bluuebunny/crossref_metadata_2025 huggingface dataset:
The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation
Authors: Shao Qiang , Qin Gao Yi
Published: October 2011

Molecular dynamics simulations using the integrated tempering sampling method were performed for the folding of wild-type B domain of protein A (BdpA). Starting from random and stretched structures, these simulations allow us to fold this protein into the native-like structure frequently, achieving very small backbone (1.7 Å) and all heavy-atom root-mean-square deviation (2.6 Å). Therefore, the method used here increases the efficiency of configuration sampling and thermodynamics characterization by molecular dynamics simulation. Although inconsistency exists between the calculation and experiments for the absolute stabilities, as a limitation of the force field parameters, the calculated order of helix stability (H3 > H2 > H1) is consistent with that determined by experiments for individual separate helices. The lowest free energy folding pathway of BdpA was found to start with a barrierless and non-cooperative structural collapse from the entirely extended (E) state, which leads to a physiologically unfolded (P) state consisting of multiple stable structures with few native inter-helical hydrophobic interactions formed. In the P state, only H3 is fully structured. The final formation of H1 (and to a lesser extent, H2) in the folded (F) state requires the packing of the inter-helical hydrophobic contacts. In addition, it was found that stabilities of backbone hydrogen bonds are significantly affected by their positions relative to the inter-helical hydrophobic core. As temperature increases, the stability of the hydrogen bonds exposed to the solvent tends to increase while that of the hydrogen bonds buried within the hydrophobic core decreases. Finally, we discuss implications of this study on the general folding mechanism of proteins.
Experimental study on polarized surface enhanced resonance Raman scattering of rhodamine 6G adsorbed on porous Al2O3 substrates
Authors: Jernshøj K. D. , Hassing S. , Hansen R. S. , Krohne-Nielsen P.
Published: October 2011

The polarization properties of surface enhanced resonance Raman scattering (SE(R)RS) of rhodamine 6G molecules, adsorbed to a hexagonally ordered gold nanostructure, are studied with the purpose to discriminate between adsorption sites with different plasmonic properties. The nanostructure is based on a self-organizing hexagonally ordered porous Al2O3 substrate sputter-coated with gold. Each hexagonal subunit has D6h symmetry, where the symmetry center may act as an isotropic site, whereas the six narrow gaps between the individual Au hemispheres may act as hot-spots. The variation of the depolarization ratio (DPR), measured in resonance for the eight most prominent vibrational modes of the xanthene moiety, is analyzed by rotating the sample. According to theory, the DPR of the SE(R)RS signal obtained from molecules physisorbed in the isotropic sites deviates from the DPR originating from molecules physisorbed in the hot-spots in two ways: 1. The DPR associated with the isotropic sites depends differently on the rotation angle than the DPR associated with the hot-spots. 2. The DPR of the SE(R)RS signal obtained from molecules physisorbed in the isotropic sites depends on the nature of the Raman modes, whereas it for molecules physisorbed in the hot-spots is independent of the nature of the Raman modes. By applying the latter in the analysis of the polarized SE(R)RS data, we conclude that the dominating SE(R)RS signal comes from molecules adsorbed in the hot-spots. However, since the DPR’s obtained for Raman modes of different symmetry are slightly different, the SE(R)RS signal must contain an additional contribution. Our analysis shows that the small mode-dependent SE(R)RS signal most likely comes from molecules adsorbed in the isotropic sites. The general result that can be derived from the present study is that by measuring the polarization properties in SE(R)RS and SERS it is possible to discriminate between adsorption sites with different plasmonic properties present in a highly symmetric nanostructure, even when the magnitude of the different contributions are highly different. The consequence of the insufficient spatial resolution with respect to a detailed mapping of the substrate often encountered in unpolarized SE(R)RS and in two-photon luminescence microscopy may thereby be circumvented.
Polarizability and alignment of dielectric nanoparticles in an external electric field: Bowls, dumbbells, and cuboids
Authors: Kwaadgras Bas W. , Verdult Maarten , Dijkstra Marjolein , van Roij René
Published: October 2011

We employ the coupled dipole method to calculate the polarizability tensor of various anisotropic dielectric clusters of polarizable atoms, such as cuboid-, bowl-, and dumbbell-shaped nanoparticles. Starting from a Hamiltonian of a many-atom system, we investigate how this tensor depends on the size and shape of the cluster. We use the polarizability tensor to calculate the energy difference associated with turning a nanocluster from its least to its most favorable orientation in a homogeneous static electric field, and we determine the cluster dimension for which this energy difference exceeds the thermal energy such that particle alignment by the field is possible. Finally, we study in detail the (local) polarizability of a cubic-shaped cluster and present results indicating that, when retardation is ignored, a bulk polarizability cannot be reached by scaling up the system.
Numerical modeling of radiation-dominated and quantum-electrodynamically strong regimes of laser-plasma interaction
Authors: Sokolov Igor V. , Naumova Natalia M. , Nees John A.
Published: October 2011

Ultra-strong laser pulses can be so intense that an electron in the focused beam loses significant energy due to γ-photon emission while its motion deviates via the radiation back-reaction. Numerical methods and tools designed to simulate radiation-dominated and quantum-electrodynamically strong laser-plasma interactions are summarized here.
Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine
Authors: Duff Nathan , Peters Baron
Published: October 2011

