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The nanoscopic structure of biodegradable choline-based naphthenic acid ionic liquids near the hexagonal boron-nitride (h-BN) surface was analyzed using quantum mechanics calculations and molecular dynamics simulations. The effects of the type of the ring (aliphatic or aromatic) and the size of the ring in the anion counterpart of the aliphatic ionic liquids (ILs) on the configurations, binding energies, orbital energies, density of states, charge transfer, and thermochemistry of adsorption of ILs on the h-BN surface were investigated. Also the significance of non-covalent interactions on the adsorption of ILs was disclosed from the quantum theory of atoms in molecule. The results of radial distribution functions, number density, and also charge density profiles showed the existence of a solid-like bottom layer in the vicinity of the surface. Angular distribution functions revealed that while the most probable orientation in aromatic anions is parallel to the h-BN sheet, the most probable orientation in aliphatic rings apparently is perpendicular to the surface. The mobility of cations and anions in the studied ILs with respect to the h-BN sheet was analyzed using their mean square displacements. For all ions near the surface, dynamics in the parallel direction were faster than those in the z-direction due to the structuring of the solid-like layer of ILs near the h-BN surface. Altogether, this study provides new insights into the physisorption of this new class of biodegradable ILs on h-BN nanosheets at the molecular level. [ABSTRACT FROM AUTHOR]

The structural and dynamic properties of water molecules in a uniformly charged nanopore have been studied using the method of classical molecular dynamics simulation. When confined in an uncharged nanopore with an appropriate radius, water molecules are aligned along the nanopore axis and form a single-file structure with the dipole vectors pointing toward the same end of the nanopore. We demonstrate here that when the nanopore is uniformly charged, the water molecules in the nanopore pack more tightly and the water molecules near the two ends of the nanopore are no longer aligned along the nanopore axis but tend to be aligned perpendicularly to the nanopore axis. The water dipole vectors do not point toward the same nanopore end. When the nanopore is positively charged, the water molecules in the nanopore align with their oxygen atoms pointing to the center of the nanopore. The central water molecule forms an L-defect. However for a negatively charged nanopore, the water molecules in the nanopore take up the opposite orientation. A D-defect is formed at the center of the nanopore. Furthermore, the water molecules in the negatively charged nanopore with moderate atomic partial charges diffuse and transport more quickly than the water molecules in an uncharged nanopore. [ABSTRACT FROM AUTHOR]

Structural and dynamical properties of interfacial water molecules near a hexagonal boron nitride sheet (h-BN) are investigated by means of Born-Oppenheimer molecular dynamics simulations. Orientational profiles in the interfacial regions reveal two distinct types of water molecules near the BN surface. Depending on the positions of the water molecules, on top of either N or B atoms, one type contains water molecules that are oriented with one OH bond pointing toward the N atoms and the other type contains water molecules that remain parallel to the BN sheet. Distinct hydrogen bonding and stabilization energies of these two types of water molecules are found from our calculations. In order to see the effects of dispersion interactions, simulations are performed with the BLYP (Becke-Lee-Yang-Parr) functional and also BLYP with Grimme's D3 corrections (BLYPD3). An enhancement of water ordering near the surface is observed with the inclusion of dispersion corrections. Further analysis of the diffusion coefficients, rotational time correlation functions, and hydrogen bond dynamics shows that water molecules near the h-BN sheet move faster compared to bulk water molecules both translationally and rotationally. The water molecules in the first layer are found to show substantial lateral diffusion. The escape dynamics of water from the solvation layer at the BN surface is also looked at in the current study. We have also investigated some of the electronic properties of interfacial water such as the charge density and dipole moment. It is found that the water molecules at the surface of the BN sheet have a lower dipole moment than bulk molecules. [ABSTRACT FROM AUTHOR]

