An approximation algorithm for sorting by reversals and transpositions

Genome rearrangement algorithms are powerful tools to analyze gene orders in molecular evolution. Analysis of genomes evolving by reversals and transpositions leads to a combinatorial problem of sorting by reversals and transpositions, the problem of finding a shortest sequence of reversals and transpositions that sorts one genome into the other. In this paper we present a 2k-approximation algorithm for sorting by reversals and transpositions for unsigned permutations where k is the approximation ratio of the algorithm used for cycle decomposition. For the best known value of k our approximation ratio becomes 2.8386+δ for any δ>0. We also derive a lower bound on reversal and transposition distance of an unsigned permutation.     

Vibrations at surfaces

This special issue is dedicated to the phenomenon of vibrations at surfaces-a topic that was indispensible a couple of decades ago, since it was one of the few phenomena capable of revealing the nature of binding at solid surfaces. For clean surfaces, the frequencies of modes with characteristic displacement patterns revealed how surface geometry, as well as the nature of binding between atoms in the surface layers, could be different from that in the bulk solid. Dispersion of the surface phonons provided further measures of interatomic interactions. For chemisorbed molecules on surfaces, frequencies and dispersion of the vibrational modes were also critical for determining adsorption sites. In other words, vibrations at surfaces served as a reliable means of extracting information about surface structure, chemisorption and overlayer formation. Experimental techniques, such as electron energy loss spectroscopy and helium-atom-surface scattering, coupled with infra-red spectroscopy, were continually refined and their resolutions enhanced to capture subtleties in the dynamics of atoms and molecules at surfaces. Theoretical methods, whether based on empirical and semi-empirical interatomic potential or on ab initio electronic structure calculations, helped decipher experimental observations and provide deeper insights into the nature of the bond between atoms and molecules in regions of reduced symmetry, as encountered on solid surfaces. Vibrations at surfaces were thus an integral part of the set of phenomena that characterized surface science. Dedicated workshops and conferences were held to explore the variety of interesting and puzzling features revealed in experimental and theoretical investigations of surface vibrational modes and their dispersion. One such conference, Vibrations at Surfaces, first organized by Harald Ibach in Juelich in 1980, continues to this day. The 13th International Conference on Vibrations at Surfaces was held at the University of Central Florida, Orlando, in March 2010. Several speakers at this meeting were invited to contribute to the special section in this issue. As is clear from the articles in this special section, the phenomenon of vibrations at surfaces continues to be a dynamic field of investigation. In fact, there is a resurgence of effort because the insights provided by surface dynamics are still fundamental to the development of an understanding of the microscopic factors that control surface structure formation, diffusion, reaction and structural stability. Examination of dynamics at surfaces thus complements and supplements the wealth of information that is obtained from real-space techniques such as scanning tunneling microscopy. Vibrational dynamics is, of course, not limited to surfaces. Surfaces are important since they provide immediate deviation from the bulk. They display how lack of symmetry can lead to new structures, new local atomic environments and new types of dynamical modes. Nanoparticles, large molecules and nanostructures of all types, in all kinds of local environments, provide further examples of regions of reduced symmetry and coordination, and hence display characteristic vibrational modes. Given the tremendous advance in the synthesis of a variety of nanostructures whose functionalization would pave the way for nanotechnology, there is even greater need to engage in experimental and theoretical techniques that help extract their vibrational dynamics. Such knowledge would enable a more complete understanding and characterization of these nanoscale systems than would otherwise be the case. The papers presented here provide excellent examples of the kind of information that is revealed by vibrations at surfaces. Vibrations at surface contents Poisoning and non-poisoning oxygen on Cu(410)L Vattuone, V Venugopal, T Kravchuk, M Smerieri, L Savio and M Rocca Modifying protein adsorption by layers of glutathione pre-adsorbed on Au(111)Anne Vallée, Vincent Humblot, Christophe Méthivier, Paul Dumas and Claire-Marie Pradier Relating temperature dependence of atom scattering spectra to surface corrugationW W Hayes and J R Manson Effects of the commensurability and disorder on friction for the system Xe/CuA Franchini, V Bortolani, G Santoro and K Xheka Switching ability of nitro-spiropyran on Au(111): electronic structure changes as a sensitive probe during a ring-opening reactionChristopher Bronner, Gunnar Schulze, Katharina J Franke, José Ignacio Pascual and Petra Tegeder High-resolution phonon study of the Ag(100) surfaceK L Kostov, S Polzin and W Widdra On the interpretation of IETS spectra of a small organic molecule Karina Morgenstern.     

Compound wall treatment with low‐Re turbulence model

A generalized treatment for the wall boundary conditions relating to turbulent flows is developed that blends the integration to a solid wall with wall functions. The blending function ensures a smooth transition between the viscous and turbulent regions. An improved low Reynolds number k?ε model is coupled with the proposed compound wall treatment to determine the turbulence field. The eddy viscosity formulation maintains the positivity of normal Reynolds stresses and Schwarz' inequality for turbulent shear stresses. The model coefficients/functions preserve the anisotropic characteristics of turbulence. Computations with fine and coarse meshes of a few flow cases yield appreciably good agreement with the direct numerical simulation and experimental data. The method is recommended for computing the complex flows where computational grids cannot satisfy a priori the prerequisites of viscous/turbulence regions. Copyright © 2011 John Wiley & Sons, Ltd.     

