Buckling, stiffening, and negative dissipation in the dynamics of a biopolymer in an active medium

We present a generic theory for the dynamics of a stiff filament under tension, in an active medium with orientational correlations, such as a microtubule in contractile actin. In sharp contrast to the case of a passive medium, we find the filament can stiffen, and possibly oscillate or buckle, depending on both the contractile or tensile nature of the activity and the filament-medium anchoring interaction. We also demonstrate a strong violation of the fluctuation-dissipation (FD) relation in the effective dynamics of the filament, including a negative FD ratio. Our approach is also of relevance to the dynamics of axons, and our model equations bear a remarkable formal similarity to those in recent work [Martin P, Hudspeth AJ, Juelicher F (2001) Proc Natl Acad Sci USA 98: 14380-14385] on auditory hair cells. Detailed tests of our predictions can be made by using a single filament in actomyosin extracts or bacterial suspensions.

On some geometric invariants associated to the space of flat connections on an open space

A geometric invariant is associated to the parabolic moduli space on a marked surface and is related to the symplectic structure of the moduli space.

A polynomial bound on the number of light cycles in an undirected graph

Let G be an undirected graph with a positive real weight on each edge. It is shown that the number of minimum-weight cycles of G is bounded above by a polynomial in the number of edges of G. A similar bound holds if we wish to count the number of cycles with weight at most a constant multiple of the minimum weight of a cycle of G.

Exploration of deleterious single nucleotide polymorphisms in the components of human P bodies: An in silico approach

P bodies are 100-300 nm sized organelles involved in mRNA silencing and degradation. A total of 60 human proteins have been reported to localize to P bodies. Several human SNPs contribute to complex diseases by altering the structure and function of the proteins. Also, SNPs alter various transcription factors binding, splicing and miRNA regulatory sites. Owing to the essential functions of P bodies in mRNA regulation, we explored computationally the functional significance of SNPs in 7 P body components such as XRN1, DCP2, EDC3, CPEB1, GEMIN5, STAU1 and TRIM71. Computational analyses of non-synonymous SNPs of these components was initiated using well utilized publicly available software programs such as the SIFT, followed by PolyPhen, PANTHER, MutPred, I-Mutant-2.0 and PhosSNP 1.0. Functional significance of noncoding SNPs in the regulatory regions were analysed using FastSNP. Utilizing miRSNP database, we explored the role of SNPs in the context that alters the miRNA binding sites in the above mentioned genes. Our in silico studies have identified various deleterious SNPs and this cataloguing is essential and gives first hand information for further analysis by in vitro and in vivo methods for a better understanding of maintenance, assembly and functional aspects of P bodies in both health and disease. (C) 2013 Elsevier B.V. All rights reserved.

Development of a low-cost portable colorimeter for the estimation of fluoride in drinking water

People in many countries are affected by fluorosis owing to the high levels of fluoride in drinking water. An inexpensive method for estimating the concentration of the fluoride ion in drinking water would be helpful in identifying safe sources of water and also in monitoring the performance of defluoridation techniques. For this purpose, a simple, inexpensive, and portable colorimeter has been developed in the present work. It is used in conjunction with the SPADNS method, which shows a color change in the visible region on addition of water containing fluoride to a reagent solution. Groundwater samples were collected from different parts of the state of Karnataka, India and analysed for fluoride. The results obtained using the colorimeter and the double beam spectrophotometer agreed fairly well. The costs of the colorimeter and of the chemicals required per test were about Rs. 250 (US$ 5) and Rs. 2.5 (US$ 0.05), respectively. In addition, the cost of the chemicals required for constructing the calibration curve was about Rs. 15 (US$ 0.3). (C) 2010 Elsevier B.V. All rights reserved.

Direction of arrival estimation in the presence of distributed noise sources: Cumulant based approach

In the past few years there have been attempts to develop subspace methods for DoA (direction of arrival) estimation using a fourth?order cumulant which is known to de?emphasize Gaussian background noise. To gauge the relative performance of the cumulant MUSIC (MUltiple SIgnal Classification) (c?MUSIC) and the standard MUSIC, based on the covariance function, an extensive numerical study has been carried out, where a narrow?band signal source has been considered and Gaussian noise sources, which produce a spatially correlated background noise, have been distributed. These simulations indicate that, even though the cumulant approach is capable of de?emphasizing the Gaussian noise, both bias and variance of the DoA estimates are higher than those for MUSIC. To achieve comparable results the cumulant approach requires much larger data, three to ten times that for MUSIC, depending upon the number of sources and how close they are. This is attributed to the fact that in the estimation of the cumulant, an average of a product of four random variables is needed to make an evaluation. Therefore, compared to those in the evaluation of the covariance function, there are more cross terms which do not go to zero unless the data length is very large. It is felt that these cross terms contribute to the large bias and variance observed in c?MUSIC. However, the ability to de?emphasize Gaussian noise, white or colored, is of great significance since the standard MUSIC fails when there is colored background noise. Through simulation it is shown that c?MUSIC does yield good results, but only at the cost of more data.

An enzymic approach to the study of sewage and sludges

The purpose of the work described here has been (a) to obtain some evidence on catalase (an oxidative enzyme) and protease, urease and phosphatase (hydrolytic enzymes) in sewage, activated sludge and septic tank sludge, and (b) to use this evidence, as a new approach, to find out the relationship between the main groups of the micro-organisms (bacteria and protozoa) and their relative influence on the purification process. To make a rapid assessment of the enzyme activities in these systems in the course of three weeks, as an experimental measure, rat tissues were added, which might serve as an additional or a ‘shock’ load of organic matter to follow broadly the development of bacteria and protozoa and the changes in the enzyme activities in the different systems. A control system with sewage alone was also run. The results showed that the initial decomposition of the fresh organic matter added to sewage and sludges was almost entirely due to bacterial activity and the later oxidative changes and removal of the suspended solids, including the bacteria, were largely due to the protozoa, such as Epistylis articulata. Analysis of the enzyme activities in the different materials showed, among other things, that the activated sludge, with its mized bacteria, protozoa and other organisms, as a whole, contained about twenty times more protease activity than an equivalent amount of the protozoan E. articulata, and that this protozoan contained five times more catalase activity than the activated sludge. The significance of these observations is discussed.

An approach for studying the mediators of pathogenesis in Mycobacterium tuberculosis

Mycobacterium tuberculosis is an example of an intracellular pathogen that mediates the disease state through complex interactions with the host's immune system. Not only does this organism replicate in the hostile environment prevailing within the infected macrophage, but it has also developed intricate mechanisms to inhibit several defence mechanisms of the host's immune system. It is postulated here that the mediators of these interactions with the host are products of differentially expressed genes in the pathogen, B and T fell responses of the host are hence to be used as tools to identify such gene products from an expression library of the Mycobacterium tuberculosis genome. The various pathways of generating a productive immune response that may be targeted by the pathogen are discussed.

Impact of Energy Expenditure Rate Constraints on the performance of Multihop Wireless Mesh Networks

In this article we study the problem of joint congestion control, routing and MAC layer scheduling in multi-hop wireless mesh network, where the nodes in the network are subjected to maximum energy expenditure rates. We model link contention in the wireless network using the contention graph and we model energy expenditure rate constraint of nodes using the energy expenditure rate matrix. We formulate the problem as an aggregate utility maximization problem and apply duality theory in order to decompose the problem into two sub-problems namely, network layer routing and congestion control problem and MAC layer scheduling problem. The source adjusts its rate based on the cost of the least cost path to the destination where the cost of the path includes not only the prices of the links in it but also the prices associated with the nodes on the path. The MAC layer scheduling of the links is carried out based on the prices of the links. We study the e�ects of energy expenditure rate constraints of the nodes on the optimal throughput of the network.

Physical chemistry of the reduction of calcium oxide with aluminium in vacuum

The physical chemistry of "aluminothermic" reduction of calcium oxide in vacuum is analyzed. Basic thermodynamic data required for the analysis have been generated by a variety of experiments. These include activity measurements in liquid AI-Ca alloys and determination of the Gibbs energies of formation of calcium aluminates. These data have been correlated with phase relations in the Ca-AI-0 system at 1373 K. The various stages of reduction, the end products and the corresponding equilibrium partial pressures of calcium have been established from thermodynamic considerations. In principle, the recovery of calcium can be improved by reducing the pressure in the reactor. However,, the cost of a high vacuum system and the enhanced time for reduction needed to achieve higher yields makes such a practice uneconomic. Aluminum contamination of calcium also increases at low pressures. The best compromise is to carry the reduction up to the stage where 3CaO-Al,O, is formed as the product. This corresponds to an equilibrium calcium partial pressure of 31.3 Pa at 1373 K and 91.6 Pa at 1460 K. Calcium can be extracted at this pressure using mechanical pumps in approximately 8 to 15 hr, depending on the size and the fill ratio of the retort and porosity of the charge briquettes.

Colloidal calcium nanoparticles: digestive ripening in the presence of a capping agent and coalescence of particles under an electron beam

The nanochemistry of calcium remains unexplored, which is largely due to the inaccessibility of calcium nanoparticles in an easy to handle form by conventional methods of synthesis as well as its highly reactive and pyrophoric nature. The synthesis of colloidal Ca nanoparticles by the solvated metal atom dispersion (SMAD) method is described. The as-prepared Ca-THF nanoparticles, which are polydisperse, undergo digestive ripening in the presence of a capping agent, hexadecyl amine (HDA) to afford highly monodisperse colloids consisting of 2-3 nm sized Ca-HDA nanoparticles. These are quite stable towards precipitation for long periods of time, thereby providing access to the study of the nanochemistry of Ca. Particles synthesized in this manner were characterized by UV-visible spectroscopy, high resolution electron microscopy, and powder X-ray diffraction methods. Under an electron beam, two adjacent Ca nanoparticles undergo coalescence to form a larger particle.