bluuebunny/crossref_metadata_2025 huggingface dataset:
Activation‐induced cytidine deaminase auto‐activates and triggers aberrant gene expression
Authors: Isobe Tomoyasu , Song Soken-Nakazawa J. , Tiwari Prabha , Ito Hiroki , Yamaguchi Yuki , Yoshizaki Kazuyuki
Published: June 2013

DNA methylation is a well‐characterized epigenetic landmark involved in transcriptional regulation; however, mechanisms underlying its regulation remain poorly characterized. Recent studies demonstrate that activation‐induced cytidine deaminase (AID) is involved in active DNA demethylation. AID is aberrantly expressed in inflammation‐associated cancers and generates point mutations; however, cellular disorders attributed to its demethylation function are largely unexplored. Here we demonstrate that ectopic AID expression perturbs tumor‐related gene expression. AID (with Gadd45) activated a methylated paired box gene 5 (Pax5) reporter construct, and induced expression and association of endogenous Pax5 with the AID promoter, suggesting that aberrant AID expression triggers an auto‐activation circuit to consolidate self‐expression.
Physician and patient use of and attitudes toward complementary and alternative medicine in the treatment of infertility
Authors: Clark Natalie A. , Will Matthew A. , Moravek Molly B. , Xu Xiao , Fisseha Senait
Published: June 2013

Objective

To determine use of and attitudes toward complementary and alternative medicine (CAM) among infertility patients and subspecialty physicians.

Methods

Infertility patients were asked to complete anonymous written surveys at an academic infertility practice; members of the Society for Reproductive Endocrinology and Infertility were electronically surveyed. Both groups were assessed regarding their use of and attitudes toward CAM.

Results

The response rate was 32.1% (115/358) among patients and 22.6% (225/995) among physicians (P < 0.05). In total, 105 (91.3%; 95% confidence interval [CI], 85.8–96.2) patients used CAM, and 84 (73.0%; 95% CI, 64.9–81.1) regarded it as beneficial to their fertility treatment. However, only 30 (26.1%; 95% CI, 18.0–34.0) patients reported CAM use to physicians, with the most common reason being that they were “never asked.” Overall, 202 (89.8%; 95% CI, 85.9–93.8) physicians reported inquiring about CAM.

Conclusion

Significant discrepancies exist between subfertile patients and physicians in attitudes toward the use of CAM. The current prevalence of CAM use among infertility patients requires greater physician attention and justifies further study on the risks and benefits of integrating CAM into the biomedical treatment of infertility.
Strengthening the organizational capacity of health professional associations: The FIGO LOGIC Toolkit
Authors: Andrews Helena , Perron Liette , Vander Plaetse Bart , Taylor David J.
Published: June 2013

Health professional associations, including national associations of obstetrics and gynecology, can have a leading role in influencing and developing health policy and practice. However, in low‐ and middle‐resource countries, the organizational capacity to facilitate this role is often insufficient. The International Federation of Gynecology and Obstetrics LOGIC (Leadership in Obstetrics and Gynaecology for Impact and Change) Initiative has been developing the capacity of national associations in Africa and Asia. Through this work, an electronic resource of materials (http://figo‐toolkit.org/) has been brought together to support organizational capacity development, addressing domains such as culture, strategic planning, human resources, project and financial management, performance, external relations, membership services, and the development and revision of clinical guidelines.
Wilderness Medical Society Practice Guidelines for Spine Immobilization in the Austere Environment
Authors: Quinn Robert , Williams Jason , Bennett Brad , Stiller Gregory , Islas Arthur , McCord Seth
Published: July 2013

In an effort to produce best-practice guidelines for spine immobilization in the austere environment, the Wilderness Medical Society convened an expert panel charged with the development of evidence-based guidelines for management of the injured or potentially injured spine in an austere (dangerous or compromised) environment. Recommendations are made regarding several factors related to spinal immobilization. These recommendations are graded based on the quality of supporting evidence and balance between the benefits and risks or burdens for each factor according to the methodology stipulated by the American College of Chest Physicians. A treatment algorithm based on the guidelines is presented.
Secondary instability of the stably stratified Ekman layer
Authors: Mkhinini Nadia , Dubos Thomas , Drobinski Philippe
Published: July 2013

The Ekman flow, an exact solution of the Boussinesq equations with rotation, is a prototype flow for both atmospheric and oceanic boundary layers. The effect of stratification on the finite-amplitude longitudinal rolls developing in the Ekman flow and their three-dimensional stability is studied by means of linearized and nonlinear numerical simulations. Similarities and differences with respect to billows developing in the Kelvin–Helmholtz (KH) unidirectional stratified shear flow are discussed. Prandtl number effects are investigated as well as the role played by the buoyant-convective instability. For low Prandtl number, the amplitude of the saturated rolls vanishes at the critical bulk Richardson number, while at high Prandtl number, finite-amplitude rolls are found. The Prandtl number also affects how the growth rate of the secondary instability evolves as the Richardson number is increased. For low Prandtl number, the growth rate decreases as the Richardson number increases while it remains significant for large Prandtl number over the range of stratification studied. This behaviour is likely a result of the differing amplitudes of the roll vortices. Furthermore, the most unstable wave vector is much lower than for the secondary instability of KH billows. Examination of the energetics of the secondary instability shows that buoyant-convective instability is present locally at high Reynolds and Prandtl numbers but plays an overall minor role despite the presence in the base flow of statically unstable regions characterized by a high Richardson number.
Landscape and patch attributes impacting medium- and large-sized terrestrial mammals in a fragmented rain forest
Authors: Garmendia Adriana , Arroyo-Rodríguez Víctor , Estrada Alejandro , Naranjo Eduardo J. , Stoner Kathryn E.
Published: July 2013

Understanding the response of biodiversity to land-use changes is an important challenge for ecologists. We assessed the effects of five landscape metrics (forest cover, number of patches, edge density, mean inter-patch isolation distance and matrix quality) and three patch metrics (patch size, shape and isolation) on the number of species and patch occupancy of medium- and large-sized terrestrial mammals in the fragmented Lacandona rain forest, Mexico. We sampled mammal assemblages in 24 forest patches and four control areas within a continuous forest. The landscape metrics were measured within a 100-ha buffer, and within a 500-ha buffer from the centre of each sampling site. A total of 21 species from 13 families was recorded. The number of species increased with shape complexity and patch size at the patch scale, and with matrix quality within 100-ha landscapes. When considering 500-ha landscapes, only the number of patches (i.e. forest fragmentation level) tended to have a negative influence at the community level. Different landscape and patch metrics predicted the occurrence of each species within the sites. Our results indicate that there is a gradient of tolerance to forest cover change, from highly sensitive species to those tolerant of, or even benefited by, forest-cover change.
Introduction: Reconsidering Recycling
Authors: OLDENZIEL RUTH , WEBER HEIKE
Published: July 2013

When citizens recycle waste, we consider this an act of responsible ‘green’ citizenship. Today's consumers query the environmental impact of their consumption. Shoppers wonder whether the goods they buy are properly recyclable; others translate their concerns for the environment into a daily practice of separating, storing, collecting and transporting reusable waste. Most European consumer-citizens have incorporated recycling into their daily routine. Today, modern recycling is usually seen as a product of the 1970s, when grass-root movements and environmental policies generated new consumer practices. The assumption is that recycling only gained widespread public support from industry, politics and consumers a few decades ago.
Norepinephrine transporter occupancy in the human brain after oral administration of quetiapine XR
Authors: Nyberg Svante , Jucaite Aurelija , Takano Akihiro , Kågedal Matts , Cselényi Zsolt , Halldin Christer , Farde Lars
Published: July 2013

Quetiapine, originally developed as an antipsychotic, demonstrates efficacy in clinical studies of schizophrenia, bipolar mania and depression, major depressive disorder and generalized anxiety disorder. This broad spectrum of efficacy was not predicted from the preclinical pharmacology of quetiapine. Binding studies in vitro show that quetiapine and its major active human metabolite, norquetiapine, have moderate to high affinity for dopamine D2 and serotonin 5-HT2A receptors, while norquetiapine alone has high affinity for the norepinephrine transporter (NET). This positron emission tomography (PET) study measured NET occupancy in human subjects treated with extended-release quetiapine (quetiapine XR) at doses relevant in the treatment of depression. PET measurements using the specific NET radioligand (S,S)-[18F]FMeNER-D2 were performed before and after quetiapine XR treatment at 150 and 300 mg/d for 6–8 d in nine healthy males (aged 21–33 yr). Regions of interest were defined for the thalamus, using the caudate as reference region. NET occupancy was calculated using a target:reference region ratio method. Plasma concentrations of quetiapine and norquetiapine were monitored during PET measurements. Following quetiapine XR treatment, the mean NET occupancy in the thalamus was 19 and 35%, respectively, at quetiapine XR doses of 150 and 300 mg/d. The estimated plasma concentration of norquetiapine corresponding to 50% NET occupancy was 161 ng/ml. This is the first demonstration of NET occupancy by an antipsychotic in the human brain. NET inhibition is accepted as a mechanism of antidepressant activity. NET occupancy may therefore contribute to the broad spectrum of efficacy of quetiapine.
LP+, K3+, FDE+, AND THEIR ‘CLASSICAL COLLAPSE’
Authors: BEALL JC
Published: July 2013

This paper is a sequel to Beall (2011), in which I both give and discuss the philosophical import of a ‘classical collapse’ result for the propositional (multiple-conclusion) logic LP+. Feedback on such ideas prompted a spelling out of the first-order case. My aim in this paper is to do just that: namely, explicitly record the first-order result(s), including the collapse results for K3+and FDE+.
Coordinating concurrent legal orders in the prosecution of international crimes
Authors: BONAFÉ BEATRICE I.
Published: July 2013

