Comparison study on surface and thermo-chemical properties of PFPE lubricants on DLC film through MD simulations

2021 ◽  
Vol 156 ◽  
pp. 106835
Author(s):  
Jingan Song ◽  
Sujoy Talukder ◽  
Shahriar Mufid Rahman ◽  
Yeonjin Jung ◽  
Chang-Dong Yeo
Keyword(s):  
Chemical Properties ◽  
Md Simulations ◽  
Comparison Study ◽  
Dlc Film ◽  
Pfpe Lubricants

scholarly journals Effects of SiO2 Contaminant on Thermo-Mechanical/Chemical Properties and Lubricity of PFPE Lubricants

Lubricants ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 90
Author(s):  
Shahriar Rahman ◽  
Dipesh Purani ◽  
Shaikh Ali ◽  
Chang-Dong Yeo
Keyword(s):  
Molecular Dynamics ◽  
Room Temperature ◽  
Chemical Properties ◽  
Md Simulations ◽  
Sliding Contact ◽  
Lower Viscosity ◽  
Different Types ◽  
Simulation Results ◽  
Sio2 Particles ◽  
Pfpe Lubricants

Using the molecular dynamics (MD) simulations with ReaxFF potential, two different types of PFPE lubricants (Ztetraol and ZTMD) are prepared on a-C film, and SiO2 particles are adsorbed onto the lubricants at room temperature. From the simulation results, it is observed that the adsorbed SiO2 particles increase the stiffness of PFPE lubricants leading to less airshear displacement. Since Ztetraol has higher mobility with lower viscosity than ZTMD, the adsorbed SiO2 particles penetrate deeper into the Ztetraol lubricants. Accordingly, the effect of SiO2 on the airshear displacement is more obvious to Ztetraol than ZTMD. In addition, the adsorbed SiO2 particles increase the friction force and the amount of lubricant pick-up during the sliding contact with a nanosized a-C tip.

scholarly journals Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

2019 ◽  
Author(s):  
Juan J Galano-Frutos ◽  
Helena García-Cebollada ◽  
Javier Sancho
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Large Scale ◽  
Binary Classification ◽  
Chemical Properties ◽  
Md Simulations ◽  
Single Amino Acid ◽  
Medical Decision ◽  
Evolutionary Information ◽  
Protein Variants

Abstract The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.

scholarly journals Molecular insight into optimizing the N- and P-doped fullerenes for urea removal in wearable artificial kidneys

2021 ◽  
Vol 32 (5) ◽  
Author(s):  
Ahmad Miri Jahromi ◽  
Pegah Zandi ◽  
Mohammad Khedri ◽  
Ebrahim Ghasemy ◽  
Reza Maleki ◽  
...  
Keyword(s):  
Kidney Diseases ◽  
Chemical Properties ◽  
Md Simulations ◽  
The Body ◽  
Radius Of Gyration ◽  
Doped Fullerenes ◽  
Artificial Kidneys ◽  
Stage Renal Disease ◽  
End Stage ◽  
Esrd Patients

AbstractUrea is the result of the breakdown of proteins in the liver, the excess of which circulates in the blood and is adsorbed by the kidneys. However, in the case of kidney diseases, some products, specifically urea, cannot be removed from the blood by the kidneys and causes serious health problems. The end-stage renal disease (ESRD) patients are not able to purify their blood, which endangers their life. ESRD patients require dialysis, a costly and difficult method of urea removal from the blood. Wearable artificial kidneys (WAKs) are consequently designed to remove the waste from blood. Regarding the great amount of daily urea production in the body, WAKs should contain strong and selective urea adsorbents. Fullerenes—which possess fascinating chemical properties—have been considered herein to develop novel urea removal adsorbents. Molecular dynamics (MD) has enabled researchers to study the interaction of different materials and can pave the way toward facilitating the development of wearable devices. In this study, urea adsorption by N-doped fullerenes and P-doped fullerenes were assessed through MD simulations. The urea adsorption was simulated by five samples of fullerenes, with phosphorous and different nitrogen dopant contents. For comparing the urea adsorption capacity in the performed simulations, detailed characteristics—including the energy analysis, radius of gyration, radial distribution function (RDF), root-mean-square fluctuation (RMSD), and H-bond analyses were investigated. It had been determined that the fullerene containing 8% nitrogen—with the highest reduction in the radius of gyration, the maximum RDF, a high adsorption energy, and a high number of hydrogen bonds—adsorbs urea more efficiently.

