Computing energy barriers for rare events from hybrid quantum/classical simulations through the virtual work principle

Hybrid quantum/classical techniques can flexibly couple ab initio simulations to an empirical or elastic medium to model materials systems that cannot be contained in small periodic supercells. However, due to electronic non-locality a total energy cannot be defined, meaning energy barriers cannot be calculated. We provide a general solution using the principle of virtual work in a modified nudged elastic band algorithm. Our method enables the first ab initio calculations of the kink formation energy for edge dislocations in molybdenum and lattice trapping barriers to brittle fracture in silicon

Hybrid quantum/classical study of hydrogen-decorated screw dislocations in tungsten : ultrafast pipe diffusion, core reconstruction, and effects on glide mechanism

The interaction of hydrogen (H) with dislocations in tungsten (W) must be understood in order to model the mechanical response of future plasma-facing materials for fusion applications. Here, hybrid quantum mechanics/molecular mechanics (QM/MM) simulations are employed to study the ⟨111⟩ screw dislocation glide in W in the presence of H, using the virtual work principle to obtain energy barriers for dislocation glide, H segregation, and pipe diffusion. We provide a convincing validation of the QM/MM approach against full DFT energy-based methods. This is possible because the compact core and relatively weak elastic fields of ⟨111⟩ screw dislocations allow them to be contained in periodic DFT supercells. We also show that H segregation stabilizes the split-core structure while leaving the Peierls barrier almost unchanged. Furthermore, we find an energy barrier of less than 0.05 eV for pipe diffusion of H along dislocation cores. Our quantum-accurate calculations provide important reference data for the construction of larger-scale material models

A first principles based polarizable O(N) interatomic force field for bulk silica

We present a reformulation of the Tangney-Scandolo interatomic force field for silica J. Chem. Phys. 117, 8898 (2002), which removes the requirement to perform an Ewald summation. We use a Yukawa factor to screen electrostatic interactions and a cutoff distance to limit the interatomic potential range to around 10 Å. A reparametrization of the potential is carried out, fitting to data from density functional theory calculations. These calculations were performed within the local density approximation since we find that this choice of functional leads to a better match to the experimental structural and elastic properties of quartz and amorphous silica than the generalized gradient approximation approach used to parametrize the original Tangney-Scandolo force field. The resulting O(N) scheme makes it possible to model hundreds of thousands of atoms with modest computational resources, without compromising the force field accuracy. The new potential is validated by calculating structural, elastic, vibrational, and thermodynamic properties of $\alpha$-quartz and amorphous silica

Design concepts and performance of NASA X-band (7162 MHz/8415 MHz) transponder for deep-space spacecraft applications

The design concepts and measured performance characteristics are summarized of an X band (7162 MHz/8415 MHz) breadboard deep space transponder (DSP) for future spacecraft applications, with the first use scheduled for the Comet Rendezvous Asteroid Flyby (CRAF) and Cassini missions in 1995 and 1996, respectively. The DST consists of a double conversion, superheterodyne, automatic phase tracking receiver, and an X band (8415 MHz) exciter to drive redundant downlink power amplifiers. The receiver acquires and coherently phase tracks the modulated or unmodulated X band (7162 MHz) uplink carrier signal. The exciter phase modulates the X band (8415 MHz) downlink signal with composite telemetry and ranging signals. The receiver measured tracking threshold, automatic gain control, static phase error, and phase jitter characteristics of the breadboard DST are in good agreement with the expected performance. The measured results show a receiver tracking threshold of -158 dBm and a dynamic signal range of 88 dB

Molecular dynamics with on-the-fly machine learning of quantum-mechanical forces

We present a molecular dynamics scheme which combines first-principles and machine-learning (ML) techniques in a single information-efficient approach. Forces on atoms are either predicted by Bayesian inference or, if necessary, computed by on-the-fly quantum-mechanical (QM) calculations and added to a growing ML database, whose completeness is, thus, never required. As a result, the scheme is accurate and general, while progressively fewer QM calls are needed when a new chemical process is encountered for the second and subsequent times, as demonstrated by tests on crystalline and molten silicon

