Twin probes as a novel tool for the detection of single-nucleotide polymorphisms

Single-nucleotide polymorphisms (SNPs) are the most common form of DNA sequence variation. There is a strong interest from both academy and industry to develop rapid, sensitive and cost effective methods for SNP detection. Here we report a novel structural concept for DNA detection based on fluorescence dequenching upon hybridization. The so-called "twin probe" consists of a central fluorene derivative as fluorophore to which two identical oligonucleotides are covalently attached. This probe architecture is applied in homogeneous hybridization assays with subsequent fluorescence spectroscopic analysis. The bioorganic hybrid structure is well suited for sequence specific DNA detection and even SNPs are identified with high efficiency. Additionally, the photophysical properties of the twin probe were investigated. The covalent attachment of two single stranded oligonucleotides leads to strong quenching of the central fluorescence dye induced by the nucleobases. The twin probe is characterized by supramolecular aggregate formation accompanied by red-shifted emission and broad fluorescence spectra.     

The Bethe lattice treatment of sound attenuation for a spin- 3/2 Ising model

The sound attenuation phenomena is investigated for a spin- 3/2 Ising model on the Bethe lattice in terms of the recursion relations by using the Onsager theory of irreversible thermodynamics. The dependencies of sound attenuation on the temperature (T$T$), frequency (w$w$), Onsager coefficient (γ$\gamma$) and external magnetic field (H$H$) near the second-order (_Tc)$\left(T_c\right)$ and first-order (_Tt)$\left(T_t\right)$ phase transition temperatures are examined for given coordination numbers q$q$ on the Bethe lattice. It is assumed that the sound wave couples to the order-parameter fluctuations which decay mainly via the order-parameter relaxation process, thus two relaxation times are obtained and which are used to obtain an expression for the sound attenuation coefficient (α)$\left(\alpha \right)$. Our investigations revealed that only one peak is obtained near _Tt$T_t$ and three peaks are found near _Tc$T_c$ when the Onsager coefficient is varied at a given constant frequency for q=3$q=3$. Fixing the Onsager coefficient and varying the frequency always leads to two peaks for q=3,4$q=3,4$ and 6 near _Tc$T_c$. The sound attenuation peaks are observed near _Tt$T_t$ at lower values of external magnetic field, but as it increases the sound attenuation peaks decrease and eventually disappear.     

A hybrid shifting bottleneck procedure algorithm for the parallel-machine job-shop scheduling problem

In practice, parallel-machine job-shop scheduling (PMJSS) is very useful in the development of standard modelling approaches and generic solution techniques for many real-world scheduling problems. In this paper, based on the analysis of structural properties in an extended disjunctive graph model, a hybrid shifting bottleneck procedure (HSBP) algorithm combined with Tabu Search (TS) metaheuristic algorithm is developed to deal with the PMJSS problem. The original-version shifting bottleneck procedure (SBP) algorithm for the job-shop scheduling (JSS) has been significantly improved to solve the PMJSS problem with four novelties: (i) a topological-sequence algorithm is proposed to decompose the PMJSS problem in a set of single-machine scheduling (SMS) and/or parallel-machine scheduling subproblems; (ii) a modified Carlier algorithm based on the proposed lemmas and the proofs is developed to solve the SMS subproblem; (iii) the Jackson rule is extended to solve the PMS subproblem; (iv) a TS metaheuristic algorithm is embedded under the framework of SBP to optimise the JSS and PMJSS cases. The computational experiments show that the proposed HSBP is very efficient in solving the JSS and PMJSS problems.     

Asymptotic behavior of a solution of the Cauchy problem for the generalized damped multidimensional Boussinesq equation

This work studies the Cauchy problem for the generalized damped multidimensional Boussinesq equation. By using a multiplier method, it is proven that the global solution of the problem decays to zero exponentially as the time approaches infinity, under a very simple and mild assumption regarding the nonlinear term.     

Critical properties of mixed spin-1 and spin-5/2 with equal and unequal crystal fields

The effects of assuming equal or unequal crystal fields (CF) on the phase diagrams of a mixed spin-1 and spin-5/2 system are investigated in terms of the recursion relations on the Bethe lattice (BL). The equal CF case was considered for the coordination numbers q=3, 4, and 6, while for q=3 the unequal CF case was also studied. It was found that for the equal CF case, the model exhibits second-order phase transitions and two compensation temperatures for all q, the reentrant behavior for q=4 and first-order phase transitions and tricritical point (TCP) for q=6. In the unequal CF case for q=3, the system yields first- and second-order phase transitions, TCP's, and three compensation temperatures. In addition, the TCP's in a very short range are classified as the stable and unstable ones depending on their free energies.     