Enhanced kinetic stability of vapor-deposited glasses has been established for a variety of glass organic formers. Several recent reports indicate that vapor-deposited glasses can be orientationally anisotropic. In this work, we present results of extensive molecular simulations that mimic a number of features of the experimental vapor deposition process. The simulations are performed on a generic coarse-grained model and an all-atom representation of N,N'-bis(3-methylphenyl)-N,N'- diphenylbenzidine (TPD), a small organic molecule whose vapor-deposited glasses exhibit considerable orientational anisotropy. The coarse-grained model adopted here is found to reproduce several key aspects reported in experiments. In particular, the molecular orientation of vapor-deposited glasses is observed to depend on substrate temperature during deposition. For a fixed deposition rate, the molecular orientation in the glasses changes from isotropic, at the glass transition temperature, Tg, to slightly normal to the substrate at temperatures just below Tg. Well below Tg, molecular orientation becomes predominantly parallel to the substrate. The all-atom model is used to confirm some of the equilibrium structural features of TPD interfaces that arise above the glass transition temperature. We discuss a mechanism based on distinct orientations observed at equilibrium near the surface of the film, which get trapped within the film during the non-equilibrium process of vapor deposition. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Staged evolution of dislocation structure in Ti crystallite subjected to scratching. • Mechanical response of Ti crystallites is governed by material fragmentation ahead of indenter. • Grain boundaries provide to rotational deformation and fragmentation of the material. Abstract Atomic scale deformation mechanisms of Ti single- and bicrystals subjected to scratch testing were studied experimentally and using molecular dynamics simulation. The numerical model explicitly considers the crystallographic orientation of Ti crystallites experimentally determined from EBSD analysis. The stage character of the evolution of dislocation structure in the Ti crystallites under loading was revealed that resulted from fragmentation of the material in the scratch groove. When the direction of easy dislocation glide is close to the scratching direction, the stages of generation and movement of dislocations alternate with the stages of dislocation pinning. It was found experimentally that the initially softer grain was characterized by a shallower residual scratch depth than the originally harder one. MD simulation revealed that the fragmentation is an origin of the observed disagreement between the residual scratch depth and the initial hardness of Ti grains with different crystallographic orientations. Grain boundaries were shown not only to be barriers for dislocation glide but also to favor the development of rotational deformation and further fragmentation of the material in the scratch groove. [ABSTRACT FROM AUTHOR]

Highlights • Pt3Al intermetallic alloy supports near-surface discrete breathers (DB). • Properies of DB depend on surface orientation and termination. • DB can localize energy about 1 eV. • DB can help to overcome potential barriers for structure transformations. Abstract It is known that defect-free crystals can support spatially localized, large amplitude vibrational modes with frequencies outside the linear phonon spectrum. Such excitations are called discrete breathers (DB) or intrinsic localized modes. So far, for 3D crystals DB were considered only in the bulk. In the present molecular dynamics study, for the first time, we demonstrate that DB can be excited at the low Miller indices surfaces of the Pt 3 Al intermetallic alloy. It is shown that properties of the DB depend essentially on the surface orientation and termination, as well as on DB polarization. The study of DB at crystal surfaces is important because they can localize energy of order of 1 eV, which can reduce the potential barrier for local structure transformation or a chemical reaction. Graphical abstract Image, graphical abstract [ABSTRACT FROM AUTHOR]

In this work, we report the electric-field effects on ionic hydration of Cl-, Na+, and Pb2+ using molecular dynamics simulations. It is found that the effect of weak fields on ionic hydration can be neglected. Strong fields greatly disturb the water orientation in the hydration shells of ions, though ion coordination number remains almost unchanged. Under strong fields, the first hydration shell of ions is significantly weakened and the ion-water interaction energy is dramatically reduced; surprisingly, the second hydration shells of Cl- and Na+ are slightly structured because of the optimal water orientation; moreover, ionic hydration structures become asymmetrical along the field direction because of the uniformly aligned water dipoles. Compared with Na+ and Pb2+, the hydration of Cl- is less disturbed by external fields, probably ascribed to the different water reorientation around anions and cations as well as the different structure-maker/breaker nature of the ions. Additionally, strong fields significantly enhance ion mobility and remarkably shorten the water residence time in the hydration shell. This work demonstrates that applying strong fields is an effective way to weaken ion hydration. [ABSTRACT FROM AUTHOR]

Actinide-lanthanide separation (ALSEP) has been a topic of interest in recent years as it has been shown to selectively extract problematic metals from spent nuclear fuel. However, the process suffers from slow kinetics, prohibiting it from being applied to nuclear facilities. In an effort to improve the process, many fundamental studies have been performed, but the majority have only focused on the thermodynamics of separation. Therefore, to understand the mechanism behind the ALSEP process, molecular dynamics (MD) simulations were utilized to obtain the dynamics and solvation characteristics for an organic extractant, 2-ethylhexylphosphonic acid mono-2-ethylhexyl ester (HEHEHP). Simulations were conducted with both pure and biphasic solvent systems to evaluate the complex solvent interactions within the ALSEP extraction method. The MD simulations revealed solvation and dynamical behaviors that are consistent with the experimentally observed chemical properties of HEHEHP for the pure solvent systems (e.g., hydrophobic/hydrophilic behaviors of the polar head group and alkyl chains and dimer formation between the ligands within an organic solvent). When present in a biphasic solvent system, interfacial behaviors of the ligand revealed that, at low concentrations, the alkyl side chains of HEHEHP were parallel to the interfacial plane. Upon increasing the concentration to 0.75 M, tendency for the parallel orientation decreased and a more perpendicular-like orientation was observed. Analysis of ligand solvation energies in different solvents through the thermodynamic integration method demonstrated favorability toward n-dodecane and biphasic solvents, which is in agreement with the previous experimental findings. [ABSTRACT FROM AUTHOR]

The strong binding of the adamantyl moiety to the cavity of β-cyclodextrin makes it a common binding motif in supramolecular chemistry and a common model system. Despite the attention, there are still unresolved questions regarding the orientation of the adamantane derivatives in the inclusion complexes--do they protrude from the wide or narrow opening of the cyclodextrin hosts? A combined analysis of ROESY NMR and molecular dynamics simulations allows the conclusion that positively charged adamantane derivatives are oriented with the hydrophilic group protruding from the wider opening of the cyclodextrin, while negatively charged adamantane derivatives form two coexisting types of complexes where the hydrophilic group respectively protrudes from the wide and narrow opening. Interestingly, structural modifications of the cyclodextrin host only have a slight impact on the guest orientation. [ABSTRACT FROM AUTHOR]

Abstract: The purpose of this study is the development of phase‐separating diblock copolymer model systems suitable for the comparison between the orientation process under shear and computer simulations of the same process. To do so, the polymer systems have to fulfill certain requirements like similar dynamics of both polymer blocks, which are associated with comparable glass transition temperatures. The development of suitable diblock copolymer systems such as poly(ethyl methacrylate)‐b‐poly(2‐vinylpyridine) or the tuning of already established polymer systems like polystyrene‐b‐poly(2‐vinylpyridine) via copolymerization with 4‐vinylpyridine is essential. Anionic polymerization is used for the sample synthesis to achieve this goal with the lowest possible polydispersity. Soft, coarse‐grained models are used to study the block dynamics in computer simulations. Within the dissipative particle dynamics methods the remaining differences in the block mobility are addressed. The experimentally determined zero‐shear viscosity η0 is used to match the simulation results to the synthesized polymer melts. [ABSTRACT FROM AUTHOR]

We study systematically the nanocutting of an Fe single crystal in dependence of the surface orientation and cut direction. We find that in the general case – where the edge dislocations formed at the cutting edge glide obliquely to it – a complex, three-dimensional dislocation network is created. If, however, the edge dislocations formed align with the cutting edge direction, then a simple (two-dimensional) cutting mechanism is realized, in which dislocations glide consecutively without interaction. The shape of the chip is governed by the direction of the activated glide systems. For strong dislocation interaction, a grain boundary may form separating the chip from the workpiece. A cutting hardness is defined; the calculated values are in good agreement with the ploughing hardness measured in scratching simulations. For selected orientations, we find that instead of dislocation plasticity, twinning is activated. This requires smaller cutting forces and the created chip surfaces are smooth. [ABSTRACT FROM AUTHOR]

Atomistic modeling is used to investigate the mechanical response to compressive and tensile straining of the Bagaryatskii orientation relationship between ferrite and cementite within pearlite. A range of interlamellar spacings and ferrite to cementite ratios are considered and values for important mechanical properties, including elastic modulus, yield stress, flow stress, and ductility, are determined. These values are fit to simple elasto-plastic models, thus allowing for the easy interpolation of states not simulated. Transverse loading can be described using simple 1-D composite theory, while longitudinal loading requires the consideration of the strain compatibility of the interface. The mechanical properties are shown to be largely dependent on the volume ratios of the cementite and ferrite, with the interlamellar spacing having an increasing role as it reaches smaller values. Additionally, the effect of the interface is discussed and characterized, including its role as a nucleation site for dislocations in both the ferrite and cementite. [ABSTRACT FROM AUTHOR]

In multiscale modeling of the morphological evolution of plasma facing materials in nuclear fusion reactors, the knowledge of the timescales of the involved physical processes is important. In the present study, a new method based on molecular dynamics simulations was developed to extract the lifetime of helium bubbles near tungsten surfaces. It was found that the lifetime of a helium bubble can be described by the Arrhenius equation. However, the lifetime of a helium bubble depends on the thickness of tungsten film above the helium bubble in the substrate and the bubble size. The influence of surface orientations on the lifetime of helium bubbles was also observed, and the performance of helium bubbles on the (1 1 1) surface is very different from on the (0 0 1) and (0 1 1) surfaces. The role of the helium bubble lifetime in other simulation techniques, such as in kinetic Monte Carlo methods and rate theory, is discussed. [ABSTRACT FROM AUTHOR]

Homoepitaxial growth film for (001), (110) and (111) Ni substrates is investigated by means of molecular dynamics (MD) simulation. Embedded atom method (EAM) is considered to represent the interaction potential between nickel atoms. The simulation is performed at 300K using an incident energy of 0.06eV. In this study, the deposition process is performed periodically and the period, , is relative to a perfect layer filling. The coverage rate of the actual expected level, , can be considered a determinant for thin-film growth of nickel. The level is the most filled level during the deposition on (001) substrate, while it is the less filled one in the case of (111) substrate. Moreover, the upper level is the one which is responsible for the surface roughness and the appearance time of an upper layer may also be a factor influencing the surface roughness. The deposition on (111) substrate induces the most rigorous surface with a rapid appearance time of the upper layers. The layers are almost completely filled for all substrates. The and lower layers are completely filled for (001) and (110) substrates while for (111) substrate the completely filled layers are and lower ones. [ABSTRACT FROM AUTHOR]

The Fe(110)-Li and Fe(111)-Li solid-liquid interfaces are investigated using molecular dynamics simulations (MD), and the results are detailedly compared with each other as well as with our previous findings obtained from the Fe(001)-Li solid-liquid interface. Due to the different intrinsic surface properties of the Fe substrates, the interface properties show remarkable orientation dependences. As for the Fe substrates, the three Fe surfaces suffer different impacts from the liquid Li on their relaxation behavior. The fine-scale density profiles suggest that the liquid Li atoms near the Fe(110)-Li solid-liquid interface are dramatically layered along the interface normal and the layers’ two-dimensional density maps indicate the layers present high degree of lateral order, which are very similar to the results acquired from the Fe(001)-Li solid-liquid interface. Interestingly, these phenomena observed in the Fe(110)-Li solid-liquid interface do not reproduce in the Fe(111)-Li solid-liquid interface, but some distinct Li layers are detected along the [110] direction at 500 K. In addition, the Li atoms near the Fe(111)-Li solid-liquid interface diffuse faster and invade into the Fe substrate easier than those near the other two interfaces. These orientation-dependent characteristics are well explained in terms of the different surface properties of the Fe substrates. [ABSTRACT FROM AUTHOR]

