Effect of the Molecular Weight and Density of Ambient Gas on Shock Wave in Laser-Assisted Nanostructuring

2008 ◽  
Author(s):  
Liying Guo ◽  
Xinwei Wang
Keyword(s):  
Shock Wave ◽  
Molecular Weight ◽  
Near Field ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Shock Wave Formation ◽  
Ambient Gas ◽  
Dynamics Simulations ◽  
Lower Ratio

This paper presents the results from molecular dynamics simulations that are performed to explore the properties of the shock wave during laser-assisted near field surface nanostructuring. A quasi-three dimensional model is constructed to study systems consisting of over 2 million atoms. This work includes studies on the velocity as well as pressure evolution of shock wave front with respect to different solid/gas molecular mass ratios and different ambient gas densities. The limitation on shock wave formation under the same laser fluence is also investigated. The results show that lower ratio of the solid/gas molecular weight weakens the strength of the shock wave during the nanostructuring process. Additionally, the formation and attenuation of the shock wave under different ambient gas conditions is studied in substantial detail.

scholarly journals Roughness effect on the efficiency of dimer antenna based biosensor

2012 ◽  
Vol 1 (2) ◽  
pp. 41 ◽  
Author(s):  
D. Barchiesi ◽  
S. Kessentini
Keyword(s):  
Surface Roughness ◽  
Near Field ◽  
Three Dimensional ◽  
Biological Molecules ◽  
Far Field ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Roughness Effect ◽  
Highly Sensitive ◽  
Local Plasmon

The fabrication process of nanodevices is continually improved. However, most of the nanodevices, such as biosensors present rough surfaces with mean roughness of some nanometers even if the deposition rate of material is more controlled. The effect of roughness on performance of biosensors was fully addressed for plane biosensors and gratings, but rarely addressed for biosensors based on Local Plasmon Resonance. The purpose of this paper is to evaluate numerically the influence of nanometric roughness on the efficiency of a dimer nano-biosensor (two levels of roughness are considered). Therefore, we propose a general numerical method, that can be applied to any other nanometric shape, to take into account the roughness in a three dimensional model. The study focuses on both the far-field, which corresponds to the experimental detected data, and the near-field, responsible for exciting and then detecting biological molecules. The results suggest that the biosensor efficiency is highly sensitive to the surface roughness. The roughness can produce important shifts of the extinction efficiency peak and a decrease of its amplitude resulting from changes in the distribution of near-field and absorbed electric field intensities.

Molecular Dynamics Simulations of Shocks and Detonations in a Model 3D Energetic Crystal with Defects

1992 ◽  
Vol 296 ◽  
Author(s):  
Lee Phillips
Keyword(s):  
Reaction Rate ◽  
Hot Spot ◽  
Detonation Front ◽  
Three Dimensional ◽  
Perfect Crystal ◽  
Chemical Activity ◽  
Chemical Bonds ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Dynamics Simulations

AbstractWe examine shock induced detonation in a three-dimensional model of a nitromethane crystal. The crystal may contain a defect in the form of a small void. Three regimes are identified: the shock can be weak enough that no chemical bonds are broken; the shock can be so strong that a detonation front is established in the perfect crystal; or the shock can be of intermediate strength, where chemical activity requires the existence of the defect. In all regimes, the defect increases the reaction rate and causes a hot spot to appear.

scholarly journals Enzymatic and structural properties of human glutamine:fructose-6-phosphate amidotransferase 2 (hGFAT2)

2020 ◽  
pp. jbc.RA120.015189
Author(s):  
Isadora A. Oliveira ◽  
Diego Allonso ◽  
Tácio V. A. Fernandes ◽  
Daniela M.S. Lucena ◽  
Gustavo T. Ventura ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Expression And Purification ◽  
Three Dimensional Model ◽  
Hexosamine Biosynthetic Pathway ◽  
E Coli ◽  
Cellular Processes ◽  
Catalytically Active ◽  
Dynamics Simulations

Glycoconjugates play a central role in several cellular processes and alteration in their composition is associated with numerous human pathologies. Substrates for cellular glycosylation are synthesized in the hexosamine biosynthetic pathway, which is controlled by the glutamine:fructose-6-phosphate amidotransfera-se (GFAT). Human isoform 2 GFAT (hGFAT2) has been implicated in diabetes and cancer; however, there is no information about structural and enzymatic properties of this enzyme. Here, we report a successful expression and purification of a catalytically active recombinant hGFAT2 (rhGFAT2) in E. coli cells fused or not to a HisTag at the C-terminal end. Our enzyme kinetics data suggest that hGFAT2 does not follow the expected ordered bi-bi mechanism, and performs the glucosamine-6-phosphate synthesis much more slowly than previously reported for other GFATs. In addition, hGFAT2 is able to isomerize fructose-6-phosphate into glucose-6-phosphate even in the presence of equimolar amounts of glutamine, which results in unproductive glutamine hydrolysis. Structural analysis of a three-dimensional model of rhGFAT2, corroborated by circular dichroism data, indicated the presence of a partially structured loop in the glutaminase domain, whose sequence is present in eukaryotic enzymes but absent in the E. coli homolog. Molecular dynamics simulations suggest that this loop is the most flexible portion of the protein, and plays a key role on conformational states of hGFAT2. Thus, our study provides the first comprehensive set of data on the structure, kinetics and mechanics of hGFAT2, which will certainly contribute to further studies on the (patho)physiology of hGFAT2.

