Longer Length Scales Research Articles

Nanometer-scale exchange interactions between spin centers in diamond

Exchange interactions between isolated pairs of spin centers in diamond have been calculated, based on an accurate atomistic electronic structure for diamond and any impurity atoms, for spin-center separations up to 2~nm. The exchange interactions exceed dipolar interactions for spin center separations less than 3~nm. NV$^-$ spin centers, which are extended defects, interact very differently depending on the relative orientations of the symmetry axis of the spin center and the radius vector connecting the pair. Exchange interactions between transition-metal dopants behave similarly to those of NV$^-$ centers. The Mn\---Mn exchange interaction decays with a much longer length scale than the Cr\---Cr and Ni\---Ni exchange interactions, exceeding dipolar interactions for Mn\---Mn separations less than 5~nm. Calculations of these highly anisotropic and spin-center-dependent interactions provide the potential for design of the spin-spin interactions for novel nanomagnetic structures.

Characteristics of the soft X-ray emission from laser-produced highly charged platinum plasmas

We characterized the spectral structure of the soft X-ray emission and determined the plasma parameters in laser-produced highly charged platinum plasmas. The spectral structure observed originated from Pt21+ to Pt34+ ions, emissions from which overlapped to produce a high output flux in the carbon-window soft X-ray spectral region. Using dual laser pulse irradiation, we observed the maximum output flux, which was 20% larger than that obtained under single-laser irradiation, and the evolution of a strongly absorbed spectral structure, which was attributed to the effects of both opacity and long-scale length of the expanding pre-plasma.

Control of the micrometric scale morphology of silicon nanowires through ion irradiation-induced metal dewetting

Abstract We propose ion-induced dewetting of Au thin films as a mechanism to modify and control the morphology of Si nanowires formed through metal-assisted chemical etching. We show that the patterns formed upon irradiation resemble those typical of dewetting phenomena, with a characteristic length in the nanometer range. Irradiated Au films are then used as a template for the fabrication of Si nanowires, and we show that a long-range order exists also in etched substrates, although at much longer length scales in the micrometer range. Investigation of the optical properties reveals that the Si nanowires emit broadband photoluminescence peaked at 700 nm. The proposed synthesis method allows tuning the morphological features of the nanowire bundles at the nanoscale without affecting the optical properties. This approach can be exploited for the engineering of nanowires-based devices where the morphological features become important.

A Note on Heat Transfer Enhancement in Laminar Impinging Flows With Shear Thinning Inelastic Fluids

A recent article presented axisymmetric numerical calculations showing substantial heat transfer enhancement in a laminar impinging flow with shear thinning inelastic fluids. This paper compares enhancement in planar and axisymmetric geometries and presents empirical dependencies correlating heat transfer rates to fluid rheology. The parametric correlation is expressed in the form ∼ ReGp. ReG is a generalized Reynolds number based on the reference strain rate and fluid rheology, and it is larger than the Newtonian Reynolds number for the same mean nozzle velocity and flow geometry. The value of p > 0 is estimated from the numerical data for weak and strong shear thinning. Within the impinging zone spanning the nozzle cross section, the value of p is essentially similar for both geometries, but in the wall jet the planar flow shows a somewhat larger value. The total heat transfer rate in the planar wall jet may be two to ten times larger for a shear thinning fluid. This is because in shear thinning flow, the primary separation vortex is able to maintain the Nusselt number at a higher average value over a significantly longer length scale in the streamwise direction.

Bone Material Properties in Osteogenesis Imperfecta.

Osteogenesis imperfecta entrains changes at every level in bone tissue, from the disorganization of the collagen molecules and mineral platelets within and between collagen fibrils to the macroarchitecture of the whole skeleton. Investigations using an array of sophisticated instruments at multiple scale levels have now determined many aspects of the effect of the disease on the material properties of bone tissue. The brittle nature of bone in osteogenesis imperfecta reflects both increased bone mineralization density-the quantity of mineral in relation to the quantity of matrix within a specific bone volume-and altered matrix-matrix and matrix mineral interactions. Contributions to fracture resistance at multiple scale lengths are discussed, comparing normal and brittle bone. Integrating the available information provides both a better understanding of the effect of current approaches to treatment-largely improved architecture and possibly some macroscale toughening-and indicates potential opportunities for alternative strategies that can influence fracture resistance at longer-length scales.

Frequency staircases in narrow-gap spherical Couette flow

Recent studies of plane parallel flows have emphasised the importance of finite-amplitude self-sustaining processes for the existence of alternative non-trivial solutions. The idea behind these mechanisms is that the motion is composed of distinct structures that interact to self-sustain. These solutions are not unique and their totality form a skeleton about which the actual realised motion is attracted. Related features can be found in spherical Couette flow between two rotating spheres in the limit of narrow-gap width. At lowest order the onset of instability is manifested by Taylor vortices localised in the vicinity of the equator. By approximating the spheres by their tangent cylinders at the equator, a critical Taylor number based on the ensuing cylindrical Couette flow problem would appear to provide a lowest order approximation to the true critical Taylor number. At next order, the latitudinal modulation of their amplitude a satisfies the complex Ginzburg-Landau equation (CGLe)where is latitude scaled on the modulation length scale, t is time and is proportional to the excess Taylor number. The amplitude a governed by our CGLe is linearly stable for all but possesses non-decaying nonlinear solutions at finite , directly analogous to plane Couette flow. Furthermore, whereas the important balance suggests that the Taylor vortices ought to propagate as waves towards the equator with frequency proportional to latitude, the realised solutions are found to exist as pulses, each locked to a discrete frequency, of spatially modulated Taylor vortices. Collectively they form a pulse train. Thus the expected continuous spatial variation of the frequency is broken into steps (forming a staircase) on which motion is dominated by the local pulse. A wealth of solutions of our CGLe have been found and some may be stable. Nevertheless, when higher-order terms are reinstated, solutions are modulated on a yet longer length scale and must evolve. So, whereas there is an underlying pulse structure in the small but finite gap limit, motion is likely to be always weakly chaotic. Our CGLe and its solution provides a paradigm for many geophysical and astrophysical flows capturing in minimalistic form interaction of phase mixing , diffusion and nonlinearity .

Regulation of Actomyosin Contractility in Non-Muscle Cells

Actomyosin contractility in non-muscle cells is involved in numerous essential processes, including maintenance of cell architecture, environmental sensing, migration, trafficking, polarization, and cytokinesis, to name but a few. An extensive network of structural and regulatory proteins is collectively responsible for the generation of actomyosin contractility forces in the appropriate time and location within the cell to facilitate these processes. We recently mined the literature and protein databases to define this network, which we termed the Contractome (J Cell Sci. 2015 Jun 15;128(12):2209-17), with 100 proteins and over 230 interactions. A systems level analysis of the Contractome highlights key regulatory pathways involved in the assembly and activation of diverse actomyosin structures.Regulation of actin and myosin structures at the molecular level can have effects on cell level dynamics. This is exemplified by the evolutionarily conserved F-actin bundling protein plastin (a.k.a. fimbrin), which we show to be essential for polarization and cytokinesis of the C. elegans zygote. PLST-1 decorates all F-actin structures in the zygote cortex. In a mutant that abrogates the bundling activity of PLST-1, myosin foci in the cortex are distinctly smaller than in the wild-type, and while cortical contractions still occur over short distances, there is a lack of coordination in the contractile network over large length scales. This results in a substantial reduction in anterior directed cortical flow, which leads to defects in the establishment of polarity. PLST-1 is also required for cell division, as loss of PLST-1 function results in a significant delay or complete failure in cytokinesis. Thus, interlinking of the cortical network by plastin allows forces to be transmitted at a much longer length scale, facilitating the integration of local contractile events throughout the meshwork into the effective cortical forces necessary for polarity establishment and cell division.

Density and temperature characterization of long-scale length, near-critical density controlled plasma produced from ultra-low density plastic foam.

The ability to produce long-scale length (i.e. millimeter scale-length), homogeneous plasmas is of interest in studying a wide range of fundamental plasma processes. We present here a validated experimental platform to create and diagnose uniform plasmas with a density close or above the critical density. The target consists of a polyimide tube filled with an ultra low-density plastic foam where it was heated by x-rays, produced by a long pulse laser irradiating a copper foil placed at one end of the tube. The density and temperature of the ionized foam was retrieved by using x-ray radiography and proton radiography was used to verify the uniformity of the plasma. Plasma temperatures of 5–10 eV and densities around 1021 cm−3 are measured. This well-characterized platform of uniform density and temperature plasma is of interest for experiments using large-scale laser platforms conducting High Energy Density Physics investigations.

Whole-Organism Cellular Pathology: A Systems Approach to Phenomics.

Phenotype is defined as the state of an organism resulting from interactions between genes, environment, disease, molecular mechanisms, and chance. The purpose of the emerging field of phenomics is to systematically determine and measure phenotypes across biology for the sake of understanding. Phenotypes can affect more than one cell type and life stage, so ideal phenotyping would include the state of every cell type within the context of both tissue architecture and the whole organism at each life stage. In medicine, high-resolution anatomic assessment of phenotype is obtained from histology. Histology's interpretative power, codified by Virchow as cellular pathology, is derived from its ability to discern diagnostic and characteristic cellular changes in diseased tissues. Cellular pathology is observed in every major human diseaseand relies on the ability of histology to detect cellular change in any cell type due to unbiased pan-cellular staining, even in optically opaque tissues. Our laboratory has shown that histology is far more sensitive than stereomicroscopy for detecting phenotypes in zebrafish mutants. Those studies have also shown that more complete sampling, greater consistency in sample orientation, and the inclusion of phenotypes extending over longer length scales would provide greater coverage of common phenotypes. We are developing technical approaches to achieve an ideal detection of cellular pathology using an improved form of X-ray microtomography that retains the strengths and addresses the weaknesses of histology as a screening tool. We are using zebrafish as a vertebrate model based on the overlaps between zebrafish and mammalian tissue architecture, and a body size small enough to allow whole-organism, volumetric imaging at cellular resolution. Automation of whole-organism phenotyping would greatly increase the value of phenomics. Potential societal benefits would include reduction in the cost of drug development, a reduction in the incidence of unexpected severe drug and environmental toxicity, and more rapid elucidation of the contributions of genes and the environment to phenotypes, including the validation of candidate disease alleles identified in population and personal genetics.

Mesoscale evolution of voids and microstructural changes in HMX-based explosives during heating through the β-δ phase transition

HMX-based explosives LX-10 and PBX-9501 were heated through the β-δ phase transition. Ultra-small angle x-ray scattering (USAXS) and molecular diffraction were simultaneously recorded as the HMX was heated. Mesoscale voids and structure dramatically change promptly with the β-δ phase transition, rather than with other thermal effects. Also, x-ray induced damage, observed in the USAXS, occurs more readily at elevated temperatures; as such, the dose was reduced to mitigate this effect. Optical microscopy performed during a similar heating cycle gives an indication of changes on longer length scales, while x-ray microtomography, performed before and after heating, shows the character of extensive microstructural damage resulting from the temperature cycle and solid-state phase transition.

Multi-Scale Theory in the Molecular Simulation of Electrolyte Solutions

To define a role for AIMD simulation on the limited time and space scales accessible to those demanding methods, this paper organizes McMillan−Mayer theory, the potential distribution approach, and quasi-chemical theory to provide theory for the thermodynamic effects associated with long-length scales. The theory treats composition fluctuations that would be accessed by larger-scale calculations, and also longer-ranged interactions that are of special interest for electrolyte solutions. The quasi-chemical organization breaks-up governing free energies into physically distinct contributions: packing, outer- shell, and chemical contributions. Here we study specifically the outer-shell contributions that express electrolyte screening. For that purpose we adopt a primitive model suggested by observation of ion-pairing in tetraethylammonium tetrafluoroborate dissolved in propylene carbonate. Gaussian statistical models are shown to be effective physical models for outer-shell contributions, and they are conclusive for the free energies within the quasi-chemical formulation. With the present data set the Gaussian physical approximation obtains more accurate mean activity coefficients than does the Bennett direct evaluation of that free energy. Figure 1

Structural characterisation of polycrystalline colloidal monolayers in the presence of aspherical impurities

Impurities in crystalline materials introduce disorder into an otherwise ordered structure due to the formation of lattice defects and grain boundaries. The properties of the resulting polycrystal can differ remarkably from those of the ideal single crystal. Here we investigate a quasi-two-dimensional system of colloidal spheres containing a small fraction of aspherical impurities and characterise the resulting polycrystalline monolayer. We find that, in the vicinity of an impurity, the underlying hexagonal lattice is deformed due to a preference for five-fold co-ordinated particles adjacent to impurities. This results in a reduction in local hexagonal ordering around an impurity. Increasing the concentration of impurities leads to an increase in the number of these defects and consequently a reduction in system-wide hexagonal ordering and a corresponding increase in entropy as measured from the distribution of Voronoi cell areas. Furthermore, through both considering orientational correlations and directly identifying crystalline domains we observe a decrease in the average polycrystalline grain size on increasing the concentration of impurities. Our data show that, for the concentrations considered, local structural modifications due to the presence of impurities are independent of their concentration, while structure on longer lengthscales (i.e. the size of polycrystalline grains) is determined by the impurity concentration.

The relationship between radar scattering and surface roughness of lunar volcanic features

AbstractLunar roughness measurements derived from the Lunar Orbiter Laser Altimeter are compared to 12.6 cm wavelength radar data collected by the Miniature Radio Frequency instrument and 70 cm wavelength radar data collected by the Arecibo Observatory. These data are compared to assess how surface and subsurface roughness are correlated and affected by parameters including age and composition at length scales between 0.1 and 100 m. A range of features are analyzed including volcanic domes (Marius Hills, Rümker Hills, Gruithuisen, and Mairan Domes); mare (Imbrium, Serenitatis, and Oceanus Procellarum); pyroclastic dark mantle deposits (Sinus Aestuum, Sulpicius Gallus, and Mare Vaporum); and two young craters (Copernicus and Tycho). Statistically significant positive correlations exist between topographic roughness and both P‐ and S‐band circular polarization ratios. The strongest correlation is observed at the longest length scales. Correlations weaken as length scales become less similar, potentially due to distinct processes controlling surface modification. Roughness is not significantly correlated with local slope. Although the Marius Hills are compositionally distinct from the Gruithuisen and Mairan domes, they are indistinguishable in roughness characteristics. Conversely, the Rümker Hills, mare, and dark mantle deposits are smoother at the length scales examined, possibly due to fine‐grained mantling of regolith or pyroclastic deposits. The floor and ejecta of Tycho are the roughest surfaces measured in this study, while the floor and ejecta of Copernicus overlap the roughness distribution of the volcanic features. This study shows that many factors control the evolution of roughness over time on various length scales.

Conserved patterns in bacterial genomes: A conundrum physically tailored by evolutionary tinkering

The proper functioning of bacteria is encoded in their genome at multiple levels or scales, each of which is constrained by specific physical forces. At the smallest spatial scales, interatomic forces dictate the folding and function of proteins and nucleic acids. On longer length scales, stochastic forces emerging from the thermal jiggling of proteins and RNAs impose strong constraints on the organization of genes along chromosomes, more particularly in the context of the building of nucleoprotein complexes and the operational mode of regulatory agents. At the cellular level, transcription, replication and cell division activities generate forces that act on both the internal structure and cellular location of chromosomes. The overall result is a complex multi-scale organization of genomes that reflects the evolutionary tinkering of bacteria. The goal of this review is to highlight avenues for deciphering this complexity by focusing on patterns that are conserved among evolutionarily distant bacteria. To this end, I discuss three different organizational scales: the protein structures, the chromosomal organization of genes and the global structure of chromosomes.

Influence of meter-scale wind-formed features on the variability of the microwave brightness temperature around Dome C in Antarctica

Abstract. Space-borne passive microwave radiometers are widely used to retrieve information in snowy regions by exploiting the high sensitivity of microwave emission to snow properties. For the Antarctic Plateau, many studies presenting retrieval algorithms or numerical simulations have assumed, explicitly or not, that the subpixel-scale heterogeneity is negligible and that the retrieved properties were representative of whole pixels. In this paper, we investigate the spatial variations of brightness temperature over a range of a few kilometers in the Dome C area. Using ground-based radiometers towed by a vehicle, we collected brightness temperature at 11, 19 and 37 GHz at horizontal and vertical polarizations along transects with meter resolution. The most remarkable observation was a series of regular undulations of the signal with a significant amplitude reaching 10 K at 37 GHz and a quasi-period of 30–50 m. In contrast, the variability at longer length scales seemed to be weak in the investigated area, and the mean brightness temperature was close to SSM/I and WindSat satellite observations for all the frequencies and polarizations. To establish a link between the snow characteristics and the microwave emission undulations, we collected detailed snow grain size and density profiles at two points where opposite extrema of brightness temperature were observed. Numerical simulations with the DMRT-ML microwave emission model revealed that the difference in density in the upper first meter explained most of the brightness temperature variations. In addition, we found that these variations of density near the surface were linked to snow hardness. Patches of hard snow – probably formed by wind compaction – were clearly visible and covered as much as 39% of the investigated area. Their brightness temperature was higher than in normal areas. This result implies that the microwave emission measured by satellites over Dome C is more complex than expected and very likely depends on the year-to-year areal proportion of the two different types of snow.

The geometry and dynamics of lifelogs: discovering the organizational principles of human experience.

A correlation dimension analysis of people’s visual experiential streams captured by a smartphone shows that visual experience is two-scaled with a smaller dimension at shorter length scales than at longer length scales. The bend between the two scales is a phase transition point where the lower scale primarily captures relationships within the same context and the higher dimensional scale captures relationships between different contexts. The dimensionality estimates are confirmed using Takens’ delay embedding procedure on the image stream, while the randomly permuted stream is shown to be space-filling thereby establishing that the two-scaled structure is a consequence of the dynamics. We note that the structure of visual experience closely resembles the structure of another domain of experience: natural language discourse. The emergence of an identical structure across different domains of human experience suggests that the two-scaled geometry reflects a general organizational principle.

Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution

Several time dependent fluorescence Stokes shift (TDFSS) experiments have reported a slow power law decay in the hydration dynamics of a DNA molecule. Such a power law has neither been observed in computer simulations nor in some other TDFSS experiments. Here we observe that a slow decay may originate from collective ion contribution because in experiments DNA is immersed in a buffer solution, and also from groove bound water and lastly from DNA dynamics itself. In this work we first express the solvation time correlation function in terms of dynamic structure factors of the solution. We use mode coupling theory to calculate analytically the time dependence of collective ionic contribution. A power law decay in seen to originate from an interplay between long-range probe–ion direct correlation function and ion–ion dynamic structure factor. Although the power law decay is reminiscent of Debye–Falkenhagen effect, yet solvation dynamics is dominated by ion atmosphere relaxation times at longer length scales (small wave number) than in electrolyte friction. We further discuss why this power law may not originate from water motions which have been computed by molecular dynamics simulations. Finally, we propose several experiments to check the prediction of the present theoretical work.