U(VI) Extraction by 8-hydroxyquinoline: a comparison study in ionic liquid and in dichloromethane

2017 ◽  
Vol 105 (6) ◽  
Author(s):  
Li-Yong Yuan ◽  
Xiang-Hong Liao ◽  
Zhi-Rong Liu ◽  
Zhi-Fang Chai ◽  
Wei-Qun Shi
Keyword(s):  
Room Temperature ◽  
Chemical Properties ◽  
Liquid Extraction ◽  
Physical And Chemical Properties ◽  
Comparison Study ◽  
New Class ◽  
Liquid Liquid Extraction ◽  
Physical And Chemical ◽  
Fuel Reprocessing ◽  
And Chemical Properties

AbstractRoom temperature ionic liquids (RTILs) represent a recent new class of solvents with potential application in liquid/liquid extraction based nuclear fuel reprocessing due to their unique physical and chemical properties. The work herein provides a comparison of U(VI) extraction by 8-hydroxyquinoline (HOX) in a commonly used RTIL, i.e. 1-butyl-3-methylimidazolium hexafluorophosphate ([C

scholarly journals Structural basis for silicon uptake by higher plants

2021 ◽  
Author(s):  
Bert van den Berg ◽  
Conrado Pedebos ◽  
Jani R Bolla ◽  
Carol V Robinson ◽  
Arnaud Basle ◽  
...  
Keyword(s):  
Crop Yields ◽  
Higher Plants ◽  
Chemical Properties ◽  
Md Simulations ◽  
Structural Basis ◽  
Intracellular Loop ◽  
Biotic Stresses ◽  
Silicon Uptake ◽  
Channel Opening ◽  
Silicon Accumulation

Metalloids are elements with physical and chemical properties that are intermediate between metals and non-metals. Silicon (Si) is the most abundant metalloid in the Earth's crust and occurs at high levels in many plants, especially those belonging to the Poaceae (grasses). Most of the world's staple food crops such as rice, barley and maize accumulate silicon to high levels, resulting in resistance to abiotic and biotic stresses and consequently better plant growth and crop yields. The first step in silicon accumulation is the uptake of silicic acid (Si), the bioavailable from of silicon, by the roots, a process mediated by the structurally uncharacterised NIP subfamily of aquaporins. Here we present the X-ray crystal structure of the archetypal NIP family member from Oryza sativa (OsNIP2;1). While the OsNIP2;1 channel is closed in the crystal by intracellular loop D, unbiased molecular dynamics (MD) simulations reveal a rapid channel opening on sub-microsecond time scales. MD simulations further show how Si interacts with an extracellular five-residue selectivity filter that provides the main barrier for transmembrane diffusion. Our data provide a foundation for understanding and potential manipulation of metalloid selectivity of an important and understudied aquaporin subfamily.

scholarly journals Computational and experimental evidence to the permeability of withanolides across the normal cell membrane

2019 ◽  
Author(s):  
R. Wadhwa ◽  
N. S. Yadav ◽  
S. P Katiyar ◽  
T. Yaguchi ◽  
C. Lee ◽  
...  
Keyword(s):  
Cell Membrane ◽  
Chemical Properties ◽  
Md Simulations ◽  
Computational Method ◽  
Withaferin A ◽  
Head Group ◽  
Polar Head Group ◽  
Drug Molecules ◽  
Natural Drugs ◽  
The Impact

AbstractPoor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in the clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs - withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that withaferin-A, but not withanone, could proficiently transverse through the model membrane. The free energy profiles obtained were in accordance with the physico-chemical properties of the investigated drug molecules. It was observed that the polar head group of the bilayer exhibits high resistance for the passage of withanone as compared to withaferin-A, while the interior of the membrane behaves similarly for both withanolides. The solvation analysis revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force. The impact of the favorable interaction of terminal oxygen (O5) of withaferin-A with the phosphate of the membrane led to its smooth passage across the bilayer. The computational predictions were validated by raising and recruiting unique antibodies that react to withaferin-A and withanone. Further, the time-lapsed analyses of control and treated human normal and cancer cells, demonstrated proficient permeation of withaferin-A, but not withanone, through normal cells. These data strongly validated our computational method for predicting permeability and hence bioavailability of candidate compounds in the drug development process.Statement of significanceWhat determines the bioavailability of a drug? Does the ability to cross cell membrane determine this? A combined simulation/experimental study of the permeability of two natural drugs - withanolides (Wi-A and Wi-N) across the cell membrane was conducted. In the computational portion of the study, steered MD simulations were performed to investigate the propensity of the two molecules to permeate across the cell. It is found that Wi-A proceeds relatively simply across the cell compared to Wi-N. This trend was found to be consistent with experiment. This work is an important step towards understanding the molecular basis of permeability of natural drug molecules.