Crystal nucleation is important for many processes including pharmaceutical crystallization, biomineralization, and material synthesis. The progression of structural changes which occur during crystal nucleation are often described using order parameters. Polymorph specific order parameters have been developed for crystallization of spherically symmetric particles; however, polymorph specific order parameters for molecular crystals remain a challenge. We introduce template based polymorph specific order parameters for molecular crystals. For each molecule in a simulation, we compute the root mean squared deviation (RMSD) between the local environment around the molecule and a template of the perfect crystal structure for each polymorph. The RMSD order parameters can clearly distinguish the α-, β-, and γ-glycine polymorph crystal structures in the bulk crystal and also in solvated crystallites. Surface melting of glycine crystallites in supersaturated aqueous solution is explored using the newly developed order parameters. The solvated α-glycine crystallite has a thinner surface melted layer than the γ-glycine crystallite. α-glycine forms first out of aqueous solution, so surface melted layer thickness may provide insight into interfacial energy and polymorph selection.
Partial information decomposition as a spatiotemporal filter
Authors: Flecker Benjamin , Alford Wesley , Beggs John M. , Williams Paul L. , Beer Randall D.
Published: October 2011

Understanding the mechanisms of distributed computation in cellular automata requires techniques for characterizing the emergent structures that underlie information processing in such systems. Recently, techniques from information theory have been brought to bear on this problem. Building on this work, we utilize the new technique of partial information decomposition to show that previous information-theoretic measures can confound distinct sources of information. We then propose a new set of filters and demonstrate that they more cleanly separate out the background domains, particles, and collisions that are typically associated with information storage, transfer, and modification in cellular automata.
Decay dynamics of excitonic polarons in InAs/GaAs quantum dots
Authors: Werner S. , Reparaz J. S. , Wagner M. R. , Zimmer P. , Ledentsov N. N. , Kabuss J. , Dachner M. R. , Richter M. , Knorr A. , Thomsen C. , Hoffmann A.
Published: October 2011

We present time-resolved studies of the exciton-phonon interaction in self-assembled InAs/GaAs quantum dots. Different scattering and luminescence processes were investigated by time-resolved spectroscopy exciting resonantly into the quantum dot’s electronic structure. By studying the characteristic decay times of the ground state and of several phonon-assisted recombinations we were able to distinguish a resonant Raman process from a phonon-assisted photoluminescence process which are always simultaneously present and can interfere with each other. While lifetimes under 30 ps were observed for the coherent Raman process, the incoherent phonon-assisted recombination exhibited typical lifetimes of around 1 ns independently of the excitation energy. We conclude that under resonant excitation the dominant radiative recombination process in this system always involves an electronic state of the ground state of the quantum dot’s electronic structure. Combining temperature-dependent and time-resolved measurements we show that a weak phonon-bottleneck is present in the low temperature regime (< 130 K), while it disappears for higher temperatures.
Franck-Condon simulation, including anharmonicity, of the photodetachment spectrum of P2H−: Restricted-spin coupled-cluster single-double plus perturbative triple and unrestricted-spin coupled-cluster single-double plus perturbative triple -F12x potential energy functions of P2H and P2H−
Authors: Mok Daniel K. W. , Lee Edmond P. F. , Chau Foo-tim , Dyke John M.
Published: October 2011

Geometry optimization and harmonic vibrational frequency calculations have been carried out on the ${\rm \tilde X}$X̃2A′ state of P2H and the ${\rm \tilde X}$X̃1A′ state of P2H− using the restricted-spin coupled-cluster single-double plus perturbative triple excitation [RCCSD(T)] and explicitly correlated unrestricted-spin coupled-cluster single-double plus perturbative triple excitation [UCCSD(T)-F12x] methods. For RCCSD(T) calculations, basis sets of up to the augmented correlation-consistent polarized valence quintuple-zeta (aug-cc-pV5Z) quality were employed, and contributions from extrapolation to the complete basis set limit and from core correlation of the P 2s22p6 electrons were also included. For UCCSD(T)-F12x calculations, different atomic orbital basis sets of triple-zeta quality with different associated complementary auxiliary basis sets and different geminal Slater exponents were used. When the P 2s22p6 core electrons were correlated in these F12x calculations, appropriate core-valence basis sets were employed. In addition, potential energy functions (PEFs) of the ${\rm \tilde X}$X̃2A′ state of P2H and the ${\rm \tilde X}$X̃1A′ state of P2H− were computed at different RCCSD(T) and UCCSD(T)-F12x levels, and were used in variational calculations of anharmonic vibrational wavefunctions, which were then utilized to calculate Franck-Condon factors (FCFs) between these two states, employing a method which includes allowance for anharmonicity and Duschinsky rotation. The photodetachment spectrum of P2H− was then simulated using the computed FCFs. Simulated spectra obtained using the RCCSD(T)/aug-cc-pV5Z and UCCSD(T)-F12x(x = a or b)/aug-cc-pCVTZ PEFs are compared and found to be essentially identical. Based on the computed FCFs, a more detailed assignment of the observed vibrational structure than previously reported, which includes “hot bands,” has been proposed. Comparison between simulated and available experimental spectra has been made, and the currently most reliable sets of equilibrium geometrical parameters for P2H and its anion have been derived. The photodetachment spectrum of P2D, yet to be recorded, has also been simulated.
Supercooled dynamics of grain boundary particles in two-dimensional colloidal crystals
Authors: Skinner Thomas O. E. , Aarts Dirk G. A. L. , Dullens Roel P. A.
Published: October 2011

