Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation.
ABSTRACT: Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This indicates that thermally activated homogeneous nucleation occurs spontaneously in MD simulations without any inducing factor, whereas most previous studies have employed factors such as pressure, surface effect, and continuous cooling to induce nucleation. Moreover, further calculations over ten nanoseconds capture the microstructure evolution on the order of tens of nanometers from the atomistic viewpoint and the grain growth exponent is directly estimated. Our novel approach based on the concept of "melting pots in a supercomputer" is opening a new phase in computational metallurgy with the aid of rapid advances in computational environments.
Project description:Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue. Here, a billion-atom molecular dynamics simulation of homogeneous nucleation from an undercooled iron melt reveals that some satellite-like small grains surrounding previously formed large grains exist in the middle of the nucleation process, which are not distributed uniformly. At the same time, grains with a twin boundary are formed by heterogeneous nucleation from the surface of the previously formed grains. The local heterogeneity in the distribution of grains is caused by the local accumulation of the icosahedral structure in the undercooled melt near the previously formed grains. This insight is mainly attributable to the multi-graphics processing unit parallel computation combined with the rapid progress in high-performance computational environments.Nucleation is a fundamental physical process, however it is a long-standing issue whether completely homogeneous nucleation can occur. Here the authors reveal, via a billion-atom molecular dynamics simulation, that local heterogeneity exists during homogeneous nucleation in an undercooled iron melt.
Project description:Molecular dynamics (MD) simulations are used to directly observe nucleation of median cracks in oxide glasses under indentation. Indenters with sharp angles can nucleate median cracks in samples with no pre-existing flaws, while indenters with larger indenter angles cannot. Increasing the tip radius increases the critical load for nucleation of the median crack. Based upon an independent set of simulations under homogeneous loading, the fracture criterion in the domain of the principal stresses is constructed. The fracture criterion, or "fracture locus", can quantitatively explain the observed effects of indenter angle and indenter tip radius on median crack nucleation. Our simulations suggest that beyond the maximum principal stress, plasticity and multi-axial stresses should also be considered for crack nucleation under indentation, even for brittle glassy systems.
Project description:In order to investigate the early phase of the amyloid formation by the short amyloidogenic octapeptide sequence ('NFGAILSS') derived from IAPP, we carried out a 100ns all-atom molecular dynamics (MD) simulations of systems that contain 27 peptides and over 30,000 water molecules. The large-scale calculations were performed for the wild type sequence and seven alanine-scanned sequences using AMBER 8.0 on RIKEN's special purpose MD-GRAPE3 supercomputer, using the all-atom point charge force field ff99, which do not favor β-structures. Large peptide clusters (size 18-26 mers) were observed for all simulations, and our calculations indicated that isoleucine at position 5 played important role in the formation of β-rich clusters. In the oligomeric state, the wild type and the S7A sequences had the highest β-structure content (~14%), as calculated by DSSP, in line with experimental observations, whereas I5A and G3A had the highest helical content (~20%). Importantly, the β-structure preferences of wild type IAPP originate from its association into clusters and are not intrinsic to its sequence. Altogether, the results of this first large-scale, multi-peptide all-atom molecular dynamics simulation appear to provide insights into the mechanism of amyloidogenic and non-amyloidogenic oligomers that mainly corroborate previous experimental observations.
Project description:While quasicrystals possess long-range orientational order they lack translation periodicity. Considerable advancements in the elucidation of their structures and formative principles contrast with comparatively uncharted interrelations, as studies bridging the spatial scales from atoms to the macroscale are scarce. Here, we report on the homogeneous nucleation of a single quasicrystalline seed from the undercooled melt of glass-forming NiZr and its continuous growth into a tenfold twinned dendritic microstructure. Observing a series of crystallization events on electrostatically levitated NiZr confirms homogeneous nucleation. Mapping the microstructure with electron backscatter diffraction suggests a unique, distortion-free structure merging a common structure type of binary alloys with a spiral growth mechanism resembling phyllotaxis. A general geometric description, relating all atomic loci, observed by atomic resolution electron microscopy, to a pentagonal [Formula: see text] module, explains how the seed's decagonal long-range orientational order is conserved throughout the symmetry breaking steps of twinning and dendritic growth.
