scholarly journals The abTEM code: transmission electron microscopy from first principles

2021 ◽  
Vol 1 ◽  
pp. 24
Author(s):  
Jacob Madsen ◽  
Toma Susi
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Open Source ◽  
Density Functional ◽  
Hexagonal Boron Nitride ◽  
Phase Reconstruction ◽  
Simulation Code ◽  
Atomic Simulation ◽  
Transmission Electron ◽  
Scattering Potential

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electrons. As instrumentation has advanced, new measurements have revealed subtle details of the scattering potential that were previously not accessible to experiment. We have created an open-source simulation code designed to meet these demands by integrating the ability to calculate the potential via density functional theory (DFT) with a flexible modular software design. abTEM can simulate most standard imaging modes and incorporates the latest algorithmic developments. The development of new techniques requires a program that is accessible to domain experts without extensive programming experience. abTEM is written purely in Python and designed for easy modification and extension. The effective use of modern open-source libraries makes the performance of abTEM highly competitive with existing optimized codes on both CPUs and GPUs and allows us to leverage an extensive ecosystem of libraries, such as the Atomic Simulation Environment and the DFT code GPAW. abTEM is designed to work in an interactive Python notebook, creating a seamless and reproducible workflow from defining an atomic structure, calculating molecular dynamics (MD) and electrostatic potentials, to the analysis of results, all in a single, easy-to-read document.  This article provides ongoing documentation of abTEM development. In this first version, we show use cases for hexagonal boron nitride, where valence bonding can be detected, a 4D-STEM simulation of molybdenum disulfide including ptychographic phase reconstruction, a comparison of MD and frozen phonon modeling for convergent-beam electron diffraction of a 2.6-million-atom silicon system, and a performance comparison of our fast implementation of the PRISM algorithm for a decahedral 20000-atom gold nanoparticle.

scholarly journals The abTEM code: transmission electron microscopy from first principles

2021 ◽  
Vol 1 ◽  
pp. 24
Author(s):  
Jacob Madsen ◽  
Toma Susi
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Open Source ◽  
Density Functional ◽  
Hexagonal Boron Nitride ◽  
Phase Reconstruction ◽  
Simulation Code ◽  
Atomic Simulation ◽  
Transmission Electron ◽  
Scattering Potential

Simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret experimental data. Since nuclear cores dominate electron scattering, the scattering potential is typically described using the independent atom model, which completely neglects valence bonding and its effect on the transmitting electrons. As instrumentation has advanced, new measurements have revealed subtle details of the scattering potential that were previously not accessible to experiment. We have created an open-source simulation code designed to meet these demands by integrating the ability to calculate the potential via density functional theory (DFT) with a flexible modular software design. abTEM can simulate most standard imaging modes and incorporates the latest algorithmic developments. The development of new techniques requires a program that is accessible to domain experts without extensive programming experience. abTEM is written purely in Python and designed for easy modification and extension. The effective use of modern open-source libraries makes the performance of abTEM highly competitive with existing optimized codes on both CPUs and GPUs and allows us to leverage an extensive ecosystem of libraries, such as the Atomic Simulation Environment and the DFT code GPAW. abTEM is designed to work in an interactive Python notebook, creating a seamless and reproducible workflow from defining an atomic structure, calculating molecular dynamics (MD) and electrostatic potentials, to the analysis of results, all in a single, easy-to-read document.  This article provides ongoing documentation of abTEM development. In this first version, we show use cases for hexagonal boron nitride, where valence bonding can be detected, a 4D-STEM simulation of molybdenum disulfide including ptychographic phase reconstruction, a comparison of MD and frozen phonon modeling for convergent-beam electron diffraction of a 2.6-million-atom silicon system, and a performance comparison of our fast implementation of the PRISM algorithm for a decahedral 20000-atom gold nanoparticle.

scholarly journals Synthesis, Computational Pharmacokinetics Report, Conceptual DFT-Based Calculations and Anti-Acetylcholinesterase Activity of Hydroxyapatite Nanoparticles Derived From Acorus Calamus Plant Extract

