Modeling of stick-slip phenomena using molecular dynamics

Molecular dynamics simulations are performed to investigate the atomic-scale stick-slip phenomenon of a pyramidal diamond tip inserted into the Ag(010) surface. The mechanisms behind the stick-slip events are investigated by considering sliding speeds between 1.0 and 5.0 ms-1 and vertical support displacements of 5 and 15 Å. The analysis of the dynamic features of the substrate shows that dislocations are extrinsically linked to the stick events, with the emission of a dislocation in the substrate region near the tip, when slip occurs after stick. For small vertical displacements, the scratch in the substrate is not continuous because the tip can jump over the surface when slipping, whereas at 15 Å, a continuous scratch is formed. The dynamic friction coefficient increases from ∼0.13 to ∼0.46 with increasing depth, but the static friction coefficient increases only from ∼0.32 to ∼0.54. At the larger depths the tip does not come to a halt during stick as it does for shallow indents. Instead the tip motion is more continuous with stick and slip manifested by periods of faster and slower motion. Although the exact points of stick and slip depend on the sliding speed, the damage to the substrate, the atomistic stick-slip mechanisms, and the friction coefficients are relatively independent of speed over the range of values considered

Gold Adatoms and Dimers on Relaxed Graphite Surfaces

The interaction of deposited gold adatoms and dimers with multilayer relaxed graphite surfaces is investigated through a density functional approach with numerical orbitals and a relativistic core pseudopotential. The energy landscape for a gold adatom along [110] agrees with scanning tunneling microscopy observations including the preferred β binding site for adatoms and the mobility difference between silver and gold adatoms. Deposited particles are shown to induce surface deformation and polarization. Static relaxation and dynamic simulations indicate that the energetically preferred binding orientation for a gold dimer is normal rather than parallel to the graphite surface. The dimer response to a simulated scanning tunneling microscopy tip is investigated by molecular dynamics simulations

Diffusion dynamics of defects in Fe and Fe-P systems

The dimer method with the Ackland EAM potential has been used to determine the diffusion mechanisms of isolated defects in the bulk of α-Fe. Three defect systems were studied, an isolated vacancy, a P-vacancy complex and a P interstitial defect. Using an event table consisting of the transitions found using the dimer method, the kinetic Monte Carlo method has been used to simulate the diffusion of these defects. Periodic boundary conditions were used to simulate Fe crystals with finite concentrations of P atoms between 0.006 at. % and 0.038 at. %. At lower temperatures of around 350 K, substitutional P atoms in Fe act as centers of attraction for vacancy defects, such that the defect moves as a P-vacancy complex for most of the time. However, as the temperature is increased, the phosphorus atom and the vacancy spend greater amounts of time dissociated. We found that P interstitial defects can also diffuse through the lattice. Diffusion constants have been calculated for these systems at various temperatures and P concentrations. These showed that an Fe-P dumbbell is the most mobile of these defect systems and a P-vacancy complex the least mobile. For the isolated vacancy and P interstitial defect systems, the diffusion constant was found to satisfy the Arrhenius relation; the P-vacancy complex, however, showed a deviation from this relation

Defect generation and pileup of atoms during nanoindentation of Fe single crystals

Complementary large scale molecular-dynamics simulations and experiments have been carried out to determine the atomistic mechanisms of the nanoindentation process in single crystal Fe{110}, {100}, and {111}. The defect formation and motion causes the complex mechanisms of plastic and elastic deformation which is reflected in the pileup patterns. The experimental results show distinct patterns of pileup material which are dependent on the individual crystal faces and the superposition of the stress field of the indenter. The highest pileup around the indenter hole occurs on the {100} surface and the shallowest on {111}. The least symmetric surface is {110} which produces an experimental pileup pattern displaying only twofold symmetry with the axially symmetric indenter. The pyramidal indenter produces an asymmetric pattern which changes as the crystal is rotated with respect to the tip but repeats with threefold rotational symmetry. Material displacement occurs primarily in planes of the {110} family. Pileup is formed by cross slip between planes of the same family which intersect in 〈111〉 directions. For the {110} surface, dislocation loops propagate in the four in-plane 〈111〉 directions and the two inclined 〈111〉 directions. The loops that propagate in the in-plane directions are terminated by edge dislocations at the surface. These transport material away from the tip but cannot produce pileup. The loops that propagate in the inclined direction cross slip and cause the observed pileup. The {100} surface has fourfold rotational symmetry and all the 〈111〉 directions are inclined. The dislocation loops propagate in these directions and cross slip readily occurs, leading to a large pileup. The {111} face shows the least pileup which is more spread out over the surface. In this case the dislocation loops propagate in shallow slip planes and do not readily cross slip. Experimentally determined force-depth curves show distinct “pop-ins” which correspond to the formation of dislocations. The contact pressure (nanohardness) is not a constant and increases with decreasing indentation depth. It also changes with crystal face. Calculated force-depth curves match the experimental trend but give estimates of the nanohardness and Young’s modulus higher than those values experimentally determined

Development of a ReaxFF potential for Ag/Zn/O and application to Ag deposition on ZnO

A new empirical potential has been derived to model an Ag–Zn–O system. Additional parameters have been included into the reactive force field (ReaxFF) parameter set established for ZnO to describe the interaction between Ag and ZnO for use in molecular dynamics (MD) simulations. The reactive force field parameters have been fitted to density functional theory (DFT) calculations performed on both bulk crystal and surface structures. ReaxFF accurately reproduces the equations of state determined for silver, silver zinc alloy and silver oxide crystals via DFT. It also compares well to DFT binding energies and works of separation for Ag on a ZnO surface. The potential was then used to model single point Ag deposition on polar (000View the MathML source1¯) and non-polar (10View the MathML source1¯0) orientations of a ZnO wurtzite substrate, at different energies. Simulation results then predict that maximum Ag adsorption on a ZnO surface requires deposition energies of ≤ 10 eV

