Atomistically motivated interface model to account for coupled plasticity and damage at grain boundaries

Grain boundary (GB) characteristics play a major role in the understanding and prediction of polycrystalline behavior [1]. GB roles become more important when it comes to nanocrystalline metals and ceramics. To gain a deeper insight into the behavior of the grain boundary, molecular dynamics (MD) simulations are utilized. The Mode I, mode II and mixed mode loading behavior is investigated using different MD simulations. By adding the unloading path to the MD simulations it was possible to differentiate between different active mechanisms at the GB. An interface model is introduced based on our understanding from the atomistic simulation of the grain boundaries. When it comes to the grain boundary (GB) behavior, the current model is able to capture the competition between the intergranular fracture and the grain boundary sliding. The interface model is thermodynamically consistent and is able to capture the complex behavior of the GB under different loading conditions.

Grain boundary induced deformation mechanisms in nanocrystalline Al by molecular dynamics simulation: From interatomic potential perspective

Diffusion, Trapping, and Dissociation Behaviours of Helium at the Σ5 Grain Boundary in Tungsten: A Molecular Dynamics Study

Molecular dynamics simulation on formation mechanism of grain boundary steps in micro-cutting of polycrystalline copper

Grain boundary energy landscape from the shape analysis of synthetically stabilized embedded grains

Applicability of interface spring and interphase models in micromechanics for predicting effective stiffness of polymer-matrix nanocomposite

Probing the micro-mechanism of precipitate-strengthened alloys with precipitate free zone: An experimental and theoretical study

Calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an alpha-galactose residue at their nonreducing end, such as the disaccharides alphaGal1-2betaGalOMe, alphaGal1-3betaGalOMe, and alphaGal1-4betaGalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics simulations and compared with those observed in available crystal structures, including PA-IL.alphaGal1-2betaGalOMe complex, which was solved at 2.4 A resolution and reported herein. The role of a structural bridge water molecule in the binding site of PA-IL was also elucidated through molecular dynamics simulations and free energy calculations. This water molecule establishes three very stable hydrogen bonds with O6 of nonreducing galactose, oxygen from Pro-51 main chain, and nitrogen from Gln-53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated, and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the free energy calculations, the simulations predicted the correct binding affinity trends with the 1-2-linked disaccharide presenting three times stronger affinity ligand than the other two. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.

As the sizes of electronic devices continue to shrink, understanding key atomic phenomena vital to macroscopic processes become increasingly important. Mass transport along grain boundaries (GBs) is such a key process. We have studied diffusion mechanisms at metallic GBs of Ag and Al with the embedded-atom method, with molecular statics (MS) and molecular dynamics (MD), as well as with massively parallel computers at Oak Ridge National Laboratory and Sandia National Laboratory. Formation and migration energies of interstitials and vacancies at the optimal symmetric tilt GBs of different angles in Ag were first obtained using MS at 0 K. Extensive MD simulations were then carried out for selected Ag GBs using massively parallel computers at different finite temperatures up to the melting point. In this way, we were able to determine the dominant diffusion mechanism within different temperature regimes by comparison of the activation energies from MS results for the identified diffusion processes with the MD simulation results. For the first time, the results of this study on Ag GBs had provided realistic explanation and simulation-based evidence for the discrepancy between the activation energies from the recent low-temperature experiments by Ma and Balluffi and those at high temperatures reported in the literature. Preliminary MD results on Al GB diffusion are in excellent agreement with experiment and on-going work on Al and Al-Cu systems aimed to further understand electromigration phenomena will be briefly discussed.

In this paper, simulated biaxial creep deformation behaviour for nanocrystalline (NC) nickel (Ni) has been performed at various applied load (i.e. 1GPa, 1.4GPa, 2GPa, 2.5GPa and 3GPa) for a particular temperature (i.e. 1210K) using molecular dynamics (MD) simulation to investigate underlying deformation mechanism based on the structural evolution during biaxial creep process. Primary, secondary and tertiary stages of creep are observed to be exhibited significantly only at 3GPa applied stress. While, only primary and secondary stages of creep are exhibited at 1GPa applied stress. Atomic structural evaluation, dislocation density, shear strains, atomic trajectory, inverse pole figures and grain orientation with texture distribution have been carried out to evaluate structural evolution. Stress exponent (m) for NC Ni is analysed for a particular creep temperature (i.e. 1210K) and obtained m value is 1.30. According to shear strains counter plot, accumulation of higher shear strains are observed at grain boundary (GB) during biaxial creep deformation. It is found that dislocation density during biaxial creep is increased with the progress of creep process. Grain rotation and texture evaluation during biaxial creep process are studied using grain tracking algorithm (GTA). Grain rotation in ultrafine-grained NC Ni specimen during biaxial creep deformation is happened and exhibits almost distinct distribution, which is occurred due to the atomic shuffling within the GBs. Grain growth of ultrafine grained NC Ni is observed during biaxial creep deformation which is caused by mechanical stress.

