Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ab initio molecular dynamics study of high-pressure melting of beryllium oxide.

ABSTRACT: We investigate, through first-principles molecular dynamics simulations, the high-pressure melting of BeO in the range 0 ≤ p ≤ 100 GPa. The wurtzite (WZ), zinc blend (ZB), and rocksalt (RS) phases of BeO are considered. It is shown that below 40 GPa, the melting temperature for the WZ phase is higher than that for the ZB and RS phases. When the pressure is beyond 66 GPa, the melting temperature for the RS phase is the highest one, in consistent with the previously reported phase diagram calculated within the quasiharmonic approximation. We find that in the medium pressure range between 40 to 66 GPa, the ZB melting data are very close to those of RS, which results from the fact that the ZB structure first transforms to RS phase before melting. The ZB-RS-liquid phase transitions have been observed directly during the molecular dynamics runs and confirmed using the pair correlation functions analysis. In addition, we propose the melting curve of BeO in the form Tm = 2696.05 (1 + P/24.67)(0.42), the zero-pressure value of 2696.05 K falling into the experimental data range of 2693 ~ 2853 K.

SUBMITTER: Li D

PROVIDER: S-EPMC3998012 | biostudies-other | 2014

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Pressure-Induced Coordination Changes in a Pyrolitic Silicate Melt From Ab Initio Molecular Dynamics Simulations.

Project description:With ab initio molecular dynamics simulations on a Na-, Ca-, Fe-, Mg-, and Al-bearing silicate melt of pyrolite composition, we examine the detailed changes in elemental coordination as a function of pressure and temperature. We consider the average coordination as well as the proportion and distribution of coordination environments at pressures and temperatures encompassing the conditions at which molten silicates may exist in present-day Earth and those of the Early Earth's magma ocean. At ambient pressure and 2,000 K, we find that the average coordination of cations with respect to oxygen is 4.0 for Si-O, 4.0 for Al-O, 3.7 for Fe-O, 4.6 for Mg-O, 5.9 for Na-O, and 6.2 for Ca-O. Although the coordination for iron with respect to oxygen may be underestimated, the coordination number for all other cations are consistent with experiments. By 15 GPa (2,000 K), the average coordination for Si-O remains at 4.0 but increases to 4.1 for Al-O, 4.2 for Fe-O, 4.9 for Mg-O, 8.0 for Na-O, and 6.8 for Ca-O. The coordination environment for Na-O remains approximately constant up to core-mantle boundary conditions (135 GPa and 4000 K) but increases to about 6 for Si-O, 6.5 for Al-O, 6.5 for Fe-O, 8 for Mg-O, and 9.5 for Ca-O. We discuss our results in the context of the metal-silicate partitioning behavior of siderophile elements and the viscosity changes of silicate melts at upper mantle conditions. Our results have implications for melt properties, such as viscosity, transport coefficients, thermal conductivities, and electrical conductivities, and will help interpret experimental results on silicate glasses.

| S-EPMC6988478 | biostudies-literature

Fragment-Based Ab Initio Molecular Dynamics Simulation for Combustion.

Project description:We develop a fragment-based ab initio molecular dynamics (FB-AIMD) method for efficient dynamics simulation of the combustion process. In this method, the intermolecular interactions are treated by a fragment-based many-body expansion in which three- or higher body interactions are neglected, while two-body interactions are computed if the distance between the two fragments is smaller than a cutoff value. The accuracy of the method was verified by comparing FB-AIMD calculated energies and atomic forces of several different systems with those obtained by standard full system quantum calculations. The computational cost of the FB-AIMD method scales linearly with the size of the system, and the calculation is easily parallelizable. The method is applied to methane combustion as a benchmark. Detailed reaction network of methane reaction is analyzed, and important reaction species are tracked in real time. The current result of methane simulation is in excellent agreement with known experimental findings and with prior theoretical studies.

| S-EPMC8197069 | biostudies-literature

TAO-DFT-Based <i>Ab Initio</i> Molecular Dynamics.

Project description:Recently, AIMD (ab initio molecular dynamics) has been extensively employed to explore the dynamical information of electronic systems. However, it remains extremely challenging to reliably predict the properties of nanosystems with a radical nature using conventional electronic structure methods (e.g., Kohn-Sham density functional theory) due to the presence of static correlation. To address this challenge, we combine the recently formulated TAO-DFT (thermally-assisted-occupation density functional theory) with AIMD. The resulting TAO-AIMD method is employed to investigate the instantaneous/average radical nature and infrared spectra of n-acenes containing n linearly fused benzene rings (n = 2-8) at 300 K. According to the TAO-AIMD simulations, on average, the smaller n-acenes (up to n = 5) possess a nonradical nature, and the larger n-acenes (n = 6-8) possess an increasing radical nature, showing remarkable similarities to the ground-state counterparts at 0 K. Besides, the infrared spectra of n-acenes obtained with the TAO-AIMD simulations are in qualitative agreement with the existing experimental data.

| S-EPMC7674663 | biostudies-literature

Ab initio investigation of CaO-ZnO alloys under high pressure.