Thermal entanglement in two-qutrit spin-1 anisotropic Heisenberg model with inhomogeneous magnetic field

The thermal entanglement of a two-qutrit spin-1 anisotropic Heisenberg XXZ chain in an inhomogeneous magnetic field is studied in detail. The effects of the external magnetic field (B), a parameter b which controls the inhomogeneity of B, and the bilinear interaction parameters J_{x=Jy≠Jz on the thermal variation of the negativity are studied in detail. It is found that negativity N decreases when the values of magnetic field, inhomogeneity b and temperature are increasing. In addition, N remains at higher temperatures for higher values of Jz and lower values of B and b.}     

Minimizing the probability of lifetime ruin under borrowing constraints

We determine the optimal investment strategy of an individual who targets a given rate of consumption and who seeks to minimize the probability of going bankrupt before she dies, also known as lifetime ruin. We impose two types of borrowing constraints: First, we do not allow the individual to borrow money to invest in the risky asset nor to sell the risky asset short. However, the latter is not a real restriction because in the unconstrained case, the individual does not sell the risky asset short. Second, we allow the individual to borrow money but only at a rate that is higher than the rate earned on the riskless asset.We consider two forms of the consumption function: (1) The individual consumes at a constant (real) dollar rate, and (2) the individual consumes a constant proportion of her wealth. The first is arguably more realistic, but the second is closely connected with Merton’s model of optimal consumption and investment under power utility. We demonstrate that connection in this paper, as well as include a numerical example to illustrate our results.     

A theoretical investigation on Pt3Sn(1 0 2) surface alloy and CO-Pt3Sn(1 0 2) system

The adsorption properties of CO on experimentally verified stepped Pt₃Sn(1 0 2) surface were investigated using quantum mechanical calculations. The two possible terminations of Pt₃Sn(1 0 2) were generated and on these terminations all types of possible adsorption sites were determined. The adsorption energies and geometries of the CO molecule for all those sites were calculated. The most favorable sites for adsorption were determined as the short bridge site on the terrace of pure-Pt row of the mixed-atom-ending termination, atop site at the step-edge of the pure row of pure-Pt-ending termination and atop site at the step-edge of the pure-Pt row of the mixed-atom-ending termination. The results were compared with those for similar sites on the flat Pt₃Sn(1 1 0) surface considering the fact that Pt₃Sn(1 0 2) has terraces with (1 1 0) orientation. The LDOS analysis of bare sites clearly shows that there are significant differences between the electronic properties of Pt atoms at stepped Pt₃Sn(1 0 2) surface and the electronic properties of Pt atoms at flat (1 1 0) surface, which leads to changes in the CO bonding energies of these Pt atoms. Adsorption on Pt₃Sn(1 0 2) surface is in general stronger compared to that on Pt₃Sn(1 1 0) surface. The difference in adsorption strength of similar sites on these two surface terminations is a result of stepped structure of Pt₃Sn(1 0 2). The local density of states (LDOS) of the adsorbent Pt and C of adsorbed CO was utilized. The LDOS of the surface metal atoms with CO-adsorbed atop and of their bare state were compared to see the effect of CO chemisorption on the electron density distribution of the corresponding Pt atom. The downward shift in energy peak in the LDOS curves as well as changes in the electron densities of the corresponding energy levels indicate the orbital mixing between CO molecular orbitals and metal d-states. The present study showed that the adsorption strength of the sites has a direct relation with their LDOS profiles.     

A multiobjective model for locating undesirable facilities

In this paper, we develop a multiobjective model to depict the tradeoffs involved when locating one or more undesirable facilities to service a region. We assume that the region requires a certain capacity of service, and that this capacity can be met by building a combination of different-sized facilities. Examples could include sanitary landfills, incinerators, and power-generating stations. Our objectives are to minimize the total cost of the facilities located, the total opposition to the facilities, and the maximum disutility imposed on any individual. Opposition and disutility are assumed to be nonlinearly decreasing functions of distance, and increasing functions of facility size. We formulate our model as a multiobjective mixed-integer program, and generate the set of efficient solutions using an enumeration algorithm. Our code can solve realistically sized problems on a microcomputer. We give an example to illustrate the tradeoffs between the three objectives, which are inevitable in such a location problem.This research was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada (OGP 25481), and by the Nova Fellowship of the Faculty of Business, University of Alberta.     

Ant Colony Optimisation for Machine Layout Problems

Flexible machine layout problems describe the dynamic arrangement of machines to optimise the trade-off between material handling and rearrangement costs under changing and uncertain production environments. A previous study used integer-programming techniques to solve heuristically reduced versions of the problem. As an alternative, this paper introduces an ant colony optimisation (ACO) algorithm to generate good solutions. Experimental results are presented, with ACO obtaining better solutions than the reduction heuristic.