PARAMETRIZATION OF THE TORSION POTENTIAL IN ALL-ATOM MODELS OF HYDROCARBON MOLECULES USING A SIMPLIFIED EXPRESSION FOR THE DEFORMATION ENERGY OF VALENCE BONDS AND ANGLES

2021 ◽  
Vol 62 (11) ◽  
pp. 1653-1666
Author(s):  
A. V. Teplukhin
Keyword(s):  
Deformation Energy ◽  
Torsion Potential ◽  
Hydrocarbon Molecules ◽  
Valence Bonds

An Attack on the Contamination Problem in the Electron Microscope

1967 ◽  
Vol 25 ◽  
pp. 368-368
Author(s):  
J. J. Kelsch ◽  
A. Holtz
Keyword(s):  
Electron Microscope ◽  
Pressure Gradient ◽  
Ionization Potential ◽  
Simple Solution ◽  
Specimen Surface ◽  
Contamination Rate ◽  
Local Pressure ◽  
High Ionization ◽  
Hydrocarbon Molecules ◽  
Contamination Problem

A simple solution to the serious problem of specimen contamination in the electron microscope is presented. This is accomplished by the introduction of clean helium into the vacuum exactly at the specimen position. The local pressure gradient thus established inhibits the migration of hydrocarbon molecules to the specimen surface. The high ionization potential of He permits the use of relatively large volumes of the gas, without interfering with gun stability. The contamination rate is reduced on metal samples by a factor of 10.

New replica method with plasma polymerized film by glow discharge

1988 ◽  
Vol 46 ◽  
pp. 414-415
Author(s):  
A. Tanaka ◽  
M. Yamaguchi ◽  
T. Hirano
Keyword(s):  
Power Supply ◽  
Plasma Polymerization ◽  
Vacuum Chamber ◽  
Complex Surface ◽  
Replica Method ◽  
Metal Extraction ◽  
High Voltage Power Supply ◽  
Negative Glow ◽  
Hydrocarbon Gas ◽  
Hydrocarbon Molecules

The plasma polymerization replica method and its apparatus have been devised by Tanaka (1-3). We have published several reports on its application: surface replicas of biological and inorganic specimens, replicas of freeze-fractured tissues and metal-extraction replicas with immunocytochemical markers.The apparatus for plasma polymerization consists of a high voltage power supply, a vacuum chamber containing a hydrocarbon gas (naphthalene, methane, ethylene), and electrodes of an anode disk and a cathode of the specimen base. The surface replication by plasma polymerization in negative glow phase on the cathode was carried out by gassing at 0.05-0.1 Torr and glow discharging at 1.5-3 kV D.C. Ionized hydrocarbon molecules diffused into complex surface configurations and deposited as a three-dimensionally polymerized film of 1050 nm in thickness.The resulting film on the complex surface had uniform thickness and showed no granular texture. Since the film was chemically inert, resistant to heat and mecanically strong, it could be treated with almost any organic or inorganic solvents.

Reduction of Specimen Contamination in Electron-Beam Instruments

1976 ◽  
Vol 34 ◽  
pp. 576-577
Author(s):  
G. Lehmpfuhl ◽  
P. J. Smith
Keyword(s):  
Electron Beam ◽  
Cold Trap ◽  
Beam Diameter ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Hydrocarbon Molecules ◽  
Electron Microscopes ◽  
Combination Of Methods ◽  
Convergent Beam ◽  
Very High

Specimens being observed with electron-beam instruments are subject to contamination, which is due to polymerization of hydrocarbon molecules by the beam. This effect becomes more important as the size of the beam is reduced. In convergent-beam studies with a beam diameter of 100 Å, contamination was observed to grow on samples at very high rates. Within a few seconds needles began forming under the beam on both the top and the underside of the sample, at growth rates of 400-500 Å/s, severely limiting the time available for observation. Such contamination could cause serious difficulty in examining a sample with the new scanning transmission electron microscopes, in which the beam is focused to a few angstroms.We have been able to reduce the rate of contamination buildup by a combination of methods: placing an anticontamination cold trap in the sample region, preheating the sample before observation, and irradiating the sample with a large beam before observing it with a small beam.

A theory of contamination in electron microscopes by surface diffusion

1978 ◽  
Vol 36 (1) ◽  
pp. 116-117
Author(s):  
J.T. Fourie
Keyword(s):  
Electron Beam ◽  
Surface Diffusion ◽  
High Vacuum ◽  
Ultra High Vacuum ◽  
Physical Parameters ◽  
Carbon Compounds ◽  
Hydrocarbon Molecules ◽  
Electron Microscopes ◽  
Primary Electrons ◽  
Long Chain

