An evaluation of the kinematic approximation in helium atom scattering using wavepacket calculations

We use 2-D wavepacket calculations to examine the scattering of helium atoms from dynamic assemblies of surface adsorbates, and in particular to explore the validity of the widely used kinematic scattering approximation. The wavepacket calculations give exact results for quasi-elastic scattering that are closely analogous to time-of-flight (TOF) experiments and they are analysed as such. A scattering potential is chosen to represent 8 meV helium atoms scattering from sodium atoms adsorbed on a Cu(001) surface and the adsorbates in the model move according to an independent Langevin equation. The energy broadening in the quasi-elastic scattering is obtained as a function of parallel momentum transfer and compared with the corresponding results using the kinematic scattering approximation. Under most circumstances the kinematic approximation and the more accurate wavepacket method are in good agreement; however, there are cases where the two methods give different results. We relate these differences to pathological features in the scattering form-factor.EPSRC Studentship, Royal Society University Research Fellowshi

PIGLE — Particles Interacting in Generalized Langevin Equation simulator

We present a package using Simulink and MATLAB to perform molecular dynamics simulations of interacting particles obeying a Generalized Langevin Equation. The package, which accounts for three spatial dimensions and rigid-body like rotation, is tuned to explore surface diffusion of co-adsorbed species. The physical parameters are species specific, and include userdefined colored noise spectra and memory friction kernels acting independently on translational and rotational degrees of freedom. We benchmark the simulations using established analytical results for dynamical correlation functions, and we use the package to numerically verify novel analytical results concerning dissipative rotational motion and mutli-exponential friction kernels. The package provides a straight-forward way to expand the modeling of ultra-fast surface diffusion problems at the atomic scale.Herchel Smith Fund, Blavatnik Foundatio

Unlocking new contrast in a scanning helium microscope.

Delicate structures (such as biological samples, organic films for polymer electronics and adsorbate layers) suffer degradation under the energetic probes of traditional microscopies. Furthermore, the charged nature of these probes presents difficulties when imaging with electric or magnetic fields, or for insulating materials where the addition of a conductive coating is not desirable. Scanning helium microscopy is able to image such structures completely non-destructively by taking advantage of a neutral helium beam as a chemically, electrically and magnetically inert probe of the sample surface. Here we present scanning helium micrographs demonstrating image contrast arising from a range of mechanisms including, for the first time, chemical contrast observed from a series of metal-semiconductor interfaces. The ability of scanning helium microscopy to distinguish between materials without the risk of damage makes it ideal for investigating a wide range of systems.This research was supported under the Australian Research Councils Discovery Projects (Project No. DP08831308) funding scheme. Postgraduate research scholarships (M.B., A.F.) from the University of Newcastle gratefully acknowledged. We thank the Newcastle and Cavendish workshops, Donald MacLaren and Kane O’Donnell for technical support, insightful discussions and assistance. This work was performed in part at both the Materials and ACT nodes of the Australian National Fabrication Facility, which is a company established under the National Collaborative Research Infrastructure Strategy to provide nano- and micro-fabrication facilities for Australia’s researchers.This is the final version of the article. It was first available from NPG via http://dx.doi.org/10.1038/ncomms1018

Structural Evolution of a Cyclooctatetraene Adlayer on Cu(111) during Isothermal Desorption

