Enhancing ab initio diffusion calculations in materials through Gaussian process regression

Saddle point search schemes are widely used to identify the transition state of different processes, like chemical reactions, surface and bulk diffusion, surface adsorption, and many more. In solid-state materials with relatively large numbers of atoms, the minimum mode following schemes such as dimer are commonly used because they alleviate the calculation of the Hessian on the high-dimensional potential energy surface. Here, we show that the dimer search can be further accelerated by leveraging Gaussian process regression (GPR). The GPR serves as a surrogate model to feed the dimer with the required energy and force input. We test the GPR- accelerated dimer method for predicting the diffusion coefficient of vacancy-mediated self-diffusion in bcc molybdenum and sulfur diffusion in hexagonal molybdenum disulfide. We use a multi-task learning approach that utilizes a shared covariance function between energy and force input, and we show that the multi-task learning significantly improves the performance of the GPR surrogate model compared to previously used learning approaches. Additionally, we demonstrate that a translation-hop sampling approach is necessary to avoid over-fitting the GPR surrogate model to the minimum-mode-following pathway and thus succeeding in locating the saddle point. We show that our method reduces the number of evaluations to a fraction of what a conventional dimer requires.Comment: 13 pages, 8 figures, 1 table, 5 supplemental figures, 2 supplemental tables, 1 supplemental not

Phonon-assisted diffusion in bcc phase of titanium and zirconium from first-principles

Diffusion is the underlying mechanism for many complicated materials phenomena, and understanding it is basic to the discovery of novel materials with desired physical and mechanical properties. Certain groups of solid phases, such as the bcc phase of IIIB and IVB metals and their alloys, which are only stable when they reach high enough temperatures and experience anharmonic vibration entropic effects, exhibit "anomalously fast diffusion". However, the underlying reason for the observed extraordinary fast diffusion is poorly understood and due to the existence of harmonic vibration instabilities in these phases the standard models fail to predict their diffusivity. Here, we indicate that the anharmonic phonon-phonon coupling effects can accurately describe the anomalously large macroscopic diffusion coefficients in the bcc phase of IVB metals, and therefore yield a new understanding of the underlying mechanism for diffusion in these phases. We utilize temperature-dependent phonon analysis by combining ab initio molecular dynamics with lattice dynamics calculations to provide a new approach to use the transition state theory beyond the harmonic approximation. We validate the diffusivity predictions for the bcc phase of titanium and zirconium with available experimental measurements, while we show that predictions based on harmonic transition state theory severely underestimates diffusivity in these phases.Comment: 11 pages, 5 figures, supplemental material of 18 pages with 11 figure

Antibiotic Resistance among <em>Escherichia coli</em> Isolates, Antimicrobial Peptides and Cell Membrane Disruption to the Control of <em>E. coli</em> Infections

The treatment of Escherichia coli infections has been seriously complicated due to the appearance of multidrug-resistant isolates and the rapid distribution of extended-spectrum β-lactamase-producing species. In recent years there has been considerable effort to develop alternative therapies to traditional antibiotics for infection diseases caused by antimicrobial agents. The mechanisms by which antimicrobial compounds induce bacterial damage have been suggested to be interaction with membranes, formation of pores lined by both lipids and peptides, or by a more general “Anionic lipid clustering,” and other specific mechanisms. The major constituents of the lipid bilayer on the outer membrane of E. coli as a Gram-negative bacteria are lipopolysaccharide, zwitterionic core oligosaccharides, saturated fatty acid chains with zwitterionic phospholipid head groups, and lipid A functionalized with anionic phosphate groups. Research findings emphasize the importance of the membrane composition of E. coli in determining the susceptibility to certain antimicrobial agents, such as antimicrobial peptides (AMPs) and successful treatment

Understanding the role of anharmonic phonons in diffusion of bcc metal

Diffusion in high-temperature bcc phase of IIIB-IVB metals such as Zr, Ti, and their alloys is observed to be orders of magnitude higher than bcc metals of group VB-VIB, including Cr, Mo, and W. The underlying reason for this higher diffusion is still poorly understood. To explain this observation, we compare the first-principles-calculated parameters of monovancy-mediated diffusion between bcc Ti, Zr, and dilute Zr- Sn alloys and bcc Cr, Mo, and W. Our results indicate that strongly anharmonic vibrations promote both the vacancy concentration and the diffusive jump rate in bcc IVB metals and can explain their markedly faster diffusion compared to bcc VIB metals. Additionally, we provide an efficient approach to calculate diffusive jump rates according to the transition state theory (TST). The use of standard harmonic TST is impractical in bcc IIIB/IVB metals due to the existence of ill-defined harmonic phonons, and most studies use classical or ab initio molecular dynamics for direct simulation of diffusive jumps. Here, instead, we use a stochastically-sampled temperature-dependent phonon analysis within the transition state theory to study diffusive jumps without the need of direct molecular dynamics simulations. We validate our first-principles diffusion coefficient predictions with available experimental measurements and explain the underlying reasons for the promotion of diffusion in bcc IVB metals/alloys compared to bcc VIB metals.Comment: 8 figures, 1 table, 5 supplementary figures, 1 supplementary table, 1 supplementary not

Flaw Insensitive Fracture in Nanocrystalline Graphene

We show from a series of molecular dynamics simulations that the tensile fracture behavior of a nanocrystalline graphene (nc-graphene) nanostrip can become insensitive to a pre-existing flaw (e.g., a hole or a notch) below a critical length scale in the sense that there exists no stress concentration near the flaw, the ultimate failure does not necessarily initiate at the flaw, and the normalized strength of the strip is independent of the size of the flaw. This study is a first direct atomistic simulation of flaw insensitive fracture in high-strength nanoscale materials and provides significant insights into the deformation and failure mechanisms of nc-graphene