Conformation of substituted polyacetylenes in solution : relationship between electronic properties and local order

A study of the chain conformation in solutions of polyphenylacetylene and poly(2-octyne) has been performed. The two polymers differ in many ways : polyphenylacetylene gives a red solution while poly(2-octyne) is transparent and, a marked difference on the chain rigidity is observed : the statistical length are 45 Å and 135 Å respectively. From the study of these two systems, one deduces that curvature fluctuations play a minor role on the π electrons localization, and that the torsion between monomer units is the pertinent parameter to understand the chain conformation and the π electrons localization.

Structure-potential relationship and nature of disorder in liquids and glassy solids

A method based on the minimal-spanning tree is extended to a collection of points in three dimensions. Two parameters, the average edge length and its standard deviation characterize the disorder. The structural phase diagram for a monatomic system of particles and the characteristic values for the uniform random distribution of points have been obtained. The method is applied to hard spheres and Lennard-Jones systems. These systems occupy distinct regions in the structural phase diagram. The structure of the Lennard-Jones system approaches that of the defective close-packed arrangements at low temperatures whereas in the liquid regime, it deviates from the close-packed configuration.

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

No-reference image quality assessment using modified extreme learning machine classifier

In this paper, we present a machine learning approach to measure the visual quality of JPEG-coded images. The features for predicting the perceived image quality are extracted by considering key human visual sensitivity (HVS) factors such as edge amplitude, edge length, background activity and background luminance. Image quality assessment involves estimating the functional relationship between HVS features and subjective test scores. The quality of the compressed images are obtained without referring to their original images ('No Reference' metric). Here, the problem of quality estimation is transformed to a classification problem and solved using extreme learning machine (ELM) algorithm. In ELM, the input weights and the bias values are randomly chosen and the output weights are analytically calculated. The generalization performance of the ELM algorithm for classification problems with imbalance in the number of samples per quality class depends critically on the input weights and the bias values. Hence, we propose two schemes, namely the k-fold selection scheme (KS-ELM) and the real-coded genetic algorithm (RCGA-ELM) to select the input weights and the bias values such that the generalization performance of the classifier is a maximum. Results indicate that the proposed schemes significantly improve the performance of ELM classifier under imbalance condition for image quality assessment. The experimental results prove that the estimated visual quality of the proposed RCGA-ELM emulates the mean opinion score very well. The experimental results are compared with the existing JPEG no-reference image quality metric and full-reference structural similarity image quality metric.

Synthesis of novel poly[(2,5-dimethoxy-p-phenylene)vinylene] precursors having two eliminatable groups: An approach for the control of conjugation length

Poly[(2,5-dimethoxy-p-phenylene)vinylene] (DMPPV) of varying conjugation length was synthesized by selective elimination of organic soluble precursor polymers that contained two eliminatable groups, namely, methoxy and acetate groups. These precursor copolymers were in turn synthesized by competitive nucleophilic substitution of the sulfonium polyelectrolyte precursor (generated by the standard Wessling route) using methanol and sodium acetate in acetic acid. The composition of the precursor copolymer, in terms of the relative amounts of methoxy and acetate groups, was controlled by varying the composition of the reaction mixture during nucleophilic substitution. Thermal elimination of these precursor copolymers at 250 degrees C, yielded partially conjugated polymers, whose color varied from light yellow to deep red. FT-IR studies confirmed that, while essentially all the acetate groups were eliminated, the methoxy groups were intact and caused the interruption in conjugation. Preliminary photoluminescence studies of the partially eliminated DMPPV samples showed a gradual shift in the emission maximum from 498 to 598 nm with increasing conjugation lengths, suggesting that the color of LED devices fabricated from such polymers can, in principle, be fine-tuned.

Telomere structure, replication and length maintenance

Telomeres are the termini of linear eukaryotic chromosomes consisting of tandem repeats of DNA and proteins that bind to these repeat sequences. Telomeres ensure the complete replication of chromosome ends, impart protection to ends from nucleolytic degradation, end-to-end fusion, and guide the localization of chromosomes within the nucleus. In addition, a combination of genetic, biochemical, and molecular biological approaches have implicated key roles for telomeres in diverse cellular processes such as regulation of gene expression, cell division, cell senescence, and cancer. This review focuses on recent advances in our understanding of the organization of telomeres, telomere replication, proteins that bind telomeric DNA, and the establishment of telomere length equilibrium.

