Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Atomistic Representation of Anomalies in the Failure Behaviour of Nanocrystalline Silicene.

ABSTRACT: Silicene, a 2D analogue of graphene, has spurred a tremendous research interest in the scientific community for its unique properties essential for next-generation electronic devices. In this work, for the first time, we present a molecular dynamics (MD) investigation to determine the fracture strength and toughness of nanocrystalline silicene (nc-silicene) sheet of varying grain sizes and pre-existing cracks at room temperature. Our results suggest a transition from an inverse pseudo Hall-Petch to a pseudo Hall-Petch behaviour in nc-silicene at a critical grain size of 17.32 nm. This phenomenon is also prevalent in nanocrystalline graphene. However, nc-silicene with pre-existing cracks exhibits anomalous crack propagation and fracture toughness behaviour. We observed two distinct types of failure mechanisms (crack sensitive and insensitive failure) and devised mechano-physical conditions under which they occur. The most striking outcome is: despite the presence of a pre-existing crack, the crack sensitivity of nc-silicene is found to be dependent on the grain size and their orientations. The calculated Fracture toughness from both Griffith's theory and MD simulations indicate that the former over-predicts the fracture toughness of nc-silicene. Finally, this study is the first direct comparison of atomistic simulations to the continuum theories to predict the anomalous behaviour in deformation and failure mechanisms of nc-silicene.

SUBMITTER: Rakib T

PROVIDER: S-EPMC5676956 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Effect of annealing treatment on mechanical properties of nanocrystalline ?-iron: an atomistic study.

Project description:Claims are often found in the literature that metallic materials can be nanocrystallized by severe plastic deformation (SPD). However, SPD does not generate a well-defined nanocrystalline (NC) material, which can be achieved by subsequent annealing/recovery treatment. In this study, molecular dynamics (MD) simulation is employed to study the effect of annealing on structure and mechanical properties of cyclic deformed NC ?-iron, which simulates SPD-processed ?-iron. It is demonstrated that grain boundaries in the deformed NC ?-iron evolve to a more equilibrium state during annealing, eliminating or minimizing the residual stress. The annealing treatment increases the system's strength by reducing dislocation emission sources, and improves material ductility through strengthening grain boundaries' resistance to intergranular cracks. The results indicate that the annealing treatment is an essential process for obtaining a well-defined NC structure with superior mechanical properties.

| S-EPMC4327417 | biostudies-literature

Silicene nanomesh.

Project description:Similar to graphene, zero band gap limits the application of silicene in nanoelectronics despite of its high carrier mobility. By using first-principles calculations, we reveal that a band gap is opened in silicene nanomesh (SNM) when the width W of the wall between the neighboring holes is even. The size of the band gap increases with the reduced W and has a simple relation with the ratio of the removed Si atom and the total Si atom numbers of silicene. Quantum transport simulation reveals that the sub-10 nm single-gated SNM field effect transistors show excellent performance at zero temperature but such a performance is greatly degraded at room temperature.

| S-EPMC4649852 | biostudies-literature

A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations.

Project description:Graphs are rapidly becoming a powerful and ubiquitous tool for the analysis of protein structure and for event detection in dynamical protein systems. Despite their rise in popularity, however, the graph representations employed to date have shared certain features and parameters that have not been thoroughly investigated. Here, we examine and compare variations on the construction of graph nodes and graph edges. We propose a graph representation based on chemical groups of similar atoms within a protein rather than residues or secondary structure and find that even very simple analyses using this representation form a powerful event detection system with significant advantages over residue-based graph representations. We additionally compare graph edges based on probability of contact to graph edges based on contact strength and analyses of the entire graph structure to an alternative and more computationally tractable node-based analysis. We develop the simplest useful technique for analyzing protein simulations based on these comparisons and use it to shed light on the speed with which static protein structures adjust to a solvated environment at room temperature in simulation.

| S-EPMC3731134 | biostudies-literature

Large-scale climatic anomalies affect marine predator foraging behaviour and demography.

Project description:Determining the links between the behavioural and population responses of wild species to environmental variations is critical for understanding the impact of climate variability on ecosystems. Using long-term data sets, we show how large-scale climatic anomalies in the Southern Hemisphere affect the foraging behaviour and population dynamics of a key marine predator, the king penguin. When large-scale subtropical dipole events occur simultaneously in both subtropical Southern Indian and Atlantic Oceans, they generate tropical anomalies that shift the foraging zone southward. Consequently the distances that penguins foraged from the colony and their feeding depths increased and the population size decreased. This represents an example of a robust and fast impact of large-scale climatic anomalies affecting a marine predator through changes in its at-sea behaviour and demography, despite lack of information on prey availability. Our results highlight a possible behavioural mechanism through which climate variability may affect population processes.

| S-EPMC4639794 | biostudies-literature

Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

Project description:Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties.

| S-EPMC4685891 | biostudies-literature

How silicene on Ag(111) oxidizes: microscopic mechanism of the reaction of O2 with silicene.

