Computational and experimental studies of fluid flow and heat transfer in a Calandria based reactor

CFD investigations are carried out to study the heat flux and temperature distribution in the calandria using a 3–Dimensional RANS code. Internal flow computations and experimental studies are carried out for a calandria embedded with a matrix of tubes working together as a reactor. Numerical investigations are carried on the Calandria reactor vessel with horizontal inlets and outlets located on top and the bottom to study the flow pattern and the associated temperature distribution. The computations have been carried out to simulate fluid flow and convective heat transfer for assigned near–to working conditions with different moderator injection rates and reacting heat fluxes. The results of computations provide an estimate of the tolerance bands for safe working limits for the heat dissipation at different working conditions by virtue of prediction of the hot spots in the calandria. The isothermal CFD results are validated by a set of experiments on a specially designed scaled model conducted over a range of flows and simulation parameters. The comparison of CFD results with experiments show good agreement.

Plant Diversity in the Sharavathi River Basin in Relation to Human Disturbance

Changes in vegetation are taking place due to anthropogenic activities since the colonization of the evergreen forest zone of Western Ghats. The forests of the Western Ghats were contiguous and uniformly rich in endemism within each climatic and physiographic regime. The region continues to be one of the biodiversity hot spots of the world. However unplanned developmental activities are altering the balance of the ecosystem. This study focuses on the floristic structure, composition and diversity of forests with varying degree of human disturbances. Based on the investigations, various strategies for conservation and sustainable utilization of forest resources were proposed.

Register File Energy Optimization for Snooping Based Clustered VLIW Architectures

Frequent accesses to the register file make it one of the major sources of energy consumption in ILP architectures. The large number of functional units connected to a large unified register file in VLIW architectures make power dissipation in the register file even worse because of the need for a large number of ports. High power dissipation in a relatively smaller area occupied by a register file leads to a high power density in the register file and makes it one of the prime hot-spots. This makes it highly susceptible to the possibility of a catastrophic heatstroke. This in turn impacts the performance and cost because of the need for periodic cool down and sophisticated packaging and cooling techniques respectively. Clustered VLIW architectures partition the register file among clusters of functional units and reduce the number of ports required thereby reducing the power dissipation. However, we observe that the aggregate accesses to register files in clustered VLIW architectures (and associated energy consumption) become very high compared to the centralized VLIW architectures and this can be attributed to a large number of explicit inter-cluster communications. Snooping based clustered VLIW architectures provide very limited but very fast way of inter-cluster communication by allowing some of the functional units to directly read some of the operands from the register file of some of the other clusters. In this paper, we propose instruction scheduling algorithms that exploit the limited snooping capability to reduce the register file energy consumption on an average by 12% and 18% and improve the overall performance by 5% and 11% for a 2-clustered and a 4-clustered machine respectively, over an earlier state-of-the-art clustered scheduling algorithm when evaluated in the context of snooping based clustered VLIW architectures.

Fluid Mechanics of Aquatic Locomotion at Large Reynolds Numbers

Abstract | There exist a huge range of fish species besides other aquatic organisms like squids and salps that locomote in water at large Reynolds numbers, a regime of flow where inertial forces dominate viscous forces. In the present review, we discuss the fluid mechanics governing the locomotion of such organisms. Most fishes propel themselves by periodic undulatory motions of the body and tail, and the typical classification of their swimming modes is based on the fraction of their body that undergoes such undulatory motions. In the angulliform mode, or the eel type, the entire body undergoes undulatory motions in the form of a travelling wave that goes from head to tail, while in the other extreme case, the thunniform mode, only the rear tail (caudal fin) undergoes lateral oscillations. The thunniform mode of swimming is essentially based on the lift force generated by the airfoil like crosssection of the fish tail as it moves laterally through the water, while the anguilliform mode may be understood using the “reactive theory” of Lighthill. In pulsed jet propulsion, adopted by squids and salps, there are two components to the thrust; the first due to the familiar ejection of momentum and the other due to an over-pressure at the exit plane caused by the unsteadiness of the jet. The flow immediately downstream of the body in all three modes consists of vortex rings; the differentiating point being the vastly different orientations of the vortex rings. However, since all the bodies are self-propelling, the thrust force must be equal to the drag force (at steady speed), implying no net force on the body, and hence the wake or flow downstream must be momentumless. For such bodies, where there is no net force, it is difficult to directly define a propulsion efficiency, although it is possible to use some other very different measures like “cost of transportation” to broadly judge performance.

High resolution multiple excitation spot optical microscopy

We propose fundamental improvements in three-dimensional (3D) resolution of multiple excitation spot optical microscopy. The excitation point spread function (PSF) is generated by two interfering counter-propagating depth-of-focus beams along the optical axis. Detection PSF is obtained by coherently interfering the emitted fluorescent light (collected by both the objectives) at the detector. System PSF shows upto 14-fold reduction in focal volume as compared to confocal, and almost 2-fold improvement in lateral resolution. Proposed PSF has the ability to simultaneously excite multiple 3D-spots of sub-femtoliter volume. Potential applications are in fluorescence microscopy and nanobioimaging. Copyright 2011 Author(s). This article is distributed under a Creative Commons Attribution 3.0 Unported License. [doi:10.1063/1.3598413]

Differential Diffractive Reflectance Modulation Sensing

We fabricated a reflectance based sensor which relies on the diffraction pattern generated from a bio-microarray where an underlying thin film structure enhances the diffracted intensity from molecular layers. The zero order diffraction represents the background signal and the higher orders represent the phase difference between the array elements and the background. By taking the differential ratio of the first and zero order diffraction signals we get a quantitative measure of molecular binding while simultaneously rejecting common mode fluctuations. We improved the signal-to-noise ratio by an order of magnitude with this ratiometric approach compared to conventional single channel detection. In addition, we use a lithography based approach for fabricating microarrays which results in spot sizes as small as 5 micron diameter unlike the 100 micron spots from inkjet printing and is therefore capable of a high degree of multiplexing. We will describe the real-time measurement of adsorption of charged polymers and bulk refractometry using this technique. The lack of moving parts for point scanning of the microarray and the differential ratiometric measurements using diffracted orders from the same probe beam allows us to make real-time measurements in spite of noise arising from thermal or mechanical fluctuations in the fluid sample above the sensor surface. Further, the lack of moving parts leads to considerable simplification in the readout hardware permitting the use of this technique in compact point of care sensors.

An Exported Heat Shock Protein 40 Associates with Pathogenesis-Related Knobs in Plasmodium falciparum Infected Erythrocytes

Cell surface structures termed knobs are one of the most important pathogenesis related protein complexes deployed by the malaria parasite Plasmodium falciparum at the surface of the infected erythrocyte. Despite their relevance to the disease, their structure, mechanisms of traffic and their process of assembly remain poorly understood. In this study, we have explored the possible role of a parasite-encoded Hsp40 class of chaperone, namely PFB0090c/PF3D7_0201800 (KAHsp40) in protein trafficking in the infected erythrocyte. We found the gene coding for PF3D7_0201800 to be located in a chromosomal cluster together with knob components KAHRP and PfEMP3. Like the knob components, KAHsp40 too showed the presence of PEXEL motif required for transport to the erythrocyte compartment. Indeed, sub-cellular fractionation and immunofluorescence analysis (IFA) showed KAHsp40 to be exported in the erythrocyte cytoplasm in a stage dependent manner localizing as punctuate spots in the erythrocyte periphery, distinctly from Maurer's cleft, in structures which could be the reminiscent of knobs. Double IFA analysis revealed co-localization of PF3D7_0201800 with the markers of knobs (KAHRP, PfEMP1 and PfEMP3) and components of the PEXEL translocon (Hsp101, PTEX150). KAHsp40 was also found to be in a complex with KAHRP, PfEMP3 and Hsp101 as confirmed by co-immunoprecipitation assay. Our results suggest potential involvement of a parasite encoded Hsp40 in chaperoning knob assembly in the erythrocyte compartment.