On the relationship between finger width, velocity, and fluxes in thermohaline convection

Double-diffusive finger convection occurs in many natural processes.The theories for double-diffusive phenomena that exist at present consider systems with linear stratification in temperature and salinity. The double-diffusive systems with step change in salinity and temperature are, however, not amenable to simple stability analysis. Hence factors that control the width of the finger, velocity, and fluxes in systems that have step change in temperature and salinity have not been understood so far. In this paper we provide new physical insight regarding factors that influence finger convection in two-layer double-diffusive system through two-dimensional numerical simulations. Simulations have been carried out for density stability ratios (R-rho) from 1.5 to 10. For each density stability ratio, the thermal Rayleigh number (Ra-T) has been systematically varied from 7x10(3) to 7x10(8). Results from these simulations show how finger width, velocity, and flux ratios in finger convection are interrelated and the influence of governing parameters such as density stability ratio and the thermal Rayleigh number. The width of the incipient fingers at the time of onset of instability has been shown to vary as Ra-T-1/3. Velocity in the finger varies as Ra(T)1/3/R-rho. Results from simulation agree with the scale analysis presented in the paper. Our results demonstrate that wide fingers have lower velocities and flux ratios compared to those in narrow fingers. This result contradicts present notions about the relation between finger width and flux ratio. A counterflow heat-exchanger analogy is used in understanding the dependence of flux ratio on finger width and velocity.

A probabilistic constrained nonlinear optimization framework to optimize RED parameters

The random early detection (RED) technique has seen a lot of research over the years. However, the functional relationship between RED performance and its parameters viz,, queue weight (omega(q)), marking probability (max(p)), minimum threshold (min(th)) and maximum threshold (max(th)) is not analytically availa ble. In this paper, we formulate a probabilistic constrained optimization problem by assuming a nonlinear relationship between the RED average queue length and its parameters. This problem involves all the RED parameters as the variables of the optimization problem. We use the barrier and the penalty function approaches for its Solution. However (as above), the exact functional relationship between the barrier and penalty objective functions and the optimization variable is not known, but noisy samples of these are available for different parameter values. Thus, for obtaining the gradient and Hessian of the objective, we use certain recently developed simultaneous perturbation stochastic approximation (SPSA) based estimates of these. We propose two four-timescale stochastic approximation algorithms based oil certain modified second-order SPSA updates for finding the optimum RED parameters. We present the results of detailed simulation experiments conducted over different network topologies and network/traffic conditions/settings, comparing the performance of Our algorithms with variants of RED and a few other well known adaptive queue management (AQM) techniques discussed in the literature.

Consolidation Behavior of Soils

Based on Terzaghi's consolidation theory, percent of consolidation, U, versus the time factor, T, relationship for constant/linear excess pore water pressure distribution, it is possible to generate theoretical log10(H2/t) versus U curves where H is the length of the drainage path of a consolidating layer, and t is the time for different known values of the coefficient of consolidation, cν. A method has been developed wherein both the theoretical and experimental behavior of soils during consolidation can be simultaneously compared and studied on the same plot. The experimental log10(H2/t) versus U curves have been compared with the theoretical curves. The deviations of the experimental behavior from the theory are explained in terms of initial compression and secondary compression. Analysis of results indicates that the secondary compression essentially starts from about 60% consolidation. A simple procedure is presented for calculating the value of cv from the δ-t data using log10(H2/t) versus U plot.

Growing length and time scales in glass-forming liquids

The glass transition, whereby liquids transform into amorphous solids at low temperatures, is a subject of intense research despite decades of investigation. Explaining the enormous increase in relaxation times of a liquid upon supercooling is essential for understanding the glass transition. Although many theories, such as the Adam-Gibbs theory, have sought to relate growing relaxation times to length scales associated with spatial correlations in liquid structure or motion of molecules, the role of length scales in glassy dynamics is not well established. Recent studies of spatially correlated rearrangements of molecules leading to structural relaxation, termed ``spatially heterogeneous dynamics,'' provide fresh impetus in this direction. A powerful approach to extract length scales in critical phenomena is finite-size scaling, wherein a system is studied for sizes traversing the length scales of interest. We perform finite-size scaling for a realistic glass-former, using computer simulations, to evaluate the length scale associated with spatially heterogeneous dynamics, which grows as temperature decreases. However, relaxation times that also grow with decreasing temperature do not exhibit standard finite-size scaling with this length. We show that relaxation times are instead determined, for all studied system sizes and temperatures, by configurational entropy, in accordance with the Adam-Gibbs relation, but in disagreement with theoretical expectations based on spin-glass models that configurational entropy is not relevant at temperatures substantially above the critical temperature of mode-coupling theory. Our results provide new insights into the dynamics of glass-forming liquids and pose serious challenges to existing theoretical descriptions.

