Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ab initio phase diagram and nucleation of gallium.

ABSTRACT: Elemental gallium possesses several intriguing properties, such as a low melting point, a density anomaly and an electronic structure in which covalent and metallic features coexist. In order to simulate this complex system, we construct an ab initio quality interaction potential by training a neural network on a set of density functional theory calculations performed on configurations generated in multithermal-multibaric simulations. Here we show that the relative equilibrium between liquid gallium, ?-Ga, ?-Ga, and Ga-II is well described. The resulting phase diagram is in agreement with the experimental findings. The local structure of liquid gallium and its nucleation into ?-Ga and ?-Ga are studied. We find that the formation of metastable ?-Ga is kinetically favored over the thermodinamically stable ?-Ga. Finally, we provide insight into the experimental observations of extreme undercooling of liquid Ga.

SUBMITTER: Niu H

PROVIDER: S-EPMC7253470 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ab initio phase diagram and nucleation of gallium.

Niu Haiyang H Bonati Luigi L Piaggi Pablo M PM Parrinello Michele M

Nature communications 20200527 1

Elemental gallium possesses several intriguing properties, such as a low melting point, a density anomaly and an electronic structure in which covalent and metallic features coexist. In order to simulate this complex system, we construct an ab initio quality interaction potential by training a neural network on a set of density functional theory calculations performed on configurations generated in multithermal-multibaric simulations. Here we show that the relative equilibrium between liquid gal ...[more]

PMID: 32461573

Similar Datasets

Ab initio prediction of the polymorph phase diagram for crystalline methanol.

Project description:Organic crystals frequently adopt multiple distinct polymorphs exhibiting different properties. The ability to predict not only what crystal forms might occur, but under what experimental thermodynamic conditions those polymorphs are stable would be immensely valuable to the pharmaceutical industry and others. Starting only from knowledge of the experimental crystal structures, this study successfully predicts the methanol crystal polymorph phase diagram from first-principles quantum chemistry, mapping out the thermodynamic regions of stability for three polymorphs over the range 0-400 K and 0-6 GPa. The agreement between the predicted and experimental phase diagrams corresponds to predicting the relative polymorph free energies to within ?0.5 kJ mol-1 accuracy, which is achieved by employing fragment-based second-order Møller-Plesset perturbation theory and coupled cluster theory plus a quasi-harmonic treatment of the phonons.

| S-EPMC5969506 | biostudies-literature

ab initio Energetics and Thermoelectric Profiles of Gallium Pnictide Polytypes.

Project description:The state-of-the-art Density Functional Theory (DFT) is utilized to investigate the structural, electronic, vibrational, thermal and thermoelectric properties of gallium pnictides GaX (X = P, As, Sb) in cubic zincblende (ZB) and hexagonal wurtzite (WZ) phases. The lattice parameters, bulk modulus, energy band nature and bandgap values, phonon, thermal and thermoelectric properties are revisited for ZB phase while for WZ phase they are predictive. Our results agree reasonably well with the experimental and theoretical data wherever they are available. The phonon dispersion curves are computed to validate the dynamic stability of these two polytypes and for further investigating the thermal and thermoelectric properties. Our computed thermoelectric figure of merit ZT gives consistent results with highest observed magnitude of 0.72 and 0.56 for GaSb compound in ZB and WZ phases respectively. The first time calculated temperature variation of lattice thermal conductivity for WZ phase shows lower value than ZB phase and hence an important factor to enhance the figure of merit of considered gallium pnictides in WZ phase. Present results validate the importance of GaX in high temperature thermoelectric applications as the figure of merit ZT shows enhancement with significant reduction in thermal conductivity at higher temperature values.

| S-EPMC6458143 | biostudies-literature

Towards fully ab initio simulation of atmospheric aerosol nucleation.

Project description:Atmospheric aerosol nucleation contributes to approximately half of the worldwide cloud condensation nuclei. Despite the importance of climate, detailed nucleation mechanisms are still poorly understood. Understanding aerosol nucleation dynamics is hindered by the nonreactivity of force fields (FFs) and high computational costs due to the rare event nature of aerosol nucleation. Developing reactive FFs for nucleation systems is even more challenging than developing covalently bonded materials because of the wide size range and high dimensional characteristics of noncovalent hydrogen bonding bridging clusters. Here, we propose a general workflow that is also applicable to other systems to train an accurate reactive FF based on a deep neural network (DNN) and further bridge DNN-FF-based molecular dynamics (MD) with a cluster kinetics model based on Poisson distributions of reactive events to overcome the high computational costs of direct MD. We found that previously reported acid-base formation rates tend to be significantly underestimated, especially in polluted environments, emphasizing that acid-base nucleation observed in multiple environments should be revisited.

| S-EPMC9568664 | biostudies-literature

Polar GaN Surfaces under Gallium Rich Conditions: Revised Thermodynamic Insights from Ab Initio Calculations.