The ESR1 (6q25) locus is associated with calcaneal ultrasound parameters and radial volumetric bone mineral density in European men

<p><b>Purpose:</b> Genome-wide association studies (GWAS) have identified 6q25, which incorporates the oestrogen receptor alpha gene (ESR1), as a quantitative trait locus for areal bone mineral density (BMD(a)) of the hip and lumbar spine. The aim of this study was to determine the influence of this locus on other bone health outcomes; calcaneal ultrasound (QUS) parameters, radial peripheral quantitative computed tomography (pQCT) parameters and markers of bone turnover in a population sample of European men.</p> <p><b>Methods:</b> Eight single nucleotide polymorphisms (SNP) in the 6q25 locus were genotyped in men aged 40-79 years from 7 European countries, participating in the European Male Ageing Study (EMAS). The associations between SNPs and measured bone parameters were tested under an additive genetic model adjusting for centre using linear regression.</p> <p><b>Results:</b> 2468 men, mean (SD) aged 59.9 (11.1) years had QUS measurements performed and bone turnover marker levels measured. A subset of 628 men had DXA and pQCT measurements. Multiple independent SNPs showed significant associations with BMD using all three measurement techniques. Most notably, rs1999805 was associated with a 0.10 SD (95%CI 0.05, 0.16; p = 0.0001) lower estimated BMD at the calcaneus, a 0.14 SD (95%CI 0.05, 0.24; p = 0.004) lower total hip BMD(a), a 0.12 SD (95%CI 0.02, 0.23; p = 0.026) lower lumbar spine BMD(a) and a 0.18 SD (95%CI 0.06, 0.29; p = 0.003) lower trabecular BMD at the distal radius for each copy of the minor allele. There was no association with serum levels of bone turnover markers and a single SNP which was associated with cortical density was also associated with cortical BMC and thickness.</p> <p><b>Conclusions:</b> Our data replicate previous associations found between SNPs in the 6q25 locus and BMD(a) at the hip and extend these data to include associations with calcaneal ultrasound parameters and radial volumetric BMD.</p&gt

Simulating radiation damage in a bcc Fe system with embedded yttria nanoparticles

This paper was accepted for publication in the journal Journal of Nuclear Materials and the definitive published version is available at http://dx.doi.org/10.1016/j.jnucmat.2013.02.016We present a molecular dynamics study of radiation damage arising from nuclear collisions close to embedded yttria nanoparticles in a bcc Fe matrix. The model assumes a perfect body-centred cubic (bcc) iron matrix in which yttria nano-particles are embedded as a simplified model of an Oxide Dispersion Strengthened steel. It is shown how the nano-particles interact with nearby initiated collision cascades, through cascade blocking and absorbing energy. Fe defects accumulate at the interface both directly from the ballistic collisions and also by attraction of defects generated close by. The nano-particles generally remain intact during a radiation event and release absorbed energy over times longer than the ballistic phase of the collision cascade

Cells of the human intestinal tract mapped across space and time

Acknowledgements We acknowledge support from the Wellcome Sanger Cytometry Core Facility, Cellular Genetics Informatics team, Cellular Generation and Phenotyping (CGaP) and Core DNA Pipelines. This work was financially supported by the Wellcome Trust (W1T20694, S.A.T.; 203151/Z/16/Z, R. A. Barker.); the European Research Council (646794, ThDefine, S.A.T.); an MRC New Investigator Research Grant (MR/T001917/1, M.Z.); and a project grant from the Great Ormond Street Hospital Children’s Charity, Sparks (V4519, M.Z.). The human embryonic and fetal material was provided by the Joint MRC/Wellcome (MR/R006237/1) Human Developmental Biology Resource (https://www.hdbr.org/). K.R.J. holds a Non-Stipendiary Junior Research Fellowship from Christ’s College, University of Cambridge. M.R.C. is supported by a Medical Research Council Human Cell Atlas Research Grant (MR/S035842/1) and a Wellcome Trust Investigator Award (220268/Z/20/Z). H.W.K. is funded by a Sir Henry Wellcome Fellowship (213555/Z/18/Z). A.F. is funded by a Wellcome PhD Studentship (102163/B/13/Z). K.T.M. is funded by an award from the Chan Zuckerberg Initiative. H.H.U. is supported by the Oxford Biomedical Research Centre (BRC) and the The Leona M. and Harry B. Helmsley Charitable Trust. We thank A. Chakravarti and S. Chatterjee for their contribution to the analysis of the enteric nervous system. We also thank R. Lindeboom and C. Talavera-Lopez for support with epithelium and Visium analysis, respectively; C. Tudor, T. Li and O. Tarkowska for image processing and infrastructure support; A. Wilbrey-Clark and T. Porter for support with Visium library preparation; A. Ross and J. Park for access to and handling of fetal tissue; A. Hunter for assistance in protocol development; D. Fitzpatrick for discussion on developmental intestinal disorders; and J. Eliasova for the graphical images. We thank the tissue donors and their families, and the Cambridge Biorepository for Translational Medicine and Human Developmental Biology Resource, for access to human tissue. This publication is part of the Human Cell Atlas: https://www.humancellatlas.org/publications.Peer reviewedPublisher PD

Cells of the human intestinal tract mapped across space and time.

Funder: Medical Research CouncilThe cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease