Structural alteration from non-B to B-form could reflect DNase I hypersensitivity

Preferential cleavage of active genes by DNase I has been correlated with a structurally altered conformation of DNA at the hypersensitive site in chromatin. To have a better understanding of the structural requirements for gene activation as probed by DNase I action, digestability by DNase I of synthetic polynucleotides having the ability to adopt B and non-B conformation (like Z-form) was studied which indicated a marked higher digestability of the B-form of DNA. Left handed Z form present within a natural sequence in supercoiled plasmid also showed marked resistance towards DNase I digestion. We show that alternating purine-pyrimidine sequences adopting Z-conformation exhibit DNAse I foot printing even in a protein free system. The logical deductions from the results indicate that 1) altered structure like Z-DNA is not a favourable substrate for DNase I, 2) both the ends of the alternating purine-pyrimidine insert showed hypersensitivity, 3) B-form with a minor groove of 12-13 A is a more favourable substrate for DNase I than an altered structure, 4) any structure of DNA deviating largely from B form with a capacity to flip over to the B-form are potential targets for the DNase I enzymic probes in naked DNA.

Phase space methods and the Hamilton-Jacobi form of dynamics

A general analysis of the Hamilton-Jacobi form of dynamics motivated by phase space methods and classical transformation theory is presented. The connection between constants of motion, symmetries, and the Hamilton-Jacobi equation is described.

Theory of unitarity bounds and low-energy form factors

We present a general formalism for deriving bounds on the shape parameters of the weak and electromagnetic form factors using as input correlators calculated from perturbative QCD, and exploiting analyticity and unitarily. The values resulting from the symmetries of QCD at low energies or from lattice calculations at special points inside the analyticity domain can be included in an exact way. We write down the general solution of the corresponding Meiman problem for an arbitrary number of interior constraints and the integral equations that allow one to include the phase of the form factor along a part of the unitarity cut. A formalism that includes the phase and some information on the modulus along a part of the cut is also given. For illustration we present constraints on the slope and curvature of the K-l3 scalar form factor and discuss our findings in some detail. The techniques are useful for checking the consistency of various inputs and for controlling the parameterizations of the form factors entering precision predictions in flavor physics.

Application of novel method for surface-ray tracing over hyperboloidal scatterers

A novel geodesic constant method has been developed for the hitherto unsolved problem of surface-ray tracing over a class of surface, namely the general hyperboloid of revolution (GHOR). All the ray-geometric parameters are obtained analytically in a one-parameter form. The ray parameters derived here for the first time can be readily used in the UTD formulation for computing the mutual coupling between the antennas located on the GHOR.

Large low-frequency resistance noise in chemical vapor deposited graphene

We report a detailed investigation of resistance noise in single layer graphene films on Si/SiO2 substrates obtained by chemical vapor deposition (CVD) on copper foils. We find that noise in these systems to be rather large, and when expressed in the form of phenomenological Hooge equation, it corresponds to Hooge parameter as large as 0.1-0.5. We also find the variation in the noise magnitude with the gate voltage (or carrier density) and temperature to be surprisingly weak, which is also unlike the behavior of noise in other forms of graphene, in particular those from exfoliation. (C) 2010 American Institute of Physics. doi:10.1063/1.3493655]

Isolation and characterization of a novel multibridged tetradentate dianionic form of pyridoxic acid. Crystal structure of tetranuclear [Cu4(PAA)2(Bipyam)4(H2O)2Cl2](NO3)2·CH3OH·10H2O

The X-ray analysis of the tetranuclear copper(II) complex formed from pyridoxic acid and 2,2′-dipyridylamine reveals a novel metal binding mode of pyridoxic acid as a multibridged tetradentate dianion. Here the pyridoxic acid moiety uses all possible sites except the pyridine nitrogen for metal coordination.

Interior Medial Axis Transform computation of 3D objects bound by free-form surfaces

This paper presents an algorithm for generating the Interior Medial Axis Transform (iMAT) of 3D objects with free-form boundaries. The algorithm proposed uses the exact representation of the part and generates an approximate rational spline description of the iMAT. The algorithm generates the iMAT by a tracing technique that marches along the object's boundary. The level of approximation is controlled by the choice of the step size in the tracing procedure. Criteria based on distance and local curvature of boundary entities are used to identify the junction points and the search for these junction points is done in an efficient way. The algorithm works for multiply-connected objects as well. Results of the implementation are provided. (C) 2010 Elsevier Ltd. All rights reserved.

Development of a structured program for conversion to prenex normal form

The method of structured programming or program development using a top-down, stepwise refinement technique provides a systematic approach for the development of programs of considerable complexity. The aim of this paper is to present the philosophy of structured programming through a case study of a nonnumeric programming task. The problem of converting a well-formed formula in first-order logic into prenex normal form is considered. The program has been coded in the programming language PASCAL and implemented on a DEC-10 system. The program has about 500 lines of code and comprises 11 procedures.

Improving the phenomenology of Kl3 form factors with analyticity and unitarity

The shape of the vector and scalar K-l3 form factors is investigated by exploiting analyticity and unitarity in a model-independent formalism. The method uses as input dispersion relations for certain correlators computed in perturbative QCD in the deep Euclidean region, soft-meson theorems, and experimental information on the phase and modulus of the form factors along the elastic part of the unitarity cut. We derive constraints on the coefficients of the parameterizations valid in the semileptonic range and on the truncation error. The method also predicts low-energy domains in the complex t plane where zeros of the form factors are excluded. The results are useful for K-l3 data analyses and provide theoretical underpinning for recent phenomenological dispersive representations for the form factors.

Critical resistivity in impurity doped binary liquid mixtures

The electrical resistance of the critical binary liquid system C6H12+(CH3CO)2O is measured both in the pure form and when the system is doped with small amounts (≈ 100 ppm) of H2O impurities. Near Tc, the resistance varies as dR/dT = A1+A2 (T-Tc)-b with b ≈ 0.35. Neither the critical exponent b nor the amplitude ratio A1/A2 are affected by the impurities. A sign reversal of dR/dT is noticed at high temperatures T much greater-than Tc.

A glossary of DNA structures from A to Z

The right-handed double-helical Watson-Crick model for B-form DNA is the most commonly known DNA structure. In addition to this classic structure, several other forms of DNA have been observed and it is clear that the DNA molecule can assume different structures depending on the base sequence and environment. The various forms of DNA have been identified as A, B, C etc. In fact, a detailed inspection of the literature reveals that only the letters F, Q, U, V and Y are now available to describe any new DNA structure that may appear in the future. It is also apparent that it may be more relevant to talk about the A, B or C type dinucleotide steps, since several recent structures show mixtures of various different geometries and a careful analysis is essential before identifying it as a 'new structure'. This review provides a glossary of currently identified DNA structures and is quite timely as it outlines the present understanding of DNA structure exactly 50 years after the original discovery of DNA structure by Watson and Crick

Probing of unusual DNA structures in topologically constrained form V DNA: use of restriction enzymes as structural probe

The ability of DNA sequences to adopt unusual structures under the superhelical torsional stress has been studied. Sequences that are forced to adopt unusual conformation in topologically constrained pBR322 form V DNA (Lk=0) were mapped using restriction enzymes as probes. Restriction enzymes such as BamHI, Pstl, Aval and HindIII could not cleave their recognition sequences. The removal of topological constraint relieved this inhibition. The influence of neighbouring sequences on the ability of a given sequence to adopt unusual DNA structure, presumably left handed Z conformation, was studied through single hit analysis. Using multiple cut restriction enzymes such as Narl and Fspl, it could be shown that under identical topological strain, the extent of structural alteration is greatly influenced by the neighbouring sequences. In the light of the variety of sequences and locations that could be mapped to adopt non-6 conformation in pBR322 form V DNA, restriction enzymes appear as potential structural probes for natural DNA sequences.

Quinoxaline: Z `=1 form

A new Z' = 1 crystal structure of quinoxaline (or 1,4-diazanaphthalene), C8H6N2, with one-fifth the volume of the earlier known Z' = 5 structure was obtained by means of an in situ cryocrystallization technique.

A note on resolving infeasibility in linear programs by constraint relaxation

We study the problem of finding a set of constraints of minimum cardinality which when relaxed in an infeasible linear program, make it feasible. We show the problem is NP-hard even when the constraint matrix is totally unimodular and prove polynomial-time solvability when the constraint matrix and the right-hand-side together form a totally unimodular matrix.