Algorithm for incremental compaction of geometrical layouts

In this paper, a new incremental algorithm for layout compaction is proposed. In addition to its linear time performance in terms of the number of rectangles in the layout, we also describe how incremental compaction can form a good feature in the design of a layout editor. The design of such an editor is also described. In the design of the editor, we describe how arrays can be used to implement quadtrees that represent VLSI layouts. Such a representation provides speed of data access and low storage requirements.

Nanoindentation study on germania-doped silica glass preforms: evidence for the compaction-densification model of photosensitivity

Nanoindentation technique was employed to measure the changes in mechanical properties of a glass preform subjected to different levels of UV exposure. The results reveal that short-term exposure leads to an appreciable increase in the Young's modulus (E), suggesting the densification of the glass, confirming the compaction-densification model. However, on prolonged exposure, E decreases, which provides what we believe to be the first direct evidence of dilation in the glass leading into the Type IIA regime. The present results rule out the hypothesis that continued exposure leads to an irreversible compaction and prove that index modulation regimes are intrinsic to the glass matrix.

Importance of local heating in the compaction of thermally sensitive solids

Local heating is an important parameter in compaction of thermally sensitive solids since local hot spots could conceivably raise the temperature of the system by several hundred degrees. To understand the importance of local hot spots, 20 g of ammonium perchlorate (AP) and potassium perchlorate (KP) were pressed together at 1500 kg cm−2 for 5 min. The surface structural examination of the compact revealed a secondary phase at the interfaces between the grains in the compositions ranging from 50% AP-50% KP to 10% AP-90% KP. The observation of the secondary phase only at the interfaces has been attributed to the short life times of temperature pulses present during the compaction. An interesting aspect of the investigation is the formation of a series of solid solutions of AP-KP.

DNA Compaction by a Dendrimer

At physiological pH, a PAMAM dendrimer is positively charged and can effectively bind negatively charged DNA. Currently, there has been great interest in understanding this complexation reaction both for fundamental (as a model for complex biological reactions) as well as for practical (as a gene delivery material and probe for sensing DNA sequence) reasons. Here, we have studied the complexation between double-stranded DNA (dsDNA) and various generations of PAMAM dendrimers (G3-05) through atomistic molecular dynamics simulations in the presence of water and ions. We report the compaction of DNA on a nanosecond time scale. This is remarkable, given the fact that such a short DNA duplex with a length close to 13 nm is otherwise thought to be a rigid rod. Using several nanoseconds long MD simulations, we have observed various binding modes of dsDNA and dendrimers for various generations of PAMAM dendrimers at varying charge ratios, and it confirms some of the binding modes proposed earlier. The binding is driven by the electrostatic interaction, and the larger the dendrimer charge, the stronger the binding affinity. As DNA wraps/binds to the dendrimer, counterions originally condensed onto DNA (Na+) and the dendrimer (Cl-) get released. We calculate the entropy of counterions and show that there is gain in entropy due to counterion release during the complexation. MD simulations demonstrate that, when the charge ratio is greater than 1 (as in the case of the G5 dendrimer), the optimal wrapping of DNA is observed. Calculated binding energies of the complexation follow the trend G5 > 04 > 03, in accordance with the experimental data. For a lower-generation dendrimer, such as G3, and, to some extent, for G4 also, we see considerable deformation in the dendrimer structure due to their flexible nature. We have also calculated the various helicoidal parameters of DNA to study the effect of dendrimer binding on the structure of DNA. The B form of the DNA is well preserved in the complex, as is evident from various helical parameters, justifying the use of the PAMAM dendrimer as a suitable delivery vehicle.

Cement stabilised rammed earth. Part A: compaction characteristics and physical properties of compacted cement stabilised soils

Rammed earth is used for load bearing walls of buildings and there is growing interest in this low carbon building material. This paper is focused on understanding the compaction characteristics and physical properties of compacted cement stabilised soil mixtures and cement stabilised rammed earth (CSRE). This experimental study addresses (a) influence of soil composition, cement content, time lag on compaction characteristics of stabilised soils and CSRE and (b) effect of moulding water content and density on compressive strength and water absorption of compacted cement stabilised soil mixes. Salient conclusions of the study are (a) compaction characteristics of soils are not affected by the addition of cement, (b) there is 50% fall in strength of CSRE for 10 h time lag, (c) compressive strength of compacted cement stabilised soil increases with increase in density irrespective of moulding moisture content and cement content, and (d) compressive strength increases with the increase in moulding water content and compaction of CSRE on the wet side of OMC is beneficial in terms of strength.

Re-examination of compaction characteristics of fine-grained soils

Standard Proctor compaction test data were generated for 3 soils with liquid limit water contents ranging from 48% to 84%. It has been established that by defining a soil by its liquid limit and coarse fraction, the path of compaction for a specific compactive effort can be predicted via a simple density-water content-liquid limit relationship. (Abstract quotes from original text)

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Thermal Response on the Microstructure and Texture of ECAP and Cold-Rolled Pure Magnesium

This paper deals with dynamic recrystallization (DRX), static recrystallization, and grain growth phenomena of pure magnesium after equal channel angular pressing (ECAP) by route A and B-C at 523 K (250 A degrees C) followed by 80 pct cold rolling. The ECAP-deformed and the subsequently rolled samples were annealed at 373 K and 773 K (100 A degrees C and 500 A degrees C). The associated changes in the microstructure and texture were studied using electron back-scattered diffraction. ECAP produced an average grain size of 12 to 18 A mu m with B and C-2 fiber textures. Subsequent rolling led to an average grain size 8 to 10 A mu m with basal texture fiber parallel to ND. There was no noticeable increase in the average grain size on annealing at 373 K (100 A degrees C). However, significant increase in the average grain size occurred at 773 K (500 A degrees C). The occurrence of different DRX mechanisms was detected: discontinuous dynamic recrystallization was attributed to basal slip activity and continuous dynamic recovery and recrystallization to prismatic/pyramidal slip systems. Only continuous static recrystallization could be observed on annealing.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Microstructural characterization of ultrafine-grain interstitial-free steel by X-ray diffraction line profile analysis

This paper highlights the microstructural features of commercially available interstitial free (IF) steel specimens deformed by equal channel angular pressing (ECAP) up to four passes following the route A. The microstructure of the samples was studied by different techniques of X-ray diffraction peak profile analysis as a function of strain (epsilon). It was found that the crystallite size is reduced substantially already at epsilon=2.3 and it does not change significantly during further deformation. At the same time, the dislocation density increases gradually up to epsilon=4.6. The dislocation densities estimated from X-ray diffraction study are found to correlate very well with the experimentally obtained yield strength of the samples.