Impressive Gelation in Organic Solvents by Synthetic, Low Molecular Mass, Self-Organizing Urethane Amides of L-Phenylalanine

Synthetic routes leading to 12 L-phenylalanine based mono- and bipolar derivatives (1-12) and an in-depth study of their structure-property relationship with respect to gelation have been presented. These include monopolar systems such as N-[(benzyloxy)carbonyl]-L-phenylalanine-N-alkylamides and the corresponding bipolar derivatives with flexible and rigid spacers such as with 1,12-diaminododecane and 4,4'-diaminodiphenylmethane, respectively. The two ends of the latter have been functionalized with N-[(benzyloxy)carbonyl]-L-phenylalanine units via amide connection. Another bipolar molecule was synthesized in which the middle portion of the hydrocarbon segment contained polymerizable diacetylene unit. To ascertain the role of the presence of urethane linkages in the gelator molecule protected L-phenylalanine derivatives were also synthesized in which the (benzyloxy)carbonyl group has been replaced with (tert-butyloxy)carbonyl, acetyl, and benzoyl groups, respectively. Upon completion of the synthesis and adequate characterization of the newly described molecules, we examined the aggregation and gelation properties of each of them in a number of solvents and their mixtures. Optical microscopy and electron microscopy further characterized the systems that formed gels. Few representative systems, which showed excellent gelation behavior was, further examined by FT-IR, calorimetric, and powder X-ray diffraction studies. To explain the possible reasons for gelation, the results of molecular modeling and energy-minimization studies were also included. Taken together these results demonstrate the importance of the presence of (benzyloxy)carbonyl unit, urethane and secondary amide linkages, chiral purities of the headgroup and the length of the alkyl chain of the hydrophobic segment as critical determinants toward effective gelation.

Approximate potential-distance relationship for clays

The conventional procedure of determining the surface potential of clay platelet and the variation of potential with distance is lengthy and time consuming. Simplified graphical procedures using Gouy theory have been developed and presented. The new procedures are simple, accurate and very much less time consuming.

On vibration of eccentrically stiffened plates with varying stiffener length

Results of a study of the variation of natural frequencies with respect to the length of the stiffener of a square panel clamped all along its boundary and stiffened in the middle by a concentric stiffener were recently reported [ 11. Significant increases in certain frequencies, namely those with modes symmetric about both the medians of the plate, were observed when small gaps were not left between the plate boundary and the stiffener end. As an extension to that work, results of a study of the effect of the eccentricity of the stiffener on the frequency variation with the length of the stiffener are reported here.

Rationale of Length Scale-Down Model Span Testing of Transmission Lines

Length scale-down (LS) model tests have been traditionally employed for laboratory studies on aeolian vibration of transmission line conductors. The span adopted is normally 30 m and is recommended by the relevant Indian, as well as other, standards. The traditionally adopted length of the LS model is reexamined herein to establish the rationale behind the choice. Based on the theoretical studies discussed, certain guidelines for the choice of model span of conductor are emphasized. In addition, the adequacy of the LS span as a tool for predicting the performance of the full span is reestablished.

Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule

We demonstrate a chain length dependent crossover in the structural properties of linear hydrocarbon (n-alkane) chains using detailed atomistic simulations in explicit water. We identify a number of exotic structures of the polymer chain through energy minimization of representative snapshots collected from molecular dynamics trajectory. While the collapsed state is ring-like (circular) for small chains (CnH2n+2; n <= 20) and spherical for very long ones (n = 100), we find the emergence of ordered helical structures at intermediate lengths (n similar to 40). We find different types of disordered helices and toroid-like structures at n = 60. We also report a sharp transition in the stability of the collapsed state as a function of the chain length through relevant free energy calculations. While the collapsed state is only marginally metastable for C20H42, a clear bistable free energy surface emerges only when the chain is about 30 monomers long. For n = 30, the polymer exhibits an intermittent oscillation between the collapsed and the coil structures, characteristic of two stable states separated by a small barrier.