Crystalline A-DNA: The X-Ray Analysis of the Fragment d(G-G-T-A-T-A-C-C)

An A-DNA type double helical conformation was observed in the single crystal X-ray structure of the octamer d(G-G-T-A-T-A-C-C), 1, and its 5-bromouracil-containing analogue, 2. The structure of the isomorphous crystals (space group P61) was solved by a search technique based on packing criteria and R-factor calculations, with use of only low order data. At the present stage of refinement the R factors are 31 % for 1 and 28 % for 2 at a resolution of 2.25 A (0.225 nm). The molecules interact through their minor grooves by hydrogen bonding and base to sugar van der Waals contacts. The stable A conformation observed in the crystal may have some structural relevance to promoter regions where the T-A-T-A sequence is frequently found.

Modeling of a pressure modulated desalination system using bond graph methodology

A desalination system is a complex multi energy domain system comprising power/energy flow across several domains such as electrical, thermal, and hydraulic. The dynamic modeling of a desalination system that comprehensively addresses all these multi energy domains is not adequately addressed in the literature. This paper proposes to address the issue of modeling the various energy domains for the case of a single stage flash evaporation desalination system. This paper presents a detailed bond graph modeling of a desalination unit with seamless integration of the power flow across electrical, thermal, and hydraulic domains. The paper further proposes a performance index function that leads to the tracking of the optimal chamber pressure giving the optimal flow rate for a given unit of energy expended. The model has been validated in steady state conditions by simulation and experimentation.

Bond graph toolbox for handling complex variable

Bond graph is an apt modelling tool for any system working across multiple energy domains. Power electronics system modelling is usually the study of the interplay of energy in the domains of electrical, mechanical, magnetic and thermal. The usefulness of bond graph modelling in power electronic field has been realised by researchers. Consequently in the last couple of decades, there has been a steadily increasing effort in developing simulation tools for bond graph modelling that are specially suited for power electronic study. For modelling rotating magnetic fields in electromagnetic machine models, a support for vector variables is essential. Unfortunately, all bond graph simulation tools presently provide support only for scalar variables. We propose an approach to provide complex variable and vector support to bond graph such that it will enable modelling of polyphase electromagnetic and spatial vector systems. We also introduced a rotary gyrator element and use it along with the switched junction for developing the complex/vector variable's toolbox. This approach is implemented by developing a complex S-function tool box in Simulink inside a MATLAB environment This choice has been made so as to synthesise the speed of S-function, the user friendliness of Simulink and the popularity of MATLAB.

Efficient algorithms for computing Reeb graphs

The Reeb graph tracks topology changes in level sets of a scalar function and finds applications in scientific visualization and geometric modeling. We describe an algorithm that constructs the Reeb graph of a Morse function defined on a 3-manifold. Our algorithm maintains connected components of the two dimensional levels sets as a dynamic graph and constructs the Reeb graph in O(nlogn+nlogg(loglogg)3) time, where n is the number of triangles in the tetrahedral mesh representing the 3-manifold and g is the maximum genus over all level sets of the function. We extend this algorithm to construct Reeb graphs of d-manifolds in O(nlogn(loglogn)3) time, where n is the number of triangles in the simplicial complex that represents the d-manifold. Our result is a significant improvement over the previously known O(n2) algorithm. Finally, we present experimental results of our implementation and demonstrate that our algorithm for 3-manifolds performs efficiently in practice.

Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1·8 and 2·25 Å, respectively. The molecules adopt an A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

An Optimal g-Guidance Scheme for Satellite Launch Vehicles

A closed-loop steering logic based on an optimal (2-guidance is developed here. The guidance system drives the satellite launch vehicle along a two- or three- dimensional trajectory for placing the payload into a specified circular orbit. The modified g-guidance algorithm makes use of the optimal required velocity vector, which minimizes the total impulse needed for an equivalent two-impluse transfer from the present state to the final orbit. The required velocity vector is defined as velocity of the vehicle on the hypothetical transfer orbit immediately after the application of the first impulse. For this optimal transfer orbit, a simple and elegant expression for the Q-matrix is derived. A working principle for the guidance algorithm in terms of the major and minor cycles, and also for the generation of the steering command, is outlined.

Flow-graph techniques for epicyclic gear train analysis

Flow-graph techniques are applied in this article for the analysis of an epicyclic gear train. A gear system based on this is designed and constructed for use in Numerical Control Systems.

Separation of sulfur-containing components of transfer ribonucleic acid on Bio-Gel P-2 and Sephadex G-10 columns

S-Labeled nucleosides of E. coli tRNA and some of the derivatives of thionucleosides were separated on Bio-Gel P-2 and Sephadex G-10 columns employing buffers of low salt concentration and high pH.

Popular Mixed Matchings

We study the problem of matching applicants to jobs under one-sided preferences: that is, each applicant ranks a non-empty subset of jobs under an order of preference, possibly involving ties. A matching M is said to be rnore popular than T if the applicants that prefer M to T outnumber those that prefer T to M. A matching is said to be popular if there is no matching more popular than it. Equivalently, a matching M is popular if phi(M,T) >= phi(T, M) for all matchings T, where phi(X, Y) is the number of applicants that prefer X to Y. Previously studied solution concepts based oil the popularity criterion are either not guaranteed to exist for every instance (e.g., popular matchings) or are NP-hard to compute (e.g., least unpopular matchings). This paper addresses this issue by considering mixed matchings. A mixed matching is simply a probability distributions over matchings in the input graph. The function phi that compares two matchings generalizes in a natural manner to mixed matchings by taking expectation. A mixed matching P is popular if phi(P,Q) >= phi(Q,P) for all mixed matchings Q. We show that popular mixed matchings always exist. and we design polynomial time algorithms for finding them. Then we study their efficiency and give tight bounds on the price of anarchy and price of stability of the popular matching problem.