International criminal law provides a particularly interesting case study for the proliferation of legal orders as it helps to understand the types of uncertainties their interaction may entail with respect to the position of the individual as well as the solutions that may be adopted in that respect. This article analyses a selected number of substantive and procedural uncertainties that originate in the relationship between international criminal law and domestic legal orders. The purpose of the discussion is to identify the particular legal devices that have been elaborated in order to ensure the coordination between these legal orders, and to suggest areas in which a better coordination is still to be achieved.
Synthesis of MOFs
Authors: Stock Norbert , Reinsch Helge , Schilling Lars‐Hendrik
Published: July 2013

A summary of important – theoretical and practical – aspects, approaches and methods is presented, which are utilized in the synthesis of MOFs. Throughout the text the needs of scientists mainly working in the field of catalysis is addressed. Thus in the first half of the chapter, general principles and methods for crystallisation are briefly summarized, followed by detailed descriptions of the important concepts of isoreticular chemistry and high‐throughput methods. Moreover some examples are given for the use of precursors and templates. Topological rules that may affect the final MOF‐structure can also be utilised for the intentional synthesis of MOFs. The second half of the chapter will cover aspects that are more strongly correlated to materials chemistry – the shaping of crystals as well as the introduction of hierarchical mesopores into the particles and the anchoring of MOFs to surfaces. Finally, some important comments on the activation procedures are given, which determine the maximum porosity of a material and thus its catalytic activity. Thus, the text intends to give an insight into the diverse and sometimes complex field of the synthesis of MOFs.
Characterization of MOFs. 1. Combined Vibrational and Electronic Spectroscopies
Authors: Bonino Francesca , Lamberti Carlo , Chavan Sachin , Vitillo Jenny G. , Bordiga* Silvia
Published: July 2013

This chapter provides an organic description of the basic theoretical background needed to understand the physical phenomena that are behind vibrational and electronic excitation of materials. Selected examples are then provided to underline the relevance of such spectroscopies in understanding porous MOF materials. As IR and UV‐Vis are the most widespread instruments for vibrational and electronic spectroscopies, respectively, most of the examples refer to these two techniques. Other laboratory techniques such as Raman, resonant Raman and XPS are also considered. Synchrotron radiation based techniques, such as X‐ray absorption (only XANES region) and X‐ray emission (XES and resonant‐XES) spectroscopies are reported as excellent techniques for investigating the occupied and non‐occupied electronic states, respectively. Inelastic neutron scattering (INS) is described as an ideal technique to characterize H2 sitting inside MOF cavities. The chapter is organized in sub‐sections that describe how the abovementioned techniques, performed in controlled atmosphere, can be applied to follow: (i) solvent removal; (ii) presence of local defects; (iii) adsorption properties towards probe molecules; (iv) reactivity in respect to simple species. The role of computational techniques in both rational design of new materials and interpretation of experimental results is testified by some relevant examples. The ensemble of the examples hopes for a wider use of porous MOFs in catalysis.
Asymmetric Catalysis with Chiral Metal Organic Frameworks
Authors: Falkowski Joseph M. , Liu Sophie , Lin* Wenbin
Published: July 2013

Metal organic frameworks (MOFs) have been demonstrated in the last decade to be competent catalysts for asymmetric transformations. In a few years, asymmetric catalysts based on MOFs have rapidly evolved from simple Lewis acid catalysts to complex and robust systems that exhibit enhanced activity, unique selectivity, enzyme‐like behavior, and a high degree of recyclability. This chapter provides a view of the current state of the art in asymmetric catalysis by MOFs.
Expanding the prion concept to cancer biology: dominant-negative effect of aggregates of mutant p53 tumour suppressor
Authors: Silva Jerson L. , Rangel Luciana P. , Costa Danielly C. F. , Cordeiro Yraima , De Moura Gallo Claudia V.
Published: July 2013

p53 is a key protein that participates in cell-cycle control, and its malfunction can lead to cancer. This tumour suppressor protein has three main domains; the N-terminal transactivation domain, the CTD (C-terminal domain) and the core domain (p53C) that constitutes the sequence-specific DBD (DNA-binding region). Most p53 mutations related to cancer development are found in the DBD. Aggregation of p53 into amyloid oligomers and fibrils has been shown. Moreover, amyloid aggregates of both the mutant and WT (wild-type) forms of p53 were detected in tumour tissues. We propose that if p53 aggregation occurred, it would be a crucial aspect of cancer development, as p53 would lose its WT functions in an aggregated state. Mutant p53 can also exert a dominant-negative regulatory effect on WT p53. Herein, we discuss the dominant-negative effect in light of p53 aggregation and the fact that amyloid-like mutant p53 can convert WT p53 into more aggregated species, leading into gain of function in addition to the loss of tumour suppressor function. In summary, the results obtained in the last decade indicate that cancer may have characteristics in common with amyloidogenic and prion diseases.
Velocity profile variations in granular flows with changing boundary conditions: insights from experiments
Authors: Schaefer Marius , Bugnion Louis
Published: June 2013

