A Numerical Study of Transient Ignition and Flame Structure in Diesel Sprays in a Constant Volume Reactor

It is well known that diesel fuel consist a large number of hydrocarbons with one or more carbon double bond in their molecular structure. Various studies have been conducted to conform that the presence of the double bond affects the fuel reactivity and its flame structure. To perform the computational fluid dynamics (CFD) analysis of the fuel combustion property with the presence of the unsaturated carbon to carbon double bond, various detailed and reduced kinetics models have developed. Along with the computational studies, numerous experimental studies have also been conducted using shock tube and RCM to study the effect of double bond on the fuel ignitability. The major outcomes from these studies are that at lower temperature the ignition delay is quite higher for alkenes (hydrocarbon containing double bond) in comparison to the alkanes. At intermediate temperature (1000 K-1200 K), the ignition delay is dependent on the radicals formed by the decomposition of the stabilized radicals present in the combustion chamber. On the other hand, at higher temperature (> 1300K), the ignition phenomenon is determined by the initiation reactions. Presence of the double bond helps in the formation of allyl radicals which are more energetic in comparison to the methyl radicals formed by the decomposition of the alkanes. Therefore, the alkenes have shorter ignition delay than alkanes at higher temperature. Numerous engine experiments using different biodiesel fuels have also been performed to study the effect of unsaturated bond on the NOx and soot emissions. But it is not feasible to study effect of presence of double bond on the flame structure through an engine experiment. Therefore a recent numerical study has been conducted using the Sandia constant volume reactor to simulate more realistic spray flames and to study the effect of the unsaturated bond on the flame structure and combustion phenomenon in spray flames under diesel engine conditions. The above mentioned study was only conducted for higher initial temperature (at 1300K) in order to study the n-heptane and 1-heptene flame characteristics on the basis of same ignition delay. But there is no numerical study has been reported yet for the lower and intermediate initial temperature. The present study focuses on the effect of presence of double bond on the ignition and flame structure of the n-heptane and 1-heptene flame at the initial temperature ranging from 1000K to 1200K in the Sandia constant volume reactor at the diesel engine condition. This reactor is being extensively used to produce the experimental results, which can be downloaded from the Engine Combustion Network (ECN) website, for the reacting and non-reacting spray simulations. N-heptane and 1-heptene flames are simulated by using the reduced CRECK mechanism. The simulations have been performed at the initial temperature of 1000K, 1100K and 1200K temperature. Since at lower temperature (<1000K) the ignition delay is too high for 1-heptene flame and therefore it is not possible to perform the simulation at that temperature because of the lack of the computational power. Therefore these three intermediate temperatures has been chosen to study the effect of initial temperature and the presence of unsaturated bond on the ignition and flame structure of the spray flames. The flame structure of n-heptane and 1-heptene flame is shown by the contour plot of temperature and the heat release rate and by the scatter plot of heat release rate in a ɸ/T plane. Finally, the formation of ignition kernels has been discussed in order to study the flame structure of the n-heptane and 1-heptene spray flame. The second part of the thesis focuses on the effect of the presence of double bond on the ignition and combustion of biodiesel/alcohol fuel blends. Partially premixed flames are simulated in a constant-volume reactors using different n-heptane/iso-pentanol and 1-heptene/iso-pentanol blends. A kinetic model for the blends is developed by combining a reduced mechanism for iso-pentanol with a reduced CRECK mechanism for n-heptane and 1-heptene. Four different blends considered include 90%n heptane/10%iso-pentanol (by volume), 80%n-heptane/20%iso-pentanol, 70%n-heptane/30%iso-pentanol, and 50%n-heptane/50%iso-pentanol. To examine the effect of the presence of double bond, similar blends are considered with 1-heptene and pentanol. The main conclusion drawn from this study is that when iso-pentanol was added with n-heptane, the ignition delay increases whereas when the blend was formed with 1-heptene, the ignition delay decreases and there was a significant variation in the location of the formation of ignition kernel. As the concentration of iso-pentanol was increased in the 1-heptene/iso-pentanol blend, the zone in which ignition occur shifts from lean premixed to non-premixed reaction zone. Fuel vapor penetration of both the fuels shows that the ignition is controlled by the presence of iso-pentanol which explains the shift in the ignition kernel formation location

Twitter Sentiment Analysis on US Presidential Candidates 2016

Our study is targeted towards the analysis of public sentiment of two presidential candidates for US Elections 2016, Hilary Clinton and Donald Trump using tweets made during their campaign.<div><br></div><div>This study provides the important insights to the candidates in improving the campaign strategy and focus on their negative sentiment.</div><div><br></div><div>R programming language has been used in the study for the sentiment analysis.</div

Overexpression of DevR_Δα10 in Mtb RKO.

<p><b>(a)</b> Vector map of integrating plasmid employed to overexpress DevR_α10 protein. <b>(b)</b> RT-qPCR analysis of aerobic DevR regulon genes expression. WT/mutant DevR expression in RKO-P_msp12DevR /RKO-P_msp12DevR_α10 strains is supported by <i>msp12</i> promoter and WT DevR in RKO-P_OperonDevR by its native promoter. <b>(c)</b> RT-qPCR analysis of DevR regulon genes under hypoxia. RT-qPCR data is Mean ± SD of 2 biological replicates.</p

<i>Mycobacterium tuberculosis</i> DevR/DosR Dormancy Regulator Activation Mechanism: Dispensability of Phosphorylation, Cooperativity and Essentiality of α10 Helix

<div><p>DevR/DosR is a well-characterized regulator in <i>Mycobacterium tuberculosis</i> which is implicated in various processes ranging from dormancy/persistence to drug tolerance. DevR induces the expression of an ~48-gene dormancy regulon in response to gaseous stresses, including hypoxia. Strains of the Beijing lineage constitutively express this regulon, which may confer upon them a significant advantage, since they would be ‘pre-adapted’ to the environmental stresses that predominate during infection. Aerobic DevR regulon expression in laboratory-manipulated overexpression strains is also reported. In both instances, the need for an inducing signal is bypassed. While a phosphorylation-mediated conformational change in DevR was proposed as the activation mechanism under hypoxia, the mechanism underlying constitutive expression is not understood. Because DevR is implicated in bacterial dormancy/persistence and is a promising drug target, it is relevant to resolve the mechanistic puzzle of hypoxic activation on one hand and constitutive expression under ‘non-inducing’ conditions on the other. Here, an overexpression strategy was employed to elucidate the DevR activation mechanism. Using a panel of kinase and transcription factor mutants, we establish that DevR, upon overexpression, circumvents DevS/DosT sensor kinase-mediated or small molecule phosphodonor-dependent activation, and also cooperativity-mediated effects, which are key aspects of hypoxic activation mechanism. However, overexpression failed to rescue the defect of C-terminal-truncated DevR lacking the α10 helix, establishing the α10 helix as an indispensable component of DevR activation mechanism. We propose that aerobic overexpression of DevR likely increases the concentration of α10 helix-mediated active dimer species to above the threshold level, as during hypoxia, and enables regulon expression. This advance in the understanding of DevR activation mechanism clarifies a long standing question as to the mechanism of DevR overexpression-mediated induction of the regulon in the absence of the normal environmental cue and establishes the α10 helix as an universal and pivotal targeting interface for DevR inhibitor development.</p></div

Mtb strains used in the study.

<p>Mtb strains used in the study.</p

Overexpression of WT/mutant DevR in Mtb RKO.

<p><b>(a)</b> Vector map of integrating plasmid overexpressing WT/mutant DevR proteins. <b>(b)</b> Mtb RKO- P_msp12DevR, RKO-P_msp12DevR D54E, RKO-P_msp12DevR D54V and RKO-P_msp12DevR T82A strains overexpress DevR variants from <i>msp12</i> promoter. RKO-P_OperonDevR strain expresses DevR from its native promoter. Western blotting of aerobic (Aer) and 5 day hypoxic (Hyp) cultures lysates. A representative blot is shown. <b>(c)</b> RT-qPCR analysis of regulon genes in aerobic cultures. <b>(d)</b> RT-qPCR analysis of DevR regulon genes under hypoxia. RT-qPCR data is Mean ± SD of 2 biological replicates. SigA was used as a loading control in (b).</p

Overexpression of DevR in Mtb DKO.