Acoustic emission source location in composite structure by Voronoi construction using geodesic curve evolution

Conventional analytical/numerical methods employing triangulation technique are suitable for locating acoustic emission (AE) source in a planar structure without structural discontinuities. But these methods cannot be extended to structures with complicated geometry, and, also, the problem gets compounded if the material of the structure is anisotropic warranting complex analytical velocity models. A geodesic approach using Voronoi construction is proposed in this work to locate the AE source in a composite structure. The approach is based on the fact that the wave takes minimum energy path to travel from the source to any other point in the connected domain. The geodesics are computed on the meshed surface of the structure using graph theory based on Dijkstra's algorithm. By propagating the waves in reverse virtually from these sensors along the geodesic path and by locating the first intersection point of these waves, one can get the AE source location. In this work, the geodesic approach is shown more suitable for a practicable source location solution in a composite structure with arbitrary surface containing finite discontinuities. Experiments have been conducted on composite plate specimens of simple and complex geometry to validate this method.

Synthesis and Evaluation of a Novel Class of G-Quadruplex-Stabilizing Small Molecules Based on the 1,3-Phenylene-Bis(piperazinyl benzimidazole) System

Achieving stabilization of telomeric DNA in G-quadruplex conformation by Various organic compounds has been an important goal for the medicinal chemists seeking to develop new anticancer agents. Several compounds are known to stabilize G-quadruplexes. However, relatively few are known to induce their formation and/or alter the topology, of the preformed quadruplex DNA. Herein, four compounds having the 1,3-phenylene-bis(piperazinyl benzimidazole) unit as a basic skeleton have been synthesized, and their interactions with the 24-mer telomeric DNA sequences from Tetrahymena thermophilia d(T(2)G(4))(4) have been investigated using high-resolution techniques Such as circular dichroism (CD) spectropolarimetry, CD melting, emission spectroscopy, and polyacrylamide gel electrophoresis. The data obtained, in the presence of one of three ions (Li+, Na+, or K+), indicate that all the new compounds have a high affinity for G-quadruplex DNA, and the strength of the binding with G-quadruplex depends on (1) phenyl ring substitution, (ii) the piperazinyl side chain, and (iii) the type of monovalent cation present in the buffer. Results further Suggest that these compounds are able to abet the conversion of the Intramolecular quadruplex into parallel stranded intermolecular G-quadruplex DNA. Notably, these compounds are also capable of inducing and stabilizing the parallel stranded quadruplex from randomly structured DNA in the absence of any stabilizing cation. The kinetics of the structural changes Induced by these compounds could be followed by recording the changes in the CD signal as a function of time. The implications of the findings mentioned above are discussed in this paper.

On the Structure of Contractible Edges in k-connected Partial k-trees

Contraction of an edge e merges its end points into a new single vertex, and each neighbor of one of the end points of e is a neighbor of the new vertex. An edge in a k-connected graph is contractible if its contraction does not result in a graph with lesser connectivity; otherwise the edge is called non-contractible. In this paper, we present results on the structure of contractible edges in k-trees and k-connected partial k-trees. Firstly, we show that an edge e in a k-tree is contractible if and only if e belongs to exactly one (k + 1) clique. We use this characterization to show that the graph formed by contractible edges is a 2-connected graph. We also show that there are at least |V(G)| + k - 2 contractible edges in a k-tree. Secondly, we show that if an edge e in a partial k-tree is contractible then e is contractible in any k-tree which contains the partial k-tree as an edge subgraph. We also construct a class of contraction critical 2k-connected partial 2k-trees.

Acyclic edge coloring of subcubic graphs

An acyclic edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycles. The acyclic chromatic index of a graph is the minimum number k such that there is an acyclic edge coloring using k colors and it is denoted by a′(G). From a result of Burnstein it follows that all subcubic graphs are acyclically edge colorable using five colors. This result is tight since there are 3-regular graphs which require five colors. In this paper we prove that any non-regular connected graph of maximum degree 3 is acyclically edge colorable using at most four colors. This result is tight since all edge maximal non-regular connected graphs of maximum degree 3 require four colors.

Analysis of the MAP/G(a,b)/1/N queue with multiple vacations

This paper deals with a batch service queue and multiple vacations. The system consists of a single server and a waiting room of finite capacity. Arrival of customers follows a Markovian arrival process (MAP). The server is unavailable for occasional intervals of time called vacations, and when it is available, customers are served in batches of maximum size ‘b’ with a minimum threshold value ‘a’. We obtain the queue length distributions at various epochs along with some key performance measures. Finally, some numerical results have been presented.

Bond graph model of doubly fed three phase induction motor using the Axis Rotator element for frame transformation

Induction motor is a typical member of a multi-domain, non-linear, high order dynamic system. For speed control a three phase induction motor is modelled as a d–q model where linearity is assumed and non-idealities are ignored. Approximation of the physical characteristic gives a simulated behaviour away from the natural behaviour. This paper proposes a bond graph model of an induction motor that can incorporate the non-linearities and non-idealities thereby resembling the physical system more closely. The model is validated by applying the linearity and idealities constraints which shows that the conventional ‘abc’ model is a special case of the proposed generalised model.