We present results of detailed velocity profile measurements in a large series of granular flow experiments in a dam-break setup. The inclination angle, bead size, and roughness of the running surface were varied. In all experiments, the downstream velocity profiles changed continuously from the head to the tail of the avalanches. On rough running surfaces, an inflection point developed in the velocity profiles. These velocity profiles cannot be modeled by the large class of constitutive laws which relate the shear stress to a power law of the strain rate. The velocity profile shape factor increased from the head to the tail of the avalanches. Its maximum value grew with increasing roughness of the running surface. We conclude that flow features such as velocity profiles are strongly influenced by the boundary condition at the running surface, which depends on the ratio of bead size to the typical roughness length of the surface. Furthermore, we show that varying velocity profile shape factors inside gravitationally driven finite-mass flows give rise to an additional term in the depth-averaged momentum equation, which is normally solved in the simulation software of hazardous geophysical flows. We therefore encourage time dependent velocity profile measurements inside hazardous geophysical flows, to learn about the importance of this “new” term in the mathematical modeling of these flows.
On the derivation of semiclassical expressions for quantum reaction rate constants in multidimensional systems
Authors: Kryvohuz Maksym
Published: June 2013

Expressions for reaction rate constants in multidimensional chemical systems are derived by applying semiclassical approximation to the quantum path integrals of the ImF formulation of reaction rate theory. First, the transverse degrees of freedom orthogonal to the reaction coordinate are treated within the steepest descent approximation, after which the semiclassical approximation is applied to the remaining reaction coordinate. Thus derived, the semiclassical expressions account for the multidimensional nature of quantum effects and accurately incorporate nuclear quantum effects such as multidimensional tunneling and zero point energies. The obtained expressions are applicable in the broad temperature range from the deep tunneling to high-temperature regimes. The present paper provides derivation of the semiclassical instanton expressions proposed by Kryvohuz [J. Chem. Phys. 134, 114103 (2011)]10.1063/1.3565425.
Nonlinear quantum-dynamical system based on the Kadomtsev-Petviashvili II equation
Authors: Zarmi Yair
Published: June 2013

The structure of soliton solutions of classical integrable nonlinear evolution equations, which can be solved through the Hirota transformation, suggests a new way for the construction of nonlinear quantum-dynamical systems that are based on the classical equations. In the new approach, the classical soliton solution is mapped into an operator, U, which is a nonlinear functional of the particle-number operators over a Fock space of quantum particles. U obeys the evolution equation; the classical soliton solutions are the eigenvalues of U in multi-particle states in the Fock space. The construction easily allows for the incorporation of particle interactions, which generate soliton effects that do not have a classical analog. In this paper, this new approach is applied to the case of the Kadomtsev-Petviashvili II equation. The nonlinear quantum-dynamical system describes a set of M = (2S + 1) particles with intrinsic spin S, which interact in clusters of 1 ≤ N ≤ (M − 1) particles.
Controlling on-surface molecular diffusion behaviors by functionalizing the organic molecules with tert-butyl groups
Authors: Sun Qiang , Zhang Chi , Li Zhiwen , Sheng Kai , Kong Huihui , Wang Likun , Pan Yunxiang , Tan Qinggang , Hu Aiguo , Xu Wei
Published: July 2013

We have performed the systematic studies on three structurally similar aromatic molecules with different functional groups on a Cu(110) surface and investigated their on-surface molecular diffusion behaviors by the interplay of scanning tunneling microscopy imaging and density functional theory calculations. We have found that the tert-butyl groups could significantly affect the molecular adsorption geometries and moreover the mobility of the molecules on the surface. These findings could give further insights into the understanding of diffusion behaviors of organic molecules specifically with tert-butyl groups on surfaces.
photon-plasma: A modern high-order particle-in-cell code
Authors: Haugbølle Troels , Frederiksen Jacob Trier , Nordlund Åke
Published: June 2013

We present the photon-plasma code, a modern high order charge conserving particle-in-cell code for simulating relativistic plasmas. The code is using a high order implicit field solver and a novel high order charge conserving interpolation scheme for particle-to-cell interpolation and charge deposition. It includes powerful diagnostics tools with on-the-fly particle tracking, synthetic spectra integration, 2D volume slicing, and a new method to correctly account for radiative cooling in the simulations. A robust technique for imposing (time-dependent) particle and field fluxes on the boundaries is also presented. Using a hybrid OpenMP and MPI approach, the code scales efficiently from 8 to more than 250.000 cores with almost linear weak scaling on a range of architectures. The code is tested with the classical benchmarks particle heating, cold beam instability, and two-stream instability. We also present particle-in-cell simulations of the Kelvin-Helmholtz instability, and new results on radiative collisionless shocks.
Shock-less interactions of ablation streams in tungsten wire array z-pinches
Authors: Swadling G. F. , Lebedev S. V. , Hall G. N. , Suzuki-Vidal F. , Burdiak G. , Harvey-Thompson A. J. , Bland S. N. , De Grouchy P. , Khoory E. , Pickworth L. , Skidmore J. , Suttle L.
Published: June 2013