Project description:We demonstrate, using first-principles molecular-dynamics simulations, that oxidation of silicene can easily take place either at low or high oxygen doses, which importantly helps clarify previous inconsistent reports on the oxidation of silicene on the Ag(111) substrate. We show that, while the energy barrier for an O2 molecule reacting with a Si atom strongly depends on the position and orientation of the molecule, the O2 molecule immediately dissociates and forms an Si-O-Si configuration once it finds a barrier-less chemisorption pathway around an outer Si atom of the silicene overlayer. A synergistic effect between the molecular dissociation and subsequent structural rearrangements is found to accelerate the oxidation process at a high oxygen dose. This effect also enhances self-organized formation of sp(3)-like tetrahedral configurations (consisting of Si and O atoms), which results in collapse of the two-dimensional silicene structure and its exfoliation from the substrate. We also find that the electronic properties of the silicene can be significantly altered by oxidation. The present findings suggest that low flux and low temperature of the oxygen gas are key to controlling oxidation of silicene.

| S-EPMC4668378 | biostudies-literature

Serum Exosomal Omics Analysis: Revealing Energy Metabolism Anomalies and Promising Diagnostic Markers for Premature Ovarian Failure

Project description:Background: Premature ovarian failure (POF) is a clinical condition characterized by the cessation of ovarian function, leading to infertility. The underlying molecular mechanisms remain unclear, and no predictable biomarkers have been identified. This study aimed to investigate the protein and metabolite contents of serum exosomes to identify underlying molecular mechanisms and explore potential biomarkers. Methods: This study was conducted on a cohort consisting of 14 POF patients and 16 healthy controls. The exosomes extracted from the serum of each group were subjected to label-free proteomic and unbiased metabolomic analysis. Differentially expressed proteins and metabolites were annotated. Pathway network clustering was conducted with further correlation analysis. The biomarkers were confirmed by ROC analysis and random forest machine learning. Results: The proteomic and metabolomic profiles of POF patients and healthy controls were compared. Two subgroups of POF patients, Pre-POF and Pro-POF, were identified based on the proteomic profile, while all patients displayed a distinguishable metabolomic profile. Signaling pathway clustering revealed progression of dysfunctional energy metabolism during the development of POF. The differentially expressed proteins and metabolites were highly correlated, with six of them selected as potential biomarkers. ROC curve analysis and random forest machine learning suggested that AFM combined with GE was a diagnostic biomarker for POF. Conclusion: Omic analysis revealed that inflammation and oxidative stress are factors that damage ovarian tissue, but progressive dysfunction of energy metabolism might be the critical pathogenetic pathway contributing to the development of POF. AFM combined with GE together serves as the best biomarker for clinical POF diagnosis.

2024-10-17 | PXD051569 | Pride

Enhanced thermoelectric efficiency of porous silicene nanoribbons.

Project description:There is a critical need to attain new sustainable materials for direct upgrade of waste heat to electrical energy via the thermoelectric effect. Here we demonstrate that the thermoelectric performance of silicene nanoribbons can be improved dramatically by introducing nanopores and tuning the Fermi energy. We predict that values of electronic thermoelectric figure of merit ZTe up to 160 are achievable, provided the Fermi energy is located approximately 100?meV above the charge neutrality point. Including the effect of phonons yields a value for the full figure of merit of ZT = 3.5. Furthermore the sign of the thermopower S can be varied with achievable values as high as S = +/- 500??V/K. As a method of tuning the Fermi energy, we analyse the effect of doping the silicene with either a strong electron donor (TTF) or a strong electron acceptor (TCNQ) and demonstrate that adsorbed layers of the former increases ZTe to a value of 3.1, which is insensitive to temperature over the range 100?K - 400?K. This combination of a high, temperature-insensitive ZTe, and the ability to choose the sign of the thermopower identifies nanoporous silicene as an ideal thermoelectric material with the potential for unprecedented performance.

| S-EPMC4377624 | biostudies-literature

Flat Zigzag Silicene Nanoribbon with Be Bridge.

Project description:The emergence of flat one- and two-dimensional materials, such as graphene and its nanoribbons, has promoted the rapid advance of the current nanotechnology. Silicene, a silicon analogue of graphene, has the great advantage of its compatibility with the present industrial processes based on silicon nanotechnology. The most significant issue for silicene is instability in the air due to the nonplanar puckered (buckled) structure. Another critical problem is that silicene is usually synthesized by epitaxial growth on a substrate, which strongly affects the π conjugated system of silicene. The fabrication of free-standing silicene with a planar configuration has long been pursued. Here, we report the strategy and design to realize the flat zigzag silicene nanoribbon. We theoretically investigated the stability of various silicene nanoribbons with substituents at the zigzag edges and found that zigzag silicene nanoribbons with beryllium (Be) bridges are very stable in a planar configuration. The obtained zigzag silicene nanoribbon has an indirect negative band gap and is nonmagnetic unlike the magnetic buckled silicene nanoribbons with zigzag edges. The linearly dispersive behavior of the π and π* bands associated with the out-of-plane 3psi and 2pBe orbitals is clearly observed, showing the existence of a Dirac point slightly above the Fermi level. We also observed that spin-orbit coupling induces a gap opening at the Dirac point.

| S-EPMC8154158 | biostudies-literature

Highly Biaxially Strained Silicene on Au(111).

Project description:Many of graphene's remarkable properties arise from its linear dispersion of the electronic states, forming a Dirac cone at the K points of the Brillouin zone. Silicene, the 2D allotrope of silicon, is also predicted to show a similar electronic band structure, with the addition of a tunable bandgap, induced by spin-orbit coupling. Because of these outstanding electronic properties, silicene is considered as a promising building block for next-generation electronic devices. Recently, it has been shown that silicene grown on Au(111) still possesses a Dirac cone, despite the interaction with the substrate. Here, to fully characterize the structure of this 2D material, we investigate the vibrational spectrum of a monolayer silicene grown on Au(111) by polarized Raman spectroscopy. To enable a detailed ex situ investigation, we passivated the silicene on Au(111) by encapsulating it under few layers hBN or graphene flakes. The observed spectrum is characterized by vibrational modes that are strongly red-shifted with respect to the ones expected for freestanding silicene. By comparing low-energy electron diffraction (LEED) patterns and Raman results with first-principles calculations, we show that the vibrational modes indicate a highly (>7%) biaxially strained silicene phase.

| S-EPMC8154839 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data