Contamination in electron microscopes can be a serious problem in STEM or in situations where a number of high resolution micrographs are required of the same area in TEM. In modern instruments the environment around the specimen can be made free of the hydrocarbon molecules, which are responsible for contamination, by means of either ultra-high vacuum or cryo-pumping techniques. However, these techniques are not effective against hydrocarbon molecules adsorbed on the specimen surface before or during its introduction into the microscope. The present paper is concerned with a theory of how certain physical parameters can influence the surface diffusion of these adsorbed molecules into the electron beam where they are deposited in the form of long chain carbon compounds by interaction with the primary electrons.

scholarly journals A deformation energy model reveals sequence-dependent property of nucleosome positioning

Chromosoma ◽  
2021 ◽  
Vol 130 (1) ◽  
pp. 27-40
Author(s):  
Guoqing Liu ◽  
Hongyu Zhao ◽  
Hu Meng ◽  
Yongqiang Xing ◽  
Lu Cai
Keyword(s):  
Budding Yeast ◽  
Nucleosome Occupancy ◽  
Nucleosome Positioning ◽  
Deformation Energy ◽  
Energy Model ◽  
Structural Parameter ◽  
High Deformation ◽  
Dna Deformation ◽  
Genome Wide ◽  
Genomic Regions

AbstractWe present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning.

scholarly journals Flow of long chain hydrocarbons through carbon nanotubes (CNTs)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pranay Asai ◽  
Palash Panja ◽  
Raul Velasco ◽  
Milind Deo
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamic ◽  
Continuum Models ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Pharmaceutical Applications ◽  
Molecular Sizes ◽  
Hydrocarbon Molecules ◽  
Pressure Driven Flow ◽  
Long Chain

AbstractThe pressure-driven flow of long-chain hydrocarbons in nanosized pores is important in energy, environmental, biological, and pharmaceutical applications. This paper examines the flow of hexane, heptane, and decane in carbon nanotubes (CNTs) of pore diameters 1–8 nm using molecular dynamic simulations. Enhancement of water flow in CNTs in comparison to rates predicted by continuum models has been well established in the literature. Our work was intended to observe if molecular dynamic simulations of hydrocarbon flow in CNTs produced similar enhancements. We used the OPLS-AA force field to simulate the hydrocarbons and the CNTs. Our simulations predicted the bulk densities of the hydrocarbons to be within 3% of the literature values. Molecular sizes and shapes of the hydrocarbon molecules compared to the pore size create interesting density patterns for smaller sized CNTs. We observed moderate flow enhancements for all the hydrocarbons (1–100) flowing through small-sized CNTs. For very small CNTs the larger hydrocarbons were forced to flow in a cork-screw fashion. As a result of this flow orientation, the larger molecules flowed as effectively (similar enhancements) as the smaller hydrocarbons.

scholarly journals Influence of niobium and yttrium on plastic deformation energy and plasticity of Ti-based amorphous alloys

China Foundry ◽  
2021 ◽  
Vol 18 (1) ◽  
pp. 60-67
Author(s):  
Sheng-feng Shan ◽  
Hao Wang ◽  
Bing Zhang ◽  
Yuan-zhi Jia ◽  
Ming-zhen Ma
Keyword(s):  
Plastic Deformation ◽  
Amorphous Alloys ◽  
Deformation Energy

Calculation of the electronic structure and energetic characteristics of hydrocarbon molecules by the CNDO/BW method

1975 ◽  
Vol 18 (1) ◽  
pp. 37-40
Author(s):  
V. P. Shcherbina ◽  
V. S. Cherkasov ◽  
Yu. A. Tishchenko ◽  
V. I. Danilova
Keyword(s):  
Electronic Structure ◽  
Hydrocarbon Molecules

scholarly journals Measurements of the 3.3 μm Diffuse Galactic Emission Feature with AROME

1990 ◽  
Vol 139 ◽  
pp. 212-213
Author(s):  
M. Giard ◽  
F. Pajot ◽  
J. M. Lamarre ◽  
G. Serra
Keyword(s):  
Surface Brightness ◽  
Galactic Plane ◽  
Elevation Angle ◽  
Emission Feature ◽  
Field Of View ◽  
Interstellar Matter ◽  
Galactic Emission ◽  
Polycyclic Aromatic ◽  
Hydrocarbon Molecules ◽  
Ir Emission

AROME∗ is a balloon-borne experiment which was built to carry out measurements of IR emission features in the diffuse galactic flux. The field of view is 0.5° and surface brightness gradients are detected through azimuthal scanning at a constant elevation angle. The detection of a feature is done by comparison of the fluxes measured in narrow and wide photometric bands centered on the feature's wavelength. Two flights have been performed (August 1987, October 1988), which detected a 3.3 μm feature in the direction of the galactic plane −6° < b < 6°, 60° > l > −50°. Since this feature is characteristic of aromatic C-H bonds, we assigned it to the emission of transiently heated polycyclic aromatic hydrocarbon molecules (PAHs). With this assumption, AROME measurements show that PAHs are an ubiquitous component of the interstellar matter which contain about 10% of the available cosmic carbon.

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