Coulomb interaction between a spherical and a deformed nuclei

We present analytic expressions of the Coulomb interaction between a spherical and a deformed nuclei which are valid for all separation distance. We demonstrate their significant deviations from commonly used formulae in the region inside the Coulomb radius, and show that they remove various shortcomings of the conventional formulae.Comment: 7 pages 4 figure

Enabling QM-accurate simulation of dislocation motion in γ−Ni and α−Fe using a hybrid multiscale approach

We present an extension of the ‘learn on the fly’ method to the study of the motion of dislocations in metallic systems, developed with the aim of producing information-efficient force models that can be systematically validated against reference QM calculations. Nye tensor analysis is used to dynamically track the quantum region centered at the core of a dislocation, thus enabling quantum mechanics/molecular mechanics simulations. The technique is used to study the motion of screw dislocations in Ni-Al systems, relevant to plastic deformation in Ni-based alloys, at a variety of temperature/strain conditions. These simulations reveal only a moderate spacing ( ∼ 5 Å ) between Shockley partial dislocations, at variance with the predictions of traditional molecular dynamics (MD) simulation using interatomic potentials, which yields a much larger spacing in the high stress regime. The discrepancy can be rationalized in terms of the elastic properties of an hcp crystal, which influence the behavior of the stacking fault region between Shockley partial dislocations. The transferability of this technique to more challenging systems is addressed, focusing on the expected accuracy of such calculations. The bcc α − Fe phase is a prime example, as its magnetic properties at the open surfaces make it particularly challenging for embedding-based QM/MM techniques. Our tests reveal that high accuracy can still be obtained at the core of a dislocation, albeit at a significant computational cost for fully converged results. However, we find this cost can be reduced by using a machine learning approach to progressively reduce the rate of expensive QM calculations required during the dynamical simulations, as the size of the QM database increases

Seed dormancy cycling in Arabidopsis : chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals

The involvement of chromatin remodelling in dormancy cycling in the soil seed bank (SSB) is poorly understood. Natural variation between the winter and summer annual Arabidopsis ecotypes Cvi and Bur was exploited to investigate the expression of genes involved in chromatin remodelling via histone 2B (H2B) ubiquitination/de-ubiquitination and histone acetylation/deacetylation, the repressive histone methyl transferases CURLY LEAF (CLF) and SWINGER (SWN), and the gene silencing repressor ROS1 (REPRESSOR OF SILENCING1) and promoter of silencing KYP/SUVH4 (KRYPTONITE), during dormancy cycling in the SSB. ROS1 expression was positively correlated with dormancy while the reverse was observed for CLF and KYP/SUVH4. We propose ROS1 dependent repression of silencing and a sequential requirement of CLF and KYP/SUVH4 dependent gene repression and silencing for the maintenance and suppression of dormancy during dormancy cycling. Seasonal expression of H2B modifying genes was correlated negatively with temperature and positively with DOG1 expression, as were histone acetyltransferase genes, with histone deacetylases positively correlated with temperature. Changes in the histone marks H3K4me3 and H3K27me3 were seen on DOG1 (DELAY OF GERMINATION1) in Cvi during dormancy cycling. H3K4me3 activating marks remained stable along DOG1. During relief of dormancy, H3K27me3 repressive marks slowly accumulated and accelerated on exposure to light completing dormancy loss. We propose that these marks on DOG1 serve as a thermal sensing mechanism during dormancy cycling in preparation for light repression of dormancy. Overall, chromatin remodelling plays a vital role in temporal sensing through regulation of gene expression

A preconditioning scheme for minimum energy path finding methods

Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum energy path for typical potential energy surfaces encountered in molecular simulation. We propose a preconditioning scheme which, combined with a new adaptive time step selection algorithm, substantially reduces the computational cost of transition path finding algorithms. We demonstrate the improved performance of our approach in a range of examples including vacancy and dislocation migration modeled with both interatomic potentials and density functional theory