Table of contents

Basic research in surface and interface science is highly interdisciplinary, covering the fields of physics, chemistry, biophysics, geo-, atmospheric and environmental sciences, material science, chemical engineering, and more. The various phenomena are interesting by themselves, and they are most important in nearly all modern technologies, as for example electronic, magnetic, and optical devices, sensors, catalysts, lubricants, hard and thermal-barrier coatings, protection against corrosion and crack formation under harsh environments. In fact, detailed understanding of the elementary processes at surfaces is necessary to support and to advance the high technology that very much founds the prosperity and lifestyle of our society.

Current state-of-the-art experimental studies of elementary processes at surfaces, of surface properties and functions employ a variety of sophisticated tools. Some are capable of revealing the location and motion of individual atoms. Others measure excitations (electronic, magnetic and vibronic), employing, for example, special light sources such as synchrotrons, high magnetic fields, or free electron lasers. The surprising variety of intriguing physical phenomena at surfaces, interfaces, and nanostructures also pose a persistent challenge for the development of theoretical descriptions, methods, and even basic physical concepts.

This second focus issue on the topic of 'Advances in Surface and Interface Science' in New Journal of Physics, following on from last year's successful collection, provides an exciting synoptic view on the latest pertinent developments in the field.

Focus on Advances in Surface and Interface Science 2008 Contents

Organic layers at metal/electrolyte interfaces: molecular structure and reactivity of viologen monolayers Stephan Breuer, Duc T Pham, Sascha Huemann, Knud Gentz, Caroline Zoerlein, Ralf Hunger, Klaus Wandelt and Peter Broekmann

Spin polarized d surface resonance state of fcc Co/Cu(001) K Miyamoto, K Iori, K Sakamoto, H Narita, A Kimura, M Taniguchi, S Qiao, K Hasegawa, K Shimada, H Namatame and S Blügel

Activated associative desorption of C + O → CO from Ru(001) induced by femtosecond laser pulses S Wagner, H Öström, A Kaebe, M Krenz, M Wolf, A C Luntz and C Frischkorn

Surface structure of Sn-doped In₂O₃ (111) thin films by STM Erie H Morales, Yunbin He, Mykola Vinnichenko, Bernard Delley and Ulrike Diebold

Coulomb oscillations in three-layer graphene nanostructures J Güttinger, C Stampfer, F Molitor, D Graf, T Ihn and K Ensslin

Adsorption processes of hydrogen molecules on SiC(001), Si(001) and C(001) surfaces Xiangyang Peng, Peter Krüger and Johannes Pollmann

Fermi surface nesting in several transition metal dichalcogenides D S Inosov, V B Zabolotnyy, D V Evtushinsky, A A Kordyuk, B Büchner, R Follath, H Berger and S V Borisenko

Probing molecule–surface interactions through ultra-fast adsorbate dynamics: propane/Pt(111) A P Jardine, H Hedgeland, D Ward, Y Xiaoqing, W Allison, J Ellis and G Alexandrowicz

A novel method achieving ultra-high geometrical resolution in scanning tunnelling microscopy R Temirov, S Soubatch, O Neucheva, A C Lassise and F S Tautz

The adsorption of viologens (1,1'-disubstituted-4,4'-bipyridinium molecules) on a chloride-modified copper electrode has been studied using a combination of cyclic voltammetry (CV), in-situ scanning tunneling microscopy (STM) and ex-situ photoemission spectroscopy (XPS). Two prototypes of viologens could be identified with respect to their redox behavior upon adsorption, namely those which retain (non-reactive adsorption) and those which change their redox state (reactive adsorption) upon interaction with the chloride-modified copper surface at given potential. The first class of viologens represented by 1,1'-dibenzyl-4,4'-bipyridinium molecules (dibenzyl-viologens, abbreviated as DBV) can be adsorbed and stabilized on this electrode surface in their di-cationic state at potentials more positive than the reduction potential of the solution species. XPS N1s core level shifts verify that the adsorbed DBV molecules on the electrode are in their oxidized di-cationic state. Electrostatic attraction between the partially solvated viologen di-cations and the anionic chloride layer is discussed as the main driving force for the DBV stabilization on the electrode surface. Analysis of the N1s and O1s core level shifts points to a non-reactive DBV adsorption leaving the DBV_ads²⁺ solvation shell partly intact. The laterally ordered DBV_ads²⁺ monolayer turns out to be hydrophilic with at least four water molecules per viologen present within this cationic organic film. The analysis of the Cl2p core level reveals that no further chloride species are present at the surface besides those which are specifically adsorbed, i.e. which are in direct contact with the metallic copper surface underneath the organic layer. The reduction of these adsorbed DBV_ads²⁺ surface species takes place only in the same potential regime where the solvated DBV_aq²⁺ bulk solution species react and is accompanied by a pronounced structural change from the di-cationic 'cavitand'-structure to a 'stripe'-structure of chains of π-stacked DBV^•+ mono-cation radicals as verified by in-situ STM. The second class of viologens represented by 1,1'-diphenyl-4,4'-bipyridinium molecules (diphenyl-viologens, abbreviated as DPV) is much more reactive upon adsorption and cannot be stabilized on the electrode surface in a di-cationic state, at least within the narrow potential window of copper. The N1s core level binding energy indicates only the presence of the corresponding mono-reduced DPV_ads^•+ species on the surface even at potentials more positive than the redox potential of the bulk solution species. This process leads to the formation of a hydrophobic viologen monolayer with stacked polymeric chains as the characteristic structural motif. The wet electrochemical reduction of viologens is further compared with a dry reduction under UHV conditions. The latter reaction inevitably affects the di-cationic viologen species in the course of the photoemission experiment. Slow photoelectrons and secondary electrons are assumed to transform the di-cationic viologens into the corresponding radical mono-cations upon irradiation.

Spin- and angle-resolved photoemission spectroscopy has been applied to the study of the surface and bulk electronic structures of a face-centered cubic (fcc) Co thin film. We have experimentally resolved a negatively spin-polarized surface resonance state of fcc Co/Cu(001) at 0.4 eV below the Fermi energy. Moreover, we have found that the surface resonance state exhibits a strong spin–orbit interaction through an investigation of magnetic dichroism in the angular distribution spectrum of Co/Cu(001).

The femtosecond (fs)-laser-induced associative desorption of CO from a C/O coadsorbate on Ru(001) has been investigated. The recombination of the atomic reactants is found to originate predominantly from oxidation of isolated 'reactive' carbon atoms, whereas oxidation of surface carbon with carbon–carbon bonds is not observed. Due to the excess of oxygen atoms (C coverage in the few-percent range) the C_ads + O_ads → CO_gas formation exhibits first-order kinetics. For both excitation wavelengths 400 and 800 nm, a strongly nonlinear fluence (F) dependence of the CO desorption yield Y is observed with exponents n≈4 in a power law parametrization Y∝⟨F⟩ⁿ. Furthermore, excitation with 400 nm pulses leads to a significantly higher desorption yield as compared to 800 nm laser light with cross sections and desorption probabilities for 400 and 800 nm excitation of σ_eff=4.9×10⁻¹⁸ cm², P_des=0.17 and σ_eff=1.1×10⁻¹⁸ cm², P_des=0.07, respectively, at an absorbed fluence of ⟨F⟩=170 J m⁻². This wavelength dependence is attributed to the shorter optical penetration of 400 nm light in the Ru substrate leading to higher surface temperatures at the same absorbed energy rather than to nonthermalized hot electrons. In addition, two-pulse-correlation measurements show a full-width at half-maximum of ∼ 20 ps excluding a purely electron-driven reaction mechanism, which should exhibit a subpicosecond response time. However, careful qualitative and quantitative analyses based on frictional modelling of the adsorbate–substrate coupling reveals that the C–O association reaction is mediated by both substrate phonons and electrons. The electronic, i.e. nonadiabatic contribution with a coupling constant of η_el=1/500 fs⁻¹ is responsible for the ultrafast activation of the reaction found in the frictional modelling to occur within ∼1 ps after excitation. Similarities to the associative desorption of N₂ (isoelectronic with CO) from N/Ru(001), a system for which density-functional calculations exist, can be drawn. Finally, the energy transfer to nuclear degrees of freedom during the C–O association process on the Ru(001) surface has been studied with time-of-flight measurements. The obtained translational energies expressed by T_trans=⟨E_trans⟩/2k_B≈700 K exhibit only a weak dependence on the absorbed laser fluence and are by a factor of ∼3 lower than the calculated surface temperatures present after fs-laser excitation. Possible origins of this discrepancy, such as unequal energy partitioning between the molecular degrees of freedom or nonadiabatic damping, are discussed.

