Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation

The dynamical origin of the x-ray diffuse scattering by crystals of a protein, Staphylococcal nuclease, is determined using molecular dynamics simulation. A smooth, nearly isotropic scattering shell at originates from equal contributions from correlations in nearest-neighbor water molecule dynamics and from internal protein motions, the latter consisting of -helix pitch and inter--strand fluctuations. Superposed on the shell are intense, three-dimensional scattering features that originate from a very small number of slowly varying (>10 ns) collective motions. The individual three-dimensional features are assigned to specific collective motions in the protein, and some of these explicitly involve potentially functional active-site deformations.     

Hydration of the chloride ion in concentrated aqueous solutions using neutron scattering and molecular dynamics

Neutron scattering experiments were performed on 6 m LiCl solutions in order to obtain the solvation structure around the chloride ion. Molecular dynamics simulations on systems mirroring the concentrated electrolyte conditions of the experiment were carried out with a variety of chloride force-fields. In each case the simulations were run with both full ionic charges and employing the electronic continuum correction (implemented through charge scaling) to account effectively for electronic polarisation. The experimental data were then used to assess the successes and shortcomings of the investigated force-fields. We found that due to the very good signal-to-noise ratio in the experimental data, they provide a very narrow window for the position of the first hydration shell of the chloride ion. This allowed us to establish the importance of effectively accounting for electronic polarisation, as well as adjusting the ionic size, for obtaining a force-field which compares quantitatively to the experimental data. The present results emphasise the utility of performing neutron diffraction with isotopic substitution as a powerful tool in gaining insight and examining the validity of force-fields in concentrated electrolyte solutions.     

A comparison of ion scattering spectra and molecular dynamics simulations at the surface of silicate glasses

Molecular dynamics simulations are correlated with experimental ion scattering spectra to elucidate the surface structure and composition of fused silica and potassium trisilicate glass. The ion scattering spectra and molecular dynamics simulations both show that the oxygen atoms dominate the surface monolayer of fused silica. The ion scattering spectra of fracture surfaces of potassium trisilicate glass show a large potassium signal with little scattering signal from the oxygen or silicon atoms indicating a predominance of potassium in the surface monolayer. This local enrichment of potassium in the surface monolayer is due to their shielding of the charged silicate tetrahedra at the surface. This is also consistent with the simulations.     

Reactive ion scattering study of physisorbed adsorbates: experiment and theory

We have studied reactive ion scattering (RIS) of hyperthermal (1–100 eV) Cs⁺ projectiles from physisorbed surfaces. RIS experiments from physisorbed water on Pt(1 1 1) reveal scattering products of Cs(H₂O)_n⁺ (n=1–3) cluster ions. The yields for RIS products are extremely high compared to those with chemisorbed species. Classical molecular dynamics simulations provide a new mechanism that explains the enhanced RIS yields with physisorbed species. Slow Cs⁺ projectiles pick up physisorbed molecules via an ion–surface abstraction reaction, preferably without direct collisions between projectile and adsorbate. This RIS process is very efficient and mechanistically different from the RIS process responsible for chemisorbed species that occurs through direct collision-induced desorption.     

A molecular dynamics study of ion migration in a doped electroactive polymer

Simulating the \hbox{BF}_{4}^{-} -doped poly(3-octylthiophene) lattice by molecular dynamics results in a structure in which dopant ions intercalate as a sandwich between thiophene rings on adjacent polymer chains. The ions occupy sites in channels parallel to the polymer main chain, which retains a high degree of planarity in contrast to the pristine (undoped) polymer. Even when lattice imperfections are created by expanding the cell, Coulomb forces ensure that the intercalation features containing the dopant channels are largely retained. On applying electric fields in the principal directions of the 'perfect lattice' it is found that the ions migrate most readily along the ion-channel directions (the lattice c axis), leaving the lattice undisturbed. Although higher electric fields cause dopant migration to occur perpendicular to the channel directions they destroy the intercalated lattice. In the reduced-order lattice regions substantial motion of the ions are predicted at a critical value of the lattice parameter.     

