Prediction of amphipathic helix—Membrane interactions with Rosetta

Amphipathic helices have hydrophobic and hydrophilic/charged residues situated on oppo site faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with the RosettaMembrane, ref2015_memb, and franklin2019 score functions on six engineered and 44 naturally-occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations for comparison. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3Å of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) of up to 0.57. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.

Investigation of the inhibitory-bactericidal effect of amidoamine-based inorganic complexes against microbiological and atmospheric corrosion

In the process, inorganic complexes of amidoamines obtained from the interaction of natural petroleum acid and oleic acids with diethylenetriamine have been developed and their effectiveness as inhibitor-bactericides has been investigated. The effect of the synthesized reagents on the kinetics of the corrosion process of steel and the activity of sulphate-reducing bacteria in 3% NaCl solution saturated with CO2 and in the biphasic water–isopropyl alcohol medium with H2S dissolved has been analyzed. The thermodynamic and kinetic parameters of the corrosion process were calculated. The adsorption of the complexes was investigated using the Langmuir isotherm and the correlation constant was determined. State of the metal surface was investigated by SEM method in CO2 and H2S media, with and without inhibitors, and the metal surface contact of complexes was studied by computer molecular simulation.

Prediction of amphipathic helix – membrane interactions with Rosetta

Amphipathic helices have hydrophobic and hydrophilic/charged residues situated on opposite faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with six engineered and 44 naturally occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations as reference. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3Å of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) up to 0.61. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.

Removal of Uranium(VI) from Aqueous Solution by Iron Nanoparticles Synthesized from Testa Extract of Annacardium occidentale: A Fluorimetric Study

Uranium(VI) is one of the most harmful and carcinogenic ion if present in water above its permissible limit. The main objective of this study is removal of uranium(VI) from water sample using nano zerovalent iron prepared by green synthesis approach with the help of Annacardium occidentale testa extract in which the whole process is completely environmental friendly and cost effective and does not involve any hazardous chemicals. Size of AO-Fe nanoparticle is characterized through UV-visible spectroscopy and FTIR analysis. Morphology of nanoparticle is studied using SEM-EDS and XRD analysis. The adsorption capacity of AO-Fe nanoparticle is studied using batch experiments. Effect of different parameters are then analyzed such as pH, adsorbent dosage, contact time and U(VI) ion concentration. Adsorption isotherm is also studied using Langmuir and Freundlich adsorption isotherm where correlation constant R2 is about 0.99.

Determination of Performance Analysis for an Underground Colliery Utilizing Mechanized Production System

Performance is one of the most important parameters for today’s business organizations. An organizationthat is low on performance, no matter how much high quality products they have, cannot take the share they desirefrom the market. It is the inevitable result for organizations with low performances to lose money and get closed down.Nowadays performance is measured in many ways. In this work; the production performance of Ömerler Colliery,which is the only government controlled mechanized lignite mine authorized under the Western Lignite Corporation(WLC) and the factors that caused performance decrease has been determined. In order to gain performancemeasurements; effectiveness, efficiency and productivity criteria have been used and performance indexes have beenacquired. As the result of the performance analysis, it is understood that there has been malfunctions with; in order; beltconveyor, chain conveyor, shearer and fortification that has been effective in the decrease of performance. Performanceindexes, which are barely derived from the multiplication of performance parameters, are examined and it is deductedthat the highest relation is achieved for the efficiency parameter with a correlation constant (r) of 0.9489 and a certaintyconstant (R²) of 0.9005 while the lowest relation is obtained for the efficiency parameter with a correlation constant (r)of 0.4621 and certainty constant (R²) 0.2135. With this acquired result it has been determined that by only measuringeffectiveness, performance detection cannot be made.

Determination of Performance Analysis for an Underground Colliery Utilizing Mechanized Production System

Performance is one of the most important parameters for today’s business organizations. An organizationthat is low on performance, no matter how much high quality products they have, cannot take the share they desirefrom the market. It is the inevitable result for organizations with low performances to lose money and get closed down.Nowadays performance is measured in many ways. In this work; the production performance of Ömerler Colliery,which is the only government controlled mechanized lignite mine authorized under the Western Lignite Corporation(WLC) and the factors that caused performance decrease has been determined. In order to gain performancemeasurements; effectiveness, efficiency and productivity criteria have been used and performance indexes have beenacquired. As the result of the performance analysis, it is understood that there has been malfunctions with; in order; beltconveyor, chain conveyor, shearer and fortification that has been effective in the decrease of performance. Performanceindexes, which are barely derived from the multiplication of performance parameters, are examined and it is deductedthat the highest relation is achieved for the efficiency parameter with a correlation constant (r) of 0.9489 and a certaintyconstant (R²) of 0.9005 while the lowest relation is obtained for the efficiency parameter with a correlation constant (r)of 0.4621 and certainty constant (R²) 0.2135. With this acquired result it has been determined that by only measuringeffectiveness, performance detection cannot be made.

Multistage Tree Model for Crime Dataset in Iraq

This research deals with the using of correlation measurement that leads to describing the degree of relationship between variables, quantities or qualities. Therefore, we implement a simple correlation coefficient and conditional correlation to introduce a regular vine copula, which gives different tree structures. Two methods to select tree structures are introduced. The first one adopts the Partial Correlation Constant (PCC) with constant, while the second method depends on the estimation of summation pathway. The proposed method makes modification on Diβmann’s algorithm to increase the dependency on each level of the tree using rank correlation measurement. Both methods are adopted to construct the best model with more than three dimensions based on the available label crime dataset in Iraq. The selected model is used for selecting the suitable tree model and generating a decision with the low dimensionality of variables.

Preparation, Characterization, and Photocatalytic Activity of TiO2/ZnO Nanocomposites

Nanoparticles of the TiO2/ZnO composite photocatalysts were prepared via sol-gel process. The crystalline structure, morphology, thermal stability, and pore structure properties of the composite photocatalysts were characterized by XRD, FE-SEM, TG-DTA, and N2physical adsorption measurements. The photocatalytic activity of the composite catalysts was evaluated by photocatalytic degradation reaction of methyl orange (MO) in aqueous solution. The best preparation parameters for the composite photocatalysts were obtained through systematical experiments. Furthermore, the photocatalytic degradation reaction of aqueous MO solution followed the first-order reaction kinetics; the relative equation can be described asln(C0/C)=0.5689t, and the calculated correlation constant (R2) is 0.9937 for the calibration curve.