Shock-less dynamics were observed during the ablation phase in tungsten wire array experiments carried out on the 1.4 MA, 240 ns MAGPIE generator at Imperial College London. This behaviour contrasts with the shock structures which were seen to dominate in previous experiments on aluminium arrays [Swadling et al., Phys. Plasmas 20, 022705 (2013)]. In this paper, we present experimental results and make comparisons both with calculations of the expected mean free paths for collisions between the ablation streams and with previously published Thomson scattering measurements of the plasma parameters in these arrays [Harvey-Thompson et al., Phys. Plasmas 19, 056303 (2012)].
Generalized hydrogen release-reaction model for the breakdown of modern gate dielectrics
Authors: Wu Ernest Y. , Suñé Jordi
Published: July 2013

In this work, we report an extensive experimental and theoretical investigation of the voltage and temperature dependence of dielectric breakdown for both high-κ/SiO2 dual-layer and SiO2 single-layer dielectrics. Based on a two-step formulation of the breakdown process, a quantitative physics-based hydrogen release-reaction model is proposed. The model is successfully compared to the experimental data over a wide range of voltage, temperature, and thickness and considering both stress polarities. The model resolves three outstanding experimental observations: (1) the decrease of voltage acceleration exponents with increasing temperature, (2) the non-Arrhenius temperature dependence at low voltages, and (3) the large activation energy of ∼1.0 eV observed at high temperatures.
Molecular dynamics simulations for CO2 spectra. IV. Collisional line-mixing in infrared and Raman bands
Authors: Lamouroux J. , Hartmann J.-M. , Tran H. , Lavorel B. , Snels M. , Stefani S. , Piccioni G.
Published: June 2013

Ab initio calculations of the shapes of pure CO2 infrared and Raman bands under (pressure) conditions for which line-mixing effects are important have been performed using requantized classical molecular dynamics simulations. This approach provides the autocorrelation functions of the dipole vector and isotropic polarizability whose Fourier-Laplace transforms yield the corresponding spectra. For that, the classical equations of dynamics are solved for each molecule among several millions treated as linear rigid rotors and interacting through an anisotropic intermolecular potential. Two of the approximations used in the previous studies have been corrected, allowing the consideration of line-mixing effects without use of any adjusted parameters. The comparisons between calculated and experimental spectra under various conditions of pressure and temperature demonstrate the quality of the theoretical model. This opens promising perspectives for first principle ab initio predictions of line-mixing effects in absorption and scattering spectra of various systems involving linear molecules.
Beam splitting target reflector based compensation for angular drift of laser beam in laser autocollimation of measuring small angle deviations
Authors: Zhu Fan , Tan Jiubin , Cui Jiwen
Published: June 2013

Beam splitting target reflector based compensation for the angular drift of laser beam in laser autocollimation is proposed in this article to improve the measurement accuracy and stability of small angle deviations. A beam splitting target reflector is used to replace the plane mirror in laser autocollimation to generate a reference beam when returning the measurement beam. The reference beam and measurement beam have the same angular drift, but have different sensitivities to the rotation angle of the reflector due to the unique characteristics of the reflector. Thus, the angular drift of laser beam in laser autocollimation can be compensated in real time by using the drift of reference beam. Experimental results indicate that an output stability of 0.085 arc sec in 2 h can be achieved after compensation. And a measurement accuracy of ±0.032 arc sec can be obtained over the range of ±1190 arc sec with an effective resolution of 0.006 arc sec. It is confirmed that the compensation method for the angular drift of laser beam is necessary for improving the measurement accuracy and stability in laser autocollimation.
Existence and concentration of semi-classical solutions for a nonlinear Maxwell-Dirac system
Authors: Ding Yanheng , Wei Juncheng , Xu Tian
Published: June 2013

We study semi-classical ground states of nonlinear Maxwell-Dirac system with critical/subcritical nonlinearities: α · (iℏ∇ + q(x)A(x))w − aβw − ωw − q(x)ϕ(x)w = f(x, |w|)w, − Δϕ = q(x)|w|2, and \documentclass[12pt]{minimal}\begin{document}$-\Delta {A_k}=q(x) (\alpha _k w) \cdot \bar{w},\break k=1,2,3,$\end{document}−ΔAk=q(x)(αkw)·w¯,k=1,2,3, where \documentclass[12pt]{minimal}\begin{document}$x\in \mathbb {R}^3$\end{document}x∈R3, A = (A1, A2, A3) is the magnetic field, ϕ is the electron field, and q is the changing point-wise charge distribution. We develop a variational argument to establish the existence of least energy solutions for ℏ small. We also describe the concentration phenomena of the solutions as ℏ → 0.
Vibration potential imaging of spherical objects
Authors: Nguyen Cuong K. , Gusev Vitalyi E. , Diebold Gerald J.
Published: June 2013