Brillouin scattering in ice and deuterated ice as a function of temperature

The elastic constants c₁₁, c₃₃, c₄₄ for ordinary ice and c₁₁ for D₂O ice between 12 and 250°K are deduced from light scattering Brillouin measurements for sound waves of wavevector q = 2.35 × 10⁵cm^?1. A range of temperature is found between 70 and 130°K where the elastic constants display an abnormal behaviour.     

Chain dynamics in a hexadecane melt as seen by neutron scattering and identified by molecular dynamics simulations

Different local and global chain dynamics in a C(16)H(34) melt could be revealed by resolution resolved time-of-flight quasielastic neutron scattering and complementary molecular dynamics simulations. Thereby it has been demonstrated that the measured intermediate scattering functions can validate the simulated data on the pico- to nanosecond timescale. Remarkably the shape of the experimentally measured intermediate scattering functions can be reproduced excellently by molecular dynamics simulations. It was found that although the extracted apparent activation energy corresponds to the long-range diffusion value, the molecular dynamics in this time range are mainly due to local bond rotations and the rotation of entire molecules.     

Predicting secondary ion formation in molecular dynamics simulations of sputtering

We present a model to incorporate the excitation and ionization of sputtered particles into molecular dynamics simulations of ion bombardment-induced collision cascades in metals. The kinetic excitation of the solid is described by electronic friction experienced by all moving particles and electron promotion in close atomic collisions. Transport of the resulting excitation energy is treated by a nonlinear diffusion equation. The resulting space- and time-dependent electron temperature is then introduced into a rate equation model describing the ionization of ejected particles. This way, secondary ion formation is described by assigning an individual ionization probability to every sputtered atom. Averaging over the entire flux, this allows the prediction of measurable quantities like integral or spectral ionization probabilities as well as velocity spectra of secondary ions.     

Laboratory-scale measurement of scattering from modelled Arctic ice ridges

An experiment is performed to measure acoustic scattering from scale modelled ice ridges in both specular (forward) and non-specular (backward) directions, for comparison with predictions from theoretical models. The experiment uses a 100 kHz transmitter emitting sinusoidal bursts. An array of miniature transducers is used to measure the scattered field as a function of scattering angle. Experimental results are obtained for scattering from different types of rods simulating ice ridges, and also the reflection coefficient from an acrylic block. The results show good agreement with the Twersky model predictions. This experiment establishes an effective technique, using scale models in the laboratory, to compare theoretical predictions and field experimental data.     

Theory of ion scattering from single crystals

The scattering of He⁺, Ne⁺ and Ar⁺ ions at 600 eV from Ni(110) in the [11̄0] direction is modeled using classical dynamics. The distributions of final scattering angles of the primary ions are displayed as contour plots over the surface impact zone. From the contour plots the regions of the surface that give rise to scattering at specific angles can be isolated. The majority of the inplane scattering arises from collisions of the primary ion with second layer or “valley” atoms. However, to correctly reproduce the experimental energy distribution curves of Heiland and Taglauer (J. Vacuum Sci. Technol. 9 (1971) 620), we must include a simple collision time correction to account for neutralization of the ion beam. This analysis predicts that the ions which collide with second layer atoms of the solid are preferentially neutralized. The energy distributions due to first layer collisions agree well with experiment. We find that a full molecular three dimensional model is needed to describe all of the ion scattering events since for most of the collisions, the ion is simultaneously interacting with at least two atoms of the solid. However, in agreement with other workers we find only a single collision is responsible for the “binary” peak in the energy distribution. In addition the relative scattering intensity at different angles is dependent on having a three-dimensional solid.     

Argon ion double scattering from polycrystalline copper

It has been found that under certain conditions the high-energy side of the polycrystal-scattered ion energy distribution may exhibit a distinct and intense peak similar to the double-scattering peak observable for single-crystalline targets.     

Theory of ion neutralisation scattering from surfaces

A method for the calculation of the probability of neutralisation of an ion, which is scattered from the surface of a solid is presented. It assumes the ion to move along a classical trajectory and solves for the time evolution operator for the electronic system. For one electron Hamiltonians the solution can be carried out exactly. Results are presented for scattering from a semi-infinite linear chain.     