Easy preparation of recyclable thermally stable visible-light-active graphitic-C3N4/TiO2 nanocomposite photocatalyst for efficient decomposition of hazardous organic industrial pollutants in aqueous medium

Research on Chemical Intermediates - Graphitic-C3N4/TiO2 nanocomposite was prepared as a photocatalyst (PC) active under visible light (λ?≥?420 nm) by preparation of...     

Evaluation of toxicity level of the polluted eco-system for an industrial city of Pakistan

The indiscriminate discharge of untreated industrial effluents and solid wastes into the open environment poses a serious threat to the ecosystem. Gujranwala is an industrial city of Pakistan wherein a large number of different industries are situated and majority of them are not equipped with proper recycling or effluent treatment plants. Unfortunately, untreated industrial effluents are locally used for the irrigation purposes which may result in higher concentrations of toxic metals in the crops and vegetables. Therefore, prime objective of the present study was to determine concentrations of toxic metals in the polluted soils, vegetables and crops grown in the vicinity of industrial areas using neutron activation analysis technique. The results obtained showed higher values of toxic metals in the studied samples. The observed highest concentration of As (0.94 ± 0.06) in spinach, Br (69 ± 9) in turnip, Co (0.83 ± 0.01) in millet, Cr (51.7 ± 4.2) in wheat, Mn (76.2 ± 7.3) in tomato, Sb (0.5 ± 0.06) in rice, Cl (31698 ± 3921) and Se (3.4 ± 0.4) in carrot. These values are higher than those reported in the literature.     

Tuning Optical Properties by Controlled Aggregation: Electroluminescence Assisted by Thermally-Activated Delayed Fluorescence from Thin Films of Crystalline Chromophores

Several photophysical properties of chromophores depend crucially on intermolecular interactions. Thermally-activated delayed fluorescence (TADF) is often influenced by close packing of the chromophore assembly. In this context, the metal-organic framework (MOF) approach has several advantages: it can be used to steer aggregation such that the orientation within aggregated structures can be predicted using rational approaches. We demonstrate this design concept for a DPA-TPE (diphenylamine-tetraphenylethylene) chromophore, which is non-emissive in its solvated state due to vibrational quenching. Turning this DPA-TPE into a ditopic linker makes it possible to grow oriented MOF thin films exhibiting pronounced green electroluminescence with low onset voltages. Measurements at different temperatures clearly demonstrate the presence of TADF. Finally, this work reports that the layer-by-layer process used for MOF thin film deposition allows the integration of the TADF-DPA-TPE in a functioning LED device.     

Preparation of magnetically doped multilayered functional silica particles via surface modification with organic polymer

Magnetically modified functional particles are emerging as one of the most promising candidate in numerous multidisciplinary applications. In this research, a simple process has been developed to prepare magnetically modified aminated silica (SiO₂) particles. Herein, submicron‐sized SiO₂ particles were modified with poly(methylmethacrylate‐methacrylic acid) by seeded polymerization without any stabilizer. The carboxyl groups localized near the particles surface were then covalently linked with ethylene diamine to prepare aminated composite particles. Iron ions were then precipitated on the surface of aminated composite particles to obtain magnetically doped functional SiO₂ particles. The preparation of such particles was confirmed by scanning electron microscopy, Fourier transform infrared, ¹H NMR, X‐ray photoelectron spectroscopy and thermogravemetric analyses. Relative measurement of adsorption study of different biomolecules suggested that magnetically doped functional silica particles are comparatively hydrophobic. Copyright © 2012 John Wiley & Sons, Ltd.     

Baking impact on photoelectrochemical cells performance of electrodeposited CdSe films

Cadmium selenide (CdSe) nanocrystalline thin films in the form of upright nanocones, perpendicular to substrate surface, are grown electrochemically onto a conducting and transparent indium-tin-oxide substrate at room temperature and impact of baking under oxygen flow on their structure, morphology, optical absorbance and dark-light photoelectrochemical cell performance is explored. Crystallinity improvement followed by enhancement in the surface roughness 11-19 nm and reduction in water contact angle from 60° to 22° (±0.2)° due to baking impact showed increase in crystallite size from 25 to 100 Å. Increase in current density from 0.07 to 5.61 mA/cm² after baking under oxygen flow has promoted the conversion efficiency to 0.5% from 0.007%.     

The incorporation of fixed cost and multilevel capacities into the discrete and continuous single source capacitated facility location problem

In this study we investigate the single source location problem with the presence of several possible capacities and the opening (fixed) cost of a facility that is depended on the capacity used and the area where the facility is located. Mathematical models of the problem for both the discrete and the continuous cases using the Rectilinear and Euclidean distances are produced. Our aim is to find the optimal number of open facilities, their corresponding locations, and their respective capacities alongside the assignment of the customers to the open facilities in order to minimise the total fixed and transportation costs. For relatively large problems, two solution methods are proposed namely an iterative matheuristic approach and VNS-based matheuristic technique. Dataset from the literature is adapted to assess our proposed methods. To assess the performance of the proposed solution methods, the exact method is first applied to small size instances where optimal solutions can be identified or lower and upper bounds can be recorded. Results obtained by the proposed solution methods are also reported for the larger instances.