Proteomic profiling of high glucose primed monocytes identifies cyclophilin A as a potential secretory marker of inflammation in type 2 diabetes

Hyperglycemia is widely recognized to be a potent stimulator of monocyte activity, which is a crucial event in the pathogenesis of atherosclerosis. We analyzed the monocyte proteome for potential markers that would enhance the ability to screen for early inflammatory status in Type 2 diabetes mellitus (T2DM), using proteomic technologies. Monocytic cells (THP-1) were primed with high glucose (HG), their protein profiles were analyzed using 2DE and the downregulated differentially expressed spots were identified using MALDI TOF/MS. We selected five proteins that were secretory in function with the help of bioinformatic programs. A predominantly downregulated protein identified as cyclophilin A (sequence coverage 98%) was further validated by immunoblotting experiments. The cellular mRNA levels of cyclophilin A in various HG-primed cells were studied using qRT-PCR assays and it was observed to decrease in a dose-dependent manner. LC-ESI-MS was used to identify this protein in the conditioned media of HG-primed cells and confirmed by Western blotting as well as ELISA. Cyclophilin A was also detected in the plasma of patients with diabetes. We conclude that cyclophilin A is secreted by monocytes in response to HG. Given the paracrine and autocrine actions of cyclophilin A, the secreted immunophilin could be significant for progression of atherosclerosis in type 2 diabetes. Our study also provides evidence that analysis of monocyte secretome is a viable strategy for identifying candidate plasma markers in diabetes.

Cannibalism can drive the evolution of behavioural phase polyphenism in locusts

During outbreaks, locust swarms can contain millions of insects travelling thousands of kilometers while devastating vegetation and crops. Such large-scale spatial organization is preceded locally by a dramatic density-dependent phenotypic transition in multiple traits. Behaviourally, low-density solitarious individuals avoid contact with one another; above a critical local density, they undergo a rapid behavioural transition to the gregarious phase whereby they exhibit mutual attraction. Although proximate causes of this phase polyphenism have been widely studied, the ultimate driving factors remain unclear. Using an individual-based evolutionary model, we reveal that cannibalism, a striking feature of locust ecology, could lead to the evolution of density-dependent behavioural phase-change in juvenile locusts. We show that this behavioural strategy minimizes risk associated with cannibalistic interactions and may account for the empirically observed persistence of locust groups during outbreaks. Our results provide a parsimonious explanation for the evolution of behavioural plasticity in locusts.

Porous Three Dimensional Arrays of Plasmonic Nanoparticles

Plasmonic interactions in a well-defined array of metallic nanoparticles can lead to interesting optical effects, such as local electric field enhancement and shifts in the extinction spectra, which are of interest in diverse technological applications, including those pertaining to biochemical sensing and photonic circuitry. Here, we report on a single-step wafer scale fabrication of a three-dimensional array of metallic nanoparticles whose sizes and separations can be easily controlled to be anywhere between fifty to a few hundred nanometers, allowing the optical response of the system to be tailored with great control in the visible region of the spectrum. The substrates, apart from having a large surface area, are inherently porous and therefore suitable for optical sensing applications, such as surface enhanced Raman scattering, containing a high density of spots with enhanced local electric fields arising from plasmonic couplings.

Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a ``spatial motif'' and several ``fold specific hot spots'' that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.

Temozolomide-modulated glioma proteome: Role of interleukin-1 receptor-associated kinase-4 (IRAK4) in chemosensitivity

The current treatment for glioblastoma includes temozolomide (TMZ) chemotherapy, yet the mechanism of action of TMZ is not thoroughly understood. Here, we investigated the TMZ-induced changes in the proteome of the glioma-derived cell line (U251) by 2D DIGE. We found 95 protein spots to be significantly altered in their expression after TMZ treatment. MS identified four upregulated spots: aspartyl tRNA synthetase glutathione synthetase, interleukin-1 receptor-associated kinase-4 (IRAK4), and breast carcinoma amplified sequence-1 and one downregulated spot: optineurin. TMZ-induced regulation of these five genes was validated by RT-qPCR andWestern blot analysis. RNAi-mediated knockdown of IRAK4, an important mediator of Toll-like receptors signaling and chemoresistance, rendered the glioma cells resistant to TMZ. High levels of IRAK4 induced upon TMZ treatment resulted in IRAK1 downregulation and inhibition of NFkB pathway. Endogenous IRAK4 protein, but not transcript levels in glioma cell lines, correlated with TMZ sensitivity. Thus, we have identified several TMZ-modulated proteins and discovered an important novel role for IRAK4 in determining TMZ sensitivity of glioma cells through its ability to inhibit Toll-like receptor signaling and NFkB pathway.

