Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization pathways of liquid-bcc transition for a model iron by fast quenching.

ABSTRACT: We report simulations on the local structural evolution in the liquid-bcc transition of a model iron. Fourteen main Voronoi polyhedra are chosen as the representatives of short-range orders (SROs) and their transformations during crystallization are also investigated. Thus, the crystallization pathways for the main SROs are drawn. Our results also show that the transformations between two SROs in the crystallization pathways can be classified into two categories, first the enlargement of coordination number, second the transformation of local symmetry from five-fold to four-fold. The former reduces the potential energy while the latter increases it. It is found that the potential energy cannot decease monotonously whatever crystallization pathway is chosen to transform the icosahedral SRO to bcc SRO. Therefore, the latter transformation might provide the energy barrier of crystallization. We propose two transformation styles among SROs. All the transformations in the crystallization pathways can be achieved according to the styles. Moreover, the two transformation styles indicates that the bcc structure is more similar to liquid than other crystals. That might be the reason why the first phase nucleated during a rapid cooling process should be bcc crystal.

SUBMITTER: Pan SP

PROVIDER: S-EPMC4652240 | biostudies-other | 2015

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Hydrogen Trapping in bcc Iron.

Project description:Fundamental understanding of H localization in steel is an important step towards theoretical descriptions of hydrogen embrittlement mechanisms at the atomic level. In this paper, we investigate the interaction between atomic H and defects in ferromagnetic body-centered cubic (bcc) iron using density functional theory (DFT) calculations. Hydrogen trapping profiles in the bulk lattice, at vacancies, dislocations and grain boundaries (GBs) are calculated and used to evaluate the concentrations of H at these defects as a function of temperature. The results on H-trapping at GBs enable further investigating H-enhanced decohesion at GBs in Fe. A hierarchy map of trapping energies associated with the most common crystal lattice defects is presented and the most attractive H-trapping sites are identified.

| S-EPMC7287698 | biostudies-literature

Shockwave generates < 100 > dislocation loops in bcc iron.

Project description:The formation mechanism of < 100 > interstitial dislocation loops in ferritic steels stemming from irradiation remains elusive, as their formations are either too short for experiments, or too long for molecular dynamics simulations. Here, we report on the formation of both interstitial and vacancy dislocation loops in high energy displacement cascades using large-scale molecular dynamics simulations with up to 220 million atoms. Riding the supersonic shockwave generated in the cascade, self-interstitial atoms are punched out to form < 100 > dislocation loops in only a few picoseconds during one single cascade event, which is several orders of magnitude faster than any existing mechanisms. The energy analysis suggests that the formation of the interstitial loops depends on kinetic energy redistribution, where higher incidence energy or larger atom mass could improve the probability of the direct nucleation of interstitial dislocation loops.

| S-EPMC6240105 | biostudies-literature

Crystallization and preliminary crystallographic analysis of histamine dehydrogenase from Natrinema gari BCC 24369.

Project description:Histamine dehydrogenase (HADH) catalyzes the oxidative deamination of histamine, resulting in the production of imidazole acetaldehyde and an ammonium ion. The enzyme isolated from the newly identified halophilic archaeon Natrinema gari BCC 24369 is significantly different from the previously described protein from Nocardioides simplex. This newly identified HADH comprises three subunits with molecular weights of 49.0, 24.7 and 23.9 kDa, respectively, and is optimally active under high-salt conditions (3.5-5 M NaCl). As a step in the exploration of the unique properties of the protein, the HADH heterotrimer was purified and crystallized. Crystals were obtained using the sitting-drop vapor-diffusion method from a solution composed of 0.2 M calcium chloride dihydrate, 0.1 M HEPES pH 7.5, 28% PEG 400. Diffraction data were collected at -173°C to a resolution limit of 2.4 Å on the Southeast Regional Collaborative Access Team (SER-CAT) beamline 22-ID at the Advanced Photon Source, Argonne National Laboratory. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a=211.9, b=58.6, c=135.4 Å, β=103.0°. The estimated Matthews coefficient is 3.21 Å3 Da(-1), corresponding to 61.7% solvent content.

| S-EPMC4089537 | biostudies-literature

Mechanisms for <100> interstitial dislocation loops to diffuse in BCC iron.

Project description:The mobility of dislocation loops in materials is a principle factor in understanding the mechanical strength, and the evolution of microstructures due to deformation and radiation. In body-centered cubic (BCC) iron, the common belief is that <100> interstitial dislocation loops are immobile once formed. However, using self-adaptive accelerated molecular dynamics (SSAMD), a new diffusion mechanism has been discovered for <100> interstitial dislocation loops. The key aspect of the mechanism is the changing of the habit planes between the {100} plane and the {110} plane, which provides a path for the <100> loops to diffuse one-dimensionally. The migration behavior modeled with SSAMD is further confirmed by in-situ transmission electron microscopy (TEM) measurements, and represents a significant step for understanding the formation of <100> loop walls and the mechanical behavior of BCC Fe under irradiation.

| S-EPMC7801622 | biostudies-literature

Carbon Nanotubes Enhance the Radiation Resistance of bcc Iron Revealed by Atomistic Study.

Project description:With extra space, a carbon nanotube (CNT) could serve as an absorber of point defects, including helium interstitials, and outgas the accumulate helium via "nano-chimneys". The radiation resistance of CNT/Fe has still not been fully understood. Herein, we investigated the influence of CNTs on low-energy helium irradiation resistance in CNT/Fe composites by molecular dynamic simulations. CNTs reduced the small and medium He clusters in the Fe matrix. When the incident energy of the He atoms was 300 eV, the He atoms aggregated at the outer surface of CNTs. CNTs postponed the formation of He bubbles. When the irradiation energy was higher than 600 eV, He atoms could penetrate the walls of CNTs and form clusters inside the single-walled CNTs or the space in double-walled CNTs-the latter presented better performance. The reduction of Frenkel pair point defects suggested the enhancement of radiation resistance by the presentation of CNTs. Our results might be useful for the material design of advanced steels for radiation resistance.

| S-EPMC6356427 | biostudies-literature

"Conjugate channeling" effect in dislocation core diffusion: carbon transport in dislocated BCC iron.