The ultrasonic vibration potential, which refers to the generation of voltages on the passage of sound through colloidal or ionic solutions, can be used as a method of imaging, where image contrast is governed by the presence of colloidal or ionic regions within a body. Here we derive an expression for the current in a pair of parallel electrodes placed externally to a spherical, colloidal body irradiated with plane acoustic waves. Experiments are reported showing the ability of the method to determine the radius of the sphere.
Coarse-grained Monte Carlo simulations of non-equilibrium systems
Authors: Liu Xiao , Crocker John C. , Sinno Talid
Published: June 2013

We extend the scope of a recent method for generating coarse-grained lattice Metropolis Monte Carlo simulations [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E 86, 026708 (2012)10.1103/PhysRevE.86.026708; X. Liu, W. D. Seider, and T. Sinno, J. Chem. Phys. 138, 114104 (2013)10.1063/1.4794686] from continuous interaction potentials to non-equilibrium situations. The original method has been shown to satisfy detailed balance at the coarse scale and to provide a good representation of various equilibrium properties in both atomic and molecular systems. However, we show here that the original method is inconsistent with non-equilibrium trajectories generated by full-resolution Monte Carlo simulations, which, under certain conditions, have been shown to correspond to Langevin dynamics. The modified coarse-grained method is generated by simultaneously biasing the forward and backward transition probability for every possible move, thereby preserving the detailed balance of the original method. The resulting coarse-grained Monte Carlo simulations are shown to provide trajectories that are consistent with overdamped Langevin (Smoluchowski) dynamics using a sequence of simple non-equilibrium examples. We first consider the purely diffusional spreading of a Gaussian pulse of ideal-gas particles and then include an external potential to study the influence of drift. Finally, we validate the method using a more general situation in which the particles interact via a Lennard-Jones interparticle potential.
Photoelectron spectroscopy and density functional calculations of AgSin− (n = 3–12) clusters
Authors: Kong Xiang-Yu , Deng Xiao-Jiao , Xu Hong-Guang , Yang Zheng , Xu Xi-Ling , Zheng Wei-Jun
Published: June 2013

We investigated the structural evolution and electronic properties of AgSin− (n = 3–12) clusters using anion photoelectron spectroscopy and density functional theory calculations. The vertical detachment energies and adiabatic detachment energies of AgSin− (n = 3–12) clusters were estimated from their photoelectron spectra. The structures of the AgSin− (n = 3–12) clusters were tentatively assigned based on the comparison of theoretical calculations and experimental measurements. The studies show that the structures of AgSin− (n = 3–12) clusters are dominated by exohedral structures with the Ag atom occupying the low coordinated sites. No endohedral structure has been found for AgSin− clusters with n ≤ 12.
Coarse-grained simulations of moderately entangled star polyethylene melts
Authors: Liu L. , Padding J. T. , den Otter W. K. , Briels W. J.
Published: June 2013

In this paper, a previous coarse-grain model [J. T. Padding and W. J. Briels, J. Chem. Phys. 117, 925 (2002)]10.1063/1.1481859 to simulate melts of linear polymers has been adapted to simulate polymers with more complex hierarchies. Bond crossings between highly coarse-grained soft particles are prevented by applying an entanglement algorithm. We first test our method on a virtual branch point inside a linear chain to make sure it works effectively when linking two linear arms. Next, we apply our method to study the diffusive and rheological behaviors of a melt of three-armed stars. We find that the diffusive behavior of the three-armed star is very close to that of a linear polymer with the same molecular weight, while its rheological properties are close to those of a linear chain with molecular mass equal to that of the longest linear sub-chain in the star.
Space-time aspects of a three-dimensional multi-modulated open cavity flow
Authors: Basley J. , Pastur L. R. , Delprat N. , Lusseyran F.
Published: June 2013

Side-band frequencies in an incompressible flow past a rectangular cavity are characterized through their space-time coherent structures. A parametric study over a range of dimensionless cavity length L/θ0 has been carried out in the incompressible regime. It yields the general evolution of self-sustained oscillations, for which primary characteristics match results in the literature. The modulating frequencies associated with side-band frequencies are usually imputed either to the two-dimensional (vortex-edge) interaction at the impingement or to three-dimensional dynamics induced by centrifugal instabilities in the inner-flow. However, secondary order features sometimes depart from commonly accepted scheme. In addition to the salient features of the flow, our observations bring to light another modulation, which may be related to the main recirculation inside the cavity. That modulation even becomes predominant for peculiar configurations. The present work focuses on such a configuration with a cavity length/depth ratio L/D = 1.5 and dimensionless cavity length L/θ0 = 76. Based on time-resolved velocity measurements, the extensive analysis is concerned with the non-linear interactions within the flow. Using laser Doppler velocimetry and time-resolved particle image velocimetry in two planes, this multi-modulated regime is so addressed through both local and global aspects. Time-resolved velocity fields provide space-time coherent data that are analysed using transfer functions, space-time diagrams, and space-extended time-Fourier decomposition.
Enhanced exchange algorithm without detailed balance condition for replica exchange method
Authors: Kondo Hiroko X. , Taiji Makoto
Published: June 2013

