Interaction energies for hollow and solid cylinders: Role of aspect ratio and particle orientation

To explore the sequence context-dependent nature of the human immunodeficiency virus type 1 (HIV-1) protease’s specificity and to provide a rationale for viral mutagenesis to study the potential role of the nucleocapsid (NC) processing in HIV-1 replication, synthetic oligopeptide substrates representing the wild-type and modified versions of the proximal cleavage site of HIV-1 NC were assayed as substrates of the HIV-1 protease (PR). The S1′ substrate binding site of HIV-1 PR was studied by an in vitro assay using KIVKCF↓NCGK decapeptides having amino acid substitutions of N17 residue of the cleavage site of the first zinc-finger domain, and in silico calculations were also performed to investigate amino acid preferences of S1′ site. Second site substitutions have also been designed to produce “revertant” substrates and convert a non-hydrolysable sequence (having glycine in place of N17) to a substrate. The specificity constants obtained for peptides containing non-charged P1′ substitutions correlated well with the residue volume, while the correlation with the calculated interaction energies showed the importance of hydrophobicity: interaction energies with polar residues were related to substantially lower specificity constants. Cleavable “revertants” showed one residue shift of cleavage position due to an alternative productive binding mode, and surprisingly, a double cleavage of a substrate was also observed. The results revealed the importance of alternative binding possibilities of substrates into the HIV-1 PR. The introduction of the “revertant” mutations into infectious virus clones may provide further insights into the potential role of NC processing in the early phase of the viral life-cycle.

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Investigation into the role of poly(vinylpyrrolidone) in the growth of high aspect ratio silver nanowires

Inorganic Chemistry Communications ◽

10.1016/j.inoche.2021.108558 ◽

2021 ◽

Vol 128 ◽

pp. 108558

Author(s):

Yuyue Guo ◽

Yangfei Hu ◽

Xiaojiong Luo ◽

Shudong Lin ◽

Jiwen Hu ◽

...

Keyword(s):

Aspect Ratio ◽

High Aspect Ratio ◽

Silver Nanowires

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Flow Measurements in a Nozzle Guide Vane Passage With a Low Aspect Ratio and Endwall Contouring

Volume 3: Heat Transfer; Electric Power; Industrial and Cogeneration ◽

10.1115/2000-gt-0213 ◽

2000 ◽

Cited By ~ 6

Author(s):

Steven W. Burd ◽

Terrence W. Simon

Keyword(s):

Aspect Ratio ◽

Flow Field ◽

Guide Vane ◽

Flow Measurements ◽

Vast Number ◽

Aspect Ratios ◽

Nozzle Guide Vane ◽

Endwall Contouring ◽

Nozzle Guide

The vast number of turbine cascade studies in the literature has been performed in straight-endwall, high-aspect-ratio, linear cascades. As a result, there has been little appreciation for the role of, and added complexity imposed by, reduced aspect ratios. There also has been little documentation of endwall profiling at these reduced spans. To examine the role of these factors on cascade hydrodynamics, a large-scale nozzle guide vane simulator was constructed at the Heat Transfer Laboratory of the University of Minnesota. This cascade is comprised of three airfoils between one contoured and one flat endwall. The geometries of the airfoils and endwalls, as well as the experimental conditions in the simulator, are representative of those in commercial operation. Measurements with hot-wire anemometry were taken to characterize the flow approaching the cascade. These measurements show that the flow field in this cascade is highly elliptic and influenced by pressure gradients that are established within the cascade. Exit flow field measurements with triple-sensor anemometry and pressure measurements within the cascade indicate that the acceleration imposed by endwall contouring and airfoil turning is able to suppress the size and strength of key secondary flow features. In addition, the flow field near the contoured endwall differs significantly from that adjacent to the straight endwall.

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Role of growth rate on the orientational alignment of Escherichia coli in a slit

Royal Society Open Science ◽

10.1098/rsos.170463 ◽

2017 ◽

Vol 4 (6) ◽

pp. 170463 ◽

Cited By ~ 7

Author(s):

Julian Sheats ◽

Bianca Sclavi ◽

Marco Cosentino Lagomarsino ◽

Pietro Cicuta ◽

Kevin D. Dorfman

Keyword(s):

Escherichia Coli ◽

Growth Rate ◽

Aspect Ratio ◽

Density Fluctuations ◽

Global Alignment ◽

Similar Amount ◽

Cell Area ◽

Nematic Ordering ◽

Side Walls

We present experimental data on the nematic alignment of Escherichia coli bacteria confined in a slit, with an emphasis on the effect of growth rate and corresponding changes in cell aspect ratio. Global alignment with the channel walls arises from the combination of local nematic ordering of nearby cells, induced by cell division and the elongated shape of the cells, and the preferential orientation of cells proximate to the side walls of the slit. Decreasing the growth rate leads to a decrease in alignment with the walls, which is attributed primarily to effects of changing cell aspect ratio rather than changes in the variance in cell area. Decreasing confinement also reduces the degree of alignment by a similar amount as a decrease in the growth rate, but the distribution of the degree of alignment differs. The onset of alignment with the channel walls is coincident with the slits reaching their steady-state occupancy and connected to the re-orientation of locally aligned regions with respect to the walls during density fluctuations.

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The Role of Geometry Parameters and Fin Aspect Ratio of Sub-20nm SOI-FinFET: An Analysis Towards Analog and RF Circuit Design

IEEE Transactions on Nanotechnology ◽

10.1109/tnano.2015.2415555 ◽

2015 ◽

Vol 14 (3) ◽

pp. 546-554 ◽

Cited By ~ 46

Author(s):

S. K. Mohapatra ◽

K. P. Pradhan ◽

D. Singh ◽

P. K. Sahu

Keyword(s):

Aspect Ratio ◽

Circuit Design ◽

Rf Circuit Design ◽

Rf Circuit

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Assessment of surface energetic heterogeneity of synthetic Na- saponites. The role of layer charge

Clay Minerals ◽

10.1180/0009855023710016 ◽

2002 ◽

Vol 37 (1) ◽

pp. 39-57 ◽

Cited By ~ 45

Author(s):

L. J. Michot ◽

F. Villiéras

Keyword(s):

Aspect Ratio ◽

Gas Adsorption ◽

High Energy ◽

Layer Charge ◽

Adsorption Mechanisms ◽

Energetic Heterogeneity ◽

Complex Adsorption ◽

Adsorption Energy Distribution ◽

Synthetic Saponite

AbstractHigh-resolution gas adsorption techniques were used to analyse the evolution of the aspect ratio and adsorption energy distribution on synthetic saponite samples with increasing layer charge. Using Ar as a gaseous probe, the aspect ratio of the saponite particles can be determined easily by decomposing the derivative adsorption isotherms and taking into account high-energy sites which can be assigned to talc-like ditrigonal cavities. Changes in the shape of the elementary particles are observed for layer charges above 1.30, i.e. when all the ditrigonal cavities contain at least one Al atom substituting for Si. When N2 is used as a probe, high-energy sites that could be wrongly interpreted as micropores on the basis of classical t-plot treatments are observed whatever the layer charge. Using the information obtained from both Ar and N2, schemes for describing adsorption can be proposed for all layer charges and suggest complex adsorption mechanisms for charged clay minerals.

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