Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

A framework for clarifying the meaning of Triple Bottom-Line, Integrated, and Sustainability Assessment

Terms such as Integrated Assessment and Sustainability Assessment are used to label 'new' approaches to impact assessment that are designed to direct planning and decision-making towards sustainable development (SD). Established assessment techniques, such as EIA and SEA, are also widely promoted as SD 'tools'. This paper presents the findings of a literature review undertaken to identify the features that are typically promoted for improving the SD-directedness of assessments. A framework is developed which reconciles the broad range of emerging approaches and tackles the inconsistent use of terminology. The framework comprises a three-dimensional space defined by the following axes: the comprehensiveness of the SD coverage; the degree of 'integration' of the techniques and themes; and the extent to which a strategic perspective is adopted. By applying the framework, assessment approaches can be positioned relative to one another, enabling comparison on the basis of substance rather than semantics. © 2007 Elsevier Inc. All rights reserved.

Measurement of the Interaction Between Recombinant I-domain from Integrin alpha 2 beta 1 and a Triple Helical Collagen Peptide with the GFOGER Binding Motif Using Molecular Force Spectroscopy.

The role of the collagen-platelet interaction is of crucial importance to the haemostatic response during both injury and pathogenesis of the blood vessel wall. Of particular interest is the high affinity interaction of the platelet transmembrane receptor, alpha 2 beta 1, responsible for firm attachment of platelets to collagen at and around injury sites. We employ single molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) to study the interaction of the I-domain from integrin alpha 2 beta 1 with a synthetic collagen related triple-helical peptide containing the high-affinity integrin-binding GFOGER motif, and a control peptide lacking this sequence, referred to as GPP. By utilising synthetic peptides in this manner we are able to study at the molecular level subtleties that would otherwise be lost when considering cell-to-collagen matrix interactions using ensemble techniques. We demonstrate for the first time the complexity of this interaction as illustrated by the complex multi-peaked force spectra and confirm specificity using control blocking experiments. In addition we observe specific interaction of the GPP peptide sequence with the I-domain. We propose a model to explain these observations.

Linking business ecosystem lifecycle with platform strategy: A triple view of technology, application and organisation

This paper explores platform strategies along the business ecosystem lifecycle (BELC), based on a multiple-case study. Developing observations on platform strategies from a firm level to a business ecosystem level, the study investigates the issue of platform strategy through three views, respectively technology, application and organisation. As a result, a general evolutional pattern of platform strategy along the BELC is identified, where an open strategy emerges at the birth and expansion phases, then a dominating strategy rises at the authority phase, and finally the opportunistic strategy takes over at the renewal phase. This paper connects the core firms in the business ecosystem with the evolutionary platform strategies. Copyright © 2013 Inderscience Enterprises Ltd.

An Arbitrary Lagrangian Eulerian Method for Three-Phase Flows with Triple Junction Points

We present a moving mesh method suitable for solving two-dimensional and axisymmetric three-liquid flows with triple junction points. This method employs a body-fitted unstructured mesh where the interfaces between liquids are lines of the mesh system, and the triple junction points (if exist) are mesh nodes. To enhance the accuracy and the efficiency of the method, the mesh is constantly adapted to the evolution of the interfaces by refining and coarsening the mesh locally; dynamic boundary conditions on interfaces, in particular the triple points, are therefore incorporated naturally and accurately in a Finite- Element formulation. In order to allow pressure discontinuity across interfaces, double-values of pressure are necessary for interface nodes and triple-values of pressure on triple junction points. The resulting non-linear system of mass and momentum conservation is then solved by an Uzawa method, with the zero resultant condition on triple points reinforced at each time step. The method is used to investigate the rising of a liquid drop with an attached bubble in a lighter liquid.

Predictive coding and the slowness principle: an information-theoretic approach.

Understanding the guiding principles of sensory coding strategies is a main goal in computational neuroscience. Among others, the principles of predictive coding and slowness appear to capture aspects of sensory processing. Predictive coding postulates that sensory systems are adapted to the structure of their input signals such that information about future inputs is encoded. Slow feature analysis (SFA) is a method for extracting slowly varying components from quickly varying input signals, thereby learning temporally invariant features. Here, we use the information bottleneck method to state an information-theoretic objective function for temporally local predictive coding. We then show that the linear case of SFA can be interpreted as a variant of predictive coding that maximizes the mutual information between the current output of the system and the input signal in the next time step. This demonstrates that the slowness principle and predictive coding are intimately related.

A duality principle for homogeneous vectorfields with applications

A duality transformation principle was proposed for converting a positive order homogeneous vectorfield into a negative order homogeneous vectorfield. The principle also converted a uniformly locally asymptotically stable differential equation into a uniformly bounded differential equation. The duality transformations included the geometric framework for homogeneity and the removal of origin from the state space.

First-principle study of native defects in CuScO2 and CuYO2

This paper studies the electronic structure and native defects intransparent conducting oxides CuScO2 and CuYO2 using the first-principle calculations. Some typical native copper-related and oxygen-related defects, such as vacancy, interstitials, and antisites in their relevant charge state are considered. The results of calculation show that, CuMO2 (M = Sc, Y) is impossible to shown-type conductivity ability. It finds that copper vacancy and oxygen interstitial have relatively low formation energy and they are the relevant defects in CuScO2 and CuYO2. Copper vacancy is the most efficient acceptor, and under O-rich condition oxygen antisite also becomes important acceptor and plays an important role in p-type conductivity.

First-principle study of extrinsic defects in CuScO2 and CuYO2

Using first-principles methods, we studied the extrinsic defects doping in transparent conducting oxides CuMO2 (M=Sc, Y). We chose Be, Mg, Ca, Si, Ge, Sn as extrinsic defects to substitute for M and Cu atoms. By systematically calculating the impurity formation energy and transition energy level, we find that Be-Cu is the most prominent extrinsic donor and Ca-M is the prominent extrinsic acceptor. In addition, we find that Mg atom substituting for Sc is the most prominent extrinsic acceptor in CuSCO2. Our calculation results are expected to be a guide for preparing n-type and p-type materials through extrinsic doping in CuMO2 (M=SC, y). (C) 2008 Elsevier B.V. All rights reserved.

1310 nm GaInNAs triple quantum well laser with 13 GHz modulation bandwidth

The emission wavelength of a GaInNAs quantum well (QW) laser was adjusted to 1310 nm, the zero dispersion wavelength of optical fibre, by an appropriate choice of QW composition and thickness and N concentration in the barriers. A triple QW design was employed to enable the use of a short cavity with a small photon lifetime while having sufficient differential gain for a large modulation bandwidth. High speed, ridge waveguide lasers fabricated from high quality material grown by molecular beam epitaxy exhibited a damped modulation response with a bandwidth of 13 GHz.

First principle study of Mg, Si and Mn co-doped GaN

Calculations of electronic structures and optical properties of Mg (or Si) and Mn co-doped GaN were carried out by means of first-principle plane-wave pesudopotential (PWP) based on density functional theory - The spin polarized impurity bands of deep energy levels were found for both systems. They are half metallic and suitable for spin injectors. Compared with GaN Mn, GaN Mn-Mg exhibits a significant increase in T-C 1 while the 1.3 eV absorption peak in GaN Mn disappears due to addition of Mg. In addition, a strong absorption peak due to T-4(1) (F) -> T-4(2) (F) transition of Mn4+ were observed near 1.1 eV. Nevertheless, GaN Mn-Si failed to show increase of T-C, and the absorption peak was not observed at the low energy side.