Search results for: Ajay Joshi

Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

Authors: Ajay V. Kolhe, R. E. Shelke, S. S. Khandare

Abstract:

The use of biodiesel in conventional diesel engines results in substantial reduction of unburned hydrocarbon, carbon monoxide and particulate matters. The performance, emission and combustion characteristics of a single cylinder four stroke variable compression ratio engine when fueled with Karanja (Pongamia) methyl ester and its 10-50 % blends with diesel (on a volume basis) are investigated and compared with standard diesel. The suitability of karanja methyl ester as a biofuel has been established in this study. The useful brake power obtained is similar to diesel fuel for all loads. Experiment has been conducted at a fixed engine speed of 1500 rpm, variable load and at compression ratios of 17.5:1 and 18.5:1. The impact of compression ratio on fuel consumption, combustion pressures and exhaust gas emissions has been investigated and presented. Optimum compression ratio which gives best performance has been identified. The results indicate longer ignition delay, maximum rate of pressure rise, lower heat release rate and higher mass fraction burnt at higher compression ratio for pongamia oil methyl ester when compared to that of diesel. The brake thermal efficiency for pongamia oil methyl ester blends and diesel has been calculated and the blend B20 is found to give maximum thermal efficiency. The blends when used as fuel results in reduction of carbon monoxide, hydrocarbon and increase in nitrogen oxides emissions. PME as an oxygenated fuel generated more complete combustion, which means increased torque and power. This is also supported with higher thermal efficiencies of the PME blends. NO_x is slightly increased due to the higher combustion temperature and the presence of fuel oxygen with the blend at full load. PME as a new Biodiesel and its blends can be used in diesel engines without any engine modification.

Keywords: Variable compression ratio CI engine, performance, combustion, emissions, biodiesel.

Authors: Ajay V. Kolhe, R. E. Shelke, S. S. Khandare

Abstract:

Various biomass based resources, which can be used as an extender, or a complete substitute of diesel fuel may have very significant role in the development of agriculture, industrial and transport sectors in the energy crisis. Use of Karanja oil methyl ester biodiesel in a CI DI engine was found highly compatible with engine performance along with lower exhaust emission as compared to diesel fuel but with slightly higher NOx emission and low wear characteristics. The combustion related properties of vegetable oils are somewhat similar to diesel oil. Neat vegetable oils or their blends with diesel, however, pose various long-term problems in compression ignition engines. These undesirable features of vegetable oils are because of their inherent properties like high viscosity, low volatility, and polyunsaturated character. Pongamia methyl ester (PME) was prepared by transesterification process using methanol for long term engine operations. The physical and combustion-related properties of the fuels thus developed were found to be closer to that of the diesel. A neat biodiesel (PME) was selected as a fuel for the tribological study of biofuels. Two similar new engines were completely disassembled and subjected to dimensioning of various vital moving parts and then subjected to long-term endurance tests on neat biodiesel and diesel respectively. After completion of the test, both the engines were again disassembled for physical inspection and wear measurement of various vital parts. The lubricating oil samples drawn from both engines were subjected to atomic absorption spectroscopy (AAS) for measurement of various wear metal traces present. The additional lubricating property of biodiesel fuel due to higher viscosity as compared to diesel fuel resulted in lower wear of moving parts and thus improved the engine durability with a bio-diesel fuel. Results reported from AAS tests confirmed substantially lower wear and thus improved life for biodiesel operated engines.

Keywords: Transesterification, PME, wear of engine parts, Metal traces and AAS.

Authors: Ajay Kumar Pandey, Mayank Kumar

Abstract:

White grub (Coleoptera: Scarabaeidae) is a major destructive pest in western Himalayan region of Uttarakhand. Beetles feed on apple, apricot, plum, walnut etc. during night while, second and third instar grubs feed on live roots of cultivated as well as non-cultivated crops. Collection and identification of scarab beetles through light trap was carried out at Crop Research Centre, Govind Ballab Pant University Pantnagar, Udham Singh Nagar (Uttarakhand) during 2018. Field trials were also conducted in 2018 to evaluate pre and post sown application of different insecticides against the white grub infesting soybean. The insecticides like Carbofuran 3 Granule (G) (750 g a.i./ha), Clothianidin 50 Water Dispersal Granule (WG) (120 g a.i./ha), Fipronil 0.3 G (50 g a.i./ha), Thiamethoxam 25 WG (80 g a.i./ha), Imidacloprid 70 WG (300 g a.i./ha), Chlorantraniliprole 0.4% G(100 g a.i./ha) and mixture of Fipronil 40% and Imidacloprid 40% WG (300 g a.i./ha) were applied at the time of sowing in pre sown experiment while same dosage of insecticides were applied in standing soybean crop during (first fortnight of July). Commutative plant mortality data were recorded after 20, 40, 60 days intervals and compared with untreated control. Total 23 species of white grub beetles recorded on the light trap and Holotrichia serrata Fabricious (Coleoptera: Melolonthinae) was found to be predominant species by recording 20.6% relative abundance out of the total light trap catch (i.e. 1316 beetles) followed by Phyllognathus sp. (14.6% relative abundance). H. rosettae and Heteronychus lioderus occupied third and fourth rank with 11.85% and 9.65% relative abundance, respectively. The emergence of beetles of predominant species started from 15th March, 2018. In April, average light trap catch was 382 white grub beetles, however, peak emergence of most of the white grub species was observed from June to July, 2018 i.e. 336 beetles in June followed by 303 beetles in the July. On the basis of the emergence pattern of white grub beetles, it may be concluded that the Peak Emergence Period (PEP) for the beetles of H. serrata was second fortnight of April for the total period of 15 days. In May, June and July relatively low population of H. serrata was observed. A decreasing trend in light trap catch was observed and went on till September during the study. No single beetle of H. serrata was observed on light trap from September onwards. The cumulative plant mortality data in both the experiments revealed that all the insecticidal treatments were significantly superior in protection-wise (6.49-16.82% cumulative plant mortality) over untreated control where highest plant mortality was 17.28 to 39.65% during study. The mixture of Fipronil 40% and Imidacloprid 40% WG applied at the rate of 300 g a.i. per ha proved to be most effective having lowest plant mortality i.e. 9.29 and 10.94% in pre and post sown crop, followed by Clothianidin 50 WG (120 g a.i. per ha) where the plant mortality was 10.57 and 11.93% in pre and post sown treatments, respectively. Both treatments were found significantly at par among each other. Production-wise, all the insecticidal treatments were found statistically superior (15.00-24.66 q per ha grain yields) over untreated control where the grain yield was 8.25 & 9.13 q per ha. Treatment Fipronil 40% + Imidacloprid 40% WG applied at the rate of 300 g a.i. per ha proved to be most effective and significantly superior over Imidacloprid 70WG applied at the rate of 300 g a.i. per ha.

Keywords: Bio efficacy, insecticide, Holotrichia, soybean, white grub.