CdS homoepitaxy growth was performed by molecular dynamics using different substrate orientations and structures in order to analyze the CdS crystallinity. As anticipated from thermodynamics of homoepitaxy, highly crystalline films with only point defects were obtained on substrates with rectangular surface geometries, including [ 11 2 ¯ ] zinc blende (ZB), [ 10 1 ¯ 0 ] wurtzite (WZ), [ 11 2 ¯ 0 ] WZ, [ 110 ] ZB, [ 010 ] ZB, and [ 1 10 1 1 10 ] ZB. In contrast, films grown on substrates with hexagonal surface geometries, corresponding to the [ 0001 ] WZ and [ 111 ] ZB growth directions, showed structures with a large number of defects including; anti-sites, vacancies, stacking faults, twinning, and polytypism. WZ and ZB transitions and grain boundaries are identified using a lattice identification algorithm and represented graphically in a structural map. A dislocation analysis was performed to detect, identify, and quantify linear defects within the atomistic data. Systematic simulations using different temperatures, deposition rates, and substrate polarities were perform to analyze the trends of dislocation densities on [ 0001 ] WZ direction and showed persistent polytypism. The polytypism observed in the films grown on the substrates with hexagonal surface geometry is attributed to the similar formation energies of the WZ and ZB phases. [ABSTRACT FROM AUTHOR]

Using molecular-dynamics simulation, we study the scratching of Ti and Mg crystals by a hard tip. Both the basal and a prismatic surface orientations are considered. We focus on the characterization of defects and plasticity in the crystal. Among the various types of dislocations generated the partials b = 1 3 〈 1 ¯ 1 0 0 〉 are most prominent. During scratch dislocation reactions constantly reorganize the dislocation network adherent to the scratch groove. Plastic activity is more pronounced for the prismatic surface, where dislocation loops – mainly consisting of b = 1 3 〈 2 ¯ 1 1 0 〉 and 1 3 〈 1 ¯ 1 0 0 〉 dislocations – are emitted into the substrate. Under the basal surface I 2 intrinsic stacking faults, corresponding to b = 1 3 〈 1 ¯ 1 0 0 〉 partials are formed parallel to the scratch groove bottom, while they are oriented perpendicular to the surface under the prismatic surface. We find that mainly the { 0 1 1 ¯ 0 } 〈 2 ¯ 1 1 0 〉 slip system is activated, and relate the form of the pile-up generated to this slip. The tangential hardness is systematically smaller than the normal hardness under scratching. The basal surface has smaller hardness than the prismatic surface. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of nanoindentation are used to study the deformation behaviors of single crystal Zr for four different surface orientations. The comparison of results for two different potentials, an embedded atom method potential and a charged optimized many body potential, reveals the influence of stable and unstable stacking fault energy on dislocation behaviors under nanoindentation. The load–displacement curve, hardness and deformation behaviors of the various surface orientations Zr are compared and the elastic and plastic deformation behaviors are analyzed. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were performed to study the dependence of migration behaviours of single helium atoms near tungsten surfaces on the surface orientation and temperature. For W{100} and W{110} surfaces, He atoms can quickly escape out near the surface without accumulation even at a temperature of 400 K. The behaviours of helium atoms can be well-described by the theory of continuous diffusion of particles in a semi-infinite medium. For a W{111} surface, the situation is complex. Different types of trap mutations occur within the neighbouring region of the W{111} surface. The trap mutations hinder the escape of He atoms, resulting in their accumulation. The probability of a He atom escaping into vacuum from a trap mutation depends on the type of the trap mutation, and the occurrence probabilities of the different types of trap mutations are dependent on the temperature. This finding suggests that the escape rate of He atoms on the W{111} surface does not show a monotonic dependence on temperature. For instance, the escape rate at T = 1500 K is lower than the rate at T = 1100 K. Our results are useful for understanding the structural evolution and He release on tungsten surfaces and for designing models in other simulation methods beyond molecular dynamics. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulation we study scratching of Fe crystals by a hard repulsive tip. Three surface orientations – (1 0 0), (1 1 0), and (1 1 1) – are studied with two scratch directions in each case. We take care to analyze the projected normal and transverse contact areas properly to take the loss of contact of the tip to the substrate beneath it and its increased contact to the pile-up into account. We find that the form of the pile-up generated depends strongly on the surface orientation and scratch direction; this dependence is analyzed with the help of the dominant slip system in bcc Fe. The normal force to keep the tip at fixed depth and the transverse scratching force vary by only 15% between the different scratch systems investigated. The normal contact area decreases considerably during the initial stage of scratching as the trailing part of the tip loses contact with the substrate. The normal hardness shows similarly small variations between the different systems studied and is smaller than the hardness during the indentation process. The transverse contact area increases continuously during the scratch as the pile-up is generated. As a consequence the tangential hardness varies more strongly (by 26%) between the systems studied. For the (1 0 0)[0 1 1] scratch system we analyze the depth dependence of scratching. We find the friction coefficient to increase with scratch depth. The dependence of the normal and tangential hardness on depth are discussed with the help of the variation of the respective projected areas with depth. [ABSTRACT FROM AUTHOR]

