THz and above THz electron or hole oscillations in DNA dimers and trimers

A non conventional source or receiver of THz and above THz electromagnetic radiation is proposed. Specifically, electron or hole oscillations in DNA dimers (two interacting DNA base‐pairs or monomers) are predicted, with frequency in the range 0.25–100 THz (period 10–4000 fs) i.e. potentially absorbing or emitting electromagnetic radiation mainly in the mid‐ and far‐infrared with wavelengths ≈ 3–1200 μm. The efficiency of charge transfer between the two monomers which make up the dimer is described with the maximum transfer percentage p  and the pure maximum transfer rate . For dimers made of identical monomers , but for dimers made of different monomers . The investigation is extended to DNA trimers (three interacting DNA base‐pairs or monomers). For trimers made of identical monomers the carrier oscillates periodically with 0.5–33 THz ( 30–2000 fs); for 0 times crosswise purines , for 1 or 2 times crosswise purines . For trimers made of different monomers the carrier movement may be non periodic. Generally, increasing the number of monomers above three, the system becomes more complex and periodicity is lost; even for the simplest tetramer the carrier movement is not periodic.     

In-plane stability of uniform steel beam-columns on a Pasternak foundation with zero end-shortening

The linearized buckling response of uniform steel beam-columns resting on a Pasternak foundation type is dealt with in this work. The corresponding two-point boundary value problem depends on the two parameters associated with the foundation model, that is, shear layer constant and Winkler spring coefficient, as well as on the axial loading. The fourth-order differential equation of buckling and the consequent characteristic one yield exact values of the buckling loads, which may lead to shape functions, being either one sinusoidal waveform or the sum of two different waveforms. The former case is associated with a single-mode response, while the latter with mode coupling. The conditions for which each of these cases characterizes the beam-column behavior are fully assessed and the dependence on the combination of the aforementioned parameters on the response is discussed in detail. It is found that regardless of the order of coupling, the corresponding mode is not related to rational values of buckling loads and hence this unfavorable phenomenon is excluded in structural design.     

Development of an egg-white bioassay for monitoring biotin levels in urine and serum.

This article reports on the development of a simple and cost-effective bioassay for the detection of biotin in urine and serum, based on the very selective binding of avidin and biotin. Avidin was allowed to react without isolating it from egg white. Egg white was treated with the dye HABA, which binds to avidin. Upon subsequent treatment with biotin, HABA is released due to the high affinity of biotin to avidin. The amount of HABA released is proportional to the amount of biotin used.     

A finite difference scheme for computing inertial manifolds

A fully discrete method is presented for computing inertial manifolds of dissipative partial differential equations. In particular, only an approximate spectral decomposition of the dominant differential operator needs to be known. The first few of the smallest eigenvalues and eigenvectors of the discretized operator are approximated using the Lanczos algorithm. Numerical experiments are performed for an equation in one space dimension by discretizing the space variable on a sufficiently fine grid. The basic ideas and techniques are exemplified for selected bifurcation diagrams of an integrated form of the Kuramoto-Sivashinsky equation.This research was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) grant OGP0036901, NSERC and Schweizerischer Nationalfonds zur Förderung der Wissenschaften BEF 0150297, and Forschungsinstitut für Mathematik, ETH Zürich.     

An effective Markov based approach for calculating the Limit Matrix in the analytic network process

Analytic network process is a multiple criteria decision analysis (MCDA) method that aids decision makers to choose among a number of possible alternatives or prioritize the criteria for making a decision in terms of importance. It handles both qualitative and quantitative criteria, that are compared in pairs, in order to forge a best compromise answer according to the different criteria and influences involved. The method has been widely applied and the literature review reveals a rising trend of ANP-related articles. The ‘power’ matrix method, a procedure necessary for the stability of the decision system, is one of the critical calculations in the mathematical part of the method. The present study proposes an alternative mathematical approach that is based on Markov chain processes and the well-known Gauss-Jordan elimination. The new approach obtains practically the same results as the power matrix method, requires slightly less time and number of calculations and handles effectively cyclic supermatrices, optimizing thus the whole procedure.     

A constrained approach to multiscale stochastic simulation of chemically reacting systems

Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address this problem, assuming that the evolution of the slow species in the system is well approximated by a Langevin process. It is based on the conditional stochastic simulation algorithm (CSSA) which samples from the conditional distribution of the suitably defined fast variables, given values for the slow variables. In the constrained multiscale algorithm (CMA) a single realization of the CSSA is then used for each value of the slow variable to approximate the effective drift and diffusion terms, in a similar manner to the constrained mean-force computations in other applications such as molecular dynamics. We then show how using the ensuing Fokker-Planck equation approximation, we can in turn approximate average switching times in stochastic chemical systems.     

A theoretical study of the XP and NEXAFS spectra of alanine: gas phase molecule, crystal, and adsorbate at the ZnO(10 ̅10) surface

The adsorption of alanine on the mixed-terminated ZnO(10 ?10) surface is studied by means of quantum-chemical ab initio calculations. Using a finite cluster model and the adsorption geometry as obtained both by periodic CPMD and embedded cluster calculations, the C1s, N1s and O1s X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectra are calculated for single alanine molecules on ZnO(10 ?10). These spectra are compared with the spectra calculated for alanine in the gas phase and in its crystalline form and with experimental XPS and NEXAFS data for the isolated alanine molecule and for alanine adsorbed on ZnO(10 ?10) at multilayer and monolayer coverage. The excellent agreement between the experimental and calculated XP and NEXAFS spectra confirms the calculated adsorption geometry: A single alanine molecule is bound to ZnO(10 ?10) in a dissociated bidentate form with the two O atoms of the acid group bound to two Zn atoms of the surface and the proton transferred to one O atom of the surface. Other possible structures, such as adsorption of alanine in one of its neutral or zwitterionic forms in which the proton of the -COOH group remains at this group or is transferred to the amino group, can be excluded since they would give rise to quite different XP spectra. In the multilayer coverage regime, on the other hand, alanine is in its crystalline form as is also shown by the analysis of the XP spectra.