An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

Background: A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure. Results: In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks. Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique `template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.

Influence of stack geometry and resonator length on the performance of thermoacoustic engine

Thermoacoustic engines convert heat energy into high amplitude sound waves, which is used to drive thermoacoustic refrigerator or pulse tube cryocoolers by replacing the mechanical pistons such as compressors. The increasing interest in thermoacoustic technology is of its potentiality of no exotic materials, low cost and high reliability compared to vapor compression refrigeration systems. The experimental setup has been built based on the linear thermoacoustic model and some simple design parameters. The engines produce acoustic energy at the temperature difference of 325-450 K imposed along the stack of the system. This work illustrates the influence of stack parameters such as plate thickness (PT) and plate spacing (PS) with resonator length on the performance of thermoacoustic engine, which are measured in terms of onset temperature difference, resonance frequency and pressure amplitude using air as a working fluid. The results obtained from the experiments are in good agreement with the theoretical results from DeltaEc. (C) 2012 Elsevier Ltd. All rights reserved.

Co-evolution of content popularity and delivery in mobile P2P networks

Mobile P2P technology provides a scalable approach for content delivery to a large number of users on their mobile devices. In this work, we study the dissemination of a single item of content (e. g., an item of news, a song or a video clip) among a population of mobile nodes. Each node in the population is either a destination (interested in the content) or a potential relay (not yet interested in the content). There is an interest evolution process by which nodes not yet interested in the content (i.e., relays) can become interested (i.e., become destinations) on learning about the popularity of the content (i.e., the number of already interested nodes). In our work, the interest in the content evolves under the linear threshold model. The content is copied between nodes when they make random contact. For this we employ a controlled epidemic spread model. We model the joint evolution of the copying process and the interest evolution process, and derive joint fluid limit ordinary differential equations. We then study the selection of parameters under the content provider's control, for the optimization of various objective functions that aim at maximizing content popularity and efficient content delivery.

Experimental and theoretical investigation of thermoacoustic prime mover

The thermoacoustic prime mover is part of an interesting class of prime movers that can be used to generate clean energy and to drive cryogenic refrigeration systems. A thermoacoustic prime mover has been built based on the linear thermoacoustic model, which consumes thermal energy and produces acoustic energy. The objective of this article is to design a thermoacoustic prime mover that can be used as a drive for a thermoacoustic refrigerator. It is found that stack plate length and its distance from the closed end have a significant effect on the thermal efficiency of the prime mover. For different stack center positions, there is an optimum length of stack plate that has a significant effect on the performance of the thermoacoustic prime mover in terms of temperature gradient, frequency, and pressure amplitude. In this study, the experiments have been done on the thermoacoustic prime mover by varying stack position and its length with constant blockage ratio and resonator length. The results obtained from the experiments have been compared to the theoretical results acquired from DeltaEc Software.

The effect of base roughness on the development of a dense granular flow down an inclined plane

The development of the flow of a granular material down an inclined plane starting from rest is studied as a function of the base roughness. In the simulations, the particles are rough frictional spheres interacting via the Hertz contact law. The rough base is made of a random configuration of fixed spheres with diameter different from the flowing particles, and the base roughness is decreased by decreasing the diameter of the base particles. The transition from an ordered to a disordered flowing state at a critical value of the base particle diameter, first reported by Kumaran and Maheshwari Phys. Fluids 24, 053302 (2012)] for particles with the linear contact model, is observed for the Hertzian contact model as well. The flow development for the ordered and disordered flows is very different. During the development of the disordered flow for the rougher base, there is shearing throughout the height. During the development of the ordered flow for the smoother base, there is a shear layer at the bottom and a plug region with no internal shearing above. In the shear layer, the particles are layered and hexagonally ordered in the plane parallel to the base, and the velocity profile is well approximated by Bagnold law. The flow develops in two phases. In the first phase, the thickness of the shear layer and the maximum velocity increase linearly in time till the shear front reaches the top. In the second phase, after the shear layer encompasses the entire flow, there is a much slower increase in the maximum velocity until the steady state is reached. (C) 2013 AIP Publishing LLC.