Hypersonic interference heating on cones with short three-dimensional protuberances

Heat fluxes around short, three-dimensional protuberances on sharp and blunt cones in hypersonic flow were experimentally measured using platinum thin-film sensors deposited on macor inserts. A parametric study of different protrusion geometries and flow conditions were conducted. Excessive heating was observed at locations near the protrusion where increased vorticity is expected, with the hottest spot being presented at the foot of the protuberance immediately upstream of it. If left unchecked, these hot spots could prove detrimental to hypersonic flight vehicles. Z-type schlieren technique was used to visualize the flow features qualitatively. New correlations to predict the heat flux at the hot spot have been proposed. (C) 2014 Elsevier Inc. All rights reserved.

Shear-imposed falling film

The study of a film falling down an inclined plane is revisited in the presence of imposed shear stress. Earlier studies regarding this topic (Smith, J. Fluid Mech., vol. 217, 1990, pp. 469-485; Wei, Phys. Fluids, vol. 17, 2005a, 012103), developed on the basis of a low Reynolds number, are extended up to moderate values of the Reynolds number. The mechanism of the primary instability is provided under the framework of a two-wave structure, which is normally a combination of kinematic and dynamic waves. In general, the primary instability appears when the kinematic wave speed exceeds the speed of dynamic waves. An equality criterion between their speeds yields the neutral stability condition. Similarly, it is revealed that the nonlinear travelling wave solutions also depend on the kinematic and dynamic wave speeds, and an equality criterion between the speeds leads to an analytical expression for the speed of a family of travelling waves as a function of the Froude number. This new analytical result is compared with numerical prediction, and an excellent agreement is achieved. Direct numerical simulations of the low-dimensional model have been performed in order to analyse the spatiotemporal behaviour of nonlinear waves by applying a constant shear stress in the upstream and downstream directions. It is noticed that the presence of imposed shear stress in the upstream (downstream) direction makes the evolution of spatially growing waves weaker (stronger).

A Comparative Study of Early Afterdepolarization-Mediated Fibrillation in Two Mathematical Models for Human Ventricular Cells

Early afterdepolarizations (EADs), which are abnormal oscillations of the membrane potential at the plateau phase of an action potential, are implicated in the development of cardiac arrhythmias like Torsade de Pointes. We carry out extensive numerical simulations of the TP06 and ORd mathematical models for human ventricular cells with EADs. We investigate the different regimes in both these models, namely, the parameter regimes where they exhibit (1) a normal action potential (AP) with no EADs, (2) an AP with EADs, and (3) an AP with EADs that does not go back to the resting potential. We also study the dependence of EADs on the rate of at which we pace a cell, with the specific goal of elucidating EADs that are induced by slow or fast rate pacing. In our simulations in two-and three-dimensional domains, in the presence of EADs, we find the following wave types: (A) waves driven by the fast sodium current and the L-type calcium current (Na-Ca-mediated waves); (B) waves driven only by the L-type calcium current (Ca-mediated waves); (C) phase waves, which are pseudo-travelling waves. Furthermore, we compare the wave patterns of the various wave-types (Na-Ca-mediated, Ca-mediated, and phase waves) in both these models. We find that the two models produce qualitatively similar results in terms of exhibiting Na-Ca-mediated wave patterns that are more chaotic than those for the Ca-mediated and phase waves. However, there are quantitative differences in the wave patterns of each wave type. The Na-Ca-mediated waves in the ORd model show short-lived spirals but the TP06 model does not. The TP06 model supports more Ca-mediated spirals than those in the ORd model, and the TP06 model exhibits more phase-wave patterns than does the ORd model.