Based on the spectra of molecular (Rayleigh) scattering of light, we investigate relaxation dynamics in the molecules of para-, meta-, and ortho-xylenes which are confined in a container and heated from room through critical temperature T c . We experimentally elucidate the successive transitions from hindered to absolutely-free rotations at temperatures up to a pre-critical temperature T *(< T c ) and then from individual to collective motions (macroscopic vibrations) of the molecules at higher temperatures above T ⁎ up to T c . Close to T c , the inner field anisotropy is the same along three axes of inertia of the ellipsoid, and the depolarization degree is universal and independent of the specific nature of xylene isomers. A marked deviation from the Rayleigh's theory is also found in the spectral intensity of scattering light. [ABSTRACT FROM AUTHOR]

Abstract: Hydrogen absorption isotherms for Pd thin films were modeled at atomistic scale by Monte Carlo (MC) simulation in the TPμN ensamble and by Molecular Dynamics (MD) simulations at 300 K. The interaction among atoms was modeled by embedded atom method (EAM) potentials. Simulated samples consisted of monocrystalline nanofilms with different thickness (2–8 nm) and two crystallographic surface orientations, (001) and (111). The isotherms were compared to bulk Pd and a few available experimental results. Instead of the plateau corresponding to the α-β PdH equilibrium in the bulk, the isotherms at nano-films show a two-plateaux behavior: a small one corresponding to a surface–subsurface hydride formation, and a larger one for the subsequent bulk hydride formation. This is strongly correlated with the atomic stress distribution induced within the thin film. The equilibrium pressures at the isotherms depend on the thin-film thickness, with pressure being larger for thicker films. The isotherms of the (001) films display lower equilibrium pressures than those for (111) films. [Copyright &y& Elsevier]

A high-purity predominantly single crystalline zirconium was subjected to controlled focused ion beam (FIB) damage. Damage estimates were obtained from electron backscattered diffraction (EBSD) and nano-indentation measurements on exactly the same area/orientation. The damage kinetics, between different crystallographic orientations, differed by one order of magnitude and a clear hierarchy of orientation sensitive ion damage emerged. Use of a simple geometric approach, linear density of atoms and corresponding scattering cross-sections to impinging gallium ions, could differentiate between extreme damage kinetics; but failed when such differences were relatively minor. Numerically intensive molecular dynamics (MD) simulations, on the other hand, were more effective. However, MD simulations or direct EBSD observations failed to justify anisotropic irradiation hardening (AIH): 3–8 times more hardening for near basal. Though explanation for AIH is indirect, evidence and rationalization for orientation-sensitive radiation damage appears clear and statistically reproducible. [ABSTRACT FROM AUTHOR]

A molecular dynamics simulation of the shock-wave propagation in the face-centered cubic (FCC) structured C60 fullerene along the <100>, <110> and <111> crystallographic directions is performed. For this purpose, the response of the material under different shock-wave loadings is studied through Hugoniot curves. Three regimes of the material behavior have been observed from fully elastic to elastic–plastic to plastic. The Hugoniot elastic limit and the phase transition are also investigated along different crystallographic directions. It is shown that the shock wave travels faster along the <110> and <111> directions than in the <100> direction in the material. Comparing the results with the experimental data, it is found that the trends of the Hugoniot data are the same as the experiments. Also, the piston velocities corresponding to different structures, such as the FCC C60 fullerene, graphite like and final diamond like, are determined based on the Hugoniot results. Moreover, it is shown that after the phase-transition occurrence, at high piston velocities the material responses along the low-index directions merge with each other; thus, an amorphous structure is expected for the final diamond-like phase. [ABSTRACT FROM AUTHOR]