Hot electron production in laser solid interactions with a controlled pre-pulse

Hot electron generation plays an important role in the fast ignition approach to inertial confinement fusion (ICF) and other applications with ultra-intense lasers. Hot electrons of temperature up to 10–20 MeV have been produced by high contrast picosecond duration laser pulses focussed to intensities of ∼1020 W cm−2 with a deliberate pre-pulse on solid targets using the Vulcan Petawatt Laser facility. We present measurements of the number and temperature of hot electrons obtained using an electron spectrometer. The results are correlated to the density scale length of the plasma produced by a controlled pre-pulse measured using an optical probe diagnostic. 1D simulations predict electron temperature variations with plasma density scale length in agreement with the experiment at shorter plasma scale lengths (<7.5μm), but with the experimental temperatures (13–17 MeV) dropping below the simulation values (20–25 MeV) at longer scale lengths. The experimental results show that longer interaction plasmas produced by pre-pulses enable significantly greater number of hot electrons to be produced.

Origins of the two simultaneous mechanisms causing glass transition temperature reductions in high molecular weight freestanding polymer films

From ellipsometry measurements, Pye and Roth [Phys. Rev. Lett. 107, 235701 (2011)] presented evidence of the presence of two glass transitions originating from two distinctly different and simultaneous mechanisms to reduce the glass transition temperature within freestanding polystyrene films with thickness less than 70 nm. The upper transition temperature T(u)(g)(h) is higher than the lower transition temperature T(l)(g)(h) in the ultrathin films. After comparing their data with the findings of others, using the same or different techniques, they concluded that new theoretical interpretation is needed to explain the two transitions and the different dependences of T(u)(g)(h) and T(l)(g)(h) on film thickness and molecular weight. We address the problem based on advance in delineating the different viscoelastic mechanisms in the glass-rubber transition zone of polymers. Theoretical considerations as well as experiments have shown in time-scales immediately following the segmental α-relaxation are the sub-Rouse modes with longer length scale but shorter than that of the Rouse modes. The existence of the sub-Rouse modes in various polymers including polystyrene has been repeatedly confirmed by experiments. We show that the sub-Rouse modes can account for the upper transition and the properties observed. The segmental α-relaxation is responsible for the lower transition. This is supported by the fact that the segmental α-relaxation in ultrathin freestanding PS films had been observed by dielectric relaxation measurements and photon correlation spectroscopy. Utilizing the temperature dependence of the segmental relaxation times from these experiments, the glass transition temperature T(α)(g)associated with the segmental relaxation in the ultrathin film is determined. It turns out that T(α)(g) is nearly the same as T(l)(g)(h) of the lower transition, and hence definitely segmental α-relaxation is the mechanism for the lower transition. Since it is unlikely that the segmental α-relaxation can give rise to two very different transitions simultaneously, a new mechanism for the upper transition is needed, and the sub-Rouse modes provide the mechanism.

Multiscale Theory in the Molecular Simulation of Electrolyte Solutions

To define a role for AIMD simulation on the limited time and space scales accessible to those demanding methods, this paper organizes McMillan-Mayer theory, the potential distribution approach, and quasi-chemical theory to provide theory for the thermodynamic effects associated with long-length scales. The theory treats composition fluctuations that would be accessed by larger-scale calculations, and also longer-ranged interactions that are of special interest for electrolyte solutions. The quasi-chemical organization breaks-up governing free energies into physically distinct contributions: packing, outer-shell, and chemical contributions. Here we study specifically the outer-shell contributions that express electrolyte screening. For that purpose we adopt a primitive model suggested by observation of ion-pairing in tetraethylammonium tetrafluoroborate dissolved in propylene carbonate. Gaussian statistical models are shown to be effective physical models for outer-shell contributions, and they are conclusive for the free energies within the quasi-chemical formulation. With the present data set the Gaussian physical approximation obtains more accurate mean activity coefficients than does the Bennett direct evaluation of that free energy.