scholarly journals Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

2018 ◽  
Vol 148 (21) ◽  
pp. 215106 ◽  
Author(s):  
Maksim Kouza ◽  
Nguyen Truong Co ◽  
Mai Suan Li ◽  
Sebastian Kmiecik ◽  
Andrzej Kolinski ◽  
...  
Keyword(s):  
Mechanical Stability ◽  
Computational Study ◽  
Fibril Formation ◽  
Formation Time ◽  
State Control ◽  
Polypeptide Chains

Computational study on unconventional superconductivity and mechanical properties of novel antiferrromagnetic (Ca,Sr,Ba)Fe2Bi2 compounds

2019 ◽  
Vol 33 (28) ◽  
pp. 1950341
Author(s):  
D. S. Jayalakshmi ◽  
M. Sundareswari ◽  
E. Viswanathan ◽  
D. Hemanand ◽  
Venkat Pranesh
Keyword(s):  
Free Energy ◽  
Transport Theory ◽  
Mechanical Stability ◽  
Computational Study ◽  
Anisotropy Constant ◽  
Coupling Factor ◽  
The Novel ◽  
Electron Phonon Coupling ◽  
Constant Relaxation Time ◽  
Electron Transport Properties

The ab initio calculation is performed to investigate about the structural and the electron transport properties of the experimentally reported (parent) compounds viz., BaFe2As2, SrFe2As2, CaFe2As2 and the novel compounds which are anticipated from our computational work namely BaFe2Bi2, SrFe2Bi2, CaFe2Bi2 with different magnetic order. The space group of the reported compounds is I4/mmm (139) and belong to ThCr2Si2 type. The formation energies of the reported compounds are compared in the anti-ferromagnetic (AFM), nonmagnetic (NM) and ferromagnetic (FM) orders. From the comparison, it reveals that the anti-ferro magnetism is the stabled state for the reported compounds. At ambient temperature with constant relaxation time, the resistivity, power factor, Seebeck coefficient and electrical conductivity are computed by using BoltzTraP transport theory code. To explain the superconducting nature of the novel compounds the transition temperature (T[Formula: see text]), electron–phonon coupling factor and Debye temperature are calculated and presented. The mechanical stability of the compounds is examined by using Young’s, bulk and shear modulus, anisotropy constant and Poisson’s ratio which are calculated by using Tetra-elastic code. The Mechanical Temperament of these compounds is analyzed by using Pugh’s ratio. The ELATE tool is used to visualize the elastic properties of these compounds. The thermodynamical stability of the compounds is examined by using Gibbs free energy, vibrational Helmholtz free energy and entropy which are calculated by using Gibbs2 code. All the properties of the theoretically predicted (novel) compounds are analyzed and compared with their parent (experimentally reported) compounds.

Porosity Manipulation in Bottom-Enclosed Vertical Porous Structure to Improve Natural Convection Cooling Efficacy: A Computational Study

2020 ◽  
Vol 142 (5) ◽  
Author(s):  
Subhashish Dasgupta ◽  
Abhishek Gupta
Keyword(s):  
Natural Convection ◽  
Mechanical Stability ◽  
Computational Study ◽  
Original System ◽  
Solid Matrix ◽  
Thermal Engineering ◽  
Flow Acceleration ◽  
Convection Cooling ◽  
Cfd Analyses ◽  
Accelerating Flow

Abstract Flow acceleration by imposing flow channelization structures like chimneys and/or solid barriers to improve natural convection cooling in pure fluids, is a well-known technique and a thoroughly investigated topic in thermal engineering. However, accelerating flow through porous media, by using such a passive technique, is challenging due to restriction imposed by the solid matrix to the erection of such structures. This study is a unique investigation into a passive method to accelerate flow in natural convection cooling through a bottom-enclosed porous medium with a vertical heated structure at the center, a configuration that is commonly encountered in industry. The porous domain is divided into distinct zones varying in porosity while retaining the average porosity of the original system, to ensure enough structural stability to the vertical heating element. Employing computational fluid dynamics (CFD) analyses, the study shows that the method has the potential to significantly improve natural convection cooling by accelerating flow in tall porous structures while at the same time improves mechanical stability of such structures.

Computational Study of Unsteady Cavitating Vortex Flow in Axisymmetric Submerged Water Jet

2005 ◽  
Author(s):  
Guoyi Peng
Keyword(s):  
High Speed ◽  
Vortex Flow ◽  
Computational Study ◽  
Near Field ◽  
Vortex Formation ◽  
Water Jet ◽  
Formation Time ◽  
Two Phase ◽  
Cavitation Bubbles ◽  
Vortex Formation Time

Unsteady cavitating and non-cavitating flows of high-speed submerged water jet have been investigated numerically by applying an approach based on the two-phase cavitation model to clarify the behavior of cavitating vortex flow in the near field of jet. The cavitation intensity is calculated by VOF method accounting for expanding and contracting of cavitation bubbles with the barotropic relation and the unsteady flow is calculated by RANS method employing the RNG k-ε turbulence model under the assumption of locally homogeneous two-phase flow. Computations are focused on the behavior of starting jet, and the validity is confirmed by comparing with experimental data. The result shows that a starting vortex ring is generated around the jet periphery, and develops with the vortex formation time. The relative standoff distance of ring-like cavity of cavitation bubbles generated in the starting vortex increases with the dimensionless vortex formation time similarly under different injection velocities.

