Ionization energies of the nucleotides

The vertical ionization energies of the four nucleotides have been computed. Geometries have been chosen to mimic orientations as they appear in B-DNA. The negative charge on the phosphate was neutralized by protonation, and also by the inclusion of counterions. Calculations have been performed with electron propagator methods (P3), M?ller-Plesset second-order perturbation theory, and density functional theory to determine the nature of the orbitals associated with the highest lying ionization energies. Calculations at the MP2/6-311G(d,p)//P3/6-311G(d,p) level of theory yield vertical ionization energies for 5'-dTMP 9.05 eV, for 5'-dCMP 8.40 eV, for 5'-dAMP 8.16 eV and for 5'-dGMP 7.96 eV. In all cases the highest occupied molecular orbital resides on the base moieties.     

Nanometre resolution using high-resolution scanning electron microscopy corroborated by atomic force microscopy

The resolving power of high-resolution scanning electron microscopy was judged using topographical height data from atomic force microscopy in order to assess the technique as a tool for understanding nanoporous crystal growth.     

An echolocation visualization and interface system for dolphin research

The present study describes the development and testing of a tool for dolphin research. This tool was able to visualize the dolphin echolocation signals as well as function as an acoustically operated "touch screen." The system consisted of a matrix of hydrophones attached to a semitransparent screen, which was lowered in front of an underwater acrylic panel in a dolphin pool. When a dolphin aimed its sonar beam at the screen, the hydrophones measured the received sound pressure levels. These hydrophone signals were then transferred to a computer where they were translated into a video image that corresponds to the dynamic sound pressure variations in the sonar beam and the location of the beam axis. There was a continuous projection of the image back onto the hydrophone matrix screen, giving the dolphin an immediate visual feedback to its sonar output. The system offers a whole new experimental methodology in dolphin research and since it is software-based, many different kinds of scientific questions can be addressed. The results were promising and motivate further development of the system and studies of sonar and cognitive abilities of dolphins.     

Biochemical and biomedical application of monodisperse polymer particles

Macroporous particles with large pores are used for size exclusion chromatography of carbohydrates with very high molecular weights. Macroporous particles of different sizes are used for multiple immunofluorometric analysis by flow cytometry. Porous magnetic particles with protein A coupled to the surface of the pores combine a high capacity in binding of IgG with easy handling of the particles. Magnetic beads with boronic acid coupled to the surface are applied for selective isolation of subclasses of cells. The beads are detached from the cells by addition of sorbitol, leaving free, pure cell fractions in good yield. The use of magnetic particles in molecular biology is described.     

Optimization of peak area precision of a GC–MS drug screening method using a nonparametric sign test

Accreditation and Quality Assurance - The optimization of a number of gas chromatography–mass spectrometry (GC–MS) parameters in order to improve peak area precision through...     

Exploiting the Aromatic Chameleon Character of Fulvenes for Computational Design of Baird‐Aromatic Triplet Ground State Compounds

Due to the reversal in electron counts for aromaticity and antiaromaticity in the closed‐shell singlet state (normally ground state, S₀) and lowest ππ* triplet state (T₁ or T₀), as given by Hückel's and Baird's rules, respectively, fulvenes are influenced by their substituents in the opposite manner in the T₁ and S₀ states. This effect is caused by a reversal in the dipole moment when going from S₀ to T₁ as fulvenes adapt to the difference in electron counts for aromaticity in various states; they are aromatic chameleons. Thus, a substituent pattern that enhances (reduces) fulvene aromaticity in S₀ reduces (enhances) aromaticity in T₁, allowing for rationalizations of the triplet state energies (E_T) of substituted fulvenes. Through quantum chemical calculations, we now assess which substituents and which positions on the pentafulvene core are the most powerful for designing compounds with low or inverted E_T. As a means to increase the π‐electron withdrawing capacity of cyano groups, we found that protonation at the cyano N atoms of 6,6‐dicyanopentafulvenes can be a route to on‐demand formation of a fulvenium dication with a triplet ground state (T₀). The five‐membered ring of this species is markedly Baird‐aromatic, although less than the cyclopentadienyl cation known to have a Baird‐aromatic T₀ state.     

