A general procedure for modified crack closure integral in 3D problems with cracks

In linear elastic fracture mechanics (LEFM), Irwin's crack closure integral (CCI) is one of the signficant concepts for the estimation of strain energy release rates (SERR) G, in individual as well as mixed-mode configurations. For effective utilization of this concept in conjunction with the finite element method (FEM), Rybicki and Kanninen [Engng Fracture Mech. 9, 931 938 (1977)] have proposed simple and direct estimations of the CCI in terms of nodal forces and displacements in the elements forming the crack tip from a single finite element analysis instead of the conventional two configuration analyses. These modified CCI (MCCI) expressions are basically element dependent. A systematic derivation of these expressions using element stress and displacement distributions is required. In the present work, a general procedure is given for the derivation of MCCI expressions in 3D problems with cracks. Further, a concept of sub-area integration is proposed which facilitates evaluation of SERR at a large number of points along the crack front without refining the finite element mesh. Numerical data are presented for two standard problems, a thick centre-cracked tension specimen and a semi-elliptical surface crack in a thick slab. Estimates for the stress intensity factor based on MCCI expressions corresponding to eight-noded brick elements are obtained and compared with available results in the literature.

A Procedure for the 3D Reconstruction of Biological Organs from 2D Image Sequences

In this work, a procedure is presented for the reconstruction of biological organs from image sequences obtained through CT-scan. Although commercial software, which can accomplish this task, are readily available, the procedure presented here needs only free software. The procedure has been applied to reconstruct a liver from the scan data available in literature. 3D biological organs obtained this way can be used for the finite element analysis of biological organs and this has been demonstrated by carrying out an FE analysis on the reconstructed liver.

Preferential condensation of SAR-DNA by histone H1 and its SPKK containing octapeptide repeat motif

Linker histone H1 binds preferentially the scaffold associated region (SAR) DNA elements that contain characteristic oligo dA . dT tracts. In the present study, we have compared the condensation brought about by histone H1 of a SAR DNA fragment in the histone spacer region of Drosophila melanogaster with that of a random DNA (pBR322 EcoRI-SalI) fragment by circular dichroism spectroscopy. The condensation of the SAR DNA fragment by histone H1 is 3-4-fold higher than that of the random DNA fragment. A 16-mer peptide, ATPKKSTKKTPKKAKK, the sequence that is present in the C-terminus of histone H1d, which has recently been shown to possess DIVA and chromatin condensing properties, also condenses the SAR DNA fragment preferentially in a highly cooperative manner. We have proposed a model for the dynamics of chromatin structure involving histone H1-SAR DNA interaction through SPKK containing peptide motifs and its competition by AT-hook peptides present in the nonhistone chromosomal proteins like HMG-I and HMG-Y.

Beckmann rearrangement of ketoximes on solid metaboric acid: a simple and effective procedure

When ketoximes admixed with solid metaboric acid (formed from boric acid at 100degreesC/0.1 Torr) are heated (similar to 140degreesC/7-42 h), the corresponding amides or lactams are produced in excellent yields (62-92%) via the Beckmann reaction. Aromatic aldoximes undergo both dehydration to the nitrile as well as (non-stereospecific) rearrangement under the above conditions. The absence of solvent, and the mildness and low toxicity of boric acid, characterise the present procedure. CO. 2002 Elsevier Science Ltd. All rights reserved.

Affinity-Chromatographic Procedure For The Purification Of The Enzyme From Mung-Bean (Phaseolus, Aureus) Seeds And Conformational-Changes On Its Interaction With Ortho-Phosphate

Flavokinase was purified, for the first time from a plant source [mung bean (Phaseolus aureus)] by affinity chromatography in the presence of orthophosphate and by using C-8 ATP-agarose (ATP linked through the C-8 position to beaded agarose), Cibacron Blue and riboflavin--Sepharoses. An altered substrates-saturation pattern was observed in the presence of K2HPO4. The conformational changes of the enzyme in the presence of K2HPO4 were monitored by fluorescence spectroscopy. These results highlight the regulatory nature of this enzyme.

A unification-based decision procedure for cryptographic protocol analysis

We present a sound and complete decision procedure for the bounded process cryptographic protocol insecurity problem, based on the notion of normal proofs [2] and classical unification. We also show a result about the existence of attacks with “high” normal cuts. Our proof of correctness provides an alternate proof and new insights into the fundamental result of Rusinowitch and Turuani [9] for the same setting.