Light scattering evidence of a central component in ice Ih

High resolution Raman spectra of ice I_h single crystal in the frequency range 0–30 cm^?1 are reported, at various temperatures. For the first time evidence is given for the existence of a Lorentzian central component in all scattering configurations. A polarization analysis of the spectra clearly shows that the central mode cannot be ascribed to the high frequency tails of the Brillouin doublet, nor to the disorder induced phonon background even accounting for renormalization of the phonon propagator. The epectral features indicate the existence of a direct coupling between the light and some relaxation mechanism of the crystal.A model is suggested to account for the excess scattering and for the activation of the acoustic phonon density of states.     

Low energy ion scattering from a Ni(100) surface

We have tudied the scattering of He and Ne ione from a clean Ni(001) surface in the energy range of 0.5 to 5 keV. The spectra are dominated by scattering from atoms in the first layer for energies belowe 2 keV, whereas for higher energies contributions from the second layer can be identified. In the impact collision mode of ion scattering spectroscopy with a scattering angle =164°, the shape of the shadow cone can be determined. These experimental shadow cone radii agree over a wide range of parameters well with calculations using a Thomas-Fermi-Molière potential with a reduced screening length.     

Light scattering from correlated ion fluctuations in ionic conductors

Inelastic light scattering spectra of CuI and AgI in the α and melt phases are reported and shown to involve two depolarized Lorentzian components centered at zero frequency. The narrow component is interpreted in terms of ionic motions and we propose that the observed depolarized scattering is caused by correlated configurations of the mobile ions.     

Determination of ion quantity by using low-temperature ion density theory and molecular dynamics simulation

In this paper, we report a method by which the ion quantity is estimated rapidly with an accuracy of 4%. This finding is based on the low-temperature ion density theory and combined with the ion crystal size obtained from experiment with the precision of a micrometer. The method is objective, straightforward, and independent of the molecular dynamics(MD)simulation. The result can be used as the reference for the MD simulation, and the method can improve the reliability and precision of MD simulation. This method is very helpful for intensively studying ion crystal, such as phase transition,spatial configuration, temporal evolution, dynamic character, cooling efficiency, and the temperature limit of the ions.     

Properties of a soft-sphere liquid from non-Newtonian molecular dynamics

A soft-sphere, inverse-12 liquid is simulated in both the isokinetic-isochoric and the isokinetic-isobaric ensemble using nonequilibrium molecular dynamics. The simulation for the isobaric ensemble is discussed in detail. The non-Newtonian characteristics of the liquid are clearly demonstrated; namely, the shear-rate-dependent pressure and density (shear dilatancy), the shear-rate-dependent shear viscosity (shear thinning), and evidence of normal pressure differences. For the first time, it is clearly shown that a significant component of isobaric shear thinning is due to shear dilatancy. The isochoric and isobaric results are checked for consistency. Simple empirical relations for the equation of state and transport properties of the fluid are presented.This is a publication in part of the National Institute of Standards and Technology (formerly NBS) and is not subject to copyright.     

Polarization ratio characteristics of electromagnetic scattering from sea ice in polar areas

In the global climate system, the polar regions are sensitive indicators of climate change, in which sea ice plays an important role. Satellite remote sensing is a significant tool for monitoring sea ice. The use of synthetic aperture radar(SAR) images to distinguish sea ice from sea water is one of the current research hotspots in this topic. To distinguish sea ice from the open sea, the polarization ratio characteristics of sea ice and sea water are studied for L-band and C-band radars, based on an electromagnetic scattering model of sea ice derived from the integral equation method(IEM) and the radiative transfer(RT) model. Numerical experiments are carried out based on the model and the results are given as follows. For L-band, the polarization ratio for sea water depends only on the incident angle, while the polarization ratio for sea ice is related to the incident angle and the ice thickness. For C-band, the sea water polarization ratio is influenced by the incident angle and the root mean square(RMS) height of the sea surface. For C-band, for small to medium incident angles,the polarization ratio for bare sea ice is mainly determined by the incident angle and ice thickness. When the incident angle increases, the RMS height will also affect the polarization ratio for bare sea ice. If snow covers the sea ice, then the polarization ratio for sea ice decreases and is affected by the RMS height of snow surface, snow thickness, volume fraction and the radius of scatterers. The results show that the sea ice and the open sea can be distinguished by using either L-band or C-band radar according to their polarization ratio difference. However, the ability of L-band to make this differentiation is higher than that of C-band.