The term molecular mechanics (MM) refers to the use of simple potential-energy functions (e.g., harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular mechanics approaches are widely applied in molecular structure refinement, molecular dynamics (MD) simulations, Monte Carlo (MC) simulations, and ligand-docking simulations. Typically, molecular mechanics models consist of spherical atoms connected by springs which represent bonds. Internal forces experienced in the model structure are described using simple mathematical functions. For example, Hooke’s law is commonly used to describe bonded interactions, and the nonbonded atoms might be treated as inelastic hard spheres or may interact according to a Lennard-Jones potential. Using these simple models, a molecular dynamics simulation numerically solves Newton’s equations of motion, thus allowing structural fluctuations to be observed with respect to time. Dynamic simulation methods are widely used to obtain information on the time evolution of conformations of proteins and other biological macromolecules1–4 and also kinetic and thermodynamic information. Simulations can provide fine detail concerning the motions of individual particles as a function of time. They can be utilized to quantify the properties of a system at a precision and on a time scale that is otherwise inaccessible, and simulation is, therefore, a valuable tool in extending our understanding of model systems. Theoretical consideration of a system additionally allows one to investigate the specific contributions to a property through “computational alchemy”,5 that is, modifying the simulation in a way that is nonphysical but nonetheless allows a model’s characteristics to be probed. One particular example is the artificial conversion of the energy function from that representing one system to that of another during a simulation. This is an important technique in free-energy calculations.6 Thus, molecular dynamics simulations, along with a range of complementary computational approaches, have become valuable tools for investigating the basis of protein structure and function. This review offers an outline of the origin of molecular dynamics simulation for protein systems and how it has developed into a robust and trusted tool. This review then covers more recent advances in theory and an illustrative selection of practical studies in which it played a central role. The range of studies in which MD has played a considerable or pivotal role is immense, and this review cannot do justice to them; MD simulations of biomedical importance were recently reviewed.4 Particular emphasis will be placed on the study of dynamic aspects of protein recognition, an area where molecular dynamics has scope to provide broad and far-ranging insights. This review concludes with a brief discussion of the future potential offered to advancement of the biological and biochemical sciences and the remaining issues that must be overcome to allow the full extent of this potential to be realized. 1.1. Historical Background MD methods were originally conceived within the theoretical physics community during the 1950s. In 1957, Alder and Wainwright7 performed the earliest MD simulation using the so-called hard-sphere model, in which the atoms interacted only through perfect collisions. Rahman8 subsequently applied a smooth, continuous potential to mimic real atomic interactions. During the 1970s, as computers became more widespread, MD simulations were developed for more complex systems, culminating in 1976 with the first simulation of a protein9,10 using an empirical energy function constructed using physics-based first-principles assumptions. MD simulations are now widely and routinely applied and especially popular in the fields of materials science11,12 and biophysics. As will be discussed later in this review, a variety of experimental conditions may be simulated with modern theories and algorithms. The initial simulations only considered single molecules in vacuo. Over time, more realistic or at least biologically relevant simulations could be performed. This trend is continuing today. The initial protein MD simulation, of the small bovine pancreatic trypsin inhibitor (BPTI), covered only 9.2 ps of simulation time. Modern simulations routinely have so-called equilibration periods much longer than that, and production simulations of tens of nanoseconds are routine, with the first microsecond MD simulation being reported in 1998.13 In addition, the original BPTI simulation included only about 500 atoms rather than the 104-106 atoms that are common today. While much of this advancement results from an immense increase in availability of computing power, major theoretical and methodological developments also contribute significantly. The number of publications regarding MD theory and application of MD to biological systems is growing at an extraordinary pace. A single review cannot do justice to the recent applications of MD. Using data from ISI Web of Science, the authors estimate that during 2005 at least 800 articles will be published that discuss molecular dynamics and proteins. The historical counts are shown in Figure 1. Open in a separate window Figure 1 Articles matching ISI Web of Science query “TS=(protein) AND TS=(molecular dynamics)”.