High-quality Sn-doped In₂O₃ (ITO) films were grown epitaxially on yttria stabilized zirconia (111) with oxygen-plasma assisted molecular beam epitaxy (MBE). The 12 nm thick films, containing 2–6% Sn, are fully oxidized. Angle-resolved x-ray photoelectron spectroscopy (ARXPS) confirms that the Sn dopant substitutes In atoms in the bixbyite lattice. From XPS peak shape analysis and spectroscopic ellipsometry measurements it is estimated that, in a film with 6 at.% Sn, ∼1/3 of the Sn atoms are electrically active. Reflection high energy electron diffraction (RHEED) shows a flat surface morphology and scanning tunneling microscopy (STM) shows terraces several hundred nanometers in width. The terraces consist of 10 nm wide orientational domains, which are attributed to the initial nucleation of the film. Low energy electron diffraction (LEED) and STM results show a bulk-terminated (1 × 1) surface, which is supported by first-principles density functional theory (DFT) calculations. Atomically resolved STM images are consistent with Tersoff–Hamann calculations that show that surface In atoms are imaged bright or dark, depending on the configuration of their O neighbors. The coordination of surface atoms on the In₂O₃(111)–1×1 surface is analyzed in terms of their possible role in surface chemical reactions.

We present transport measurements on a tunable three-layer graphene single electron transistor (SET). The device consists of an etched three-layer graphene flake with two narrow constrictions separating the island from source and drain contacts. Three lateral graphene gates are used to electrostatically tune the device. An individual three-layer graphene constriction has been investigated separately showing a transport gap near the charge neutrality point. The graphene tunneling barriers show a strongly nonmonotonic coupling as a function of gate voltage indicating the presence of localized states in the constrictions. We show Coulomb oscillations and Coulomb diamond measurements proving the functionality of the graphene SET. A charging energy of ≈0.6 meV is extracted.

Adsorption processes of hydrogen molecules on the Si(001)-(2×1) and C(001)-(2×1) surfaces are discussed in light of our previous studies of H₂ adsorption on the related SiC(001)-c(4×2) surface. Very amazingly, there are pathways above the latter on which hydrogen molecules can adsorb dissociatively at room temperature. One of these pathways has not been considered before for adsorption of H₂ on the Si(001)-(2×1) or C(001)-(2×1) surface. Therefore, we report first-principles investigations of the reaction of molecular hydrogen with the Si(001)-(2×1) and C(001)-(2×1) surfaces on this new adsorption pathway in addition to those that have been studied before. In spite of a number of similarities, the three surfaces show distinct differences as well, giving rise to spectacularly different reactivities with hydrogen molecules. This is due to the fact that the reaction of H₂ with semiconductor surfaces depends crucially on intricate combined effects of the arrangement of surface dimers, as well as the orientation of their dangling bond orbitals. In addition, the chemical nature of the surface atoms has a pronounced effect on the spatial extent of dangling bond orbitals which influences the adsorption behaviour markedly as well. In agreement with experiments, our results show that Si(001)-(2×1) and C(001)-(2×1) are inert to H₂ adsorption at room temperature for all investigated pathways which exhibit substantial energy barriers. For the two reaction pathways that have been investigated before, our results are in good accord with those of previous density functional and quantum Monte Carlo (QMC) calculations. As a matter of fact, the new reaction channel studied in this work for the first time turns out to have the lowest energy barrier for H₂ adsorption on the diamond surface and should thus be the most important channel for sticking of H₂ on C(001)-(2×1).

By means of high-resolution angle-resolved photoelectron spectroscopy (ARPES), we have studied the fermiology of 2H transition metal dichalcogenide polytypes TaSe₂, NbSe₂ and Cu_0.2NbS₂. The tight-binding model of the electronic structure, extracted from ARPES spectra for all three compounds, was used to calculate the Lindhard function (bare spin susceptibility), which reflects the propensity to charge density wave (CDW) instabilities observed in TaSe₂ and NbSe₂. We show that though the Fermi surfaces of all three compounds possess an incommensurate nesting vector in the close vicinity of the CDW wave vector, the nesting and ordering wave vectors do not exactly coincide, and there is no direct relationship between the magnitude of the susceptibility at the nesting vector and the CDW transition temperature. The nesting vector persists across the incommensurate CDW transition in TaSe₂ as a function of temperature despite the observable variations of the Fermi surface geometry in this temperature range. In Cu_0.2NbS₂, the nesting vector is present despite different doping levels, which leads us to expect a possible enhancement of the CDW instability with Cu intercalation in the Cu_xNbS₂ family of materials.

³He spin echo measurements of the atomic scale motion of propane on a Pt(111) surface are presented. The measurements provide both the height of the energy barriers to diffusion and the strength of the frictional coupling of propane to the substrate. We show that both the rate and the nature of the dynamics we measure cannot be reproduced by an existing empirical potential. Using numerical simulation we derive a potential energy surface which is capable of reproducing the main features of our dataset.

We investigate rapid energy transfer (ET) and its temperature dependence in a star-shaped stilbenoid phthalocyanine (SSS1Pc) dendrimer having π-conjugated light-harvesting (LH) antennas, and develop an appropriate model. In SSS1Pc, an intense core photoluminescence (PL) band appears under the selective excitation of the absorption bands of the LH antenna due to highly efficient ET at room temperature (RT). The transient response of core-absorption bleaching and the temporal behaviours of the PL intensities of the core and antenna reveal that ET from the LH antenna occurs rapidly prior to achieving quasi-equilibrium in the photoexcited state of the LH antenna. In addition, it is also clarified that the ET quantum efficiency in SSS1Pc degrades at temperatures lower than ∼100 K. To understand these results, we develop an ET model based on a π-conjugating network between the LH antenna and the core that accounts for steric hindrance between the LH antenna and the torsional vibration of the LH-antenna subunit. This model reveals that highly efficient ET occurs at RT through the π-conjugated network mediated by the thermally activated torsional vibration of the LH-antenna subunit.

The specific heat C(T) of a BaFe₂As₂ single crystal and hole-doped superconducting Ba_0.5K_0.5Fe₂As₂ and Ca_0.5Na_0.5Fe₂As₂ polycrystals were measured. For the undoped BaFe₂As₂ single crystal, a very sharp specific heat peak was observed at 136 K. This is attributed to the structural and antiferromagnetic transitions occurring at the same temperature. For the superconducting Ba_0.5K_0.5Fe₂As₂ polycrystal, a clear peak of C/T was observed at T_c=36 K, which is the highest peak seen at a superconducting transition for iron-based high-T_c superconductors so far. For the superconducting Ca_0.5Na_0.5Fe₂As₂ sample with lower T_c=18 K, there is no obvious anomaly in C/T below T_c, which may be due to its low superfluid density. The electronic specific heat coefficients γ and Debye temperatures Θ_D of these compounds were obtained from the low-temperature data.

DyBaCo₂O_5.5 has shown a complex phase diagram, which is based on the interplay of different energy scales, related to magnetism, orbital ordering and for example Co spin-state transitions. For a detailed understanding of these fascinating materials it is therefore necessary to identify the order of the different energy scales. Small changes in the corresponding energy relations strongly influence the electronic structure and ground state properties, like low and high spin configurations, which have been controversially discussed in order to interpret the metal-to-insulator (MIT) transition in REBaCo₂O_5.5 (RE = rare earths). To clarify unambiguously the microscopic nature of the spin-state evolution associated with this MIT, we performed detailed temperature and angular dependent x-ray magnetic circular dichroism measurements in DyBaCo₂O_5.5 single crystals above and below the MIT and at the onset of the ferromagnetic phase. Anisotropic contributions of spin and orbital moments have been observed with an extremely high signal-to-noise ratio. We can identify a higher-spin- to lower-spin-state change across the MIT, which is in contrast to previous macroscopic experimental findings. Only the Co ions in octahedral environment are found to be in a reduced spin configuration in the high-temperature metallic state.

The emission of positronium negative ions from Cs deposited W(100) surfaces has been studied. A dramatic change in the emission efficiency was observed upon coating a W(100) surface with Cs. The conversion efficiency (the fraction of incident slow positrons yielding the ions) of the W(100) target with a 2.2×10¹⁴ atoms cm^{- 2} Cs coverage, measured over a time interval of 3×10³ s immediately after deposition, was found to be 1.25%, which is two orders of magnitude higher than that obtained for the clean, uncoated W(100) surface and 45 times greater than the highest efficiency reported thus far.

Collections of micrometer-sized solid particles immersed in plasma are used to mimic many systems from solid state and fluid physics, due to their strong electrostatic interaction, their large inertia, and the fact that they are large enough to be visualized with ordinary optics. On Earth, gravity restricts the so-called dusty plasma systems to thin, two-dimensional (2D) layers, unless special experimental geometries are used, involving heated or cooled electrons, and/or the use of dielectric materials. In micro-gravity experiments, the formation of a dust-free void breaks the isotropy of 3D dusty plasma systems. In order to do real 3D experiments, this void has somehow to be closed. In this paper, we use a fully self-consistent fluid model to study the closure of a void in a micro-gravity experiment, by lowering the driving potential. The analysis goes beyond the simple description of the 'virtual void', which describes the formation of a void without taking the dust into account. We show that self-organization plays an important role in void formation and void closure, which also allows a reversed scheme, where a discharge is run at low driving potentials and small batches of dust are added. No hysteresis is found this way. Finally, we compare our results with recent experiments and find good agreement, but only when we do not take charge-exchange collisions into account.

Much experimental effort is invested these days in fabricating nanoelectromechanical systems (NEMS) that are sufficiently small, cold and clean, so as to approach quantum mechanical behavior as their typical quantum energy scale becomes comparable with that of the ambient thermal energy k_BT. Such systems will hopefully enable one to observe the quantum behavior of human-made objects, and test some of the basic principles of quantum mechanics. Here, we expand and elaborate on our recent suggestion (Katz et al 2007 Phys. Rev. Lett. 99 040404) to exploit the nonlinear nature of a nanoresonator in order to observe its transition into the quantum regime. We study this transition for an isolated resonator, as well as one that is coupled to a heat bath at either zero or finite temperature. We argue that by exploiting nonlinearities, quantum dynamics can be probed using technology that is almost within reach. Numerical solutions of the equations of motion display the first quantum corrections to classical dynamics that appear as the classical-to-quantum transition occurs. This provides practical signatures to look for in future experiments with NEMS resonators.

In this paper, we empirically study the evolution of large scale Internet topology at the autonomous system (AS) level. The network size grows in an exponential form, obeying the famous Moore's law. We theoretically predict that the size of the AS-level Internet will double every 5.32 years. We apply the k-core decomposition method on the real Internet, and find that the size of a k-core with larger k is nearly stable over time. In addition, the maximal coreness is very stable after 2003. In contrast to the predictions of most previous models, the maximal degree of the Internet is also relatively stable versus time. We use the edge-exchange operation to obtain the randomized networks with the same degree sequence. A systematical comparison is drawn, indicating that the real Internet is more loosely connected, and both the full Internet and the nucleus are more disassortative than their randomized versions.

We investigate the fundamental statistical features of tagged (or annotated) networks having a rich variety of attributes associated with their nodes. Tags (attributes, annotations, properties, features, etc) provide essential information about the entity represented by a given node, thus, taking them into account represents a significant step towards a more complete description of the structure of large complex systems. Our main goal here is to uncover the relations between the statistical properties of the node tags and those of the graph topology. In order to better characterize the networks with tagged nodes, we introduce a number of new notions, including tag-assortativity (relating link probability to node similarity), and new quantities, such as node uniqueness (measuring how rarely the tags of a node occur in the network) and tag-assortativity exponent. We apply our approach to three large networks representing very different domains of complex systems. A number of the tag related quantities display analogous behaviour (e.g. the networks we studied are tag-assortative, indicating possible universal aspects of tags versus topology), while some other features, such as the distribution of the node uniqueness, show variability from network to network allowing for pin-pointing large scale specific features of real-world complex networks. We also find that for each network the topology and the tag distribution are scale invariant, and this self-similar property of the networks can be well characterized by the tag-assortativity exponent, which is specific to each system.

Biological systems such as single cells must function in the presence of fluctuations. It has been shown in a two-dimensional experimental setup that sea urchin sperm cells move toward a source of chemoattractant along planar trochoidal swimming paths, i.e. drifting circles. In these experiments, a pronounced variability of the swimming paths is observed. We present a theoretical description of sperm chemotaxis in two dimensions which takes fluctuations into account. We derive a coarse-grained theory of stochastic sperm swimming paths in a concentration field of chemoattractant. Fluctuations enter as multiplicative noise in the equations for the sperm swimming path. We discuss the stochastic properties of sperm swimming and predict a concentration-dependence of the effective diffusion constant of sperm swimming which could be tested in experiments.

The Doppler effect of moving atoms can create irreversibility of light. We show that the laser field in an electromagnetic induced transparency (EIT) scheme with atomic motion can control the directional propagation of two counter-propagating output probe fields in an atomic gas. Quantum coherence and the Doppler effect enable the system to function like an optical transistor with two outputs that can generate states analogous to the Bell basis. Interference of the two output fields from the gas provides useful features for determining the mean atomic velocity and can be used as a sensitive quantum velocimeter. Some subtle physics of EIT is also discussed. In particular, the sign of the dispersive phase in EIT is found to have a unique property, which helps to explain certain features in the interference.

We study how to detect groups in a complex network each of which consists of component nodes sharing a similar connection pattern. Based on the mixture models and the exploratory analysis set up by Newman and Leicht (2007 Proc. Natl. Acad. Sci. USA 104 9564), we develop an algorithm that is applicable to a network with any degree distribution. The partition of a network suggested by this algorithm also applies to its complementary network. In general, groups of similar components are not necessarily identical with the communities in a community network; thus partitioning a network into groups of similar components provides additional information of the network structure. The proposed algorithm can also be used for community detection when the groups and the communities overlap. By introducing a tunable parameter that controls the involved effects of the heterogeneity, we can also investigate conveniently how the group structure can be coupled with the heterogeneity characteristics. In particular, an interesting example shows a group partition can evolve into a community partition in some situations when the involved heterogeneity effects are tuned. The extension of this algorithm to weighted networks is discussed as well.

Electrosurgery is broadly used in a wide variety of surgical procedures, yet its underlying mechanisms of interaction are poorly characterized. Fundamentals of electrosurgery have not changed much since the 1930s—cutting is still performed using continuous RF waveforms, leaving a collateral damage zone of hundreds of micrometers in depth. Pulsed waveforms with variable duty cycle are used mostly for tissue coagulation. Recently, we have demonstrated that electrosurgery with microsecond bursts applied via microelectrodes can provide cellular precision in soft tissue dissection. This paper examines dynamics of pulsed electrical discharges in conductive medium, and accompanying phenomena, such as vaporization, cavitation and ionization. It is demonstrated that ionization of the vapor cavity around the electrode is essential for energy delivery beyond the vaporization threshold. It is also shown that the ionization threshold voltage and resistance of the plasma-mediated discharge are much lower in the negative phase of the discharge than in the positive one. Capacitive coupling of the ac waveform to the electrode compensates for this asymmetry by shifting the medium voltage on the electrode, thus increasing the positive and decreasing the negative amplitudes to achieve charge balance in the opposite phases. With planar insulated electrodes having exposed edges of 12.5 μm in width and bursts of 40 μs in duration even tough biological tissues can be dissected with cellular precision. For example, cartilage dissection is achieved with pulse energy of 2.2 mJ per millimeter of length of the blade, and leaves a thermal damage zone of only 5–20 μm in width.

Using a sub-5 fs pulse laser, the pump–probe experiment was performed on a quinoid thiophene derivative and both electronic relaxation and vibrational dynamics were clarified with the same experimental data. From the data, two population decay times of the lowest electronic excited state were determined to be 200 fs and 1.8 ps, which can be explained by the assumption that the 2¹A_g state lies below the exciton 1¹B_u state together with the very low fluorescence quantum efficiency. The relaxation process after excitation by the pump pulse was studied to be 1¹B_u→1¹B^*_u→2¹A_g→1¹A_g. According to the experimental data, the location of the energy level was also discussed. The electronic dephasing time was determined to be 64 ± 4 fs by utilizing the data in the 'negative time' range. The vibrational dephasing time constant of the most strongly coupled mode with frequency of 1466 cm^-1 was determined to be 520 ± 20 fs from the widths of the corresponding Fourier power spectra.

In this paper, we introduce a new class of nonlinear Schrödinger equations (NLSEs), with an electromagnetic potential , both depending on the wavefunction Ψ. The scalar potential Φ depends on |Ψ|², whereas the vector potential satisfies the equation of magnetohydrodynamics with coefficient depending on Ψ.

In Madelung variables, the velocity field comes to be not irrotational in general and we prove that the vorticity induces dissipation, until the dynamical equilibrium is reached. The expression of the rate of dissipation is common to all NLSEs in the class.

We show that they are a particular case of the one-particle dynamics out of dynamical equilibrium for a system of N identical interacting Bose particles, as recently described within stochastic quantization by Lagrangian variational principle.

The cubic case is discussed in particular. Results of numerical experiments for rotational excitations of the ground state in a finite two-dimensional trap with harmonic potential are reported.

The Kerr nonlinearity of an optical-fibre Sagnac loop can be utilized to engineer a variety of two-photon quantum states. These include correlated, identical photon pairs as well as degenerate, maximally entangled states—both of which are used in quantum information processing. In fact, their underlying principle—the reverse Hong–Ou–Mandel effect—can also be applied to free-space, down-conversion-based analogues of either identical or entangled photon-pair sources. Due to their simple structure, such versatile devices are expected to find widespread applications in quantum-state engineering.

Enhanced fluorescence is observed from dye molecules interacting with optical nanoantenna arrays. Elliptical gold dimers form individual nanoantennae with tunable plasmon resonances depending upon the geometry of the two particles and the size of the gap between them. A fluorescent dye, Rhodamine 800, is uniformly embedded in a dielectric host that coats the nanoantennae. The nanoantennae act to enhance the dye absorption. In turn, emission from the dye drives the plasmon resonance of the antennae; the nanoantennae act to enhance the fluorescence signal and change the angular distribution of emission. These effects depend upon the overlap of the plasmon resonance with the excitation wavelength and the fluorescence emission band. A decreased fluorescence lifetime is observed along with highly polarized emission that displays the characteristics of the nanoantenna's dipole mode. Being able to engineer the emission of the dye–nanoantenna system is important for future device applications in both bio-sensing and nanoscale optoelectronic integration.

We investigate the Feshbach conversion of fermionic atom pairs to condensed bosonic molecules with a microscopic model that accounts for the repulsive interactions among all the particles involved. We find that the conversion efficiency is enhanced by the interaction between bosonic molecules, while it is suppressed by the interactions between fermionic atoms and between atoms and molecules. In the adiabatic limit, the combined effect of these interactions can lead to a ceiling of less than 100% on the conversion efficiency for a narrow Feshbach resonance. Our theory agrees with the recent Rice experiment on ⁶Li.

We investigate experimentally and theoretically the fluorescence emitted by molecular ensembles as well as spatially isolated, single molecules of an organic dye immobilized in a quasi-planar optical microresonator at room temperature. The optically excited dipole emitters couple simultaneously to on- and off-axis cavity resonances of the microresonator. The multi-spectral radiative contributions are strongly modified with respect to free (non-confined) space due to enhancement and inhibition of the molecular spontaneous emission (SpE) rate. By varying the mirror spacing of the microresonator on the nanometer-scale, the SpE rate of the cavity-confined molecules and, consequently, the spectral line width of the microresonator-controlled broadband fluorescence can be tuned by up to one order of magnitude. Stepwise reducing the optical confinement, we observe that the microresonator-controlled molecular fluorescence line shape converges towards the measured fluorescence line shape in free space. Our results are important for research on and application of broadband emitters in nano-optics and -photonics as well as microcavity-enhanced (single molecule) spectroscopy.

High-pressure angle-dispersive x-ray diffraction measurements have been performed on bulk and nanocrystalline cubic CeO₂ with mean sizes of 4.7 and 5.6 nm. It is found that the compressibility of the nanocrystals is lower than the bulk when a threshold pressure is reached. This critical pressure is found to be 10 GPa for 4.7 nm and 16 GPa for 5.6 nm CeO₂ nanocubes. The particle size dependence of the threshold pressure for the hardening of CeO₂ nanoparticles is quite unusual. First-principles electronic calculations show that the increased bulk modulus of the nanocrystal is due to the strengthening of the surface Ce–O bonds resulting in a much larger shear modulus than in the bulk and consequently hardening the shell surface.

We studied the effects of long-chain polymers on the small scales of turbulence by experimental measurements of Lagrangian accelerations in the bulk of turbulent flows of dilute polymer solutions. Lagrangian accelerations were measured by following tracer particles with a high-speed optical tracking system. We observed a significant decrease in the acceleration variance in dilute polymer solutions as compared with in pure water. The shape of the normalized acceleration probability density functions, however, remained the same as in Newtonian water flows. We also observed an increase in the turbulent Lagrangian acceleration autocorrelation time with polymer concentration. The decrease of acceleration variance and the increase of acceleration autocorrelation time are consistent with a suppression of viscous dissipation, and cannot be explained by a mere increase of effective viscosity due to the polymers.

