Room temperature plasticity in amorphous SiO2 and amorphous Al2O3 : A computational and topological study

Requirements for room temperature plasticity in oxides glasses have been only recently established. While atomistic mechanisms of this type of plasticity have been reported, it remains challenging to translate this knowledge between different structures and predict what other oxide glasses can be ductile and by which principle. Here we show that a coarse-grained analysis at the polyhedral level gives valuable information to accompany the atomistic characterization of plasticity, and we propose the analysis of polyhedral neighbor change events (PNCE) as a tool to allow comparison of the room temperature plasticity in various oxide glasses. Classical atomistic simulations with around 1 million atoms provided primitive data for coarse-grained analysis. Based on the PNCE analysis, the edge-sharing polyhedra are found to be up to 2 orders of magnitude more active in enabling plasticity, and combined with the occurrence of edge-sharing polyhedra, is shown to explain the brittle to ductile transition in a-SiO2 and the intrinsically high ductility of a-Al2O3. Finally, the coarse-grained analysis enables the benefit of using additional topological constraint theory analysis to yield more in-depth information regarding the ductile features of each glass structure. Quantitative comparison between amorphous Al2O3 and SiO2 shows a consistent trend between the materials and shows that the approach can be extended to the designing of other damage tolerant oxide glass materials.Peer reviewe

Exceptional Microscale Plasticity in Amorphous Aluminum Oxide at Room Temperature

Oxide glasses are an elementary group of materials in modern society, but brittleness limits their wider usability at room temperature. As an exception to the rule, amorphous aluminum oxide (a-Al2O3) is a rare diatomic glassy material exhibiting significant nanoscale plasticity at room temperature. Here, it is shown experimentally that the room temperature plasticity of a-Al2O3 extends to the microscale and high strain rates using in situ micropillar compression. All tested a-Al2O3 micropillars deform without fracture at up to 50% strain via a combined mechanism of viscous creep and shear band slip propagation. Large-scale molecular dynamics simulations align with the main experimental observations and verify the plasticity mechanism at the atomic scale. The experimental strain rates reach magnitudes typical for impact loading scenarios, such as hammer forging, with strain rates up to the order of 1 000 s−1, and the total a-Al2O3 sample volume exhibiting significant low-temperature plasticity without fracture is expanded by 5 orders of magnitude from previous observations. The discovery is consistent with the theoretical prediction that the plasticity observed in a-Al2O3 can extend to macroscopic bulk scale and suggests that amorphous oxides show significant potential to be used as light, high-strength, and damage-tolerant engineering materials.Peer reviewe

Using steered molecular dynamics to predict and assess Hsp70 substrate-binding domain mutants that alter prion propagation.

Genetic screens using Saccharomyces cerevisiae have identified an array of cytosolic Hsp70 mutants that are impaired in the ability to propagate the yeast [PSI(+)] prion. The best characterized of these mutants is the Ssa1 L483W mutant (so-called SSA1-21), which is located in the substrate-binding domain of the protein. However, biochemical analysis of some of these Hsp70 mutants has so far failed to provide major insight into the specific functional changes in Hsp70 that cause prion impairment. In order to gain a better understanding of the mechanism of Hsp70 impairment of prions we have taken an in silico approach and focused on the Escherichia coli Hsp70 ortholog DnaK. Using steered molecular dynamics simulations (SMD) we demonstrate that DnaK variant L484W (analogous to SSA1-21) is predicted to bind substrate more avidly than wild-type DnaK due to an increase in numbers of hydrogen bonds and hydrophobic interactions between chaperone and peptide. Additionally the presence of the larger tryptophan side chain is predicted to cause a conformational change in the peptide-binding domain that physically impairs substrate dissociation. The DnaK L484W variant in combination with some SSA1-21 phenotypic second-site suppressor mutations exhibits chaperone-substrate interactions that are similar to wild-type protein and this provides a rationale for the phenotypic suppression that is observed. Our computational analysis fits well with previous yeast genetics studies regarding the functionality of the Ssa1-21 protein and provides further evidence suggesting that manipulation of the Hsp70 ATPase cycle to favor the ADP/substrate-bound form impairs prion propagation. Furthermore, we demonstrate how SMD can be used as a computational tool for predicting Hsp70 peptide-binding domain mutants that impair prion propagation

Simulation of crystallization in Ge2Sb2Te5{\mathrm{Ge}}_{2}{\mathrm{Sb}}_{2}{\mathrm{Te}}_{5}: A memory effect in the canonical phase-change material

Crystallization of amorphous Ge2Sb2Te5 (GST) has been studied using four extensive (460 atoms, up to 4 ns) density functional/molecular dynamics simulations at 600 K. This phase change material is a rare system where crystallization can be simulated without adjustable parameters over the physical time scale, and the results could provide insight into order-disorder processes in general. Crystallization is accompanied by an increase in the number of ABAB squares (A:Ge,Sb;B:Te), percolation, and the occurrence of low-frequency localized vibration modes. A sample with a history of order crystallizes completely in 1.2 ns, but ordering in others was less complete, even after 4 ns. The amorphous starting structures without memory display phases (>1ns) with subcritical nuclei (10–50 atoms) ranging from nearly cubical blocks to stringlike configurations of ABAB squares and AB bonds extending across the cell. Percolation initiates the rapid phase of crystallization and is coupled to the directional p-type bonding in metastable GST. Cavities play a crucial role, and the final ordered structure is distorted rock salt with a face-centered cubic sublattice containing predominantly Te atoms. We comment on earlier models based on smaller and much shorter simulations