The use of helium diffraction patterns to study desorption processes is explored as a novel extension to traditional methods based on helium specular reflection. The sample, cyclooctatetraene adsorbed on Cu(111), provides a rich but complex structure. The modulation of cyclooctatetraene by Cu(111) is manifested as a convolution in the diffraction pattern, displaying an averaged super-cell symmetry of (7 √3 × 7 √3)R30◦. The adlayer expands during isothermal desorption, and the change in lattice constant provides a direct measure of the coverage as a function of time. We find a desorption energy of 0:96 ± 0:01 eV at saturation of the first layer, and an upper limit of 1:62 ± 0:07 eV for isolated molecules. These values, and details of the assigned structure, indicate chemisorbed molecules with a planar conformation.For financial support, N. Avidor gratefully acknowledges the Blavatnik Foundation, J.A. Lau acknowledges the ICASEC, P.S.M. Townsend acknowledges the UK EPSRC, I. Calvo-Almaz´an acknowledges the Ram´on Areces Foundation, BJ Hinch acknowledges the NSF (CHE-1565673). The authors thank G. Alexandrowicz for useful discussions. EPSRC (EP/E004962/1) EPSRC (1363145

How Atomic Steps Modify Diffusion and Inter-adsorbate Forces: Empirical Evidence from Hopping Dynamics in Na/Cu(115).

We followed the collective atomic-scale motion of Na atoms on a vicinal Cu(115) surface within a time scale of pico- to nanoseconds using helium spin echo spectroscopy. The well-defined stepped structure of Cu(115) allows us to study the effect that atomic steps have on the adsorption properties, the rate for motion parallel and perpendicular to the step edge, and the interaction between the Na atoms. With the support of a molecular dynamics simulation we show that the Na atoms perform strongly anisotropic 1D hopping motion parallel to the step edges. Furthermore, we observe that the spatial and temporal correlations between the Na atoms that lead to collective motion are also anisotropic, suggesting the steps efficiently screen the lateral interaction between Na atoms residing on different terraces.This work was supported by the German-Israeli Foundation for Scientific Research and Development, the Israeli Science Foundation (Grant No. 2011185), the German Science Foundation (DFG) through contract MO 960/18-1, the Cluster of Excellence RESOLV (EXC 1069), and the European Research Council under the European Union’s seventh framework program (FP/2007-2013)/ERC Grant 307267.This is the author accepted manuscript. The final version is available from ACS via http://dx.doi.org/10.1021/acs.jpclett.5b0193

Vibrational lifetimes and friction in adsorbate motion determined from quasi-elastic scattering

The vibrational excitation of molecules adsorbed on a surface is typically probed by spectroscopic techniques such as infrared or Raman spectroscopy. In the present article we demonstrate an alternative method to determine vibrational lifetimes of adsorbate molecules using quasi-elastic helium atom scattering (QHAS). As a probe of diffusive motion of molecules on surfaces QHAS is well established. Here, we demonstrate that QHAS can also be used to probe the vibrational lifetime of a molecule in its adsorption well. Measurements of cyclopentadienyl, C5H5, on Cu(111) allow us to distinguish two substrate phonon modes as well as two molecular vibrational modes, perpendicular and parallel to the surface. We further find that the dephasing of the vibrational motion corresponds to the friction determined in previous diffusion measurements.Financial support by the EPSRC (EP/E0049621), the Austrian Academy of Sciences (BAJL), the Royal Society (APJ) and the US National Science Foundation (CHE1124879, BJH) is gratefully acknowledged

Note: A simple sample transfer alignment for ultra-high vacuum systems

The alignment of ultra-high-vacuum sample transfer systems can be problematic when there is no direct line of sight to assist the user. We present the design of a simple and cheap system which greatly simplifies the alignment of sample transfer devices. Our method is based on the adaptation of a commercial digital camera which provides live views from within the vacuum chamber. The images of the camera are further processed using an image recognition and processing code which determines any misalignments and reports them to the user. Installation has proven to be extremely useful in order to align the sample with respect to the transfer mechanism. Furthermore, the alignment software can be easily adapted for other systems.One of us (A.T.) acknowledges financial support provided by the FWF (Austrian Science Fund) within Project No. J3479-N20

Global distribution of the sickle cell gene and geographical confirmation of the malaria hypothesis

