PdC(x) phase in Pd nanoparticles upon CO and O2 exposure

The structure and chemical composition of Pd nanoparticles exposed to pure CO and mixtures of CO and O(2) at elevated temperatures have been studied in situ by a combination of X-ray Diffraction and X-ray Photoelectron Spectroscopy in pressures ranging from ultra high vacuum to 10 mbar and from room temperature to a few hundred degrees celsius. Our investigation shows that under CO exposure, above a certain temperature, carbon dissolves into the Pd particles forming a carbide phase. Upon exposure to CO and O(2) mixtures, the carbide phase forms and disappears reversibly, switching at the stoichiometric ratio for CO oxidation. This finding opens new scenarios for the understanding of catalytic oxidation of C-based molecules.     

All-silica nanofluidic devices for DNA-analysis fabricated by imprint of sol-gel silica with silicon stamp

We present a simple and cheap method for fabrication of silica nanofluidic devices for single-molecule studies. By imprinting sol-gel materials with a multi-level stamp comprising micro- and nanofeatures, channels of different depth are produced in a single process step. Calcination of the imprinted hybrid sol-gel material produces purely inorganic silica, which has very low autofluorescence and can be fusion bonded to a glass lid. Compared to top-down processing of fused silica or silicon substrates, imprint of sol-gel silica enables fabrication of high-quality nanofluidic devices without expensive high-vacuum lithography and etching techniques. The applicability of the fabricated device for single-molecule studies is demonstrated by measuring the extension of DNA molecules of different lengths confined in the nanochannels.     

Ni(HF2)(3-Clpy)4]BF4 (py = pyridine): evidence for spin exchange along strongly distorted F···H···F- bridges in a one-dimensional polymeric chain

[Ni(HF(2))(3-Clpy)(4)]BF(4) (py = pyridine) is a simple one-dimensional (1D) coordination polymer composed of compressed NiN(4)F(2) octahedra that form chains with bridging HF(2)(-) ligands. In spite of significant distortion of the HF(2)(-) bridge, a quasi-1D antiferromagnetic (AFM) behavior was observed with J(FHF) = 4.86 K.     

Pre-equilibrium capillary zone electrophoresis or frontal analysis: advantages of plateau peak conditions in affinity capillary electrophoresis

The feasibility of using the affinity CE methodologies pre-equilibrium CZE and CE frontal analysis was tested on interaction systems exhibiting rapid on-and-off kinetics. Experimentally, the methodologies differ only with respect to the volume of sample introduced into the capillary. Pre-equilibrium CZE has been considered amendable to interactions with slow on-and-off kinetics only; however, it has recently been applied in studies of interactions with fast on-and-off kinetics. The effect of varying the sample volume introduced hydrodynamically into the capillary on the apparent degree of complexation was studied. For two different binding systems, the fraction of free analyte was found to be overestimated using pre-equilibrium CZE as compared to volumes providing plateau peak conditions as used with frontal analysis. Results indicate that frontal analysis conditions lead to more robust binding assays and thus more reliable data. The validity of data obtained by pre-equilibrium CZE may be low, thus the use of an experimental setup providing plateau peaks is highly recommended. It is suggested that the effect of altering the sample volume on the degree of binding should be investigated as part of method development and validation.     

Determination of SFC, FFA, and equivalent reaction time for enzymatically interestified oils using NIRS

The use of near infrared spectroscopy (NIRS) for rapid determination of the degree of interesterification of blends of palm stearin, coconut oil, and rapeseed oil obtained using an immobilized Thermomyces lanuginosa lipase at 70 °C was investigated. Interesterification was carried out by applying both fixed bed and batch reactors. Calibrations were developed for quantitative determination of solid fat content (SFC) at 10, 20, 30, 35, and 40 °C and free fatty acid (FFA) resulting in root mean square errors of prediction of 1.0, 1.3, 1.4, 1.6, 1.7, and 0.19% (w/w), respectively. The data showed that NIRS could be used to replace the traditional methods for determining FFA and SFC in vegetable oils.It was possible to monitor the activity of the immobilized enzyme for interesterification of margarine oils by predicting the equivalent reaction time in a batch reactor from NIR spectra. Root mean square errors of prediction for two different oil blends interesterified for 300 and 170 min were 21 and 12 min, respectively.     

Novel optical and statistical methods reveal colloid-wall interactions inconsistent with DLVO and Lifshitz theories

We present an experimental method based on video microscopy to perform nanometer scale position detection of a micrometer bead in the direction along the propagation of the detection light. Using the same bead for calibration and detection significantly improves the in depth resolution in comparison to video microscopy methods from literature. This method is used together with an optical trap to measure interaction potentials between a glass surface and colloids made of polystyrene or silica at different electrolyte concentrations. The results are confirmed by an independent method where the optical trap is used in connection with a quadrant photodiode. Also, we present a maximum likelihood analysis method which considerably improves the spatial resolution of interaction potentials by optimizing the underlying potential function to fit all observed position distributions. The measured interaction potentials agree well with DLVO theory for small electrolyte concentrations; however, for larger electrolyte concentrations the potentials differ qualitatively from both DLVO and Lifshitz theory.