Assimilation of endmember variability in spectral for urban land cover extraction mixture analysis

Variable Endmember Constrained Least Square (VECLS) technique is proposed to account endmember variability in the linear mixture model by incorporating the variance for each class, the signals of which varies from pixel to pixel due to change in urban land cover (LC) structures. VECLS is first tested with a computer simulated three class endmember considering four bands having small, medium and large variability with three different spatial resolutions. The technique is next validated with real datasets of IKONOS, Landsat ETM+ and MODIS. The results show that correlation between actual and estimated proportion is higher by an average of 0.25 for the artificial datasets compared to a situation where variability is not considered. With IKONOS, Landsat ETM+ and MODIS data, the average correlation increased by 0.15 for 2 and 3 classes and by 0.19 for 4 classes, when compared to single endmember per class. (C) 2013 COSPAR. Published by Elsevier Ltd. All rights reserved.

Study on ride comfort assessment of multiple occupants using lumped parameter analysis

Growing consumer expectations continue to fuel further advancements in vehicle ride comfort analysis including development of a comprehensive tool capable of aiding the understanding of ride comfort. To date, most of the work on biodynamic responses of human body in the context of ride comfort mainly concentrates on driver or a designated occupant and therefore leaves the scope for further work on ride comfort analysis covering a larger number of occupants with detailed modeling of their body segments. In the present study, governing equations of a 13-DOF (degrees-of-freedom) lumped parameter model (LPM) of a full car with seats (7-DOF without seats) and a 7-DOF occupant model, a linear version of an earlier non-linear occupant model, are presented. One or more occupant models can be coupled with the vehicle model resulting into a maximum of 48-DOF LPM for a car with five occupants. These multi-occupant models can be formulated in a modular manner and solved efficiently using MATLAB/SIMULINK for a given transient road input. The vehicle model and the occupant model are independently verified by favorably comparing computed dynamic responses with published data. A number of cases with different dispositions of occupants in a small car are analyzed using the current modular approach thereby underscoring its potential for efficient ride quality assessment and design of suspension systems.

An enthalpy method for modeling eutectic solidification

This paper presents a new micro-scale model for solidification of eutectic alloys. The model is based on the enthalpy method and simulates the growth of adjacent alpha and beta phases from a melt of eutectic composition in a two-dimensional Eulerian framework. The evolution of the two phases is obtained from the solution of volume averaged energy and species transport equations which are formulated using the nodal enthalpy and concentration potential values. The three phases are tracked using the beta-phase fraction and the liquid fraction values in all the computational nodes. Solutal convection flow field in the domain is obtained from the solution of volume-averaged momentum and continuity equations. The governing equations are solved using a coupled explicit-implicit scheme. The model is qualitatively validated with Jackson-Hunt theory. Results show expected eutectic growth pattern and proper species transfer and diffusion field ahead of the interface. Capabilities of the model such as lamella width selection, division of lamella into thinner lamellae and the presence of solutal convection are successfully demonstrated. The present model can potentially be incorporated into the existing framework of enthalpy based micro-scale dendritic solidification models thus leading to an efficient generalized microstructure evolution model. (C) 2014 Elsevier Inc. All rights reserved.