A computational procedure to generate difference equations from differential equations

In this paper we have developed methods to compute maps from differential equations. We take two examples. First is the case of the harmonic oscillator and the second is the case of Duffing's equation. First we convert these equations to a canonical form. This is slightly nontrivial for the Duffing's equation. Then we show a method to extend these differential equations. In the second case, symbolic algebra needs to be used. Once the extensions are accomplished, various maps are generated. The Poincare sections are seen as a special case of such generated maps. Other applications are also discussed.

Stabilization and Structural Alteration of the G-Quadruplex DNA Made from the Human Telomeric Repeat Mediated by Troger's Base Based Novel Benzimidazole Derivatives

Ligand-induced stabilization of the G-quadruplex DNA structure derived from the single-stranded 3'-overhang of the telomeric DNA is an attractive strategy for the inhibition of the telomerase activity. The agents that can induce/stabilize a DNA sequence into a G-quadruplex structure are therefore potential anticancer drugs. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2) based on Troger's base skeleton with the G-quadruplex DNA (G4DNA). These Troger's base molecules stabilize the G4DNA derived from a human telomeric sequence. Evidence of their strong interaction with the G4DNA has been obtained from CD spectroscopy, thermal denaturation, and UV-vis titration studies. These ligands also possess significantly higher affinity toward the G4DNA over the duplex DNA. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Furthermore, the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. Computational studies suggested that the adaptive scaffold might allow these ligands to occupy not only the G-quartet planes but also the grooves of the G4DNA.

Novel procedure for the estimation of swelling pressures of compacted bentonites based on diffuse double layer theory

Bentonite clays are proven to be attractive as buffer and backfill material in high-level nuclear waste repositories around the world. A quick estimation of swelling pressures of the compacted bentonites for different clay-water-electrolyte interactions is essential in the design of buffer and backfill materials. The theoretical studies on the swelling behavior of bentonites are based on diffuse double layer (DDL) theory. To establish theoretical relationship between void ratio and swelling pressure (e versus P), evaluation of elliptic integral and inverse analysis are unavoidable. In this paper, a novel procedure is presented to establish theoretical relationship of e versus P based on the Gouy-Chapman method. The proposed procedure establishes a unique relationship between electric potentials of interacting and non-interacting diffuse clay-water-electrolyte systems. A procedure is, thus, proposed to deduce the relation between swelling pressures and void ratio from the established relation between electric potentials. This approach is simple and alleviates the need for elliptic integral evaluation and also the inverse analysis. Further, application of the proposed approach to estimate swelling pressures of four compacted bentonites, for example, MX 80, Febex, Montigel and Kunigel V1, at different dry densities, shows that the method is very simple and predicts solutions with very good accuracy. Moreover, the proposed procedure provides continuous distributions of e versus P and thus it is computationally efficient when compared with the existing techniques.

RepEx: Repeat extractor for biological sequences

Genomic sequences are far from being random but are made up of systematically ordered and information rich patterns. These repeated sequence patterns have been vastly utilized for their fundamental importance in understanding the genome function and organization. To this end, a comprehensive toolkit, RepEx, has been developed which extracts repeat (inverted, everted and mirror) patterns from the given genome sequence(s) without any constraints. The toolkit can also be used to fetch the inverted repeats present in the protein sequence (s). Further, it is capable of extracting exact and degenerate repeats with a user defined spacer intervals. It is remarkably more precise and sensitive when compared to the existing tools. An example with comprehensive case studies and a performance evaluation of the proposed toolkit has been presented to authenticate its efficiency and accuracy. (C) 2013 Elsevier Inc. All rights reserved.

A PRACTICAL PROCEDURE TO ESTIMATE THE BEARING CAPACITY OF FOOTINGS ON SAND-APPLICATION TO 87 CASE STUDIES

Following the recent work of the authors in development and numerical verification of a new kinematic approach of the limit analysis for surface footings on non-associative materials, a practical procedure is proposed to utilize the theory. It is known that both the peak friction angle and dilation angle depend on the sand density as well as the stress level, which was not the concern of the former work. In the current work, a practical procedure is established to provide a better estimate of the bearing capacity of surface footings on sand which is often non-associative. This practical procedure is based on the results obtained theoretically and requires the density index and the critical state friction angle of the sand. The proposed practical procedure is a simple iterative computational procedure which relates the density index of the sand, stress level, dilation angle, peak friction angle and eventually the bearing capacity. The procedure is described and verified among available footing load test data.

Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species-Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast.