scholarly journals The Fingerprints of Resonant Frequency for Atomic Vacancy Defect Identification in Graphene

Nanomaterials ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3451
Author(s):  
Liu Chu ◽  
Jiajia Shi ◽  
Eduardo Souza de Cursi
Keyword(s):  
Resonant Frequency ◽  
Element Model ◽  
Vacancy Defect ◽  
Supplementary Information ◽  
Experimental Conditions ◽  
Defect Identification ◽  
Vacancy Defects ◽  
Detection And Identification ◽  
Atomic Vacancy ◽  
Defects Identification

The identification of atomic vacancy defects in graphene is an important and challenging issue, which involves inhomogeneous spatial randomness and requires high experimental conditions. In this paper, the fingerprints of resonant frequency for atomic vacancy defect identification are provided, based on the database of massive samples. Every possible atomic vacancy defect in the graphene lattice is considered and computed by the finite element model in sequence. Based on the sample database, the histograms of resonant frequency are provided to compare the probability density distributions and interval ranges. Furthermore, the implicit relationship between the locations of the atomic vacancy defects and the resonant frequencies of graphene is established. The fingerprint patterns are depicted by mapping the locations of atomic vacancy defects to the resonant frequency magnitudes. The geometrical characteristics of computed fingerprints are discussed to explore the feasibility of atomic vacancy defects identification. The work in this paper provides meaningful supplementary information for non-destructive defect detection and identification in nanomaterials.

scholarly journals The Effects of Random Porosities in Resonant Frequencies of Graphene Based on the Monte Carlo Stochastic Finite Element Model

2021 ◽  
Vol 22 (9) ◽  
pp. 4814
Author(s):  
Liu Chu ◽  
Jiajia Shi ◽  
Yue Yu ◽  
Eduardo Souza De Cursi
Keyword(s):  
Finite Element ◽  
Monte Carlo ◽  
Finite Element Model ◽  
Element Model ◽  
Working Environment ◽  
Probability Density Distribution ◽  
Resonant Frequencies ◽  
Vacancy Defects ◽  
Porous Graphene ◽  
Atomic Vacancy

With the distinguished properties in electronics, thermal conductivity, optical transparence and mechanics, graphene has a powerful potential in nanosensors, nano-resonators, supercapacitors, batteries, etc. The resonant frequency of graphene is an important factor in its application and working environment. However, the random dispersed porosities in graphene evidently change the lattice structure and destroy the integrity and geometrical periodicity. This paper focuses on the effects of random porosities in resonant frequencies of graphene. Monte Carlo simulation is applied to propagate the porosities in the finite element model of pristine graphene. The statistical results and probability density distribution of porous graphene with atomic vacancy defects are computed based on the Monte Carlo finite element model. The results of porous graphene with atomic vacancy defects are compared and discussed with the results of graphene with bond vacancy defects. The enhancement effects of atomic vacancy defects are confirmed in porous graphene. The influences of atomic vacancy defects on displacement and rotation vector sums of porous graphene are more concentrated in local places.

scholarly journals Ribo-ODDR: Oligo design pipeline for experiment-specific rRNA depletion in ribo-seq

2021 ◽  
Author(s):  
Ferhat Alkan ◽  
Joana Silva ◽  
Eric Pintó Barberà ◽  
William J Faller
Keyword(s):  
Ribosome Profiling ◽  
Supplementary Information ◽  
Experimental Conditions ◽  
Computational Framework ◽  
Rna Translation ◽  
Rrna Depletion ◽  
Selection For ◽  
Nucleotide Resolution ◽  
User Friendly ◽  
Oligo Design

Abstract Motivation Ribosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of rRNA fragments. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, they may perform suboptimally in Ribo-seq. In order to overcome this, it is possible to use custom biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos. Results Here, we first show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a “one-size-fits-all” approach may be inefficient. Therefore we developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We experimentally show that Ribo-ODDR designed oligos outperform commercially available kits and lead to a significant increase in rRNA depletion in Ribo-seq. Availability Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR Supplementary information Supplementary data are available at Bioinformatics online.

Modal Analysis and Modeling of a Parallel Kinematic Machine

1999 ◽  
Author(s):  
David S. Hardage ◽  
Gloria J. Wiens
Keyword(s):  
Finite Element ◽  
Resonant Frequency ◽  
Structural Dynamics ◽  
Preliminary Data ◽  
Element Model ◽  
Parallel Kinematic Machine ◽  
Parallel Kinematic ◽  
Machine Configuration ◽  
Stiffness Characteristics ◽  
The Finite Element Model

Abstract This paper presents the results of a mini-modal survey on the Hexel Tornado 2000, a parallel kinematic machine tool located at Sandia National Laboratories, and discusses the finite element model that is used to simulate the structural dynamics of this machine. Preliminary data suggests a dependency of resonant frequency and stiffness characteristics on machine configuration.