The replica exchange method (REM) is a powerful tool for the conformational sampling of biomolecules. In this study, we propose an enhanced exchange algorithm for REM not meeting the detailed balance condition (DBC), but satisfying the balance condition in all considered exchanges between two replicas. Breaking the DBC can minimize the rejection rate and make an exchange process rejection-free as the number of replicas increases. To enhance the efficiency of REM, all possible pairs—not only the nearest neighbor—were considered in the exchange process. The test simulations of the alanine dipeptide confirmed the correctness of our method. The average traveling distance of each replica in the temperature distribution was also increased in proportion to an increase in the exchange rate. Furthermore, we applied our algorithm to the conformational sampling of the 10-residue miniprotein, chignolin, with an implicit solvent model. The results showed a faster convergence in the calculation of its free energy landscape, compared to that achieved using the normal exchange method of adjacent pairs. This algorithm can also be applied to the conventional near neighbor method and is expected to reduce the required number of replicas.
The interactions of phenylalanines in β-sheet-like structures from molecular orbital calculations using density functional theory (DFT), MP2, and CCSD(T) methods
Authors: Pohl Gabor , Plumley Joshua A. , Dannenberg J. J.
Published: June 2013

We present density functional theory calculations designed to evaluate the importance of π-stacking interactions to the stability of in-register Phe residues within parallel β-sheets, such as amyloids. We have used a model of a parallel H-bonded tetramer of acetylPheNH2 as a model and both functionals that were specifically designed to incorporate dispersion effects (DFs), as well as, several traditional functionals which have not been so designed. None of the functionals finds a global minimum for the π-stacked conformation, although two of the DFs find this to be a local minimum. The stacked phenyls taken from the optimized geometries calculated for each functional have been evaluated using MP2 and CCSD(T) calculations for comparison. The results suggest that π-stacking does not make an important contribution to the stability of this system and (by implication) to amyloid formation.
A high spatial resolution Stokes polarimeter for motional Stark effect imaging
Authors: Thorman Alex , Michael Clive , Howard John
Published: June 2013

We describe an enhanced temporally switched interfero-polarimeter that has been successfully deployed for high spatial resolution motional Stark effect imaging on the KSTAR superconducting tokamak. The system utilizes dual switching ferroelectric liquid crystal waveplates to image the full Stokes vector of elliptically polarized and Doppler-shifted Stark-Zeeman Balmer-alpha emission from high energy neutral beams injected into the magnetized plasma. We describe the optical system and compare its performance against a Mueller matrix model that takes account of non-ideal performance of the switching ferro-electric liquid crystal waveplates and other polarizing components.
Predicting longevity of submerged superhydrophobic surfaces with parallel grooves
Authors: Emami B. , Hemeda A. A. , Amrei M. M. , Luzar A. , Gad-el-Hak M. , Vahedi Tafreshi H.
Published: June 2013

A mathematical framework is developed to predict the longevity of a submerged superhydrophobic surface made up of parallel grooves. Time-dependent integro-differential equations predicting the instantaneous behavior of the air–water interface are derived by applying the balance of forces across the air–water interface, while accounting for the dissolution of the air in water over time. The calculations start by producing a differential equation for the initial steady-state shape and equilibrium position of the air–water interface at t = 0. Analytical and/or numerical solutions are then developed to solve the time-dependent equations and to compute the volume of the trapped air in the grooves over time until a Wenzel state is reached as the interface touches the groove's bottom. For demonstration, a superhydrophobic surface made of parallel grooves is considered, and the influence of the groove's dimensions on the longevity of the surface under different hydrostatic pressures is studied. It was found that for grooves with higher width-to-depth ratios, the critical pressure (pressure at which departure from the Cassie state starts) is higher due to stronger resistance to deflection of the air–water interface from the air trapped in such grooves. However, grooves with higher width-to-depth ratios reach the Wenzel state faster because of their greater air–water interface areas.
Adsorption of polyelectrolytes onto oppositely charged cylindrical macroions
Authors: de Carvalho Sidney Jurado , Caetano Daniel Lucas Zago
Published: June 2013

In this work we investigate the adsorption of polyelectrolyte chains onto uniformly charged cylindrical macroions by means of the Metropolis Monte Carlo simulations and weighted histogram analysis method. Adopting a simplified model for macromolecules and treating the electrolytic solution in the Debye-Hückel level, conformational properties of the adsorbed chain, such as the radius of gyration and the thickness of the adsorbed layer, are provided as a function of ionic strength and macroion charge density. By analysis of the free energy profile as a function of the radius of gyration it was possible to identify first-order-like transitions between adsorbed and desorbed states and obtain a macroion charge density dependence of the critical ionic strength in good agreement with experiments.
Rapid integrated rheo-optical and polarized Fourier-transform infrared spectrometry measurement system for polymer films undergoing chemo-mechanical changes
Authors: Unsal E. , Nugay I. I. , Offenbach I. , Gross M. , Manning C. , Cakmak M.
Published: July 2013