It has been 100 years since the first report of sickle haemoglobin (HbS). More than 50 years ago, it was suggested that the gene responsible for this disorder could reach high frequencies because of resistance conferred against malaria by the heterozygous carrier state. This traditional example of balancing selection is known as the 'malaria hypothesis'. However, the geographical relationship between the transmission intensity of malaria and associated HbS burden has never been formally investigated on a global scale. Here, we use a comprehensive data assembly of HbS allele frequencies to generate the first evidence-based map of the worldwide distribution of the gene in a Bayesian geostatistical framework. We compare this map with the pre-intervention distribution of malaria endemicity, using a novel geostatistical area-mean comparison. We find geographical support for the malaria hypothesis globally; the relationship is relatively strong in Africa but cannot be resolved in the Americas or in Asia

The dynamics of benzene on Cu(111): a combined helium spin echo and dispersion-corrected DFT study into the diffusion of physisorbed aromatics on metal surfaces

We use helium spin-echo spectroscopy (HeSE) to investigate the dynamics of the diffusion of benzene adsorbed on Cu(111). The results of these measurements show that benzene moves on the surface through an activated jump-diffusion process between the adsorption sites on a Bravais lattice. Density Functional Theory (DFT) calculations with van der Waals (vdW) corrections help us understand that the molecule diffuses by jumping through non-degenerate hollow sites. The results of the calculations shed light on the nature of the binding interaction between this prototypical aromatic molecule and the metallic surface. The highly accurate HeSE experimental data provide a quantitatively stringent benchmark for the vdW correction schemes applied to the DFT calculations and we compare the performances of several dispersion interaction schemes.MS would like to thank the Royal Society for his University Research Fellowship. HH acknowledges the support of the Leverhulme Trust. This work used the ARCHER UK National Supercomputing Service via our membership of the UK’s HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202)

Modeling the morphodynamics of coastal responses to extreme events: what shape are we in?

This paper is not subject to U.S. copyright. The definitive version was published in Sherwood, C. R., van Dongeren, A., Doyle, J., Hegermiller, C. A., Hsu, T.-J., Kalra, T. S., Olabarrieta, M., Penko, A. M., Rafati, Y., Roelvink, D., van der Lugt, M., Veeramony, J., & Warner, J. C. Modeling the morphodynamics of coastal responses to extreme events: what shape are we in? Annual Review of Marine Science, 14, (2022): 457–492, https://doi.org/10.1146/annurev-marine-032221-090215.This review focuses on recent advances in process-based numerical models of the impact of extreme storms on sandy coasts. Driven by larger-scale models of meteorology and hydrodynamics, these models simulate morphodynamics across the Sallenger storm-impact scale, including swash,collision, overwash, and inundation. Models are becoming both wider (as more processes are added) and deeper (as detailed physics replaces earlier parameterizations). Algorithms for wave-induced flows and sediment transport under shoaling waves are among the recent developments. Community and open-source models have become the norm. Observations of initial conditions (topography, land cover, and sediment characteristics) have become more detailed, and improvements in tropical cyclone and wave models provide forcing (winds, waves, surge, and upland flow) that is better resolved and more accurate, yielding commensurate improvements in model skill. We foresee that future storm-impact models will increasingly resolve individual waves, apply data assimilation, and be used in ensemble modeling modes to predict uncertainties.All authors except D.R. were partially supported by the IFMSIP project, funded by US Office of Naval Research grant PE 0601153N under contracts N00014-17-1-2459 (Deltares), N00014-18-1-2785 (University of Delaware), N0001419WX00733 (US Naval Research Laboratory, Monterey), N0001418WX01447 (US Naval Research Laboratory, Stennis Space Center), and N0001418IP00016 (US Geological Survey). C.R.S., C.A.H., T.S.K., and J.C.W. were supported by the US Geological Survey Coastal/Marine Hazards and Resources Program. A.v.D. and M.v.d.L. were supported by the Deltares Strategic Research project Quantifying Flood Hazards and Impacts. M.O. acknowledges support from National Science Foundation project OCE-1554892