Assessment of Seismically Induced Landslide Hazard for the State of Karnataka Using GIS Technique

Landslide hazards are a major natural disaster that affects most of the hilly regions around the world. In India, significant damages due to earthquake induced landslides have been reported in the Himalayan region and also in the Western Ghat region. Thus there is a requirement of a quantitative macro-level landslide hazard assessment within the Indian subcontinent in order to identify the regions with high hazard. In the present study, the seismic landslide hazard for the entire state of Karnataka, India was assessed using topographic slope map, derived from the Digital Elevation Model (DEM) data. The available ASTER DEM data, resampled to 50 m resolution, was used for deriving the slope map of the entire state. Considering linear source model, deterministic seismic hazard analysis was carried out to estimate peak horizontal acceleration (PHA) at bedrock, for each of the grid points having terrain angle 10A degrees and above. The surface level PHA was estimated using nonlinear site amplification technique, considering B-type NEHRP site class. Based on the surface level PHA and slope angle, the seismic landslide hazard for each grid point was estimated in terms of the static factor of safety required to resist landslide, using Newmark's analysis. The analysis was carried out at the district level and the landslide hazard map for all the districts in the Karnataka state was developed first. These were then merged together to obtain a quantitative seismic landslide hazard map of the entire state of Karnataka. Spatial variations in the landslide hazard for all districts as well as for the entire state Karnataka is presented in this paper. The present study shows that the Western Ghat region of the Karnataka state is found to have high landslide hazard where the static factor of safety required to resist landslide is very high.

Factors affecting distribution of fish within a tidally drained mangrove forest in the Andaman and Nicobar Islands, India

Mangrove forests in meso-tidal areas are completely drained during low tides, forming only temporary habitats for fish. We hypothesised that in such temporary habitats, where stranding risks are high, distance from tidal creeks that provided access to inundated areas during receding tides would be the primary determinant of fish distribution. Factors such as depth, root density and shade were hypothesised to have secondary effects. We tested these hypotheses in a tidally drained mangrove patch in the Andaman Islands, India. Using stake nets, we measured fish abundance and species richness relative to distance from creeks, root density/m(2), shade, water depth and size (total length) of fish. We also predicted that larger fish (including potential predators) would be closer to creeks, as they faced a greater chance of mortality if stranded. Thus we conducted tethering trials to examine if predation would be greater close to the creeks. Generalised linear mixed effects models showed that fish abundance was negatively influenced by increasing creek distance interacting with fish size and positively influenced by depth. Quantile regression analysis showed that species richness was limited by increasing creek distance. Proportion of predation was greatest close to the creeks (0-25 m) and declined with increasing distance. Abundance was also low very close to the creeks, suggesting that close to the creeks predation pressure may be an important determinant of fish abundance. The overall pattern however indicates that access to permanently inundated areas, may be an important determinant of fish distribution in tidally drained mangrove forests.

Fruit Trait Preference in Rhesus Macaques (Macaca mulatta) and its Implications for Seed Dispersal

Primates constitute 25-40 % of the frugivore biomass of tropical forests. Primate fruit preference, as a determinant of seed dispersal, can therefore have a significant impact on these ecosystems. Although the traits of fruits included in primate diets have been described, fruit trait preference has been less studied with respect to fruit availability. We examined fruit trait preference and its implications for seed dispersal in the rhesus macaque (Macaca mulatta), a dietarily flexible species and important seed disperser, at the Buxa Tiger Reserve, India. Over a year, we monitored the phenology of selected trees in the study area, observed the feeding behavior of rhesus macaques using scans and focal animal sampling, and documented morphological traits of the fruits/seeds consumed. Using generalized linear modeling, we found that the kind of edible tissue was the chief determinant of fruit consumption, with M. mulatta feeding primarily on fruits with juicy-soft pulp and acting as seed predators for those with no discernible pulp. Overall, the preferred traits were external covers that could be easily pierced by a fingernail, medium to large seeds, true stone-like seeds, and juicy-soft edible tissue, thereby implying that fruit taxa with these traits had a higher probability of being dispersed. Macaques were more selective during the high fruit availability period than the low fruit availability period, preferentially feeding on soft-skinned fruits with juicy-soft pulp. We suggest that further studies be conducted across habitats and time to understand the consistency of interactions between primates and fruits with specific traits to determine the degree of selective pressure (if any) that is exerted by primates on fruit traits.