Project description:Thermophysical properties of highly doped Si50Ge50 melt were measured contactlessly in the electromagnetic levitation facility ISS-EML on board the International Space Station. The sample could be melted, overheated by about 375?K, and cooled down in 350?mbar Argon atmosphere. A large undercooling of about 240?K was observed and a quasi-homogeneous nucleation on the droplet surface occurred. During the cooling phase, high-resolution videos were taken from the side and the top. The density and thermal expansion were evaluated with digital image processing; the viscosity and the surface tension were measured by means of the oscillating drop technique. Inductive measurements of the electrical resistivity were conducted by a dedicated electronics. All data were taken as a function of temperature T from the overheated melt down to the undercooled range. We found a nonlinear thermal expansion, suggesting a many body effect in the liquid beyond the regular pair interaction, an enhanced damping of surface oscillations likely related to an internal turbulent flow, and an increment of the electrical resistivity with decreased T in the undercooled range regarding a demixing of the components.
Project description:The structural and dynamical behavior of the 41-56 beta-hairpin from the protein G B1 domain (GB1) has been studied at different temperatures using molecular dynamics (MD) simulations in an aqueous environment. The purpose of these simulations is to establish the stability of this hairpin in view of its possible role as a nucleation site for protein folding. The conformation of the peptide in the crystallographic structure of the protein GB1 (native conformation) was lost in all simulations. The new equilibrium conformations are stable for several nanoseconds at 300K (>10 ns), 350 K (>6.5 ns), and even at 450 K (up to 2.5 ns). The new structures have very similar hairpin-like conformations with properties in agreement with available experimental nuclear Overhauser effect (NOE) data. The stability of the structure in the hydrophobic core region during the simulations is consistent with the experimental data and provides further evidence for the role played by hydrophobic interactions in hairpin structures. Essential dynamics analysis shows that the dynamics of the peptide at different temperatures spans basically the same essential subspace. The main equilibrium motions in this subspace involve large fluctuations of the residues in the turn and ends regions. Of the six interchain hydrogen bonds, the inner four remain stable during the simulations. The space spanned by the first two eigenvectors, as sampled at 450 K, includes almost all of the 47 different hairpin structures found in the database. Finally, analysis of the hydration of the 300 K average conformations shows that the hydration sites observed in the native conformation are still well hydrated in the equilibrium MD ensemble.
Project description:Bringing a liquid into contact with a solid is known to generally promote crystal nucleation at the freezing temperature. In contrast, it is much more difficult to conceive that a solid surface may hinder nucleation and favor large undercooling effects. Here we report on ab initio and classical molecular dynamic simulations to capture the underlying structural mechanism responsible for this striking effect. We find that the substrate/liquid interactions exert an important influence on in-plane ordering of the adjacent liquid layers in the undercooling regime. In particular, we identify that the presence of atomic arrangements with five-fold symmetry (FFS) on the substrate surface in the form of pentagonal atomic motifs allows the liquid to be undercooled well below its freezing temperature. Our findings clearly demonstrate that this pentagonal-coordinated surface enhances the presence of local arrangements with FFS in the adjacent liquid layers that prevents the crystal nucleation. Finally we suggest new technological developments to attain large undercooling effects.
Project description:The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.
Project description:Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure.
Project description:Molecular dynamics (MD) simulations are carried out to investigate the effects of the type and spacing of FCC/BCC interfaces on the deformation and spall behavior. The simulations are carried out using model Cu/Ta multilayers with six different types of interfaces. The results suggest that interface type can significantly affect the structure and intensity of the incoming shock wave, change the activated slip systems, alter dislocation slip and twinning behavior, affect where and how voids are nucleated during spallation and the resulting spall strength. Moreover, the above aspects are significantly affected by the interface spacing. A transition from homogeneous to heterogeneous dislocation nucleation occurs as the interface spacing is decreased to 6?nm. Depending on interface type and spacing, damage (voids) nucleation and spall failure is observed to occur not only at the Cu/Ta interfaces, but also in the weaker Cu layer interior, or even in the stronger Ta layer interior, although different mechanisms underlie each of these three distinct failure modes. These findings point to the fact that, depending on the combination of interface type and spacing, interfaces can lead to both strengthening and weakening of the Cu/Ta multilayered microstructures.