<p><b>(a)</b> Vector map of integrating plasmid overexpressing DevR. <b>(b)</b> Western blotting of lysates from aerobic Mtb cultures. A representative blot is shown. <b>(c)</b> Total DevR levels (DevR + DevR-Myc) in DKO-complemented strains. <b>(d)</b> DevR (endo) level in DKO-complemented strains. <b>(e)</b> RT-qPCR analysis of select DevR regulon genes in DKO-complemented strains. <b>(f)</b> RT-qPCR analysis of additional DevR regulon genes in DKO-P_msp12DevR. Data is Mean ± SD of 2 biological replicates. SigA was used as a loading control in (b). In panels (c) to (f), protein and transcript levels are shown relative to that in DKO (considered as 1).</p

Structure-based identification of potential natural compound inhibitors targeting bacterial cytoskeleton protein FtsZ from <i>Acinetobacter baumannii</i> by computational studies

Acinetobacter baumannii is one of the multi-drug-resistant pathogens responsible for hospital-acquired infections reported worldwide. Clinically it is challenging to treat these pathogens as they have developed resistance against the existing class of antibiotics. Hence, there is an urgent need to develop a new class of antibiotics against these pathogens to prevent the spread of infections and mortality. In Acinetobacter baumannii, the filamentous temperature-sensitive mutant Z protein polymerizes at the imminent division site to form a Z-ring at the mid-point of the cell and act as a scaffold to recruit other cell division proteins involved in orchestrating septum synthesis in bacteria. Perturbation in the assembly of FtsZ affects bacterial cell dynamics and survival. Hence, FtsZ has emerged as a new drug target in antibiotic discovery to identify compounds that inhibit bacterial cell division. In this study, we have performed a virtual screening of 30,000 compounds from the ZINC Biogenic natural compound library targeting the nucleotide-binding site of FtsZ from Acinetobacter baumannii. We have identified 8 new natural compounds with binding energy in the range of −8.66 to −6.953 kcal/mol and analyzed them by 200 ns molecular dynamics simulations. Out of these eight compounds, ZINC14708526 showed the best binding with relatively optimal drug-likeness and medicinal chemistry as a potent inhibitor of abFtsZ. Thus, the identified FtsZ inhibitor ZINC14708526 is a promising lead compound to develop potent antimicrobial agents against Acinetobacter baumannii infections. Communicated by Ramaswamy H. Sarma</p

Identification of Novel Autoantigen in the Synovial Fluid of Rheumatoid Arthritis Patients Using an Immunoproteomics Approach

<div><p>Rheumatoid arthritis (RA) is a chronic, autoimmune and inflammatory joint disease with a poorly understood etiology. Despite widespread diagnostic use of anti-citrullinated protein antibodies and rheumatoid factor proteins there is a strong demand for novel serological biomarkers to improve the diagnosis this disease. The present study was aimed to identify novel autoantigens involved in rheumatoid arthritis (RA) pathogenesis through immune-proteomic strategy. Synovial fluid samples from clinically diagnosed RA patients were separated on two-dimensional gel electrophoresis (2-DE). Samples from patients with non-RA rheumatisms (osteoarthritis and trauma) were used as controls. Immunoreactive proteins were spotted by Western blotting followed by identification through Q-TOF mass spectrometer analysis. Forty Western blots were generated using plasma from ten individual RA patients and 33 reactive spots were identified, 20 from the high molecular weight (HMW) gel and 13 from the low molecular weight (LMW) gel. Among the 33 common immunogenic spots, 18 distinct autoantigens were identified, out of which 14 are novel proteins in this context. Expression analysis of five important proteins, vimentin, gelsolin, alpha 2 HS glycoprotein (AHSG), glial fibrillary acidic protein (GFAP), and α1B-glycoprotein (A1BG) by Western blot analysis using their specific antibodies revealed their higher expression in RA synovial fluid as compared to non-RA samples. Recombinantly expressed GFAP and A1BG protein were used to develop an in-house ELISA to quantify the amount of autoantibodies in the RA patients. RA patients revealed an increase in the expression of GFAP and A1BG in the plasma as compared to osteoarthritis patients. Therefore, GFAP and A1BG can be proposed as potential new autoantigens of diagnostic importance for RA subjects. Further characterization of these proteins in rheumatoid arthritis will be helpful in understanding the role of these proteins in the disease pathogenesis providing new diagnostic tool with better specificity and accurate detection of the disease.</p> </div

Identified high and low molecular weight RA antigens.

<p>Identification of high molecular weight (HMW) and low molecular weight (LMW) antigens using Q-TOF mass spectrometric (MS) analysis followed by online MASCOT search against the SwissProt and NCBInr protein databases (kDa-kilo Dalton, MW-molecular weight, Obs-observed, Thr- theoretical, pI- isoelectric point, MOWSE- Molecular Weight Search).</p