Project description:Ca(x)Zn(1-x)O alloys are potential candidates to achieve wide band-gap, which might significantly promote the band gap engineering and heterojunction design. We performed a crystal structure search for CaO-ZnO system under pressure, using an ab initio evolutionary algorithm implemented in the USPEX code. Four stable ordered Ca(x)Zn(1-x)O structures are found in the pressure range of 8.7-60?GPa. We further constructed the pressure vs. composition phase diagram of CaO-ZnO alloys based on the detailed enthalpy calculations. With the increase in Ca concentration, the CaO-ZnO alloy first undergoes a hexagonal to monoclinic transition, and then transforms back to a hexagonal phase. At Above 9?GPa, there is no cubic structure in the alloys, in contrast to the insostructural components (B1-B1). The band gap of the Ca(x)Zn(1-x)O alloy shows an almost linear increase as a function of the Ca concentration. We also investigated the variation regularity of the band gap under pressure.

| S-EPMC4505315 | biostudies-literature

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study.

Project description:The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.

| S-EPMC5389128 | biostudies-literature

Ab initio molecular dynamics: concepts, recent developments, and future trends.

Project description:The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given.

| S-EPMC1100773 | biostudies-literature

Ultrafast intersystem crossing dynamics in uracil unravelled by ab initio molecular dynamics.

Project description:Ab initio molecular dynamics simulations have been performed in order to investigate the relaxation dynamics of uracil after UV excitation in gas phase. Intersystem crossing (ISC) has been included for the first time into time-dependent simulations of uracil, allowing the system to relax in the singlet as well as in the triplet states. The results show a qualitatively different picture than similar simulations that include singlet states only. The inclusion of ISC effectively quenches the relaxation to the singlet ground state and instead privileges transitions from the low-lying n?* state (S1) to a ??* triplet state (T2) followed by rapid internal conversion to the lowest triplet state.

| S-EPMC4391640 | biostudies-literature

How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study.

Project description:Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic signals by reducing the effective concentration of ACh in the synaptic clefts. Organophosphate compounds irreversibly inhibit AChEs, leading to irreparable damage to nerve cells. By employing Born-Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have characterized the covalent inhibition mechanism between AChE and the nerve toxin soman and determined its free energy profile for the first time. Our results indicate that phosphonylation of the catalytic serine by soman employs an addition-elimination mechanism, which is highly associative and stepwise: in the initial addition step, which is also rate-limiting, His440 acts as a general base to facilitate the nucleophilic attack of Ser200 on the soman's phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate; in the subsequent elimination step, Try121 of the catalytic gorge stabilizes the leaving fluorine atom prior to its dissociation from the active site. Together with our previous characterization of the aging mechanism of soman inhibited AChE, our simulations have revealed detailed molecular mechanistic insights into the damaging function of the nerve agent soman.

| S-EPMC4183371 | biostudies-literature

Assessment of ab initio models of protein complexes by molecular dynamics.

Project description:Determining how proteins interact to form stable complexes is of crucial importance, for example in the development of novel therapeutics. Computational methods to determine the thermodynamically stable conformation of complexes from the structure of the binding partners, such as RosettaDock, might potentially emerge to become a promising alternative to traditional structure determination methods. However, while models virtually identical to the correct experimental structure can in some cases be generated, the main difficulty remains to discriminate correct or approximately correct models from decoys. This is due to the ruggedness of the free-energy landscape, the approximations intrinsic in the scoring functions, and the intrinsic flexibility of proteins. Here we show that molecular dynamics simulations performed starting from a number top-scoring models can not only discriminate decoys and identify the correct structure, but may also provide information on an initial map of the free energy landscape that elucidates the binding mechanism.

| S-EPMC6002105 | biostudies-literature

Insights into H2 formation in space from ab initio molecular dynamics.

Project description:Hydrogen formation is a key process for the physics and the chemistry of interstellar clouds. Molecular hydrogen is believed to form on the carbonaceous surface of dust grains, and several mechanisms have been invoked to explain its abundance in different regions of space, from cold interstellar clouds to warm photon-dominated regions. Here, we investigate direct (Eley-Rideal) recombination including lattice dynamics, surface corrugation, and competing H-dimers formation by means of ab initio molecular dynamics. We find that Eley-Rideal reaction dominates at energies relevant for the interstellar medium and alone may explain observations if the possibility of facile sticking at special sites (edges, point defects, etc.) on the surface of the dust grains is taken into account.

| S-EPMC3637713 | 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