Adsorption of DNA into mesoporous silica

In these experiments, double-stranded, linear DNA sequences were adsorbed into the pores of spherically shaped acid-prepared mesoporous silica (APMS). The lengths of the sequences were either 760 base pairs or 2000 base pairs. DNA adsorption into the interior of the mesoporous material was confirmed using confocal microscopy of sequences containing fluorescently labeled DNA molecules. Additional characterization with N(2) physisorption and powder X-ray diffraction supported this finding. The extent of adsorption was measured at various concentrations using UV-visible spectrophotometry to establish adsorption isotherms. APMS alone adsorbed a negligible amount of DNA; however, exchanging divalent cations such as Mg(2+) and Ca(2+) into the pores of APMS prior to DNA uptake was found to cause a significant amount of DNA to be adsorbed. Using Na(+) caused a lower amount of DNA to be adsorbed. DNA adsorption was also dependent on the pore diameter of APMS. Adsorption increased upon expansion of the pore size of the metal ion-exchanged material from 34 to 54 A; however, no additional uptake was measured by further increasing the pore size to 100 A. The amount of DNA adsorbed could also be significantly increased by using (aminopropyl)triethoxysilane to covalently link ammonium ions to the surface. Postsynthetic modification of the silica surface with aminopropyl groups increased the maximum DNA adsorption to 15.7 microg/mg silica, for materials with pore diameters of 100 A, which is 2 to 3 times more adsorbed DNA than for metal ion-exchanged material. This indicated that DNA binds more strongly in the presence of the ammonium group compared to the metal counterions. Finally, calculation and comparison of Freundlich and Langmuir constants for these adsorption processes indicate that intermolecular interactions between the DNA molecules within the pores are significant when the effective pore diameter is small, including materials with larger pores that were modified with organosilane.     

Cross-reactive arrays based on three-way junctions

We report herein a novel system for the parallel processing of molecular recognition events utilizing arrays of oligonucleotide-based fluorescent sensors to characterize hydrophobic molecules in solution. The binding domains of the sensors were based on three-way junctions that utilize double helical stems as framework regions to reliably fold regardless of variations in or around the binding domain. A reporting domain was introduced by the specific substitution of a single phosphodiester group with a phosphorothioate, followed by selective functionalization with a fluorophore. The sensors were organized into cross-reactive arrays to yield characteristic fingerprints for samples containing hydrophobic molecules. The fingerprints can be used to characterize steroids in solution, including complex biologically important fluids. Arrays have the potential for clinical applications such as the detection of gross errors in steroidogenesis.     

First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.     

Simultaneous correction of the influence of skin color and fat on tissue spectroscopy by use of a two-distance fiber-optic probe and orthogonalization technique

We have demonstrated simultaneous correction for the optical interference of skin and fat in tissue spectra by using a two-distance fiber-optic probe. We obtained the correction by orthogonalizing the spectra collected at a long source-detector distance (SD) to the spectra collected at a short SD and mapped to the long SD space. The method was validated in tissuelike three-layer phantoms as well as preliminarily in human tissue. After the correction, a partial-least-squares model of the phantoms showed enhanced prediction performance.     

Production of (4)(double Lambda)H hypernuclei

An experiment demonstrating the production of double-Lambda hypernuclei in (K(-),K(+)) reactions on (9)Be was carried out at the D6 line in the BNL alternating-gradient synchrotron. The technique was the observation of pions produced in sequential mesonic weak decay, each pion associated with one unit of strangeness change. The results indicate the production of a significant number of the double hypernucleus (4)(double Lambda)H and the twin hypernuclei (4)(Lambda)H and (3)(Lambda)H. The relevant decay chains are discussed and a simple model of the production mechanism is presented. An implication of this experiment is that the existence of an S = -2 dibaryon more than a few MeV below the double Lambda mass is unlikely.     

Dynamic optimization and event location in atmospheric chemistry

A model coupling differential equations and an optimization problem with equality and inequality constraints is described. The first order optimality conditions are coupled with the differential equations to form a differential-algebraic system. Inequality constraints for the optimization variables induce discontinuities in the first derivatives of the solution in time. Tracking techniques based on sensitivity analysis and second order multistep methods are proposed to locate the discontinuities. Application to the dynamics of organic atmospheric aerosol particles is given to illustrate the detection of the activation of constraints. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

具有切向控制的局部四点插值曲线设计方法

Ｎｉｒａ Ｄｙｎ等提出的四点插值法是一种典型的自由曲线离散造型方法，但该方法不能控制插值点的切向。本文利用薄板样很可能 量的极小化原理给出了具有切向控制的四点分插值条件。用户可以方便地交互控制任一插值点的切向，使得四点插值法更为有效和实用。     

Laser Nitriding of Iron,Stainless Steel,and Plain Carbon Steel Investigated by Mössbauer Spectroscopy

Nitriding is a common method for improving the hardness, mechanical properties, wear and corrosion resistance of metals. Laser nitriding of metals is an efficient process, where the irradiation of surfaces in air or nitrogen atmospheres with short laser pulses leads to a fast take-up of nitrogen into the irradiated surfaces. This process has been extensively investigated for pure iron, but usually, no tools or functional parts are made of pure iron. Mainly steel or cast iron is used as a base material. Therefore, when looking for technical applicability, also the influence of alloying elements on the laser nitriding process is of great interest. Besides the pure iron various carbon steels and an austenitic stainless steel were studied in laser nitriding experiments in order to investigate the influence of the material itself. Here, the process is investigated via Conversion Electron and X-ray Mössbauer Spectroscopy (CEMS and CXMS), Resonant Nuclear Reaction Analysis (RNRA), and X-Ray Diffraction (XRD). It appears that carbon steels are even better suited for the laser nitriding process than pure iron, and the laser nitriding also works efficiently for the stainless steel which is normally difficult to be nitrided.     

Communication: Standard surface hopping predicts incorrect scaling for Marcus' golden-rule rate: the decoherence problem cannot be ignored

We evaluate the accuracy of Tully's surface hopping algorithm for the spin-boson model for the case of a small diabatic coupling parameter (V). We calculate the transition rates between diabatic surfaces, and we compare our results to the expected Marcus rates. We show that standard surface hopping yields an incorrect scaling with diabatic coupling (linear in V), which we demonstrate is due to an incorrect treatment of decoherence. By modifying standard surface hopping to include decoherence events, we recover the correct scaling (~V(2)).