Influence of intrinsic strain on irradiation induced damage: the role of threshold displacement and surface binding energies

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Atomistic simulations of focused ion beam machining of strained silicon

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A new method for microscale cyclic crack growth characterization from notched microcantilevers and application to single crystalline tungsten and a metallic glass

The lifetime of most metals is limited by cyclic loads, ending in fatigue failure. The progressive growth of cracks ends up in catastrophic failure. An advanced method is presented for the determination of cyclic crack growth on the microscale using a nanoindenter, which allows the characterization of > 10,000 loading cycles. It uses focused ion beam fabricated notched microcantilevers. The method has been validated by cyclic bending metallic glass and tungsten microcantilevers. The experiments reveal a stable crack growth during the lifetime of both samples. The metallic glass shows less plasticity due to the absence of dislocations, but shows shearing caused by the deformation. The crack growth rates determined in the tests follow Paris' power law relationship. The results are reliable, reproducible and comparable with macroscopic setups. Due to the flexibility of the method, it is suitable for the characterization of specific microstructural features, like single phases, grain boundaries or different grain orientations

Equation of motion for dislocations with inertial effects

An approximate equation of motion is proposed for screw and edge dislocations, which accounts for retardation and for relativistic effects in the subsonic range. Good quantitative agreement is found, in accelerated or in decelerated regimes, with numerical results of a more fundamental nature.Comment: 6 pages, 4 figures, LaTe

Depinning transition for a screw dislocation in a model solid solution

On the basis of the classical dislocation theory, the Solid Solution Hardening (SSH) is commonly ascribed to the pinning of the edge dislocations. At the atomic level, the theoretical study of the dislocation cores contrasts with such a prediction. Using the static molecular simulations with some interatomic effective potentials, we demonstrate numerically that the critical resolved shear stress associated to a screw dislocation in a random Ni(Al) single crystal has same order as the edge one. Such a result is imposed by the details of the dislocation stacking fault and the core dissociation into Shockley partials. The SSH statistical theory is employed to tentatively predict analytically the data acquired through our atomistic simulations at different Al concentration

Atomic super-resolution tomography

We consider the problem of reconstructing a nanocrystal at atomic resolution from electron microscopy images taken at a few tilt angles. A popular reconstruction approach called discrete tomography confines the atom locations to a coarse spatial grid, which is inspired by the physical a priori knowledge that atoms in a crystalline solid tend to form regular lattices. Although this constraint has proven to be powerful for solving this very under-determined inverse problem in many cases, its key limitation is that, in practice, defects may occur that cause atoms to deviate from regular lattice positions. Here we propose a grid-free discrete tomography algorithm that allows for continuous deviations of the atom locations similar to super-resolution approaches for microscopy. The new formulation allows us to define atomic interaction potentials explicitly, which results in a both meaningful and powerful incorporation of the available physical a priori knowledge about the crystal's properties. In computational experiments, we compare the proposed grid-free method to established grid-based approaches and show that our approach can indeed recover the atom positions more accurately for common lattice defects

“Conjugate Channeling” Effect in Dislocation Core Diffusion: Carbon Transport in Dislocated BCC Iron

Dislocation pipe diffusion seems to be a well-established phenomenon. Here we demonstrate an unexpected effect, that the migration of interstitials such as carbon in iron may be accelerated not in the dislocation line direction [symbol], but in a conjugate diffusion direction. This accelerated random walk arises from a simple crystallographic channeling effect. [c] is a function of the Burgers vector b, but not [symbol], thus a dislocation loop possesses the same everywhere. Using molecular dynamics and accelerated dynamics simulations, we further show that such dislocation-core-coupled carbon diffusion in iron has temperature-dependent activation enthalpy like a fragile glass. The 71° mixed dislocation is the only case in which we see straightforward pipe diffusion that does not depend on dislocation mobility.National Science Foundation (U.S.) (Grant No. CMMI-0728069)National Science Foundation (U.S.) (Grant No. DMR-1008104)National Science Foundation (U.S.) (Grant No. DMR-1120901

Anisotropy effects on the plasmonic response of nanoparticle dimers

We present an ab initio study of the anisotropy and atomic relaxation effects on the optical properties of nanoparticle dimers. Special emphasis is placed on the hybridization process of localized surface plasmons, plasmon-mediated photoinduced currents, and electric-field enhancement in the dimer junction. We show that there is a critical range of separations between the clusters (0.1–0.5 nm) in which the detailed atomic structure in the junction and the relative orientation of the nanoparticles have to be considered to obtain quantitative predictions for realistic nanoplasmonic devices. It is worth noting that this regime is characterized by the emergence of electron tunneling as a response to the driven electromagnetic field. The orientation of the particles not only modifies the attainable electric field enhancement but can lead to qualitative changes in the optical absorption spectrum of the system.We thankfully acknowledge financial support by the European Research Council (ERC-2010-AdG Proposal No. 267374 and ERC-2011-AdG Proposal No. 290891), the Spanish Government (Grants MAT2011-28581-C02-01, FIS2013-46159-C3-1-P, and MAT2014-53432-C5-5-R), and the Basque Country Government (Grupos Consolidados IT-578-13).Peer Reviewe

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals