Short-scale Roughness Research Articles

Diffusion of tRNA inside the ribosome is position-dependent

In recent years, there has been a growing interest to quantify the energy landscape that governs ribosome dynamics. However, in order to quantitatively integrate theoretical predictions and experimental measurements, it is essential that one has a detailed understanding of the associated diffusive properties. Here, all-atom explicit-solvent simulations (50 μs of aggregate sampling) predict that the diffusion coefficient of a tRNA molecule will depend on its position within the ribosome. Specifically, during aa-tRNA accommodation (i.e., the process by which tRNA enters the ribosome), the apparent diffusion coefficient decreases by approximately an order of magnitude. By comparing these to values obtained with an energetically "smooth" model, we show that the observed nonuniform behavior likely arises from electrostatic and solvation interactions between the tRNA and ribosome. These calculations also reveal the hierarchical character of ribosomal energetics, where steric interactions induce a large-scale free-energy barrier, and short-scale roughness determines the rate of diffusive movement across the landscape.

On predicting receptivity to surface roughness in a compressible infinite swept wing boundary layer

The receptivity of crossflow disturbances on an infinite swept wing is investigated using solutions of the adjoint linearised Navier-Stokes equations. The adjoint based method for predicting the magnitude of stationary disturbances generated by randomly distributed surface roughness is described, with the analysis extended to include both surface curvature and compressible flow effects. Receptivity is predicted for a broad spectrum of spanwise wavenumbers, variable freestream Reynolds numbers, and subsonic Mach numbers. Curvature is found to play a significant role in the receptivity calculations, while compressible flow effects are only found to marginally affect the initial size of the crossflow instability. A Monte Carlo type analysis is undertaken to establish the mean amplitude and variance of crossflow disturbances generated by the randomly distributed surface roughness. Mean amplitudes are determined for a range of flow parameters that are maximised for roughness distributions containing a broad spectrum of roughness wavelengths, including those that are most effective in generating stationary crossflow disturbances. A control mechanism is then developed where the short scale roughness wavelengths are damped, leading to significant reductions in the receptivity amplitude.

Breaking waves and near-surface sea spray aerosol dependence on changing winds: Wave breaking efficiency and bubble-related air-sea interaction processes

Simultaneous measurements of sea spray aerosol (SSA), wind, wave, and microwave brightness temperature are obtained in the open ocean on-board Floating Instrument Platform (FLIP). These data are analysed to clarify the ocean surface processes important to SSA production. Parameters are formulated to represent surface processes with characteristic length scales spanning a broad range. The investigation reveals distinct differences of the SSA properties in rising winds and falling winds, with higher SSA volume in falling winds. Also, in closely related measurements of whitecap coverage, higher whitecap fraction as a function of wind speed is found in falling winds than in rising winds or in older seas than in younger seas. Similar trend is found in the short scale roughness reflected in the microwave brightness temperature data. In the research of length and velocity scales of breaking waves, it has been observed that the length scale of wave breaking is shorter in mixed seas than in wind seas. For example, source function analysis of short surface waves shows that the characteristic length scale of the dissipation function shifts toward higher wavenumber (shorter wavelength) in mixed seas than in wind seas. Similarly, results from feature tracking or Doppler analysis of microwave radar sea spikes, which are closely associated with breaking waves, show that the magnitude of the average breaking wave velocity is smaller in mixed seas than in wind seas. Furthermore, breaking waves are observed to possess geometric similarity. Applying the results of breaking wave analyses to the SSA and whitecap observations described above, it is suggestive that larger air cavities resulting from the longer breakers are entrained in rising high winds. The larger air cavities escape rapidly due to buoyancy before they can be fully broken down into small bubbles for the subsequent SSA production or whitecap manifestation. In contrast, in falling winds (with mixed seas more likely), the shorter breaker entrains smaller and more numerous air cavities that stay underwater longer for more efficient bubble breakup by turbulence and prolonging the surface disturbances attributable to wave breaking. For low winds, the breaking scale is small and with high efficiency for SSA or whitecap generation; the trend of rising or falling wind is less important.

Combined short scale roughness and surface dielectric function gradient effects on the determination of tip-sample force in atomic force microscopy

The contribution of tip roughness to the van der Waals force between an atomic force microscopy probe tip and the sample is calculated using the multilayer effective medium model, which allows us to consider the relevant case of roughness characterized by correlation length and amplitude in the nanometer scale. The effect of the surface dielectric function gradient is incorporated in the tip-sample force model. It is concluded that for rms roughness in the few nanometers range the effect of short scale tip roughness is quite significant.

A multilayered effective medium model for the roughness effect on the Casimir force

A multilayered effective medium model is proposed to calculate the contribution of surface roughness to the Casimir force. In this model the rough layer has its optical properties derived from an effective medium approximation, with the rough layer considered as the mixing of voids and solid material. The rough layer can be divided into sublayers consisting of different volume fractions of voids and solid material as a function of the roughness surface profile. The Casimir force is then calculated using the generalizations of the Lifshitz theory for multilayered planar systems. Predictions of the Casimir force based on the proposed model are compared with those of well-known methods of calculation, usually restricted to be used with large-scale roughness. It is concluded that the effect of short-scale roughness as predicted by this model is considerably larger than what could be expected from the extrapolation of the results obtained by the other methods.

Joint sun-glitter and radar imagery of surface slicks

A method is proposed to retrieve and interpret fine spatial variations of the sea surface roughness in sun glitter imagery. Observed sun glitter brightness anomalies are converted using a transfer function determined from the smoothed shape of sun glitter brightness. The method is applied to MODIS and MERIS sun glitter imagery of natural oil seeps and the catastrophic Deepwater Horizon oil spill in the Gulf of Mexico. The short-scale roughness variations in the presence of mineral oils slicks are consistently extracted and compared to variations associated with the biogenic slicks. In doing so, the wind speed dependency on the roughness anomalies is also considered. A comparison to normalized radar cross section (NRCS) anomalies taken from the corresponding high resolution ASAR images is performed, and similarities as well as differences are investigated. The results document significant benefit from the synergetic use of sun glitter and radar imagery for detection and monitoring of surface slicks.

Tunable Wetting of Nanoparticle-Decorated Polymer Films

In this paper, amine-modified silica nanoparticles (NPs) with diameters (d) from 15 to 230 nm are covalently linked to poly(styrene-random-acrylic acid) (P(S-ran-AA)) films, and wettability is studied as a function of diameter and NP surface coverage. During attachment, films swell and exhibit long and short scale roughness, consisting of a ridged, honeycomb structure, approximately 1 mum wide and 45-50 nm deep, which encircles nanoscale features 10-15 nm high and approximately 50 nm apart. A maximum NP coverage of approximately 70% was achieved for d less than or nearly equal to the nanoscale roughness induced by surface swelling. For d several times greater than this nanoscale roughness, the maximum coverage was limited by interparticle repulsion and reached only approximately 30%. For NPs with diameters of 15-106 nm, the water contact angle increased from 75 degrees to 120 degrees as NP coverage increased from 0 to 70%. At low and high NP coverage, the Wenzel and Cassie models, respectively, accurately describe the data. However, at intermediate NP coverage, neither model is satisfactory. An increase in surface roughness alone cannot account for this discrepancy. Atomic force microscopy (AFM) studies show that the NPs partially embed into the swollen P(S-ran-AA) surface, suggesting that the amine-coated NPs are wet by the copolymer, exposing low surface energy styrene. These studies demonstrate that control over surface properties of coatings, such as wetting, can be achieved by selecting NP sizes that complement film roughness.

Use of anomalous scattering for synchrotron X-ray reflectivity studies of Fe–Cr and Co–Cu double layers

Double layers of Fe–Cr and Co–Cu, respectively, were prepared on oxidized Si substrates by pulsed laser deposition (PLD). The interfacial roughness structure was studied by synchrotron X-ray reflectivity measurements at the absorption K-edges using the contrast enhancement due to resonant scattering. The results are determined from simulations of the measured specular and diffuse scans. Whereas in Fe–Cr double layers the σ rms-interface width for Fe deposition on Cr ( σ Cr=0.70±0.1 nm) is not very different from that of Cr deposition on Fe ( σ Fe=0.85±0.1 nm), in Co–Cu double layers, in contrast, for Cu deposition on Co, the width ( σ Co=0.65±0.1 nm) is much smaller than for Co deposition on Cu ( σ Cu=1.5±0.15 nm). On the basis of the fractal model to describe the interface roughness morphology, from the off-specular scans the lateral roughness correlation length, ξ and the roughness exponent, h, were determined. For both types of double layers extremely high ξ-values (larger than 2 μm) were found. However, the flatness is accompanied by a high short-scale roughness (jaggedness), expressed by a small h-parameter ( h=0.25±0.05). Both facts were found to be characteristic for the ‘as-deposited’ state of such metal/metal layers prepared by PLD.

Phenomenology of squeezing and sliding of molecularly thin Xe, CH4 and C16H34 lubrication films between smooth and rough curved solid surfaces with long-range elasticity

The properties of Xe, CH4 and C16H34 lubricant confined between two approaching solids are investigated by a model that accounts for the curvature and elastic properties of the solid surfaces. We consider both smooth surfaces, and surfaces with short-scale roughness. In most cases we observe well defined molecular layers develop in the lubricant film when the width of the film is of the order of a few atomic diameters, but in some cases atomic scale roughness inhibit the formation of these layers, and the lubricant exhibit liquid-like properties. An external squeezing-pressure induces discontinuous, thermally activated changes in the number n of lubricant layers. We observe that the layering transition tends to nucleate in disordered or imperfect regions in the lubrication film. We also present and discuss results of sliding dynamics for Xe and C16H34 lubrication films.

Large terrace formation and modulated electronic states in (110) GaAs quantum wells

Interface roughness and local electronic states formed in GaAs quantum wells (QWs) grown on (110) cleaved surfaces were characterized by high-resolution microscopic photoluminescence (micro-PL) imaging and spectroscopy assisted by a solid immersion lens. From macroscopic PL spectra and micro-PL images, it was found that well width fluctuation of about 0.6 to 0.7 nm, which corresponds to 3 to 3.5 monolayers (ML), with laterally sub-$\ensuremath{\mu}\mathrm{m}$- to $\ensuremath{\mu}\mathrm{m}$-scale ML terraces existed in the (110) GaAs/AlAs QWs, and this was also supported by the results of atomic force microscopy measurements performed on the (110) GaAs surface. In high-resolution solid-immersion micro-PL spectroscopy, sharp PL peaks were observed at low excitation power and their temperature and excitation power dependence showed a localized quantum-dot-like (QD-like) nature in the (110) GaAs QWs. The spatial and spectral distribution of these sharp PL peaks indicated that the localized QD-like states were formed by short-scale roughness in the bottom GaAs-on-AlAs interface of the (110) GaAs/AlAs QWs on each $\ensuremath{\mu}\mathrm{m}$-scale large ML terrace in the top AlAs-on-GaAs interface.

Sliding versus till deformation in the fast motion of an ice stream over a viscous till

AbstractThe partitioning between till deformation and sliding in the fast flow of ice streams with active basal melting is examined assuming no adhesion of the till to the ice base and incompressible viscous fluid behavior for the till. For deforming-till thickness of 10 m or less the predicted contribution to basal motion by sliding is larger than shearing in the till unless there is short-scale roughness with wavelengths less than order 0.1 m on the ice sole. At such short scales strain heating within the till and focused melting on the ice sole would quickly eliminate the roughness. Thus, fast flow over a till bed would be expected to be mostly by sliding over the subglacial till. More realistic continuum behavior of the till including non-linear and compressible deformation strengthens the conclusion. If sliding is not dominant, then there must be adhesion of the till to the ice base, some mechanism that continuously generates short-scale roughness on the ice–till interface, or very weak internal slip boundaries within the till.

Heat pulse scattering from rough surfaces with long-range irregularity

We have modelled the scattering of heat pulses from rough surfaces. Scattering from long-range irregularities was calculated in the eikonal approximation whilst the effect of short-scale roughness was treated by extending Nakayama's approach to shorter wavelengths. The model was used to interpret experimental data on buried amorphous-crystalline interfaces in silicon.

Rain measurement on buoys using hydrophones

The impact of rain and spray on the ocean disturbs the sea surface and generates underwater ambient noise. The short scale roughness is influenced by impacting drops due to the momentum transfer. Radar and sonar signals are scattered by the short elements of the sea surface. Spray and rain impact change their characteristics, and consequently affect radar and sonar backscatter. In situ measurements of rain and spray impact are necessary to study their effects on the sea surface. Accurate sea measurements of rain momentum fluxes and drop size distributions are a complex problem, especially on buoys. A new measuring technique has been developed using hydrophones. Exposed to precipitation, these instruments are affected directly by the impact of rain. A drop falling on the hydrophone deforms its surface and is sensed by a piezoelectric transducer. The voltage output of the sensor is a rapidly decaying oscillation. The integral value of this signal is a measure of the drop momentum, and the drop size can be deduced. Laboratory studies of defined drops as well as field measurements of natural rain have shown that hydrophones can be used to determine drop momentums and drop size distributions. Based on simultaneous rain measurements by a Joss-Waldvogel Disdrometer and a hydrophone, an analytical function has been derived which relates drop size and hydrophone voltage output. >

Characterization of the Au surface structure of Al–I–Au light-emitting tunnel junctions

Visible light is emitted from the Au-air interface of Al–I–Au thin-film tunnel junctions (deposited over a thin layer of CaF2 on glass) as a result of the decay of surface plasmon polaritons (SPPs). We show the surface topography of such a Au film and relate its large-scale features to the outcoupling of fast SPP’s to photons. The absence of short-scale roughness features is explained by their disappearance through surface diffusion. To confirm this a controlled sequence of 5-nm, 20-ms scanning tunneling microscope (STM) W tip crashes has been used to produce indentations 3 nm deep with a lateral dimension of 5–7 nm on a Au crystal in air at room temperature. Four sequences of indentations were drawn in the form of a square box. Right from the start, feature decay is observed and over a period of 2 h a succession of images shows that the structure disappears into the background as a result of surface diffusion. The surface diffusion constant is estimated to be 10−18 cm2 s−1. The lack of light output via slow mode SPPs is an inevitable consequence of surface annealing.

Extreme UV and x-ray scattering measurements from a rough LiF crystal surface characterized by electron micrography

XUV and x-ray scattering by a LiF crystal is measured. The angular distribution of the scattered radiation (ADSR) reveals characteristic features, side peaks or asymmetry. The surface of the sample is statistically characterized by a microdensitometer analysis of electron micrographs resolving the short spatial wavelengths of the surface roughness. This analysis shows that the surface has a large microroughness with an autocovariance function which is Gaussian in its initial portion. The first-order perturbation vector theory of the roughness-induced scattering leads to an interpretation of the ADSR features in terms of the modulation of the surface power spectral density function associated with the microroughness by an optical factor. The possibility of obtaining short scale roughness characterization from XUV or x-ray measurements is discussed.