First-Principles Study of Interaction of Lithium Atoms with (3, 3) Carbon Nanotubes

2014 ◽  
Vol 687-691 ◽  
pp. 4311-4314 ◽  
Author(s):  
Shun Fu Xu ◽  
Ling Min Li
Keyword(s):  
Carbon Nanotubes ◽  
First Principles ◽  
Density Functional ◽  
Vacancy Defect ◽  
Single Wall Carbon Nanotubes ◽  
Generalized Gradient ◽  
Hydrogen Atoms ◽  
Functional Theory ◽  
Vacancy Defects ◽  
Adsorption Mechanisms

In this paper, we have employed first-principles calculations to investigate the adsorption mechanisms of one lithium atom on the sidewalls of 1/2/3 H-adsorbed indefective/defective (3, 3) single-wall carbon nanotubes (CNTs) which have vacancy defects. Our calculations are performed within density functional theory (DFT) under the generalized gradient approximation (GGA) of Perdew, Burke, and Ernzerhof (PBE).Our results show that the lithium atoms strongly binds to the H-adsorbed (3, 3) nanotube. Lithium atoms can chemically adsorb on (3, 3) nanotube with the vacancy defect (MVD) without any energy barrier. The lithium adsorption will enhance the electrical conductivity of the nanotube. Further more, the structure of the (3, 3) nanotube with the MVD and hydrogen atoms will become more stable after the three kinds of lithium adsorption.

Influence of Defects on Elastic Buckling Properties of Single-Layered Graphene Sheets

2014 ◽  
Vol 636 ◽  
pp. 11-14 ◽  
Author(s):  
Bao Long Li ◽  
Li Jun Zhou ◽  
Jian Gao Guo
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Vacancy Defect ◽  
Elastic Buckling ◽  
Graphene Sheets ◽  
Effect Factors ◽  
Vacancy Defects ◽  
Size Dependent ◽  
Buckling Stress ◽  
Geometrical Dimensions

Molecular structural mechanics based finite element method has been applied to study the effects of two types of Stone-Wales (SW) defects and vacancy defect on elastic buckling properties of single-layered graphene sheets (SLGSs). The defect effect factors of critical buckling stresses are calculated for the defective SLGSs with different chirality and geometrical dimensions. It is proved that defect effect factors are size-dependent and chirality-dependent. The results show that the vacancy defects will always weaken the SLGSs’ stability, and two types of SW defects have different effects on zigzag and armchair SLGSs. What’s more, the positions of defects also have remarkable influence on the critical buckling stress of SLGSs.

scholarly journals Monte Carlo-Based Finite Element Method for the Study of Randomly Distributed Vacancy Defects in Graphene Sheets

2018 ◽  
Vol 2018 ◽  
pp. 1-12
Author(s):  
Liu Chu ◽  
Jiajia Shi ◽  
Eduardo Souza de Cursi ◽  
Xunqian Xu ◽  
Yazhou Qin ◽  
...  
Keyword(s):  
Finite Element Method ◽  
Finite Element ◽  
Monte Carlo ◽  
Natural Frequencies ◽  
Vacancy Defect ◽  
Honeycomb Lattice ◽  
Graphene Sheets ◽  
Pristine Graphene ◽  
Vacancy Defects ◽  
Element Method

This paper proposed an effective stochastic finite element method for the study of randomly distributed vacancy defects in graphene sheets. The honeycomb lattice of graphene is represented by beam finite elements. The simulation results of the pristine graphene are in accordance with literatures. The randomly dispersed vacancies are propagated and performed in graphene by integrating Monte Carlo simulation (MCS) with the beam finite element model (FEM). The results present that the natural frequencies of different vibration modes decrease with the augment of the vacancy defect amount. When the vacancy defect reaches 5%, the regularity and geometrical symmetry of displacement and rotation in vibration behavior are obviously damaged. In addition, with the raise of vacancy defects, the random dispersion position of vacancy defects increases the variance in natural frequencies. The probability density distributions of natural frequencies are close to the Gaussian and Weibull distributions.

Sign in / Sign up

Export Citation Format

Share Document