IS IT POSSIBLE TO PREDICT AMYLOIDOGENIC REGIONS FROM SEQUENCE ALONE?

2006 ◽  
Vol 04 (02) ◽  
pp. 373-388 ◽  
Author(s):  
OXANA V. GALZITSKAYA ◽  
SERGIY O. GARBUZYNSKIY ◽  
MICHAIL YU. LOBANOV
Keyword(s):  
Amino Acid ◽  
Protein Sequence ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Fibril Formation ◽  
Amino Acid Sequences ◽  
Amyloid Formation ◽  
Amyloid Fibril Formation ◽  
Polypeptide Chains ◽  
Proteins And Peptides

Identification of potentially amyloidogenic regions in polypeptide chains is very important because the amyloid fibril formation can be induced in most normal proteins. In our work we suggest a new method to detect amyloidogenic regions in protein sequence. It is based on the assumption that packing is tight inside an amyloid and therefore regions which could potentially pack well would have a tendency to form amyloids. This means that the regions with strong expected packing of residues would be responsible for the amyloid formation. We use this property to identify potentially amyloidogenic regions in proteins basing on their amino acid sequences only. Our predictions are consistent with known disease-related amyloidogenic regions for 8 of 11 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Predictions of the regions which are responsible for the formation of amyloid fibrils in proteins unrelated to disease have been also done.

Immunocytochemical Localization of Amyloid Protein AA in the “Dense Fibrillar Inclusions” of the Reticuloendothelical Cells

1977 ◽  
Vol 35 ◽  
pp. 438-439
Author(s):  
T. Shirahama ◽  
M. Skinner ◽  
A.S. Cohen
Keyword(s):  
Amyloid Fibril ◽  
Close Association ◽  
Gel Filtration ◽  
Fibril Formation ◽  
Amyloid Protein ◽  
Electron Microscopic ◽  
Amyloid Deposits ◽  
Amyloid Fibril Formation ◽  
Electron Microscopic Technique ◽  
Lysosomal System

A1thought the mechanisms of amyloidogenesis have not been entirely clarified, proteolysis of the parent proteins may be one of the important steps in the amyloid fibril formation. Recently, we reported that "dense fibrillar inclusions" (DFI), which had the characteristics of lysosomes and contained organized fibrillar profiles as well, were observed in the reticuloendothelial cells in close association with the foci of new amyloid deposits. We considered the findings as evidence for the involvement of lysosomal system in amyloid fibril formation (l). In the present study, we attempted to determine the identity of the contents of the DFI by the use of antisera against the amyloid protein (AA) and an immuno-electron microscopic technique.Amyloidosis was induced in CBA/J mice by daily injections of casein (l). AA was isolated from amyloid-laden spleens by gel filtration and antibody to it was produced in rabbits (2). For immunocytochemistry, the unlabeled antibody enzyme method (3) was employed.

An improved design for an Scanning Tunnelling Microscope (STM) for use in a Transmission Electron Microscope (TEM)

1991 ◽  
Vol 49 ◽  
pp. 384-385
Author(s):  
W.K. Lo ◽  
J.C.H. Spence
Keyword(s):  
Electron Microscope ◽  
Transmission Electron Microscope ◽  
Mechanical Stability ◽  
Scanning Tunnelling Microscope ◽  
Reflection Mode ◽  
Specimen Holder ◽  
Transmission Electron ◽  
Scanning Tunnelling ◽  
Improved Design

An improved design for a combination Scanning Tunnelling Microscope/TEM specimen holder is presented. It is based on earlier versions which have been used to test the usefulness of such a device. As with the earlier versions, this holder is meant to replace the standard double-tilt specimen holder of an unmodified Philips 400T TEM. It allows the sample to be imaged simultaneously by both the STM and the TEM when the TEM is operated in the reflection mode (see figure 1).The resolution of a STM is determined by its tip radii as well as its stability. This places strict limitations on the mechanical stability of the tip with respect to the sample. In this STM the piezoelectric tube scanner is rigidly mounted inside the endcap of the STM holder. The tip coarse approach to the sample (z-direction) is provided by an Inchworm which is located outside the TEM vacuum.

Experiments with a scanning tunneling microscope (STM) mounted in a scanning electron microscope (SEM)

1986 ◽  
Vol 44 ◽  
pp. 636-639
Author(s):  
Oliver C. Wells ◽  
Mark E. Welland
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Mechanical Stability ◽  
Tunneling Current ◽  
Feedback System ◽  
Scanning Tunneling ◽  
Surface Profiling ◽  
Close Proximity ◽  
Metal Tip ◽  
Scanning Electron

Scanning tunneling microscopes (STM) exist in two versions. In both of these, a pointed metal tip is scanned in close proximity to the specimen surface by means of three piezos. The distance of the tip from the sample is controlled by a feedback system to give a constant tunneling current between the tip and the sample. In the low-end STM, the system has a mechanical stability and a noise level to give a vertical resolution of between 0.1 nm and 1.0 nm. The atomic resolution STM can show individual atoms on the surface of the specimen.A low-end STM has been put into the specimen chamber of a scanning electron microscope (SEM). The first objective was to investigate technological problems such as surface profiling. The second objective was for exploratory studies. This second objective has already been achieved by showing that the STM can be used to study trapping sites in SiO2.

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