Separation in homogeneous systems with independent identical elements

The paper considers strategic defense and attack of a system which can be separated into independent identical homogeneous parallel elements. The defender distributes its resource between separation of the elements and their protection from outside attacks. The attacker distributes its effort evenly among all attacked elements. The vulnerability of each element is determined by a contest success function between the attacker and the defender. The defender can choose a subset of the elements to defend. The attacker does not know which elements are protected and can choose a number of randomly chosen elements to attack. Separation efficiency conditions are formulated dependent on the defender’s and attacker’s budgets, separation costs, contest intensity, and system demand. An algorithm for determining the optimal number of protected elements is suggested for the case when both the defender and the attacker can choose the number of protected and attacked elements freely. The article considers both the cases without and with performance redundancy. Illustrative numerical examples are presented.     

Adduct formation in quantitative bioanalysis: Effect of ionization conditions on paclitaxel

Quantitative analysis of target compounds with liquid chromatography atmospheric pressure ionization mass spectrometry is sometimes hampered by adduct formation. In these situations, cationization with alkali metal ions instead of proton addition is often observed in the positive ion mode. This work studies the process of adduct formation and investigates potential strategies to control this phenomenon. Paclitaxel, a pharmaceutical chemotherapeutic agent, was used as a model compound. Electrospray (ESI), atmospheric pressure chemical ionization (APCI) and sonic spray ionization (SSI) are evaluated and compared. The work was performed on two different instruments, allowing the evaluation of different ionization behavior for different source design for electrospray, if any. Different mobile phase additives were compared, including acetic acid, formic acid, ammonium formate, and a range of primary amines. Continuous infusion was used for a fast screening, to detect optimal conditions. These were then further investigated in detail by LC-MS. The results indicate that electrospray is the more sensitive interface for this compound on the investigated apparatus. Unacceptable quantitative data were acquired without additives in the mobile phase. Generally, additives increased the reproducibility significantly. A response of mainly one ion was achieved with dodecylamine/acetic acid and acetic acid/sodium acetate. The data also point out the importance of evaluating adduct formation for compounds prone to this phenomenon during method development, especially in view of accurate quantitation.     

Letter: A Moving Medium Simulation of Schwarzschild Black Hole Optics

An explicit fluid flow simulation of electromagnetic wave propagation in the gravitational field of a Schwarzschild black hole is given. The fluid has a constant refractive index and a spherically symmetric inward directed flow. The resulting form of the metric leads to a new coordinate system in which the Schwarzschild vacuum is written in Gordon's form. It is shown that a closely related coordinate system interpolates between the Kerr-Schild and Painlevé-Gullstrand coordinates.     

Ensemble Linear Subspace Analysis of High-Dimensional Data

Regression models provide prediction frameworks for multivariate mutual information analysis that uses information concepts when choosing covariates (also called features) that are important for analysis and prediction. We consider a high dimensional regression framework where the number of covariates (p) exceed the sample size (n). Recent work in high dimensional regression analysis has embraced an ensemble subspace approach that consists of selecting random subsets of covariates with fewer than p covariates, doing statistical analysis on each subset, and then merging the results from the subsets. We examine conditions under which penalty methods such as Lasso perform better when used in the ensemble approach by computing mean squared prediction errors for simulations and a real data example. Linear models with both random and fixed designs are considered. We examine two versions of penalty methods: one where the tuning parameter is selected by cross-validation; and one where the final predictor is a trimmed average of individual predictors corresponding to the members of a set of fixed tuning parameters. We find that the ensemble approach improves on penalty methods for several important real data and model scenarios. The improvement occurs when covariates are strongly associated with the response, when the complexity of the model is high. In such cases, the trimmed average version of ensemble Lasso is often the best predictor.