scholarly journals Updates on enzymatic and structural properties of human glutamine: fructose-6-phosphate amidotransferase 2 (hGFAT2)

2020 ◽  
Author(s):  
Isadora A. Oliveira ◽  
Diego Allonso ◽  
Tácio V. A. Fernandes ◽  
Daniela M. S. Lucena ◽  
Gustavo T. Ventura ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Expression And Purification ◽  
Three Dimensional Model ◽  
Hexosamine Biosynthetic Pathway ◽  
E Coli ◽  
Cellular Processes ◽  
Catalytically Active ◽  
Dynamics Simulations

AbstractGlycoconjugates play a central role in several cellular processes and alteration in their composition is associated to human pathologies. The hexosamine biosynthetic pathway is a route through which cells obtain substrates for cellular glycosylation, and is controlled by the glutamine: fructose-6-phosphate amidotransferase (GFAT). Human isoform 2 GFAT (hGFAT2) has been implicated in diabetes and cancer, however, there is no information about structural and enzymatic properties of this enzyme. Here, we report a successful expression and purification of a catalytically active recombinant hGFAT2 (rhGFAT2) in E. coli cells fused or not to a HisTag at the C-terminal end. Our enzyme kinetics data suggest that hGFAT2 does not follow the ordered bi-bi mechanism, and performs the glucosamine-6-phosphate synthesis much slowly than previously reported for other GFATs. In addition, hGFAT2 is able to isomerase fructose-6-phosphate into glucose-6-phosphate even in presence of equimolar amounts of glutamine, in an unproductive glutamine hydrolysis. Structural analysis of the generated three-dimensional model rhGFAT2, corroborated by circular dichroism data, indicated the presence of a partially structured loop in glutaminase domain, whose sequence is present in eukaryotic enzymes but absent in the E. coli homolog. Molecular dynamics simulations show such loop as the most flexible portion of the protein, which interacts with the protein mainly through the interdomain region, and plays a key role on conformational states of hGFAT2. Altogether, our study provides the first comprehensive set of data on the structure, kinetics and mechanics of hGFAT2, which will certainly contribute for further studies focusing on drug development targeting hGFAT2.

FDTD Study of the Surface Waves Detection in Apertureless Scanning Near-Field Microscopy

2008 ◽  
Author(s):  
G. Parent ◽  
S. Fumeron ◽  
D. Lacroix
Keyword(s):  
Surface Waves ◽  
Near Field ◽  
Fdtd Method ◽  
Three Dimensional ◽  
Far Field ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Experimental Tool ◽  
Field Transformation ◽  
Difference Time

Recent studies have shown the importance of surface waves in heat transfer near interfaces. The scanning near field optical microscopy (SNOM) provides an experimental tool to investigate the thermal electromagnetic field near surfaces. In this work, we present a three dimensional model of SNOM devices. This model is based on the finite-difference-time domain (FDTD) method associated to a near to far field transformation. Near field and far field scattered by a silicon tetrahedral tip and by a pecfectly conducting one are presented and discussed.

scholarly journals Three-Dimensional Model of Lanosterol 14α-Demethylase from Cryptococcus neoformans: Active-Site Characterization and Insights into Azole Binding

2009 ◽  
Vol 53 (8) ◽  
pp. 3487-3495 ◽  
Author(s):  
Chunquan Sheng ◽  
Zhenyuan Miao ◽  
Haitao Ji ◽  
Jianzhong Yao ◽  
Wenya Wang ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Active Site ◽  
Antifungal Agents ◽  
Fungal Infections ◽  
Three Dimensional ◽  
Rational Drug Design ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Functional Regions ◽  
Dynamics Simulations

ABSTRACT Cryptococcus neoformans is one of the most important causes of life-threatening fungal infections in immunocompromised patients. Lanosterol 14α-demethylase (CYP51) is the target of azole antifungal agents. This study describes, for the first time, the 3-dimensional model of CYP51 from Cryptococcus neoformans (CnCYP51). The model was further refined by energy minimization and molecular-dynamics simulations. The active site of CnCYP51 was well characterized by multiple-copy simultaneous-search calculations, and four functional regions important for rational drug design were identified. The mode of binding of the natural substrate and azole antifungal agents with CnCYP51 was identified by flexible molecular docking. A G484S substitution mechanism for azole resistance in CnCYP51, which might be important for the conformation of the heme environment, is suggested.

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