Correlating the five parameter grain boundary character distribution and the intergranular corrosion behaviour of a stainless steel using 3D orientation microscopy based on mechanical polishing serial sectioning

Grain boundaries (GBs) are important microstructure features and can significantly affect the properties of nanocrystalline materials. Molecular dynamics simulation was carried out in this study to investigate the shear response and deformation mechanisms of symmetric and asymmetric Σ11<1 1 0> tilt GBs in copper bicrystals. Different deformation mechanisms were reported, depending on GB inclination angles and equilibrium GB structures, including GB migration coupled to shear deformation, GB sliding caused by local atomic shuffling, and dislocation nucleation from GB. The simulation showed that migrating Σ11(1 1 3) GB under shear can be regarded as sliding of GB dislocations and their combination along the boundary plane. A non-planar structure with dissociated intrinsic stacking faults was prevalent in Σ11 asymmetric GBs of Cu. This type of structure can significantly increase the ductility of bicrystal models under shear deformation. A grain boundary can be a source of dislocation and migrate itself at different stress levels. The intrinsic free volume involved in the grain boundary area was correlated with dislocation nucleation and GB sliding, while the dislocation nucleation mechanism can be different for a grain boundary due to its different equilibrium structures.

Garnet-type Li7La3Zr2O12 (LLZO) and its derivatives are considered promising candidate materials for all-solid-state Li-ion batteries as solid electrolytes due to their high Li+ conductivities of around 10-4 S cm-1 at room temperature and wide electrochemical window. Despite the larger number of detailed studies utilizing various experimental and theoretical approaches, the experimentally evaluated Li+ conductivities did not precisely match the computationally predicted values. The discrepancy between the ion conductivities can be attributed to the ambivalent properties of grain boundaries (GBs). GB structure is a critical parameter that controls the macroscopic properties of materials. However, various technological limitations of both the experimental and theoretical approaches utilized for elucidating the Li+ conduction behavior of GBs have restricted our ability of reaching a deeper understanding of the processes occurring at the atomic level. In this study, we investigated the Li+conducting behaviors of various tilted GBs of cubic LLZO with a garnet framework by using molecular dynamics approaches. Nine stoichiometric equilibrium GB models were used to determine Li+conductivity. It was found that the GB conductivity was smaller than the bulk one regardless of the orientation. In particular, the conductivities perpendicular to the GBs were characterized by the lowest values. Some factors affecting Li conductivity near the tilted GBs may be related to their stability. The relationship between the structural distortions at the GBs and the Li+ conducting characteristics were evaluated in terms of the GB energies and radial distribution function for the La-La, Zr-Zr, and O-O interactions in the LLZO bulk and GBs. We found that the Li+ conductivities are highly correlate with the structural distortions at the GBs. In order to elucidate the Li+ diffusion characteristics at the GBs in more detail, the variations of the atomic concentration near the GBs were calculated along the axis perpendicular to the GB surface. The atomic population at bulk region was constantly modulated, while that at GB region was anomalously dispersed. The average atomic concentration at the GBs was lower than that at the bulk. In particular, the observed decrease in the Li+ concentration suggests the formation of Li-deficient sites across the GB center, which represents the primary reason for the degraded ionic conductivity in the GB region. In fact, the Li ionic conductivity perpendicular to the GBs decreased with decreasing Li+ concentration at the GBs, which was caused by the slower diffusion of Li+. Thus, preventing the distortion of the GB crystallographic structure and the related drop in the Li+concentration should be considered one of the top priorities when designing GBs with desirable properties. Acknowledgement This work was partially supported by CREST, JST Grant Number JPMJCR1322, Japan.

The cubic silicon carbide (3C-SiC) has been considered as a candidate structural material for several types of advanced nuclear reactors. The effects of cascade collision on thermal conductivity in symmetrical tilt grain boundary (GB) were studied by Molecular dynamics (MD) simulations. The thermal conductivity of 3C-SiC at Σ5(210)[001] GB was calculated using non-equilibrium molecular dynamics (NEMD) methods. A relatively small simulation unit was used to analyze the effect of different energies of incident PKA (primary knock-on atoms) on the thermal conductivity of 3C-SiC and to compare the results with perfect structure GB system. Finally, the vibrational density of states (VDOS) of atoms in the GB region was calculated to analyze the phonon mismatch at the interface. Calculations show that cascade collisions generated by energetic atoms will result in a decrease in thermal conductivity of the Σ5(210) GB system, but the effect varies in different regions, with a sharp decrease in thermal conductivity and an increase in thermal resistance for the intracrystalline region, while the magnitude of change in either thermal resistance or thermal conductivity is not significant in the GB region. Irradiated model shows a higher GB energy compared to the unirradiated model. For all irradiated models, lattice defects have a significant effect on the thermal conductivity of the GB system, depending on the spatial structure of the GBs. the results of the VDOS analysis suggest that an increase in the degree of atomic lattice mismatch near the interface is responsible for a further increase in the thermal resistance of the irradiated GB system.