Project description:Dislocation pipe diffusion seems to be a well-established phenomenon. Here we demonstrate an unexpected effect, that the migration of interstitials such as carbon in iron may be accelerated not in the dislocation line direction ξ, but in a conjugate diffusion direction. This accelerated random walk arises from a simple crystallographic channeling effect. c is a function of the Burgers vector b, but not ξ, thus a dislocation loop possesses the same everywhere. Using molecular dynamics and accelerated dynamics simulations, we further show that such dislocation-core-coupled carbon diffusion in iron has temperature-dependent activation enthalpy like a fragile glass. The 71° mixed dislocation is the only case in which we see straightforward pipe diffusion that does not depend on dislocation mobility.

| S-EPMC3623912 | biostudies-literature

Cleavages along {110} in bcc iron emit dislocations from the curved crack fronts.

Project description:Body-centered-cubic (bcc) transition metals, such as [Formula: see text]-Fe and W, cleave along the {100} plane, even though the surface energy is the lowest along the {110} plane. To unravel the mechanism of this odd response, large-scale atomistic simulations of curved cleavage cracks of [Formula: see text]-Fe were conducted in association with stress intensity factor analyses of straight crack fronts using an interatomic potential created by an artificial neural network technique. The study provides novel findings: Dislocations are emitted from the crack fronts along the {110} cleavage plane, and this phenomenon explains why the {100} plane can be the cleavage plane. However, the simple straight crack-front analyses did not yield the same conclusion. It is suggested that atomistic modeling, at sufficiently large scales to capture the inherent complexities of materials using highly accurate potentials, is necessary to correctly predict the mechanical strength. The method adopted in this study is generally applicable to the cleavage problem of bcc transition metals and alloys.

| S-EPMC9668986 | biostudies-literature

Signatures of a liquid-liquid transition in an ab initio deep neural network model for water.

Project description:The possible existence of a metastable liquid-liquid transition (LLT) and a corresponding liquid-liquid critical point (LLCP) in supercooled liquid water remains a topic of much debate. An LLT has been rigorously proved in three empirically parametrized molecular models of water, and evidence consistent with an LLT has been reported for several other such models. In contrast, experimental proof of this phenomenon has been elusive due to rapid ice nucleation under deeply supercooled conditions. In this work, we combined density functional theory (DFT), machine learning, and molecular simulations to shed additional light on the possible existence of an LLT in water. We trained a deep neural network (DNN) model to represent the ab initio potential energy surface of water from DFT calculations using the Strongly Constrained and Appropriately Normed (SCAN) functional. We then used advanced sampling simulations in the multithermal-multibaric ensemble to efficiently explore the thermophysical properties of the DNN model. The simulation results are consistent with the existence of an LLCP, although they do not constitute a rigorous proof thereof. We fit the simulation data to a two-state equation of state to provide an estimate of the LLCP's location. These combined results-obtained from a purely first-principles approach with no empirical parameters-are strongly suggestive of the existence of an LLT, bolstering the hypothesis that water can separate into two distinct liquid forms.

| S-EPMC7584908 | biostudies-literature

Dynamics of the fcc-to-bcc phase transition in single-crystalline PdCu alloy nanoparticles

Project description:Two most common crystal structures in metals and metal alloys are body-centered cubic (bcc) and face-centered cubic (fcc) structures. The phase transitions between these structures play an important role in the production of durable and functional metal alloys. Despite their technological significance, the details of such phase transitions are largely unknown because of the challenges associated with probing these processes. Here, we describe the nanoscopic details of an fcc-to-bcc phase transition in PdCu alloy nanoparticles (NPs) using in situ heating transmission electron microscopy. Our observations reveal that the bcc phase always nucleates from the edge of the fcc NP, and then propagates across the NP by forming a distinct few-atoms-wide coherent bcc–fcc interface. Notably, this interface acts as an intermediate precursor phase for the nucleation of a bcc phase. These insights into the fcc-to-bcc phase transition are important for understanding solid − solid phase transitions in general and can help to tailor the functional properties of metals and their alloys. Phase transitions in crystals are challenging to study with atomic resolution. Here, the authors reveal that the transition from fcc to bcc occurs across a few-atoms-wide coherent interface, which serves as a precursor phase for the nucleation of the bcc phase.

| S-EPMC9822937 | biostudies-literature

Liquid-liquid-solid transition in viscoelastic liquids.

Project description:Liquid-liquid-solid transitions (LLST) are known to occur in confined liquids, exist in supercooled liquids and emerge in liquids driven from equilibrium. Molecular dynamics (MD) simulations claim many successes in forecasting the phenomena. The transitions are also studied in the framework of thermodynamics based methods and minimalistic models. In here, the proposed approach is derived in the framework of continuum and includes spatial and temporal dynamic heterogeneities; the approach is meant to capture the material behavior at small scales. We conjecture that the liquid-like and solid-like behaviors are dissimilar enough for the two to be governed by different constitutive relations. In this way, we gain additional degree of freedom, which is found essential when predicting the transitional phenomena. As a result, we derive the LLST criteria for liquids in equilibrium, during steady flow and at transient conditions. Lastly, we forecast short-lived LLSTs in human blood during cardiac cycle.

| S-EPMC3579185 | biostudies-other

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