Project description:This paper presents an improved theoretical view of ab initio thermodynamics for polar GaN surfaces under gallium-rich conditions. The study uses density functional theory (DFT) calculations to systematically investigate the adsorption of gallium atoms on GaN polar surfaces, starting from the clean surface and progressing to the metallic multilayer. First principles phonon calculations are performed to determine vibrational free energies. Changes in the chemical potential of gallium adatoms are determined as a function of temperature and surface coverage. Three distinct ranges of Ga coverage with very low, medium, and high chemical potential are observed on the GaN(000-1) surface, while only two ranges with medium and high chemical potential are observed on the GaN(000-1) surface. The analysis confirms that a monolayer of Ga adatoms on the GaN(000-1) surface is highly stable over a wide range of temperatures. For a second adlayer at higher temperatures, it is energetically more favorable to form liquid droplets than a uniform crystalline adlayer. The second Ga layer on the GaN(0001) surface shows pseudo-crystalline properties even at a relatively high temperature. These results provide a better thermodynamic description of the surface state under conditions typical for molecular beam epitaxy and offer an interpretation of the observed growth window.

| S-EPMC10489001 | biostudies-literature

Ab initio generalized Langevin equation.

Project description:We introduce a machine learning-based approach called ab initio generalized Langevin equation (AIGLE) to model the dynamics of slow collective variables (CVs) in materials and molecules. In this scheme, the parameters are learned from atomistic simulations based on ab initio quantum mechanical models. Force field, memory kernel, and noise generator are constructed in the context of the Mori-Zwanzig formalism, under the constraint of the fluctuation-dissipation theorem. Combined with deep potential molecular dynamics and electronic density functional theory, this approach opens the way to multiscale modeling in a variety of situations. Here, we demonstrate this capability with a study of two mesoscale processes in crystalline lead titanate, namely the field-driven dynamics of a planar ferroelectric domain wall, and the dynamics of an extensive lattice of coarse-grained electric dipoles. In the first case, AIGLE extends the reach of ab initio simulations to a regime of noise-driven motions not accessible to molecular dynamics. In the second case, AIGLE deals with an extensive set of CVs by adopting a local approximation for the memory kernel and retaining only short-range noise correlations. The scheme is computationally more efficient than molecular dynamics by several orders of magnitude and mimics the microscopic dynamics at low frequencies where it reproduces accurately the dominant far-infrared absorption frequency.

| S-EPMC10998567 | biostudies-literature

Accurate ab Initio Spin Densities.

Project description:We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].

| S-EPMC3373140 | biostudies-literature

How fragility makes phase-change data storage robust: insights from ab initio simulations.

Project description:Phase-change materials are technologically important due to their manifold applications in data storage. Here we report on ab initio molecular dynamics simulations of crystallization of the phase change material Ag4In3Sb67Te26 (AIST). We show that, at high temperature, the observed crystal growth mechanisms and crystallization speed are in good agreement with experimental data. We provide an in-depth understanding of the crystallization mechanisms at the atomic level. At temperatures below 550 K, the computed growth velocities are much higher than those obtained from time-resolved reflectivity measurements, due to large deviations in the diffusion coefficients. As a consequence of the high fragility of AIST, experimental diffusivities display a dramatic increase in activation energies and prefactors at temperatures below 550 K. This property is essential to ensure fast crystallization at high temperature and a stable amorphous state at low temperature. On the other hand, no such change in the temperature dependence of the diffusivity is observed in our simulations, down to 450 K. We also attribute this different behavior to the fragility of the system, in combination with the very fast quenching times employed in the simulations.

| S-EPMC4185410 | biostudies-literature

Ab initio nonrigid X-ray nanotomography.

Project description:Reaching the full potential of X-ray nanotomography, in particular for biological samples, is limited by many factors, of which one of the most serious is radiation damage. Although sample deformation caused by radiation damage can be partly mitigated by cryogenic protection, it is still present in these conditions and, as we exemplify here using a specimen extracted from scales of the Cyphochilus beetle, it will pose a limit to the achievable imaging resolution. We demonstrate a generalized tomographic model, which optimally follows the sample morphological changes and attempts to recover the original sample structure close to the ideal, damage-free reconstruction. Whereas our demonstration was performed using ptychographic X-ray tomography, the method can be adopted for any tomographic imaging modality. Our application demonstrates improved reconstruction quality of radiation-sensitive samples, which will be of increasing relevance with the higher brightness of 4th generation synchrotron sources.

| S-EPMC6565693 | biostudies-literature

AIDA: ab initio domain assembly server.

Project description:AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization.

| S-EPMC4086082 | biostudies-literature

Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers.

Project description:The conformational landscape of phenylisoserine (PhIS) was studied. Trial structures were generated by allowing for all combinations of single-bond rotamers. Based on the B3LYP/aug-cc-pVDZ calculations 54 conformers were found to be stable in the gas phase. The six most stable conformers were further optimized at the B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVDZ levels for which characteristic intramolecular hydrogen bond types were classified. To estimate the influence of water on PhIS conformation, the IEF-PCM/B3LYP/aug-cc-pVDZ calculations were carried out and showed 51 neutral and six zwitterionic conformers to be stable in water solution. According to DFT calculations, the conformer equilibrium in the gas phase is dominated by one conformer, whereas the MP2 calculations suggest three PhIS structures to be significantly populated. Comparison of DFT and MP2 energies of all 57 structures stable in water indicates that, in practice, one zwitterionic and one neutral conformer determine the equilibrium in water. Based on the AIM calculations, we found that for the neutral conformers in vacuum and in water, d(H...B) is linearly correlated with Laplacian at the H-bond critical point. Figure Phenylisoserine (PhIS) is an active side chain of cytotoxic Paclitaxel medicine. The conformational landscape of phenylisoserine was studied. One zwitterionic and one neutralconformer determine the equilibrium in water whereas in the gas phase the MP2 calculations suggest three PhIS structures to be significantly populated.

| S-EPMC3094660 | 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