We experimentally investigate the dynamics of particles constituting grain boundaries in a two-dimensional colloidal crystal, using video-microscopy. A clear plateau in the mean square displacement of the grain boundary particles is found, followed by an upswing indicative of cage breaking. The van Hove correlation functions and the non-Gaussian parameter show that grain boundary particle dynamics are highly heterogeneous. Furthermore, we identified clusters of cooperatively moving particles and analyzed the time-dependence of the weight-averaged mean cluster size. We find good correlation between the behavior of the mean square displacement, and the time dependence of the non-Gaussian parameter and the cluster size, as also reported for various supercooled systems. Our results therefore provide experimental support for the similarity between particle dynamics in grain boundaries and in supercooled liquids as suggested by recent computer simulations.
Effective theories for circuits and automata
Authors: DeDeo Simon
Published: October 2011

Abstracting an effective theory from a complicated process is central to the study of complexity. Even when the underlying mechanisms are understood, or at least measurable, the presence of dissipation and irreversibility in biological, computational, and social systems makes the problem harder. Here, we demonstrate the construction of effective theories in the presence of both irreversibility and noise, in a dynamical model with underlying feedback. We use the Krohn-Rhodes theorem to show how the composition of underlying mechanisms can lead to innovations in the emergent effective theory. We show how dissipation and irreversibility fundamentally limit the lifetimes of these emergent structures, even though, on short timescales, the group properties may be enriched compared to their noiseless counterparts.
Rotational predissociation of extremely weakly bound atom-molecule complexes produced by Feshbach resonance association
Authors: Wallis Alisdair O. G. , Krems Roman V.
Published: October 2011

We study the rotational predissociation of atom–molecule complexes with very small binding energy. Such complexes can be produced by Feshbach resonance association of ultracold molecules with ultracold atoms. Numerical calculations of the predissociation lifetimes based on the computation of the energy dependence of the scattering matrix elements become inaccurate when the binding energy is smaller than the energy width of the predissociating state. We derive expressions that represent accurately the predissociation lifetimes in terms of the real and imaginary parts of the scattering length and effective range for molecules in an excited rotational state. Our results show that the predissociation lifetimes are the longest when the binding energy is positive, i.e., when the predissociating state is just above the excited state threshold.
Magnetorotational instability in a collisionless plasma with heat flux vector and an isotropic plasma with self-gravitational effect
Authors: Ren Haijun , Cao Jintao , Wu Zhengwei , Chu Paul K.
Published: October 2011

The linear stability of a differential rotating magnetized plasma is analyzed in the collisionless approximation along with heat flux vector. The dispersion relation is derived and simplified cases are discussed with instability criteria presented. Anisotropic pressures are shown to not only alter the classical instability criterion but also induce new unstable regions. The shear rotating instability in a collisional magnetized plasma with a scalar kinetic pressure in the presence of self-gravitational effect is then considered. Three cases are discussed specifically according to the general dispersion relation. The effects of Jeans term and compressibility on the local shear instability induced by differential rotation are examined and the analytic instability criteria are presented.
Arbitrary amplitude kinetic Alfvén solitons in a plasma with a q-nonextensive electron velocity distribution
Authors: Liu Y. , Liu S. Q. , Dai B.
Published: October 2011

Arbitrary amplitude solitary kinetic Alfvén waves (KAWs) in a plasma with q–nonextensive electrons are investigated by the conventional Sagdeev pseudopotential method, through which the existence of solitary KAWs is analyzed theoretically and numerically. It is shown only solitons with density hump can exist, the amplitude of which depends sensitively on the parameter q and the plasma β. There is an upper limit for the amplitude of solitary wave which decreases with the increase of q and β. The results obtained in the framework of Maxwellian distribution are reproduced when q → 1.
Comparative studies on charged particle flow in a double plasma device
Authors: Chakraborty M. , Das B. K.
Published: October 2011

An experiment is conducted to study the comparative effect of a transverse magnetic field (TMF) and stainless steel (ss) plates in a filament discharge in a double plasma device (DPD). A variable transverse magnetic field is setup between the source and the target regions of the DPD using permanent magnets. By changing the distance between magnetic pole separations, the magnetic field is varied in the range of 80 Gauss to 300 Gauss. Plasma diffuses from the source to the target region through this field. Changing the discharge voltage and the discharge current varies the discharge conditions. Langmuir probes are placed in the source and target regions to measure the plasma parameters. Ss plates of similar surface area then replace the TMF and these data are compared with the TMF data to show the effect of the TMF on plasma parameters in comparison to the ss plates. It is seen that the magnetic field causes the plasma parameters to vary in a consistent way when the discharge parameters are varied.
Electron current extraction from a permanent magnet waveguide plasma cathode
Authors: Weatherford B. R. , Foster J. E. , Kamhawi H.
Published: October 2011

An electron cyclotron resonance plasma produced in a cylindrical waveguide with external permanent magnets was investigated as a possible plasma cathode electron source. The configuration is desirable in that it eliminates the need for a physical antenna inserted into the plasma, the erosion of which limits operating lifetime. Plasma bulk density was found to be overdense in the source. Extraction currents over 4 A were achieved with the device. Measurements of extracted electron currents were similar to calculated currents, which were estimated using Langmuir probe measurements at the plasma cathode orifice and along the length of the external plume. The influence of facility effects and trace ionization in the anode-cathode gap are also discussed.
Microstructural comparison of silicon solar cells’ front-side Ag contact and the evolution of current conduction mechanisms
Authors: Li Z. G. , Liang L. , Ionkin A. S. , Fish B. M. , Lewittes M. E. , Cheng L. K. , Mikeska K. R.
Published: October 2011

Microstructures of front-side Ag contact of crystalline Si solar cells fired at temperatures from below to above optimal were systematically investigated using advanced electron microscopy. Ag pastes studied included commercial pastes and an experimental paste containing nano-sized metallic Zn additive. Microstructures of optimally fired cells determined from cross-sectional and top-view images were found to be consistent with a primary tunneling mechanism for current flow (a “nano-Ag colloids assisted tunneling” model) due to the lack of Ag crystallites connecting the silver conductor line to the silicon emitter. We mapped the evolution of the interfacial microstructures across the firing temperature window and correlated it with cell performance. Our result sheds light on the relative importance of the two current transport models as the peak firing temperature was swept from below to above optimal.
Liquid crystal bubbles forming a tunable micro-lenses array
Authors: Hamdi R. , Petriashvili G. , Lombardo G. , De Santo M. P. , Barberi R.
Published: October 2011

Cholesteric liquid crystals with long pitch confined in homeotropic cells can be used to generate stable but distorted and localized liquid crystal structures exhibiting spherulitic textures, known as “bubbles.” As these bubbles can be induced by an external electric field with a narrow range following the confinement ratio C=d/p ≈1 (d representing cell thickness and p representing cholesteric pitch), it is possible to obtain electrically controlled micro-lenses. Here we investigated the optical and electro-optical properties of such liquid crystal bubbles for creating an array of micro-lenses with electrically tunable focal length.
Raman spectra and dielectric function of BiCrO3: Experimental and first-principles studies
Authors: Himcinschi Cameliu , Vrejoiu Ionela , Weißbach Torsten , Vijayanandhini Kannan , Talkenberger Andreas , Röder Christian , Bahmann Silvia , Zahn Dietrich R. T. , Belik Alexei A. , Rafaja David , Kortus Jens
Published: October 2011

We present the complex dielectric function of BiCrO3 thin films in the energy range of 0.73–9.8 eV determined using spectroscopic ellipsometry. By analyzing the absorption onset region, it is shown that the optical bandgap of BiCrO3 is indirect, with a value of 2.27 eV. The imaginary part of the BiCrO3 dielectric function, ɛ2, calculated using density functional theory in the generalized gradient approximation with an Hubbard potential of 3 eV agrees well with the experimentally determined one. Raman spectra of both polycrystalline and epitaxial thin films of BiCrO3 are reported. The temperature dependent Raman measurements indicate a structural phase transition at ∼400 K which was confirmed also by x-ray diffraction investigations.
Plastic flow in shock-loaded silver at strain rates from 104 s−1 to 107 s−1 and temperatures from 296 K to 1233 K
Authors: Zaretsky E. B. , Kanel G. I.
Published: October 2011

The evolution of elastic-plastic shock waves in 99.9% purity silver samples of 0.127 to 2.0 mm thickness has been studied in a series of VISAR-instrumented planar impact experiments with initial sample temperature varied from 296 to 1233 K. The decay of elastic precursor wave at 933, 1173, and 1233 K temperatures is approximately inversely proportional to the square root of the propagation distance. The latter corresponds to the cubic dependence of initial plastic strain rate, ranged from 104 s−1 to 106 s−1, on the shear stress. At fixed strain rates, the flow stress grows linearly with the temperature but the dependence becomes stronger near the silver melting point, 1234 K. An analysis of the rise times of the plastic shock waves shows that for the same level of shear stress the plastic strain rate at the shock front is significantly higher than that at the top of the elastic precursor wave.
Transmission of terahertz wave through one-dimensional photonic crystals containing single and multiple metallic defects
Authors: Liu Hai-Ying , Liang Sen , Dai Qiao-Feng , Wu Li-Jun , Lan Sheng , Venu Gopal Achanta , Trofimov Vyacheslav A. , Lysak Tatiana M.
Published: October 2011

We investigated numerically and experimentally the transmission of terahertz (THz) waves through single and multiple metallic defects created in a one-dimensional (1D) photonic crystal (PC) by inserting single metallic wires or arrays of parallel metallic wires into the air-gap defect of the 1D PC. The transmission properties of the metallic defect modes generated in the photonic bandgap (PBG) were characterized by using THz time-domain spectroscopy. For single metallic defects, it was found that the appearance the defect mode depends not only on the diameter of the metallic wires but also on the polarization of the THz wave. For transverse magnetic (TM) polarized waves whose electric fields are parallel to the metallic wires, the incident THz wave is generally split into two identical parts. In sharp contrast, the excitation of surface plasmon polaritons (SPPs) with enhanced field intensity is observed for transverse electric (TE) polarized waves whose electric fields are perpendicular to the metallic wires. In both cases, two resonant modes with reduced transmittance are observed in the PBG. While the resonant mode related to SPPs is found at the long-wavelength side of the original defect mode, the resonant mode without the excitation of SPPs appears at the short-wavelength side. Numerical simulation based on the finite-difference time-domain (FDTD) technique revealed that the electric field of SPPs is more tightly confined at the surface of the metallic wire when it is placed in the PC, implying that the confinement of a THz wave in the propagation direction will facilitate the localization of SPPs in the transverse direction. For two parallel metallic wires, the defect mode was found to depend on the separation between them. If they are widely separated, then the excitation of SPPs is similar to that observed in single metallic wires. However, the excitation of dipole-like SPPs does not occur for two closely packed metallic wires because of their large lateral size. It was also revealed that two parallel metallic wires with a small diameter and a narrow separation could be employed to achieve a significant enhancement, as large as 21.6, for the electric field in between them. More interestingly, the enhancement factor becomes larger when the confinement of the electric field in the propagation direction is increased. For an array of four widely separated wires whose lateral dimension is wider than the diameter of the THz beam, only one resonant mode is observed at the long-wavelength side of the original defect mode. The experimental observations are in good agreement with the simulation results based on the FDTD technique. The enhanced concentration of the electric field of SPPs at the surfaces of metallic defects may be useful for focusing and sensing of THz waves.
Self-heating and athermal effects on the electroluminescence spectral modulation of an AlGaInP light-emitting diode
Authors: Vaitonis Z. , Vitta P. , Jakštas V. , Žukauskas A.
Published: October 2011

We report on the investigation of electroluminescence (EL) modulation depth as a function of photon energy in a high-power double-heterojunction AlGaInP light-emitting diode (LED). At low frequencies, the modulation spectrum exhibits the features as follows: (i) a dip at the photon energy close to the EL spectrum peak; (ii) an almost wavelength-independent modulation enhancement in the long-wavelength wing of the EL spectrum; and (iii) a linear increase of the modulation depth with photon energy in the short-wavelength wing of the EL spectrum. With increasing modulation frequency, these features diminish but do not disappear. A model, which quantitatively accounts for the experimental data has been introduced. At low frequencies, the spectral modulation features are due mainly to the modulation of EL efficiency, bandgap energy and the carrier distribution function caused by the oscillation of junction temperature. In the high-frequency limit when the oscillation of junction temperature fades, the spectral modulation features can be understood in terms of asymmetrical EL band broadening due to athermal many-body effects. The investigation of spectrally resolved EL modulation was shown to be applicable for the estimation of small (∼0.1 K) junction temperature oscillation and thermal relaxation time constants of LEDs emitting due to band-to-band recombination of free carriers.
Growth of single-crystalline cobalt silicide nanowires with excellent physical properties
Authors: Liang Yu-Hsin , Yu Shih-Ying , Hsin Cheng-Lun , Huang Chun-Wei , Wu Wen-Wei
Published: October 2011

With the miniaturization of electron devices, the minuscule structures are important to state-of-the-art science and technology. Therefore, the growth methods and properties of nanomaterials have been extensively studied recently. Here, we use chemical vapor transport (CVT) methods to synthesize single-crystalline cobalt silicide nanowires (NWs) by using (CoCl2·6 H2O) as a single-source precursor. By changing reaction temperature and ambient pressure, we can obtain different morphology of cobalt silicide NWs under the appropriate concentration of silicon and cobalt. The field emission measurement of CoSi NWs shows low turn-on field (5.02 V/μm) and it is outstanding for magnetic properties that differ from the bulk CoSi. The CoSi nanowires with different diameters have diverse magnetic saturation (Ms) and coercive force (Hc).
Challenges for complexity measures: A perspective from social dynamics and collective social computation
Authors: Flack Jessica C. , Krakauer David C.
Published: October 2011

We review an empirically grounded approach to studying the emergence of collective properties from individual interactions in social dynamics. When individual decision-making rules, strategies, can be extracted from the time-series data, these can be used to construct adaptive social circuits. Social circuits provide a compact description of collective effects by mapping rules at the individual level to statistical properties of aggregates. This defines a simple form of social computation. We consider the properties that complexity measures would need to have to best capture regularities at different level of analysis, from individual rules to circuits to population statistics. One obvious benefit of using the properties and structure of biological and social systems to guide the development of complexity measures is that it is more likely to produce measures that can be applied to data. Principled but pragmatic measures would allow for a rigorous investigation of the relationship between adaptive features at the micro, meso, and macro scales, a long standing goal of evolutionary theory. A second benefit is that empirically grounded complexity measures would facilitate quantitative comparisons of strategies, circuits, and aggregate properties across social systems.
Introduction to Focus Issue on “Randomness, Structure, and Causality: Measures of Complexity from Theory to Applications”
Authors: Crutchfield James P. , Machta Jon
Published: October 2011

We introduce the contributions to this Focus Issue and describe their origin in a recent Santa Fe Institute workshop.
Dynamics of glass-forming liquids. XV. Dynamical features of molecular liquids that form ultra-stable glasses by vapor deposition
Authors: Chen Zhen , Richert Ranko
Published: October 2011

The dielectric relaxation behavior of ethylbenzene (EBZ) in its viscous regime is measured, and the glass transition temperature (Tg = 116 K) as well as fragility (m = 98) are determined. While the Tg of EBZ from this work is consistent with earlier results, the fragility is found much higher than what has been assumed previously. Literature data is supplemented by the present results on EBZ to compile the dynamic behavior of those glass formers that are known to form ultra-stable glasses by vapor deposition. These dynamics are contrasted with those of ethylcyclohexane, a glass former for which a comparable vapor deposition failed to produce an equally stable glassy state. In a graph that linearizes Vogel-Fulcher-Tammann behavior, i.e., the derivative of −logτ with respect to T/Tg raised to the power of −1/2 versus T/Tg, all ultra-stable glass formers fall onto one master curve in a wide temperature range, while ethylcyclohexane deviates for T ≫ Tg. This result suggests that ultra-stable glass formers share common behavior regarding the dynamics of their supercooled liquid state if scaled to their respective Tg values, and that fragility and related features are linked to the ability to form ultra-stable materials.
The trans-HOCO radical: Quartic force fields, vibrational frequencies, and spectroscopic constants
Authors: Fortenberry Ryan C. , Huang Xinchuan , Francisco Joseph S. , Crawford T. Daniel , Lee Timothy J.
Published: October 2011

In the search for a full mechanism creating CO2 from OH + CO, it has been suggested that creation of the hydroxyformyl or HOCO radical may be a necessary step. This reaction and its transient intermediate may also be responsible for the regeneration of CO2 in such high quantities in the atmosphere of Mars. Past spectroscopic observations of this radical have been limited and a full gas phase set of the fundamental vibrational frequencies of the HOCO radical has not been reported. Using established, highly accurate quantum chemical coupled cluster techniques and quartic force fields, we are able to compute all six fundamental vibrational frequencies and other spectroscopic constants for trans-HOCO in the gas phase. These methods have yielded rotational constants that are within 0.01 cm−1 for A0 and 10−4 cm−1 for B0 and C0 compared with experiment as well as fundamental vibrational frequencies within 4 cm−1 of the known gas phase experimental ν1 and ν2 modes. Such results lead us to conclude that our prediction of the other four fundamental modes of trans-HOCO are also quite reliable for comparison to future experimental observation, though the discrepancy for the torsional mode may be larger since it is fairly anharmonic. With the upcoming European Space Agency/NASA ExoMars Trace Gas Orbiter, these data may help to establish whether HOCO is present in the Martian sky and what role it may play in the retention of a CO2-rich atmosphere. Furthermore, these data may also help to clear up questions built around the fundamental chemical process of how exactly the OH + CO reaction progresses.
Van der Waals interactions: Evaluations by use of a statistical mechanical method
Authors: Høye Johan S.
Published: October 2011

In this work the induced van der Waals interaction between a pair of neutral atoms or molecules is considered by use of a statistical mechanical method. With use of the Schrödinger equation this interaction can be obtained by standard quantum mechanical perturbation theory to second order. However, the latter is restricted to electrostatic interactions between dipole moments. So with radiating dipole-dipole interaction where retardation effects are important for large separations of the particles, other methods are needed, and the resulting induced interaction is the Casimir-Polder interaction usually obtained by field theory. It can also be evaluated, however, by a statistical mechanical method that utilizes the path integral representation. We here show explicitly by use of this method the equivalence of the Casimir-Polder interaction and the van der Waals interaction based upon the Schrödinger equation. The equivalence is to leading order for short separations where retardation effects can be neglected. In recent works [J. S. Høye, Physica A 389, 1380 (2010)10.1016/j.physa.2009.12.003; Phys. Rev. E 81, 061114 (2010)]10.1103/PhysRevE.81.061114, the Casimir-Polder or Casimir energy was added as a correction to calculations of systems like the electron clouds of molecules. The equivalence to van der Waals interactions indicates that the added Casimir energy will improve the accuracy of calculated molecular energies. Thus, we give numerical estimates of this energy including analysis and estimates for the uniform electron gas.
Field programmable gate array based reconfigurable scanning probe/optical microscope
Authors: Nowak Derek B. , Lawrence A. J. , Dzegede Zechariah K. , Hiester Justin C. , Kim Cliff , Sánchez Erik J.
Published: October 2011

The increasing popularity of nanometrology and nanospectroscopy has pushed researchers to develop complex new analytical systems. This paper describes the development of a platform on which to build a microscopy tool that will allow for flexibility of customization to suit research needs. The novelty of the described system lies in its versatility of capabilities. So far, one version of this microscope has allowed for successful near-field and far-field fluorescence imaging with single molecule detection sensitivity. This system is easily adapted for reflection, polarization (Kerr magneto-optical (MO)), Raman, super-resolution techniques, and other novel scanning probe imaging and spectroscopic designs. While collecting a variety of forms of optical images, the system can simultaneously monitor topographic information of a sample with an integrated tuning fork based shear force system. The instrument has the ability to image at room temperature and atmospheric pressure or under liquid. The core of the design is a field programmable gate array (FPGA) data acquisition card and a single, low cost computer to control the microscope with analog control circuitry using off-the-shelf available components. A detailed description of electronics, mechanical requirements, and software algorithms as well as examples of some different forms of the microscope developed so far are discussed.
Thin film CdTe solar cells with an absorber layer thickness in micro- and sub-micrometer scale
Authors: Bai Zhizhong , Yang Jun , Wang Deliang
Published: October 2011

CdTe thin film solar cell with an absorber layer as thin as 0.5 μm was fabricated. An efficiency of 7.9% was obtained for a 1-μm-thick CdTe solar cell. An increased intensity of deep recombination states in the band gap, which was responsible for the reduced open-circuit voltage and fill factor for ultra-thin solar cells, was induced due to the not-well-developed polycrystalline CdTe microstructure and the CdS/CdTe heterojunction and the presence of Cu in the back contact. The experimental results presented in this study demonstrated that 1-μm-thick absorber layer is thick enough to fabricate CdTe solar cell with a decent efficiency.
Density functional theory calculations of dynamic first hyperpolarizabilities for organic molecules in organic solvent: Comparison to experiment
Authors: Lu Shih-I , Chiu Cheng-Chang , Wang Ying-Fung
Published: October 2011

Against experimental values obtained from solution-phase dc electric field induced second-harmonic generation measurements at a fundamental wavelength of 1910 nm, the performance of 20 exchange-correlation functionals in density functional theory in evaluation of solvent modulated dynamic first hyperpolarizabilities of 82 organic molecules in chloroform, 1,4-dioxane, and/or dichloromethane was evaluated. The used exchange-correlation functionals consisted of generalized gradient approximation (GGA), meta-GGA, global hybrids, and range-separated hybrids. The PCM-X/6-311+G(2d,p)//PCM-B3LYP/6-31G(2df,p) level of theory was employed. The calculated results showed functionals with the exact asymptote of the exchange potential gave satisfying linear correlation with R2 of 0.95 between experimental data and theoretical values. With a linear correction, these functionals also provided a better accuracy with mean absolute error of 5 × 10−30 esu than other functionals. The solvent effect and solvation scheme on the calculated property were also studied.
Dual-lag synchronization between coupled chaotic lasers due to path-delay interference
Authors: Tiana-Alsina J. , Garcia-Lopez J. H. , Torrent M. C. , Garcia-Ojalvo J.
Published: October 2011

We study experimentally the synchronization dynamics of two semiconductor lasers coupled unidirectionally via two different delayed paths. The emitter laser operates in a chaotic regime characterized by low-frequency fluctuations due to optical feedback and induces a synchronized dynamical activity in the receiver laser, which operates in the continuous-wave regime when uncoupled. Different delays in the two coupling paths lead to the coexistence of two time lags in the synchronized dynamics of the oscillators. This dual-lag synchronization degrades the average synchronization quality of the system of coupled lasers and hinders the transmission of information between them. Numerical simulation results agree with the experimental observations, and allow us to explore this phenomenon in a wide parameter range, and quantify the degree of signal transmission degradation caused by this chaotic path-delay interference.
Monte Carlo simulation of osmotic equilibria
Authors: Schreiber Sebastian , Hentschke Reinhard
Published: October 2011

We present a Metropolis Monte Carlo simulation algorithm for the Tpπ-ensemble, where T is the temperature, p is the overall external pressure, and π is the osmotic pressure across the membrane. The algorithm, which can be applied to small molecules or sorption of small molecules in polymer networks, is tested for the case of Lennard-Jones interactions.
Ion-specific colloidal aggregation: Population balance equations and potential of mean force
Authors: Odriozola Gerardo
Published: October 2011

Recently reported colloidal aggregation data obtained for different monovalent salts (NaCl, NaNO3, and NaSCN) and at high electrolyte concentrations are matched with the stochastic solutions of the master equation to obtain bond average lifetimes and bond formation probabilities. This was done for a cationic and an anionic system of similar particle size and absolute charge. Following the series Cl−, \documentclass[12pt]{minimal}\begin{document}${\rm NO}_3^-$\end{document} NO 3−, SCN−, the parameters obtained from the fitting procedure to the kinetic data suggest: (i) The existence of a potential of mean force (PMF) barrier and an increasing trend for it for both lattices. (ii) An increasing trend for the PMF at contact, for the cationic system, and a practically constant value for the anionic system. (iii) A decreasing trend for the depth of the secondary minimum. This complex behavior is in general supported by Monte Carlo simulations, which are implemented to obtain the PMF of a pair of colloidal particles immersed in the corresponding electrolyte solution. All these findings contrast the Derjaguin, Landau, Verwey, and Overbeek theory predictions.
The destabilization of an initially thick liquid sheet edge
Authors: Lhuissier Henri , Villermaux Emmanuel
Published: October 2011

By forcing the sudden dewetting of a free soap film attached on one edge to a straight solid wire, we study the recession and subsequent destabilization of its free edge. The newly formed rim bordering the sheet is initially thicker than the film to which it is attached, because of the Plateau border preexisting on the wire. The initial condition is thus that of an immobile massive toroidal rim connected to a thin liquid film of thickness h. The terminal Taylor-Culick receding velocity V=2σ/ρh, where σ and ρ are the liquid surface tension and density, respectively, is only reached after a transient acceleration period which promotes the rim destabilization. The selected wavelength and associated growth time coincide with those of an inertial instability driven by surface tension.
Spectroscopy of lithium atoms sublimated from isolation matrix of solid Ne
Authors: Sacramento R. L. , Scudeller L. A. , Lambo R. , Crivelli P. , Cesar C. L.
Published: October 2011

We have studied, via laser absorption spectroscopy, the velocity distribution of 7Li atoms released from a solid neon matrix at cryogenic temperatures. The Li atoms are implanted into the Ne matrix by laser ablation of a solid Li precursor. A heat pulse is then applied to the sapphire substrate sublimating the matrix together with the isolated atoms at around 12 K. We find interesting differences in the velocity distribution of the released Li atoms from the model developed for our previous experiment with Cr [R. Lambo, C. C. Rodegheri, D. M. Silveira, and C. L. Cesar, Phys. Rev. A 76, 061401–R (2007)]10.1103/PhysRevA.76.061401. This may be due to the sublimation regime, which is at much lower flux for the Li experiment than for the Cr experiment, as well as to the different collisional cross sections between those species to the Ne gas. We find a drift velocity compatible with Li being thermally sublimated at 11–13 K, while the velocity dispersion around this drift velocity is low, around 5–7 K. With a slow sublimation of the matrix we can determine the penetration depth of the laser ablated Li atoms into the Ne matrix, an important information that is not usually available in most matrix isolation spectroscopy setups. The present results with Li, together with the previous results with Cr suggest this to be a general technique for obtaining cryogenic atoms, for spectroscopic studies, as well as for trap loading. The release of the isolated atoms is also a useful tool to study and confirm details of the matrix isolated atoms which are masked or poorly understood in the solid.
Compliant substrate versus plastic relaxation effects in Ge nanoheteroepitaxy on free-standing Si(001) nanopillars
Authors: Kozlowski G. , Zaumseil P. , Schubert M. A. , Yamamoto Y. , Bauer J. , Matejova J. , Schulli T. , Tillack B. , Schroeder T.
Published: October 2011

We report on the structural characterization of Ge clusters selectively grown by chemical vapor deposition on free-standing 50 nm wide Si(001) nanopillars. Synchrotron based x-ray diffraction studies and transmission electron microscopy were performed to experimentally verify the nanoheteroepitaxy theory as a technique to grow high quality Ge on Si(001). Although the structure dimensions are comparable to the theoretical values required for the strain partitioning phenomenon, the compliant character of Si is not unambiguously proven. In consequence, the strain is relieved by nucleation of misfit dislocations at the Ge/Si interface. By gliding out of threading arms, high quality Ge nanostructures are achieved.
Stress migration model for Cu interconnect reliability analysis
Authors: Walter Yao H. , Yiang Kok-Yong , Justison Patrick , Rayasam Mahidhar , Aubel Oliver , Poppe Jens
Published: October 2011

Stress migration (SM) reliability data have been treated qualitatively to define pass or fail criteria in the past. However, realistic quantitative SM analysis and lifetime estimates for products were not available due to lack of a suitable SM model. In this paper, we establish a comprehensive SM model for quantitative stress-induced-voiding (SIV) risk analysis for 32 nm technology and beyond. It was found that the SIV risk is dependent on both stress temperatures and geometric structural line widths as driving forces. Based on the new SM model, the SM lifetime can be estimated from measurable SM data and accelerated SM test methods can be designed to meet the qualification criteria.
Buckling of poly(methyl methacrylate) in stimulus-responsive shape recovery
Authors: Zhao Yong , Chun Wang Chang , Min Huang Wei , Purnawali Hendra
Published: October 2011

We investigate buckling phenomenon during shape recovery in a poly(methyl methacrylate) upon immersing in ethanol (chemo-responsive) and heating (thermo-responsive). The underlying mechanism is revealed and the influential factors are discussed. Such buckling phenomenon is generic and applicable to all materials during shape recovery when certain conditions (as discussed here) are satisfied.
Enhance performance of organic solar cells based on an isoindigo-based copolymer by balancing absorption and miscibility of electron acceptor
Authors: Ma Zaifei , Wang Ergang , Vandewal Koen , Andersson Mats R , Zhang Fengling
Published: October 2011

Superior absorption of PC71BM in visible region to that of PC61BM makes PC71BM a predominant acceptor for most high efficient polymer solar cells (PSCs). However, we will demonstrate that power conversion efficiencies (PCEs) of PSCs based on poly[N,N′-bis(2-hexyldecyl)isoindigo-6,6′-diyl-alt-thiophene-2,5-diyl] (PTI-1) with PC61BM as acceptor are 50% higher than their PC71BM counterparts under illumination of AM1.5G. AFM images reveal different topographies of the blends between PTI-1:PC61BM and PTI-1:PC71BM, which suggests that acceptor’s miscibility plays a more important role than absorption. The photocurrent of 9.1 mA/cm2 is among the highest value in PSCs with a driving force for exciton dissociation less than 0.2 eV.