We experimentally demonstrate the high-sensitivity optical monitoring of moving micromirrors, made of low-loss dielectric coatings upon silicon resonators of various shapes and sizes. The very high optical finesses obtained () have allowed us to measure the thermal noise of the micromirrors at room temperature with a shot-noise limited sensitivity at the level and to completely characterize their mechanical behavior, in excellent agreement with the results of a finite-element computation. Applications of such optomechanical systems range from quantum optics experiments to the experimental demonstration of the quantum ground state of a macroscopic mechanical resonator.

We study the dynamics of a pair of molecular ensembles trapped inside a superconducting resonator through which they are strongly coupled via a microwave field mode. We find that entanglement can be generated via 'vacuum fluctuations' even when the molecules and cavity field are initially prepared in their ground state. This entanglement is created in a relatively short time and without the need for further manipulation of the system. It therefore provides a convenient scheme to entangle two mesoscopic systems, and may well be useful for quantum information processing.

In this paper, a scalable photonic crystal cavity array, in which single embedded quantum dots (QDs) are coherently interacting, is studied theoretically. Firstly, we examine the spectral character and optical delay brought about by the coupled cavities interacting with single QDs, in an optical analogue to electromagnetically induced transparency. Secondly, we then examine the usability of this coupled QD–cavity system for quantum phase gate operation and our numerical examples suggest that a two-qubit system with fidelity above 0.99 and photon loss below 0.04 is possible.

The coherent exciton transport on a class of deterministic and random scale-free networks (DSFNs and RSFNs) generated by simple rules is studied in this paper. The coherent exciton dynamics is modeled by continuous-time quantum walks, and we calculate the transition probabilities between two nodes of the networks. We find that the transport depends on the initial nodes of the excitation. For DSFNs, the probabilities of finding the excitation at the initial central nodes are nearly periodic, in contrast to the flat behavior found for RSFNs. In the long time limit, the transition probabilities on DSFNs show characteristic patterns with identical values. For RSFNs, we find that the excitation is most likely to be found at the initial nodes with high connectivity. All these features of quantum transport are significantly different from those of the classical transport modeled by continuous-time random walks.

Wide-ranging measurements of sub-picosecond laser interactions with large noble gas cluster targets have been conducted in order to help clarify the nature and extent of the underlying laser–plasma heating. Within the sub-relativistic vacuum irradiance range of 10¹⁶–10¹⁷ W cm^-2, we find that electron temperatures measured with continuum x-ray spectroscopy exhibit a pronounced multi-keV enhancement. Analysis indicates this behaviour to be consistent with collisional or collisionless resonant heating mechanisms. We also present the first measurements of laser-to-cluster energy deposition at relativistic vacuum irradiances, our data demonstrating absorption fractions of 90% or more. Optical probing was used to resolve the onset of a supersonic ionization front resulting from this very high absorption, and shows that despite significant pre-focus heating, the greatest plasma energy densities can be generated about the vacuum focus position. Electron energy spectra measurements confirm that laser–plasma super-heating occurs, and together with ion data establish that relativistic laser–plasma coupling in atomic clusters can take place without significant MeV particle beam production. In conjunction with optical self-emission data, the optical probing also indicates laser pre-pulse effects at peak vacuum irradiance of 5 × 10¹⁹ W cm^-2. Laser absorption, plasma heating and energy transport data are supported throughout with analytical and numerical modelling.

A stochastic theory for the toppling activity in sandpile models is developed, based on a simple mean-field assumption about the toppling process. The theory describes the process as an anti-persistent Gaussian walk, where the diffusion coefficient is proportional to the activity. It is formulated as a generalization of the Itô stochastic differential equation with an anti-persistent fractional Gaussian noise source and a deterministic drift term. An essential element of the theory is rescaling to obtain a proper thermodynamic limit. When subjected to the most relevant statistical tests, the signal generated by the stochastic equation is indistinguishable from the temporal features of the toppling process obtained by numerical simulation of the Bak–Tang–Wiesenfeld sandpile.

A recent experiment performed by Afshar et al (2007 Found. Phys. 37 295–305) has been interpreted as a violation of Bohr's complementarity principle between interference visibility and which-path information (WPI) in a two-path interferometer. We have reproduced this experiment, using true single-photon pulses propagating in a two-path wavefront-splitting interferometer realized with a Fresnel's biprism, and followed by a grating with adjustable transmitting slits. The measured values of interference visibility V and WPI, characterized by the distinguishability parameter D, are found to obey the complementarity relation V²+D²⩽1. This result demonstrates that the experiment can be perfectly explained by the standard interpretation of quantum mechanics.

Time-resolved emissive probe measurements have been performed to study the spatio-temporal development of the plasma potential in an asymmetric bipolar pulsed magnetron discharge. The influence of the substrate potential as well as of the substrate position has been investigated while the further conditions were the same. To access the entire potential range which was between -100 V and + 400 V and to obtain sufficient time-resolution of the emissive probe, different heating currents had to be used. The plasma potential has been found to be typically close to zero in the 'on' phase, about +  40 V in the stable 'off' phase and up to +  400 V at the beginning of the 'off' phase, which is in agreement with the results of other authors. However, the positive values in the 'off' phase are generally lower than those reported and stay mostly below the target potential. This is explained by macroscopic considerations of the quasineutrality of the plasma taking into account a magnetic and geometrical shielding of the target, acting as an anode in the 'off' phase, and the potential and position of the substrate holder and environment.

We determine infrared transmission amplitude and phase spectra of metamaterial samples at well-defined incidence and polarization with a vector ('asymmetric') frequency-comb Fourier-transform spectrometer (c-FTS) that uses no moving elements. The metamaterials are free-standing metallic hole arrays; we study their resonances in the 7–13 μm and 100–1000 μm wavelength regions due both to interaction with bulk waves (Wood anomaly) and with leaky surface plasmon polaritons (near-unity transmittance, coupling features and dispersion). Such complex-valued transmission and reflection spectra could be used to compute a metamaterial's complex dielectric function directly, as well as its magnetic and magneto-optical permeability functions.

The operator annihilating a single quantum of excitation in a bosonic field is one of the cornerstones for the interpretation and prediction of the behavior of the microscopic quantum world. Here we present a systematic experimental study of the effects of single-photon annihilation on some paradigmatic light states. In particular, by demonstrating the invariance of coherent states by this operation, we provide the first direct verification of their definition as eigenstates of the photon annihilation operator.

Relativistic heavy ions of high charge (Z) and energy (E) (HZE) in galactic cosmic rays (GCR) are important contributors to space radiation risk because they cannot be shielded completely and their relative biological effectiveness is very high. To understand these risks, Monte Carlo track structure simulations by radiation transport codes are widely used in radiation biology to provide information on energy deposition and production of radiolytic species that damage cellular structures. In this paper, we show that relativistic corrections can be applied to existing semi-empirical cross section models for the ionization and excitation of water molecules by ions to extend the validity of their energy range up to ∼10⁴ MeV amu⁻¹. Similarly, an effective charge value correction is applied for Z>2 ions. Simulations of HZE tracks have been performed by a new C++ Monte Carlo transport code, named RITRACKS, that uses these cross sections to calculate the stopping power, radial dose, XY-plane projections of track segments and radial distributions of primary radiolytic species (H^•, ^•OH, H₂, H₂O₂ and e⁻_aq) at ∼10⁻¹² s. These new data will be useful to understand results from experiments performed at ion accelerators by discriminating the role of the so-called core and penumbra of the tracks.

