Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Xenon Diffusion Mechanism and Xenon Bubble Nucleation and Growth Behaviors in Molybdenum via Molecular Dynamics Simulations.

ABSTRACT: The behaviors of xenon in molybdenum were studied using molecular statics andmolecular dynamics simulations. The diffusion mechanism of xenon atoms was studied combiningmolecular dynamics, nudged elastic band, and temperature-accelerated dynamics methods. Thevacancy-assisted diffusion mechanism was analyzed and the corresponding energy barriers werecalculated. The clustering process of scattered xenon atoms was studied at an elevated temperature.Xenon bubbles were observed to form when the concentration of xenon atoms exceeded a thresholdconcentration value. Meanwhile, the interaction of xenon bubble and vacancies was investigated viathe nudged elastic band method. The results showed that there exists a region around the xenonbubble where the migration energy of vacancy is significantly influenced. This work provides usefulinsights towards a better understanding of the behaviors of xenon in molybdenum.

SUBMITTER: Zhang W

PROVIDER: S-EPMC6696071 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Xenon Diffusion Mechanism and Xenon Bubble Nucleation and Growth Behaviors in Molybdenum via Molecular Dynamics Simulations.

Zhang Wenhua W Yun Di D Liu Wenbo W

Materials (Basel, Switzerland) 20190724 15

The behaviors of xenon in molybdenum were studied using molecular statics andmolecular dynamics simulations. The diffusion mechanism of xenon atoms was studied combiningmolecular dynamics, nudged elastic band, and temperature-accelerated dynamics methods. Thevacancy-assisted diffusion mechanism was analyzed and the corresponding energy barriers werecalculated. The clustering process of scattered xenon atoms was studied at an elevated temperature.Xenon bubbles were observed to form when the conce ...[more]

PMID: 31344951

Similar Datasets

A general mechanism for transcription bubble nucleation in bacteria.

Project description:Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ70, nucleates DNA melting via recognition of conserved bases of the promoter -10 motif, which are unstacked and captured in pockets of σ70. By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σN-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σN, like σ70, captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.

| S-EPMC10083551 | biostudies-literature

Bubble nucleation and growth on microstructured surfaces under microgravity.

Project description:Understanding the dynamics of surface bubble formation and growth on heated surfaces holds significant implications for diverse modern technologies. While such investigations are traditionally confined to terrestrial conditions, the expansion of space exploration and economy necessitates insights into thermal bubble phenomena in microgravity. In this work, we conduct experiments in the International Space Station to study surface bubble nucleation and growth in a microgravity environment and compare the results to those on Earth. Our findings reveal significantly accelerated bubble nucleation and growth rates, outpacing the terrestrial rates by up to ~30 times. Our thermofluidic simulations confirm the role of gravity-induced thermal convective flow, which dissipates heat from the substrate surface and thus influences bubble nucleation. In microgravity, the influence of thermal convective flow diminishes, resulting in localized heat at the substrate surface, which leads to faster temperature rise. This unique condition enables quicker bubble nucleation and growth. Moreover, we highlight the influence of surface microstructure geometries on bubble nucleation. Acting as heat-transfer fins, the geometries of the microstructures influence heat transfer from the substrate to the water. Finer microstructures, which have larger specific surface areas, enhance surface-to-liquid heat transfer and thus reduce the rate of surface temperature rise, leading to slower bubble nucleation. Our experimental and simulation results provide insights into thermal bubble dynamics in microgravity, which may help design thermal management solutions and develop bubble-based sensing technologies.

| S-EPMC10827752 | biostudies-literature

Disclosing crystal nucleation mechanism in lithium disilicate glass through molecular dynamics simulations and free-energy calculations.

Project description:Unraveling detailed mechanism of crystal nucleation from amorphous materials is challenging for both experimental and theoretical approaches. In this study, we have examined two methods to understand the initial stage of crystal precipitation from lithium disilicate glasses using molecular dynamics simulations. One of the methods is a modified exploring method to find structurally similar crystalline clusters in the glass models, enabling us to find three different embryos, such as Li2Si2O5 (LS2), Li2SiO3 (LS) and Li3PO4 (LP), in the 33Li2O·66SiO2·1P2O5 glass (LS2P1), in which P2O5 is added as a nucleating agent. Interestingly, LS2 and LP crystals were found inside the LS2P1 glass while LS crystal appeared on the glass surface, which agrees with experimental observations. The other method is free energy calculation using a subnano-scale spherical crystal embedded in the glass model. This method, which we called Free-Energy Seeding Method (FESM), allows us to evaluate free energy change as a function of crystal radius and to identify critical size of the crystal precipitation. The free energy profiles for LS and LS2 crystal nuclei in the LS2 glass models possess maximum energy at a critical radius as expected by classical nucleation theory. Furthermore, the critical radius and the energy barrier height agree well with recent experimental investigation, proving the applicability of this method to design glass-ceramics by atomistic modeling.

| S-EPMC7576157 | biostudies-literature

Molecular-dynamics simulations of urea nucleation from aqueous solution.

Project description:Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

| S-EPMC4291617 | biostudies-other

Plasmonic Bubble Nucleation in Binary Liquids.