Highlights: [•] The bulk vacancy formation energy was calculated for Al, Ni, Cu, Pd, Ag, and Pt. [•] Vacancy formation energies (Ev ) were calculated using the Sutton–Chen potential. [•] Vacancy formation energies (Ev ) show surface orientation dependency, . [•] Vacancy formation energies (Ev ) decrease with a temperature increase. [ABSTRACT FROM AUTHOR]

Experimentalresults by Fisher et al. [Faraday Discuss. Chem. Soc.1979, 68, 26] showed the existence of local orientationalcorrelations of segmentsof the n-alkane molecules in the liquid state. Sincethe estimated correlation volume is below 103Å3, molecular dynamics simulations appear to be a suitable methodfor their identification and characterization. We used molecular dynamicsto fully characterize short-range order in polyethylene melts. Thecharacterization started by identifying sequences of aligned segmentsin chains, each one having at least one Kuhn monomer in length. Afterward,a search was made for interactions of a tagged aligned chain segmentwith others fulfilling the same condition, laying within a limitingseparation distance (18 Å) and making a limiting orientationangle (40°). When, at least, four interactions are counted, ashort-range ordered region is defined. Chain placement in these regionshas similarities to that of the unit cell at the solid phase, althoughwith different separation distances and angle. Overall, short-rangeorder resembles a dynamic uniaxial nematic phase, the local orderparameter increasing with the chain length in agreement with experimentalresults. Segments at the ordered regions persist over time, for timeslonger than the Rouse relaxation time of the chain. Those in randomconformational sequences between the ordered regions have a mass distributionin agreement with the Flory distribution, with a number-average valuecomparable to experimental results for the molecular mass betweenentanglements. [ABSTRACT FROM AUTHOR]

Highlights: [•] Amino acid residue 882 in the B-loop is strain-conserved. [•] Substituting amino acid residue 882 affects the receptor-binding site. [•] Amino acid orientation at residue 882 also affects the receptor-binding site. [Copyright &y& Elsevier]

The growth process of twins is studied in magnesium using atomistic simulations. It is shown that a specific interface, which places prismatic and basal planes face-to-face, plays an important role. This interface has a low energy, forming a cusp in the orientation-dependent interface energy of a twinned bicrystal. This interface appears in several published twin structures and, for instance, accommodates the large deviations of twin interfaces from planes reported recently (Zhang et al., Scr. Mater. 67 (2012) 862). [Copyright &y& Elsevier]

Equilibrium molecular dynamics simulationswere employed to investigatethe structural properties of interfacial liquid ethanol on two aluminasurfacesthe (0001) and the (11̅02) terminations of α-Al2O3both described using the CLAYFF forcefield. The resultant atomic density profiles show that ethanol moleculesin the first monolayer are well ordered and that their distributiondepends on the surface OH groups. A pronounced dipolar orientationis found for the ethanol molecules in the first layer and also, althoughto a smaller extent, among the ethanol molecules in the second molecularlayer. The orientational distribution predicted for the methyl groupof ethanol on α-Al2O3(11̅02) isconsistent with that observed experimentally by Shen and co-workers.The orientation of molecules in the second layer is opposite comparedto that found in the first adsorbed molecular layer. Our simulationsshow long residence times and slowly decaying reorientation autocorrelationfunctions for ethanol molecules in the first adsorbed layer, suggestingthat within the first adsorbed layer ethanol molecules are stronglycoordinated with both α-Al2O3(0001) andα-Al2O3(11̅02) surfaces. Analysisof the hydrogen bond network confirms that preferential surface–ethanolinteractions are responsible for such observations. [ABSTRACT FROM AUTHOR]

