The role of nucleobase carboradical and carbanion on DNA lesions: a theoretical study

DNA base release induced by H and OH radical addition to thymine and their corresponding electron adducts is studied at the DFT B3LYP/6-31+G(d,p) level in gas phase and in solution. H atom transfer after radical formation from C2' on the sugar to the C6 site on the base is shown to be prohibited for the radical species. Their corresponding electron adducts, albeit minor events in cellular systems, show excellent capabilities to proton transfer from C2' on the sugar to the C6 site on the base. The barriers for subsequent N-glycosidic bond dissociation range from 0.1 to 1.6 kcal mol(-1) at the B3LYP level and around 5 kcal mol(-1) using the BB1K functional, implying that these reactions can serve as a source to abasic sites. Analysis of bond dissociation energies show that all the reactions are exothermic, which is consistent with the changes in N-glycosidic bond lengths during the proton-transfer reactions. Bulk solvation plays a reverse influence on proton transfer and the bond rupture reactions. Molecular orbitals, NPA charges, and electron affinities are calculated to shed further light on the properties leading up to the intramolecular reactions.     

Theoretical study of the antioxidant properties of pyridoxine

Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of utmost importance in the living cell. The antioxidative properties of pyridoxine (vitamin B6) have recently been discovered. In this study, we have analyzed the reactivity of pyridoxine toward the ROS (.-)OH, (.-)OOH, and (.-)O(2)- at the density functional theory level (functionals B3LYP and MPW1B95). Two reaction types have been studied as follows: addition to the aromatic ring atoms and hydrogen/proton abstraction. Our results show that (.-)OH is the most reactive species, while (.-)OOH displays low reactivity and (.-)O2(-) does not react at all with pyridoxine. The most exergonic reactions are those where (.-)H is removed from the CH(2)OH groups or the ring-bound OH group and range from -33 to -39 kcal/mol. The most exergonic addition reactions occur by attacking the carbon atoms bonded to nitrogen but with an energy gain of only 6 kcal/mol.     

Measuring energy differences by BEC interferometry on a chip

We investigate the use of a Bose-Einstein condensate trapped on an atom chip for making interferometric measurements of small energy differences. We measure and explain the noise in the energy difference of the split condensates, which derives from statistical noise in the number difference. We also consider systematic errors. A leading effect is the variation of the rf magnetic field in the trap with distance from the wires on the chip surface. This can produce energy differences that are comparable with those due to gravity.     

Megavariate Analysis of Environmental QSAR Data. Part II – Investigating Very Complex Problem Formulations Using Hierarchical, Non-Linear and Batch-Wise Extensions of PCA and PLS

Summary Three extensions of the basic PCA and PLS methodologies are described. These extensions are hierarchical, non-linear and batch-based in nature. The objectives of these methods are to assist in problem understanding and problem solving in very complex (QSAR) problem formulations. The method extensions are illustrated using two example QSAR data sets containing many X- and Y-variables.     

Bentley’s conjecture on popularity toplist turnover under random copying

Bentley et al. studied the turnover rate in popularity toplists in a ‘random copying’ model of cultural evolution. Based on simulations of a model with population size N, list length ? and invention rate μ, they conjectured a remarkably simple formula for the turnover rate: $\ell \sqrt{\mu}$ . Here we study an overlapping generations version of the random copying model, which can be interpreted as a random walk on the integer partitions of the population size. In this model we show that the conjectured formula, after a slight correction, holds asymptotically.     

Entropy driven stabilization of energetically unstable crystal structures explained from first principles theory

Conventional methods to calculate the thermodynamics of crystals evaluate the harmonic phonon spectra and therefore do not work in frequent and important situations where the crystal structure is unstable in the harmonic approximation, such as the body-centered cubic (bcc) crystal structure when it appears as a high-temperature phase of many metals. A method for calculating temperature dependent phonon spectra self-consistently from first principles has been developed to address this issue. The method combines concepts from Born's interatomic self-consistent phonon approach with first principles calculations of accurate interatomic forces in a supercell. The method has been tested on the high-temperature bcc phase of Ti, Zr, and Hf, as representative examples, and is found to reproduce the observed high-temperature phonon frequencies with good accuracy.     

Increasing the equilibrium solubility of dopants in semiconductor multilayers and alloys

We have theoretically studied the possibility to control the equilibrium solubility of dopants in semiconductor alloys, by strategic tuning of the alloy concentration. From the modeled cases of C(0) in Si(x)Ge(1-x), Zn(-) and Cd(-) in Ga(x)In(1-x)P it is seen that under certain conditions the dopant solubility can be orders of magnitude higher in an alloy or multilayer than in either of the elements of the alloy. This is found to be due to the solubility's strong dependence on the lattice constant for size mismatched dopants. The equilibrium doping concentration in alloys or multilayers could therefore be increased significantly. More specifically, Zn- in a Ga(x)In(1-x)P multilayer is found to have a maximum solubility for x = 0.9, which is 5 orders of magnitude larger than that of pure InP.     

Solvent‐Dependent Structure of the I3− Ion Derived from Photoelectron Spectroscopy and Ab Initio Molecular Dynamics Simulations

Ab initio molecular dynamics (MD) simulations of the solvation of LiI₃ in four different solvents (water, methanol, ethanol, and acetonitrile) are employed to investigate the molecular and electronic structure of the I₃^? ion in relation to X‐ray photoelectron spectroscopy (XPS). Simulations show that hydrogen‐bond rearrangement in the solvation shell is coupled to intramolecular bond‐length asymmetry in the I₃^? ion. By a combination of charge analysis and I 4 d core‐level XPS measurements, the mechanism of the solvent‐induced distortions has been studied, and it has been concluded that charge localization mediates intermolecular interactions and intramolecular distortion. The approach involving a synergistic combination of theory and experiment probes the solvent‐dependent structure of the I₃^? ion, and the geometric structure has been correlated with the electronic structure.     

Surface integral analogy approaches for predicting noise from 3D high-lift low-noise wings

Three surface integral approaches of the acoustic analogies are studied to predict the noise from three concep- tual configurations of three-dimensional high-lift low-noise wings. The approaches refer to the Kirchhoff method, the Ffowcs Williams and Hawkings （FW-H） method of the permeable integral surface and the Curle method that is known as a special case of the FW-H method. The first two approaches are used to compute the noise generated by the core flow region where the energetic structures exist. The last approach is adopted to predict the noise specially from the pressure perturbation on the wall. A new way to con- struct the integral surface that encloses the core region is proposed for the first two methods. Considering the local properties of the flow around the complex object-the actual wing with high-lift devices-the integral surface based on the vorticity is constructed to follow the flow structures. The surface location is discussed for the Kirchhoff method and the FW-H method because a common surface is used for them. The noise from the core flow region is studied on the basis of the dependent integral quantities, which are indicated by the Kirchhoff formulation and by the FW-H formulation. The role of each wall component on noise contribution is analyzed using the Curle formulation. Effects of the volume integral terms of Lighthill＇s stress tensors on the noise pre-diction are then evaluated by comparing the results of the Curle method with the other two methods.     

Lecture Hall Partitions II

For a non-decreasing integer sequence a=(a₁,...,a_n) we define L_a to be the set of n-tuples of integers = (₁,...,_n) satisfying . This generalizes the so-called lecture hall partitions corresponding to a_i=i and previously studied by the authors and by Andrews. We find sequences a such that the weight generating function for these a-lecture hall partitions has the remarkable form In the limit when n tends to infinity, we obtain a family of identities of the kind the number of partitions of an integer m such that the quotient between consecutive parts is greater than is equal to the number of partitions of m into parts belonging to the set P, for certain real numbers and integer sets P. We then underline the connection between lecture hall partitions and Ehrhart theory and discuss some reciprocity results.