2021 ◽  
Vol 9 ◽  
Author(s):  
Sushma Pradeep ◽  
Anisha S. Jain ◽  
Chandan Dharmashekara ◽  
Shashanka K. Prasad ◽  
Nagaraju Akshatha ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Acetylcholinesterase Activity ◽  
Acorus Calamus ◽  
Hydroxyapatite Nanoparticles ◽  
Transmission Electron ◽  
In Silico Studies ◽  
Crystalline Nature

Over the years, Alzheimer’s disease (AD) treatments have been a major focus, culminating in the identification of promising therapeutic targets. A herbal therapy approach has been required by the demand of AD stage-dependent optimal settings. Present study describes the evaluation of anti-acetylcholinesterase (AChE) activity of hydroxyapatite nanoparticles derived from an Acorus calamus rhizome extract (AC-HAp NPs). The structure and morphology of as-prepared (AC-HAp NPs) was confirmed using powder X-ray diffractometer (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and high-resolution transmission electron microscopy (HR-TEM). The crystalline nature of as-prepared AC-HAp NPs was evident from XRD pattern. The SEM analysis suggested the spherical nature of the synthesized material with an average diameter between 30 and 50 nm. Further, the TEM and HR-TEM images revealed the shape and size of as-prepared (AC-HAp NPs). The interplanar distance between two lattice fringes was found to be 0.342 nm, which further supported the crystalline nature of the material synthesized. The anti-acetylcholinesterase activity of AC-HAp NPs was greater as compared to that of pure HAp NPs. The mechanistic evaluation of such an activity carried out using in silico studies suggested that the anti-acetylcholinesterase activity of phytoconstituents derived from Acorus calamus rhizome extract was mediated by BNDF, APOE4, PKC-γ, BACE1 and γ-secretase proteins. The global and local descriptors, which are the underpinnings of Conceptual Density Functional Theory (CDFT), have been predicted through the MN12SX/Def2TZVP/H2O model chemistry to help in the comprehension of the chemical reactivity properties of the five ligands considered in this study. With the further objective of analyzing their bioactivity, the CDFT studies are complemented with the estimation of some useful computed pharmacokinetics indices, their predicted biological targets, and the ADMET parameters related to the bioavailability of the five ligands are also reported.

scholarly journals Pure Acetylene Semihydrogenation over Ni–Cu Bimetallic Catalysts: Effect of the Cu/Ni Ratio on Catalytic Performance

Nanomaterials ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 509 ◽  
Author(s):  
Shuzhen Zhou ◽  
Lihua Kang ◽  
Xuening Zhou ◽  
Zhu Xu ◽  
Mingyuan Zhu
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Bimetallic Catalysts ◽  
Density Functional ◽  
Calcium Carbide ◽  
Raw Material ◽  
Impregnation Method ◽  
X Ray ◽  
Transmission Electron ◽  
Ethylene Selectivity

Ethylene is an important chemical raw material and with the increasing consumption of petroleum resources, the production of ethylene through the calcium carbide acetylene route has important research significance. In this work, a series of bimetallic catalysts with different Cu/Ni molar ratios are prepared by co-impregnation method for the hydrogenation of calcium carbide acetylene to ethylene. The introduction of an appropriate amount of Cu effectively inhibits not only the formation of ethane and green oil, thus increasing the selectivity of ethylene, but also the formation of carbon deposits, which improves the stability of the catalyst. The ethylene selectivity of the Ni–Cu bimetallic catalyst increases from 45% to 63% compared with the Ni monometallic counterpart and the acetylene conversion still can reach 100% at the optimal conditions of 250 °C, 8000 mL·g−1·h−1 and V(H2)/V(C2H2) = 3. X-ray diffraction and transmission electron microscopy confirmed that the metal particles were highly dispersed on the support, High-resolution transmission electron microscopy and H2-Temperature programmed reduction proved that there was an interaction between Ni and Cu, combined with X-ray photoelectron spectroscopy and density functional theory calculations results, Cu transferred electrons to Ni changed the Ni electron cloud density in NiCux catalysts, thus reducing the adsorption of acetylene and ethylene, which is favorable to ethylene selectivity.

The Structure and Passivation Effects of Double-Positioning Twin Boundaries in CdTe

2005 ◽  
Vol 865 ◽  
Author(s):  
Yanfa Yan ◽  
M.M. Al-Jassim ◽  
K.M. Jones
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
High Resolution ◽  
First Principles ◽  
Density Functional ◽  
Dangling Bonds ◽  
Twin Boundaries ◽  
Transmission Electron ◽  
Cl Atoms ◽  
Image Simulations

AbstractUsing the combination of high-resolution transmission electron microscopy, first-principles density-functional total-energy calculations, and image simulations, we studied the atomic structure and passivation effects of double-positioning (DP) twin boundaries in CdTe. The DP twin boundaries are found to contain more Te dangling bonds than Cd dangling bonds, resulting in energy states in the bandgap that are detrimental to the electronic properties of CdTe. We found that I, Br, Cl, S, and O atoms present passivation effects on the DP twin boundaries to differing degrees, whereas H does not passivate the boundaries. Of all these impurities, I and Cl atoms present the best passivation effects on the DP twin boundaries. The superior passivation effects are realized by either terminating the Cd atoms with dangling bonds, or substituting the Te atoms with dangling bonds in the DP twin boundaries in CdTe by Cl and I atoms.

scholarly journals Acid-Free Hydrothermal-Extraction and Molecular Structure of Carbon Quantum Dots Derived from Empty Fruit Bunch Biochar

Materials ◽  
2020 ◽  
Vol 13 (15) ◽  
pp. 3356
Author(s):  
Norhanisah Jamaludin ◽  
Tong Ling Tan ◽  
Alif Syafiq Kamarol Zaman ◽  
Amir Reza Sadrolhosseini ◽  
Suraya Abdul Rashid
Keyword(s):  
Molecular Structure ◽  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Quantum Dots ◽  
Photoelectron Spectroscopy ◽  
Density Functional ◽  
Hydrothermal Process ◽  
Carbon Quantum Dots ◽  
Empty Fruit Bunch ◽  
Transmission Electron

Carbon quantum dots (CQD) have great potential to be used in various applications due to their unique electrical and optical properties. Herein, a facile, green and eco-friendly hydrothermal method for the preparation of carbon quantum dots was achieved using empty fruit bunch (EFB) biochar as a renewable and abundant carbon source. In the current study, the role of the hydrothermal process was observed and studied by comparing the morphology and optical characteristics of CQD obtained from EFB biochar. Interestingly, based on the high-resolution transmission electron microscopy (HRTEM) result, a considerably similar carbon quantum dots structure can be observed for the EFB biochar sample, showing the similar size and distribution of CQD. To further discuss the extraction of CQD from EFB biochar, a mechanism based on hydrothermal-induced extraction of CQD is proposed. The optimal structure of CQD deduced by density functional theory (DFT) in energy and dipole momentum was about 2057.4905 Hatree and 18.1699 Debye, respectively. This study presents a practical experimental approach in elucidating the molecular structure of photoluminescence CQD based on the Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) results.

scholarly journals Point defects in turbostratic stacked bilayer graphene

Nanoscale ◽  
2017 ◽  
Vol 9 (36) ◽  
pp. 13725-13730 ◽  
Author(s):  
Chuncheng Gong ◽  
Sungwoo Lee ◽  
Suklyun Hong ◽  
Euijoon Yoon ◽  
Gun-Do Lee ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Point Defects ◽  
Density Functional ◽  
Tight Binding ◽  
Bilayer Graphene ◽  
Dynamics Simulation ◽  
Functional Theory ◽  
Transmission Electron ◽  
Aberration Corrected

The point defects in turbostratic bilayer graphene are characterized using aberration-corrected transmission electron microscopy, density functional theory, and tight-binding molecular dynamics simulation.

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