Statistical criteria of stellar population types

1966 ◽  
Vol 24 ◽  
pp. 101-110
Author(s):  
W. Iwanowska
Keyword(s):  
Stellar Population ◽  
Chemical Properties ◽  
Spectrophotometric Study ◽  
Physical And Chemical Properties ◽  
Population Type ◽  
The Galaxy ◽  
Distribution Parameters ◽  
Physical And Chemical ◽  
Statistical Criteria ◽  
And Chemical Properties

In connection with the spectrophotometric study of population-type characteristics of various kinds of stars, a statistical analysis of kinematical and distribution parameters of the same stars is performed at the Toruń Observatory. This has a twofold purpose: first, to provide a practical guide in selecting stars for observing programmes, second, to contribute to the understanding of relations existing between the physical and chemical properties of stars and their kinematics and distribution in the Galaxy.

Biophysical Measurement of Molecular Weight of Foot-and-Mouth Disease RNA Fragments

1974 ◽  
Vol 32 ◽  
pp. 262-263
Author(s):  
Sydney S. Breese ◽  
Howard L. Bachrach
Keyword(s):  
Chemical Properties ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Distilled Water ◽  
Bovine Plasma ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Carbon Coated ◽  
Rna Fragments ◽  
Physical And Chemical

Continuing studies on the physical and chemical properties of foot-and-mouth disease virus (FMDV) have included electron microscopy of RNA strands released when highly purified virus (1) was dialyzed against demlneralized distilled water. The RNA strands were dried on formvar-carbon coated electron microscope screens pretreated with 0.1% bovine plasma albumin in distilled water. At this low salt concentration the RNA strands were extended and were stained with 1% phosphotungstic acid. Random dispersions of strands were recorded on electron micrographs, enlarged to 30,000 or 40,000 X and the lengths measured with a map-measuring wheel. Figure 1 is a typical micrograph and Fig. 2 shows the distributions of strand lengths for the three major types of FMDV (A119 of 6/9/72; C3-Rezende of 1/5/73; and O1-Brugge of 8/24/73.

Decoration of specific sites on freeze-fractured membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 140-141
Author(s):  
H. Gross ◽  
H. Moor
Keyword(s):  
Pure Water ◽  
Freeze Fracture ◽  
Chemical Properties ◽  
Surface Forces ◽  
Sulfate Pentahydrate ◽  
Copper Sulfate Pentahydrate ◽  
Physico Chemical ◽  
Water Of Hydration ◽  
Small Container ◽  
Binding Forces

Fracturing under ultrahigh vacuum (UHV, p ≤ 10-9 Torr) produces membrane fracture faces devoid of contamination. Such clean surfaces are a prerequisite foe studies of interactions between condensing molecules is possible and surface forces are unequally distributed, the condensate will accumulate at places with high binding forces; crystallites will arise which may be useful a probes for surface sites with specific physico-chemical properties. Specific “decoration” with crystallites can be achieved nby exposing membrane fracture faces to water vopour. A device was developed which enables the production of pure water vapour and the controlled variation of its partial pressure in an UHV freeze-fracture apparatus (Fig.1a). Under vaccum (≤ 10-3 Torr), small container filled with copper-sulfate-pentahydrate is heated with a heating coil, with the temperature controlled by means of a thermocouple. The water of hydration thereby released enters a storage vessel.

Cathodoluminescence of Catalyst Crystallites

1982 ◽  
Vol 40 ◽  
pp. 664-665
Author(s):  
E.D. Boyes ◽  
P.L. Gai ◽  
D.B. Darby ◽  
C. Warwick
Keyword(s):  
Defect Density ◽  
Chemical Properties ◽  
Operating Conditions ◽  
Semiconductor Materials ◽  
Environmental Cell ◽  
High Resolution Structure ◽  
Commercially Important ◽  
Crystallographic Defects ◽  
Resolution Structure

The extended crystallographic defects introduced into some oxide catalysts under operating conditions may be a consequence and accommodation of the changes produced by the catalytic activity, rather than always being the origin of the reactivity. Operation without such defects has been established for the commercially important tellurium molybdate system. in addition it is clear that the point defect density and the electronic structure can both have a significant influence on the chemical properties and hence on the effectiveness (activity and selectivity) of the material as a catalyst. SEM/probe techniques more commonly applied to semiconductor materials, have been investigated to supplement the information obtained from in-situ environmental cell HVEM, ultra-high resolution structure imaging and more conventional AEM and EPMA chemical microanalysis.

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