The dependence of the reaction initiation mechanism ofpentaerythritoltetranitrate (PETN) on shock orientation and shock strength is investigatedwith molecular dynamics simulations using a reactive force field andthe multiscale shock technique. In the simulations, a single crystalof PETN is shocked along the [110], [001], and [100] orientationswith shock velocities in the range 3–10 km/s. Reactions occurwith shock velocities of 6 km/s or stronger, and reactions initiatethrough the dissociation of nitro and nitrate groups from the PETNmolecules. The most sensitive orientation is [110], while [100] isthe most insensitive. For the [001] orientation, PETN decompositionvia nitro group dissociation is the dominant reaction initiation mechanism,while for the [110] and [100] orientations the decomposition is viamixed nitro and nitrate group dissociation. For shock along the [001]orientation, we find that CO–NO2bonds initiallyacquire more kinetic energy, facilitating nitro dissociation. Forthe other two orientations, C–ONO2bonds acquiremore kinetic energy, facilitating nitrate group dissociation. [ABSTRACT FROM AUTHOR]

Near edge X-ray absorption fine structure (NEXAFS) coupled withmolecular dynamics simulations were utilized to probe the orientationat the exposed surface of the polymer film for polystyrene type polymerswith various pendant functional groups off the phenyl ring. For allthe polymers, the surface was oriented so that the rings are nominallynormal to the film surface and pointing outward from the surface.The magnitude of this orientation was small and dependent on the sizeof the pendant functional group. Bulky functional groups hinderedthe surface orientation, leading to nearly unoriented surfaces. Depthdependent NEXAFS measurements demonstrated that the surface orientationwas localized near the interface. Molecular dynamics simulations showedthat the phenyl rings were not oriented strongly around a particular“average tilt angle”. In contrast, simulations demonstratethat the phenyl rings exhibit a broad distribution of tilt angles,and that changes in the tilt angle distribution with pendant functionalitygive rise to the observed NEXAFS response. The more oriented samplesexhibit a higher probability of phenyl ring orientation at anglesgreater than 60 degrees relative to the plane of the films surface. [ABSTRACT FROM AUTHOR]

Summary Membrane proteins play important roles in various cellular functions. To analyze membrane proteins, nanodisc technology using membrane scaffold proteins allows single membrane protein units to be embedded into the lipid bilayer disc without detergents. Recent advancements in high-speed atomic force microscopy (HS-AFM) have enabled us to monitor the real-time dynamics of proteins in solution at the nanometer scale. In this study, we report HS-AFM imaging of membrane proteins reconstituted into nanodiscs using two membrane protein complexes, SecYEG complex and MgtE dimer. The observed images showed single particles of membrane protein-embedded nanodiscs in an end-up orientation whereby the membrane was fixed parallel to the supporting solid surface and in a side-on orientation whereby the membrane plane was vertically fixed to the solid surface, enabling the elucidation of domain fluctuations in membrane proteins. This technique provides a basic method for the high-resolution imaging of single membrane proteins by HS-AFM. Graphical Abstract Highlights • Membrane protein-embedded nanodiscs were used for high-speed (HS)-AFM observation • Nanodiscs in an end-up and side-on orientation were observed by HS-AFM in real time • HS-AFM combined with nanodiscs is a powerful tool for membrane protein dynamics Haruyama et al. established a procedure for the observation of membrane proteins in nanodiscs by high-speed AFM in real time. Using the two-dimensional crystal of streptavidin as well as mica as a solid support surface, dynamic structural changes of membrane proteins in the lipid environment were visualized from two distinct angles. [ABSTRACT FROM AUTHOR]

While at small collision velocities collisions of nanoparticles (NPs) are elastic, they become plastic at higher velocities. We study the elastic-plastic threshold and the onset of plasticity using molecular dynamics simulation for a Lennard-Jones material. The reasons behind the R-2/3 increase of the threshold velocity for small NP radii R found recently are discussed. At the threshold, NP orientation strongly influences the generation of plasticity, and averaging over many orientations is required to predict the critical velocity for dislocation generation. The onset of plasticity is governed by the generation of isolated stacking faults and nanotwins spanning the entire NP. At higher velocities, the fraction of defects becomes proportional to the total number of atoms in the NP. [ABSTRACT FROM AUTHOR]