Project description:Metal nanoparticles under laser irradiation can produce enormous heat due to surface plasmon resonance. When submerged in a liquid, this can lead to the nucleation of plasmonic bubbles. In the very early stage, the nucleation of a giant vapor bubble was observed with an ultrahigh-speed camera. In this study, the formation of this giant bubble on gold nanoparticles in six binary liquid combinations has been investigated. We find that the time delay between the beginning of the laser heating and the bubble nucleation is determined by the absolute amount of dissolved gas in the liquid. Moreover, the bubble volume mainly depends on the vaporization energy of the liquid, consisting of the latent heat of vaporization and the energy needed to reach the boiling temperature. Our results contribute to controlling the initial giant bubble nucleation and have strong bearings on applications of such bubbles.

| S-EPMC6996646 | biostudies-literature

Strong Transient Flows Generated by Thermoplasmonic Bubble Nucleation.

Project description:The challenge of inducing and controlling localized fluid flows for generic force actuation and for achieving efficient mass transport in microfluidics is key to the development of next-generation miniaturized systems for chemistry and life sciences. Here we demonstrate a methodology for the robust generation and precise quantification of extremely strong flow transients driven by vapor bubble nucleation on spatially isolated plasmonic nanoantennas excited by light. The system is capable of producing peak flow speeds of the order mm/s at modulation rates up to ∼100 Hz in water, thus allowing for a variety of high-throughput applications. Analysis of flow dynamics and fluid viscosity dependence indicates that the transient originates in the rapid bubble expansion that follows nucleation rather than being strictly thermocapillary in nature.

| S-EPMC7760215 | biostudies-literature

Reconciling bubble nucleation in explosive eruptions with geospeedometers.

Project description:Magma from Plinian volcanic eruptions contains an extraordinarily large numbers of bubbles. Nucleation of those bubbles occurs because pressure decreases as magma rises to the surface. As a consequence, dissolved magmatic volatiles, such as water, become supersaturated and cause bubbles to nucleate. At the same time, diffusion of volatiles into existing bubbles reduces supersaturation, resulting in a dynamical feedback between rates of nucleation due to magma decompression and volatile diffusion. Because nucleation rate increases with supersaturation, bubble number density (BND) provides a proxy record of decompression rate, and hence the intensity of eruption dynamics. Using numerical modeling of bubble nucleation, we reconcile a long-standing discrepancy in decompression rate estimated from BND and independent geospeedometers. We demonstrate that BND provides a record of the time-averaged decompression rate that is consistent with independent geospeedometers, if bubble nucleation is heterogeneous and facilitated by magnetite crystals.

| S-EPMC7803785 | biostudies-literature

Fracture behaviors of pre-cracked monolayer molybdenum disulfide: A molecular dynamics study.

Project description:The fracture strength and crack propagation of monolayer molybdenum disulfide (MoS2) sheets with various pre-existing cracks are investigated using molecular dynamics simulation (MDS). The uniaxial tensions of pre-cracked monolayer MoS2 sheets with different crack tips, different locations of crack, different crack lengths and angled cracks are simulated and studied. The results show that the configuration of crack tip can influence significantly the fracture behaviors of monolayer MoS2 sheets while the location of crack does not influence the fracture strength. With the increase of crack length, the fracture strength of monolayer MoS2 sheets reduces almost linearly, and the fracture of monolayer MoS2 sheets is transformed from almost brittle to ductile. By making comparison between the MDS results and the predictions of continuum fracture mechanics theories, including Inglis' model, Griffith's model with and without finite size effect, it is found that MDS results agree well with the predictions of Griffith's model with finite size effect, differ from the predictions of Inglis' model and Griffith's model without finite size effect. Finally, the MDS results of monolayer MoS2 sheets with different angled crack are also analyzed based on the continuum fracture mechanics model.

| S-EPMC5082624 | biostudies-literature

Ethanol as a Probe for the Mechanism of Bubble Nucleation in the Diet Coke and Mentos Experiment.

Project description:The Diet Coke and Mentos experiment involves dropping Mentos candies into carbonated beverages to produce a fountain. This simple experiment has enjoyed popularity with science teachers and the general public. Studies of the physicochemical processes involved in the generation of the fountain have been largely informed by the physics of bubble nucleation. Herein, we probe the effect of ethanol addition on the Diet Coke and Mentos experiment to explore the impact that beverage surface tension and viscosity have on the heights of fountains achieved. Our results indicate that current descriptions of the effects of surface tension and viscosity are not completely understood. We also extend and apply a previously reported, simplified version of Brunauer-Emmett-Teller theory to investigate kinetic and mechanistic aspects of bubble nucleation on the surface of Mentos candies in carbonated beverages. A combination of this new theory and experiment allows for the estimation that the nucleation sites on the Mentos candy that catalyze degassing are 1-3 μm in size, and that between 50,000 and 300,000 of these sites actively nucleate bubbles on a single Mentos candy. While the methods employed are not highly sophisticated, they have potential to stimulate fresh investigations and insights into bubble nucleation in carbonated beverages.

| S-EPMC8002754 | 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

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