We present a cluster-based approach to model charge transport through molecular and atomic contacts. The electronic structure of the contacts is determined in the framework of density functional theory, and the parameters needed to describe transport are extracted from finite clusters. A similar procedure, restricted to nearest-neighbor interactions in the electrodes, has been presented by Damle et al (2002 Chem. Phys. 281 171). Here, we show how to systematically improve the description of the electrodes by extracting bulk parameters from sufficiently large metal clusters. In this way, we avoid problems arising from the use of nonorthogonal basis functions. For demonstration, we apply our method to electron transport through Au contacts with various atomic-chain configurations and to a single-atom contact of Al.

An ultracold three-species Bose–Fermi–Fermi degenerate atomic mixture ⁸⁷Rb–⁴⁰K–⁶Li was realized very recently (Tagliber M et al 2008 Phys. Rev. Lett. 100 010401). Here, we study the creation of heteronuclear triatomic molecules in this mixture, and show that a constructive triple-path interference can lead to an almost ideal conversion rate, in comparison with the single- or double-path cases. The important effect of the initial population imbalance on the atom–molecule dark state is also investigated.

In this work, the laser-induced magnetization dynamics of nanostructured nickel films is investigated. The influence of the nanosize is discussed considering the timescale of hundreds of femtoseconds as well as the GHz regime. While no nanosize effect is observed on the short timescale, the excited magnetic mode in the GHz regime can be identified by comparison with micromagnetic simulations. The thickness dependence reveals insight into the dipole interaction between single nickel structures. Also, transient reflectivity changes are discussed.

We consider a nanomechanical analogue of a nonlinear interferometer, consisting of two parallel, flexural nanomechanical resonators, each with an intrinsic Duffing nonlinearity and with a switchable beamsplitter-like coupling between them. We calculate the precision with which the strength of the nonlinearity can be estimated and show that it scales as 1/n^3/2, where n is the mean phonon number of the initial state. This result holds even in the presence of dissipation, but assumes the ability to make measurements of the quadrature components of the nanoresonators.

An all mechanical signal mixing device is described which uses only linear springs as fundamental building blocks. Two input oscillators are coupled to an orthogonally vibrating output oscillator via a linear spring, which results in an effective nonlinear multiplicative mixing function. Numerical simulations have been performed for studying the performance characteristics of the mixer. A modified version of the mixer acting as a mechanical modulator is also numerically investigated for application as a mechanical power amplifier. The viability of the concept is demonstrated in a centimeter scale experimental setup and a micromechanical scale polymer embodiment has been built using two-photon polymerization lithographic methods.

EuFe₂As₂ is a member of the ternary iron arsenide family. Similar to BaFe₂As₂ and SrFe₂As₂, EuFe₂As₂ exhibits a clear anomaly in resistivity near 200 K. Here, we report the discovery of superconductivity in Eu_0.7Na_0.3Fe₂As₂ by partial substitution of the europium site with sodium. ThCr₂Si₂ tetragonal structure, as expected for EuFe₂As₂, is formed as the main phase for the composition Eu_0.7Na_0.3Fe₂As₂. Resistivity measurements reveal that the transition temperature T_c as high as 34.7 K is observed in this compound. The rate of T_c suppression with the applied magnetic field is 3.87 T K⁻¹, giving an extrapolated zero-temperature upper critical field of 100 T. It demonstrates a very encouraging application of the new superconductors.

Fingering instabilities arising from local perturbations to planar reaction fronts in the CO oxidation reaction on Pt(100) are presented. CO oxidation represents a heterogeneous nonlinear system with the necessary kinetic and diffusive transport properties to support the development of fingered wave fronts. External forcing was utilized to create CO wave fronts on an otherwise monostable, O-covered surface, which, upon destabilization, gave rise to fingers of adsorbed CO extending into the O adlayer ahead of the reaction front. Finger spreading and tip-splitting were observed as the finger pattern evolved towards an intrinsic wavelength, independent of the length of the reaction front, calculated to be approximately 40 μm. Our data also show the presence of a shielding process, where at wavelengths less than twice the observed intrinsic value, additional fingers were created on the reaction front through a tip-splitting bifurcation of an existing finger. At wavelengths greater than twice the intrinsic value, additional fingers formed in the troughs between adjacent fingers, apparently unaffected by the presence of the larger surrounding fingers.

We propose and demonstrate white-light-generating nonradiative energy transfer (ET) from epitaxial quantum wells (QWs) to colloidal quantum dots (QDs) in their close proximity. This proof-of-concept hybrid color-converting system consists of chemically synthesized red-emitting CdSe/ZnS core/shell heteronanocrystals intimately integrated on epitaxially grown cyan-emitting InGaN/GaN QWs. The white light is generated by the collective luminescence of QWs and QDs, for which the dot emission is further increased by 63% with nonradiative ET, setting the operating point in the white region of CIE chromaticity diagram. Using cyan emission at 490 nm from the QWs and red emission at 650 nm from the nanocrystal (NC) luminophors, we obtain warm white light generation with a correlated color temperature of T_c = 3135 K and tristimulus coordinates of (x,y) = (0.42, 0.39) in the white region. By analyzing the time-resolved radiative decay of these NC emitters in our hybrid system with a 16 ps time resolution, the luminescence kinetics reveals a fast ET with a rate of (2 ns)^-1 using a multiexponential fit with χ ² = 1.0171.

Advances in physics are intimately connected with developments in a new technology, the telescope, precision clocks, even the computer all have heralded a shift in thinking. These landmark developments open new opportunities accelerating research and in turn new scientific directions. These technological drivers often correspond to new instruments, but equally might just as well flag a new mathematical tool, an algorithm or even means to visualize physics in a new way.

Early on in this twenty-first century, scientific communities are just starting to explore the potential of digital visualization. Whether visualization is used to represent and communicate complex concepts, or to understand and interpret experimental data, or to visualize solutions to complex dynamical equations, the basic tools of visualization are shared in each of these applications and implementations.

High-performance computing exemplifies the integration of visualization with leading research. Visualization is an indispensable tool for analyzing and interpreting complex three-dimensional dynamics as well as to diagnose numerical problems in intricate parallel calculation algorithms. The effectiveness of visualization arises by exploiting the unmatched capability of the human eye and visual cortex to process the large information content of images. In a brief glance, we recognize patterns or identify subtle features even in noisy data, something that is difficult or impossible to achieve with more traditional forms of data analysis.

Importantly, visualizations guide the intuition of researchers and help to comprehend physical phenomena that lie far outside of direct experience. In fact, visualizations literally allow us to see what would otherwise remain completely invisible. For example, artificial imagery created to visualize the distribution of dark matter in the Universe has been instrumental to develop the notion of a cosmic web, and for helping to establish the current standard model of cosmology wherein this (in principle invisible) dark matter dominates the cosmic matter content.

The advantages of visualization found for simulated data also hold for real world data as well. With the application of computerized acquisition many scientific disciplines are witnessing exponential growth rates of the volume of accumulated raw data, which often makes it daunting to condense the information into a manageable form, a challenge that can be addressed by modern visualization techniques. Such visualizations are also often an enticing way to communicate scientific results to the general public. This need for visualization is especially true in basic science, with its reliance on a benevolent and interested general public that drives the need for high-quality visualizations.

Despite the widespread use of visualization, this technology has suffered from a lack of the unifying influence of shared common experiences. As with any emerging technology practitioners have often independently found solutions to similar problems. It is the aim of this focus issue to celebrate the importance of visualization, report on its growing use by the broad community of physicists, including biophysics, chemical physics, geophysics, astrophysics, and medical physics, and provide an opportunity for the diverse community of scientists using visualization to share work in one issue of a journal that itself is in the vanguard of supporting visualization and multimedia.

A remarkable breadth and diversity of visualization in physics is to be found in this issue spanning fundamental aspects of relativity theory to computational fluid dynamics. The topics span length scales that are as small as quantum phenomena to the entire observable Universe. We have been impressed by the quality of the submissions and hope that this snap-shot will introduce, inform, motivate and maybe even help to unify visualization in physics.

Readers are also directed to the December issue of Physics World which includes the following features highlighting work in this collection and other novel uses of visualization techniques:   'A feast of visualization' Physics World December 2008 pp 20–23   'Seeing the quantum world' by Barry Sanders Physics World December 2008 pp 24–27   'A picture of the cosmos' by Mark SubbaRao and Miguel Aragon-Calvo Physics World December 2008 pp 29–32   'Thinking outside the cube' by César A Hidalgo Physics World December 2008 pp 34–37

Focus on Visualization in Physics Contents

Visualization of spiral and scroll waves in simulated and experimental cardiac tissue E M Cherry and F H Fenton

Visualization of large scale structure from the Sloan Digital Sky Survey M U SubbaRao, M A Aragón-Calvo, H W Chen, J M Quashnock, A S Szalay and D G York

How computers can help us in creating an intuitive access to relativity Hanns Ruder, Daniel Weiskopf, Hans-Peter Nollert and Thomas Müller

Lagrangian particle tracking in three dimensions via single-camera in-line digital holography Jiang Lu, Jacob P Fugal, Hansen Nordsiek, Ewe Wei Saw, Raymond A Shaw and Weidong Yang

Quantifying spatial heterogeneity from images Andrew E Pomerantz and Yi-Qiao Song

Disaggregation and scientific visualization of earthscapes considering trends and spatial dependence structures S Grunwald

Strength through structure: visualization and local assessment of the trabecular bone structure C Räth, R Monetti, J Bauer, I Sidorenko, D Müller, M Matsuura, E-M Lochmüller, P Zysset and F Eckstein

Thermonuclear supernovae: a multi-scale astrophysical problem challenging numerical simulations and visualization F K Röpke and R Bruckschen

Visualization needs and techniques for astrophysical simulations W Kapferer and T Riser

Flow visualization and field line advection in computational fluid dynamics: application to magnetic fields and turbulent flows Pablo Mininni, Ed Lee, Alan Norton and John Clyne

Splotch: visualizing cosmological simulations K Dolag, M Reinecke, C Gheller and S Imboden

Visualizing a silicon quantum computer Barry C Sanders, Lloyd C L Hollenberg, Darran Edmundson and Andrew Edmundson

Colliding galaxies, rotating neutron stars and merging black holes—visualizing high dimensional datasets on arbitrary meshes Werner Benger

A low complexity visualization tool that helps to perform complex systems analysis M G Beiró, J I Alvarez-Hamelin and J R Busch

Visualizing astrophysical N-body systems John Dubinski

The heart is a nonlinear biological system that can exhibit complex electrical dynamics, complete with period-doubling bifurcations and spiral and scroll waves that can lead to fibrillatory states that compromise the heart's ability to contract and pump blood efficiently. Despite the importance of understanding the range of cardiac dynamics, studying how spiral and scroll waves can initiate, evolve, and be terminated is challenging because of the complicated electrophysiology and anatomy of the heart. Nevertheless, over the last two decades advances in experimental techniques have improved access to experimental data and have made it possible to visualize the electrical state of the heart in more detail than ever before. During the same time, progress in mathematical modeling and computational techniques has facilitated using simulations as a tool for investigating cardiac dynamics. In this paper, we present data from experimental and simulated cardiac tissue and discuss visualization techniques that facilitate understanding of the behavior of electrical spiral and scroll waves in the context of the heart. The paper contains many interactive media, including movies and interactive two- and three-dimensional Java appletsDisclaimer: IOP Publishing was not involved in the programming of this software and does not accept any responsibility for it. You download and run the software at your own risk. If you experience any problems with the software, please contact the author directly. To the fullest extent permitted by law, IOP Publishing Ltd accepts no responsibility for any loss, damage and/or other adverse effect on your computer system caused by your downloading and running this software. IOP Publishing Ltd accepts no responsibility for consequential loss..

We will discuss the challenges of visualizing large cosmological datasets. These include observational issues such as the masks and incomplete nature of the survey volume, cosmological issues such as redshift distortions and the difficulty of visualizing datasets that span cosmological epochs, as well as the inherent visualization challenges in presenting dense three-dimensional (3D) datasets. Two case studies will be presented. The first will feature the identification of filamentary structures in the large scale distribution of galaxies. The second case study will feature visualizations of the correlations between quasar absorption line systems and luminous red galaxies. Finally, we will give an overview of our visualization work-flow which features the use of the open-source 3D modeling program Blender.

Computers have added many new possibilities to the tool box used for visualizing science in general and relativity in particular. We present some new results from our own work: (2+1) dimensional Minkowski diagrams showing two spatial dimensions, extended wormhole visualization, and the illustration of accretion discs by using the approximation via a rigidly rotating disc of dust. We also discuss some related examples from our earlier work, such as interactive and immersive visualization, or the visualization of the warp drive metric.

Lagrangian particle trajectories are measured in three spatial dimensions with a single camera using the method of digital in-line holography. Lagrangian trajectories of 60–120 μm diameter droplets in turbulent air obtained with data from one camera compare favorably with tracks obtained from a simultaneous dual-camera data set, the latter having high spatial resolution in all three dimensions. Using the single-camera system, particle motion along the optical axis is successfully tracked, allowing for long, continuous 3D tracks, but the depth resolution based on standard reconstruction methods is not sufficient to obtain accurate acceleration measurements for that component. Lagrangian velocity distributions for all three spatial components agree within reasonable sampling uncertainties and Lagrangian acceleration distributions agree for the two lateral components. An equivalent single-camera, imaging-based 2D tracking system would be challenged by the particle densities tested, but the holographic configuration allows for 3D tracking in the dilute limit. The method also allows particle size, shape and orientation to be measured along the trajectory. Lagrangian measurements of particle size provide a direct measure of particle size uncertainty under realistic conditions sampled from the entire measurement volume.

Visualization techniques are extremely useful for characterizing natural materials with complex spatial structure. Although many powerful imaging modalities exist, simple display of the images often does not convey the underlying spatial structure. Instead, quantitative image analysis can extract the most important features of the imaged object in a manner that is easier to comprehend and to compare from sample to sample. This paper describes the formulation of the heterogeneity spectrum to show the extent of spatial heterogeneity as a function of length scale for all length scales to which a particular measurement is sensitive. This technique is especially relevant for describing materials that simultaneously present spatial heterogeneity at multiple length scales. In this paper, the heterogeneity spectrum is applied for the first time to images from optical microscopy. The spectrum is measured for thin section images of complex carbonate rock cores showing heterogeneity at several length scales in the range 10–10 000 μm.

Earth attributes show complex, heterogeneous spatial patterns generated by exogenous environmental factors and formation processes. This study investigates various strategies to quantify the underlying spatial patterns of simulated fields resembling real earthscapes and to compare their performance for describing them. The approach is to disaggregate the variability of earth attributes into two components, deterministic trend m(x_i) and spatial dependence ε(x_i), and determine the effects of m(x_i) and ε(x_i) on prediction accuracy under various combinations of spatial fields of earth attributes encountered in different earthscapes. We illustrate that cross-dependencies exist between spatial and feature accuracy. Scientific visualization is used to transpose quantitative results into visual space.

The visualization and subsequent assessment of the inner human bone structures play an important role for better understanding the disease- or drug-induced changes of bone in the context of osteoporosis giving prospect for better predictions of bone strength and thus of the fracture risk of osteoporotic patients. In this work, we show how the complex trabecular bone structure can be visualized using μCT imaging techniques at an isotropic resolution of 26 μm. We quantify these structures by calculating global and local topological and morphological measures, namely Minkowski functionals (MFs) and utilizing the (an-)isotropic scaling index method (SIM) and by deriving suitable texture measures based on MF and SIM. Using a sample of 151 specimens taken from human vertebrae in vitro, we correlate the texture measures with the mechanically measured maximum compressive strength (MCS), which quantifies the strength of the bone probe, by using Pearson's correlation coefficient. The structure parameters derived from the local measures yield good correlations with the bone strength as measured in mechanical tests. We investigate whether the performance of the texture measures depends on the MCS value by selecting different subsamples according to MCS. Considering the whole sample the results for the newly defined parameters are better than those obtained for the standard global histomorphometric parameters except for bone volume/total volume (BV/TV). If a subsample consisting only of weak bones is analysed, the local structural analysis leads to similar and even better correlations with MCS as compared to BV/TV. Thus, the MF and SIM yield additional information about the stability of the bone especially in the case of weak bones, which corroborates the hypothesis that the bone structure (and not only its mineral mass) constitutes an important component of bone stability.

The numerical modeling of type Ia supernovae is a demanding astrophysical task. Relevant physical processes take place on vastly different length- and timescales. This multi-scale character of the object poses challenges to the numerical approaches. We discuss an implementation that accounts for these problems by employing a large eddy simulation (LES) strategy for treating turbulence effects and a level-set technique to represent the thin thermonuclear flames. It is demonstrated that this approach works efficiently in simulations of the deflagration model and the delayed detonation model of type Ia supernovae. The resulting data reflect the multi-scale nature of the problem. Therefore, visualization has to be tackled with special techniques. We describe an approach that enables the interactive exploration of large datasets on commodity hardware. To this end, out-of-core methods are employed and the rendering of the data is achieved by a hybrid particle-based and texture-based volume-rendering technique.

Numerical simulations have evolved continuously towards being an important field in astrophysics, equivalent to theory and observation. Due to the enormous developments in computer sciences, both hardware- and software-architecture, state-of-the-art simulations produce huge amounts of raw data with increasing complexity. In this paper some aspects of problems in the field of visualization in numerical astrophysics in combination with possible solutions are given. Commonly used visualization packages along with a newly developed approach to real-time visualization, incorporating shader programming to uncover the computational power of modern graphics cards, are presented. With these techniques at hand, real-time visualizations help scientists to understand the coherences in the results of their numerical simulations. Furthermore a fundamental problem in data analysis, i.e. coverage of metadata on how a visualization was created, is highlighted.

Accurately interpreting three dimensional (3D) vector quantities output as solutions to high-resolution computational fluid dynamics (CFD) simulations can be an arduous, time-consuming task. Scientific visualization of these fields can be a powerful aid in their understanding. However, numerous pitfalls present themselves ranging from computational performance to the challenge of generating insightful visual representations of the data. In this paper, we briefly survey current practices for visualizing 3D vector fields, placing particular emphasis on those data arising from CFD simulations of turbulence. We describe the capabilities of a vector field visualization system that we have implemented as part of an open source visual data analysis environment. We also describe a novel algorithm we have developed for illustrating the advection of one vector field by a second flow field. We demonstrate these techniques in the exploration of two sets of runs. The first comprises an ideal and a resistive magnetohydrodynamic (MHD) simulation. This set is used to test the validity of the advection scheme. The second corresponds to a simulation of MHD turbulence. We show the formation of structures in the flows, the evolution of magnetic field lines, and how field line advection can be used effectively to track structures therein.

We present a light and fast, publicly available, ray-tracer Splotch software tool which supports the effective visualization of cosmological simulations data. We describe the algorithm it relies on, which is designed in order to deal with point-like data, optimizing the ray-tracing calculation by ordering the particles as a function of their 'depth', defined as a function of one of the coordinates or other associated parameters. Realistic three-dimensional impressions are reached through a composition of the final colour in each pixel properly calculating emission and absorption of individual volume elements. We describe several scientific as well as public applications realized with Splotch. We emphasize how different datasets and configurations lead to remarkably different results in terms of the images and animations. A few of these results are available online.

Quantum computation is a fast-growing, multi-disciplinary research field. The purpose of a quantum computer is to execute quantum algorithms that efficiently solve computational problems intractable within the existing paradigm of 'classical' computing built on bits and Boolean gates. While collaboration between computer scientists, physicists, chemists, engineers, mathematicians and others is essential to the project's success, traditional disciplinary boundaries can hinder progress and make communicating the aims of quantum computing and future technologies difficult. We have developed a four minute animation as a tool for representing, understanding and communicating a silicon-based solid-state quantum computer to a variety of audiences, either as a stand-alone animation to be used by expert presenters or embedded into a longer movie as short animated sequences. The paper includes a generally applicable recipe for successful scientific animation production.

Visualization of datasets stemming from diverse sources is challenged by the large variety of substantial differences in topology, geometry and nature of the associated data fields. Since there is no standard on how to formulate and treat data for scientific visualization, algorithms are frequently implemented in a highly domain-specific way. Here, we explore the potential of point-wise rendering as a generic way to represent single or multiple fields instantaneously on arbitrary mesh types. This approach is discussed within the terminology of fiber bundles as a general mathematical concept to model scalar-, vector- and tensorfields given on topological spaces (with manifolds as a particular case). We give application examples based on datasets originating from astrophysics and show first results of a tensor field visualization of a recently produced complex dataset of colliding black holes in their final orbit. We finally propose a data layout representing the mathematical concept of a 'field' generic enough to handle all cases involved.

In this paper, we present an extension of large network visualization (LaNet-vi), a tool to visualize large scale networks using the k-core decomposition. One of the new features is how vertices compute their angular position. While in the later version it is done using shell clusters, in this version we use the angular coordinate of vertices in higher k-shells, and arrange the highest shell according to a cliques decomposition. The time complexity goes from to O(n) upon bounds on a heavy-tailed degree distribution. The tool also performs a k-core-connectivity analysis, highlighting vertices that are not k-connected; e.g. this property is useful to measure robustness or quality of service (QoS) capabilities in communication networks. Finally, the actual version of LaNet-vi can draw labels and all the edges using transparencies, yielding an accurate visualization. Based on the obtained figure, it is possible to distinguish different sources and types of complex networks at a glance, in a sort of 'network iris-print'.

I begin with a brief history of N-body simulation and visualization and then go on to describe various methods for creating images and animations of modern simulations in cosmology and galactic dynamics. These techniques are incorporated into a specialized particle visualization software library called MYRIAD that is designed to render images within large parallel N-body simulations as they run. I present several case studies that explore the application of these methods to animations in star clusters, interacting galaxies and cosmological structure formation.