The design and performance of a multisensory instrument to track physical and chemical changes of thin polymer films (typically 5 μm < thickness < 100 μm) subjected to thermal and mechanical treatments are described in this paper. For the first time, real-time measurements of spectral birefringence, true stress, true strain, and temperature are integrated together with ultra-rapid-scan polarized FT-IR spectrometer (URS-FT-IR) to investigate the relationships between true mechanical measures and structural features at different length scales. The rheo-optical properties (birefringence-true stress-true strain) are collected at a rate of 10 data points/s and URS-FT-IR data are collected at a rate of 300 complete spectra/s. The IR dichroism measurement is performed by exposing the sample to non-polarized IR beam in transmission mode with two mutually perpendicular polarizations, parallel and perpendicular to the stretching direction, received by detector unit. This design allows to analyze both polarizations simultaneously wavenumbers in the range of 500 cm−1–4000 cm−1. Controlled processing parameters include air speed, air temperature, stretching rate, stretching ratio, stretch cycling, and holding times; while simultaneously measuring optical retardation, sample width, temperature, load cell, and both parallel and perpendicular IR spectra. Calibration and performance of this instrument is demonstrated with several film samples. These are: A polystyrene standard, an atactic polystyrene (homo-polymer), a polyurethane (consists of hard and soft segments) for physical changes during uniaxial deformation, and a polyamic acid during imidization reaction. This measurement system is particularly useful in unraveling molecular level details of complex physical and chemical events that take place during very fast deformation schemes (uniaxial stretching, retraction, relaxation, annealing, etc.) relevant to industrial processes. These include specific orientation behavior of each phase, block or filler, crystallization, relaxation and orientation state. It is also suited to track reaction rates and products in polymers undergoing thermal or photo curing.
Stability of viscous long liquid filaments
Authors: Driessen Theo , Jeurissen Roger , Wijshoff Herman , Toschi Federico , Lohse Detlef
Published: June 2013

We study the collapse of an axisymmetric liquid filament both analytically and by means of a numerical model. The liquid filament, also known as ligament, may either collapse stably into a single droplet or break up into multiple droplets. The dynamics of the filament are governed by the viscosity and the aspect ratio, and the initial perturbations of its surface. We find that the instability of long viscous filaments can be completely explained by the Rayleigh-Plateau instability, whereas a low viscous filament can also break up due to end pinching. We analytically derive the transition between stable collapse and breakup in the Ohnesorge number versus aspect ratio phase space. Our result is confirmed by numerical simulations based on the slender jet approximation and explains recent experimental findings by Castréjon-Pita et al. [Phys. Rev. Lett. 108, 074506 (2012)]10.1103/PhysRevLett.108.074506.
Measurement of threshold voltage in organic thin film transistors
Authors: Kumar Singh Vinay , Mazhari Baquer
Published: June 2013

Conventional method used for measurement of linearly extrapolated threshold voltage from the slope of ISD vs. VGS characteristics in organic thin film transistors (OTFTs) suffers from the influence of gate dependence of field mobility and its use for comparing different devices can result in anomalous trends. In the present work, an improved method is described, which eliminates the effects of mobility and yields a unique value of threshold voltage. Experimental results obtained with pentacene OTFTs with two different dielectric materials are presented, which show that actual threshold voltage can be very different than the values estimated using the conventional technique.
Coupled multiphysics, barrier localization, and critical radius effects in embedded nanowire superlattices
Authors: Prabhakar Sanjay , Melnik Roderick , Bonilla Luis L
Published: June 2013

The new contribution of this paper is to develop a cylindrical representation of an already known multiphysics model for embedded nanowire superlattices (NWSLs) of wurtzite structure that includes a coupled, strain dependent 8-band k·p Hamiltonian in cylindrical coordinates and investigate the influence of coupled piezo-electromechanical effects on the barrier localization and critical radius in such NWSLs. The coupled piezo-electromechanical model for semiconductor materials takes into account the strain, piezoelectric effects, and spontaneous polarization. Based on the developed 3D model, the band structures of electrons (holes) obtained from results of modeling in Cartesian coordinates are in good agreement with those values obtained from our earlier developed 2D model in cylindrical coordinates. Several parameters such as lattice mismatch, piezo-electric fields, valence, and conduction band offsets at the heterojunction of AlxGa1–xN/GaN superlattice can be varied as a function of the Al mole fraction. When the band offsets at the heterojunction of AlxGa1–xN/GaN are very small and the influence of the piezo-electromechanical effects can be minimized, then the barrier material can no longer be treated as an infinite potential well. In this situation, it is possible to visualize the penetration of the Bloch wave function into the barrier material that provides an estimation of critical radii of NWSLs. In this case, the NWSLs can act as inversion layers. Finally, we investigate the influence of symmetry of the square and cylindrical NWSLs on the band structures of electrons in the conduction band.
Planar silicon nitride mid-infrared devices
Authors: Tai Lin Pao , Singh Vivek , Kimerling Lionel , Murthy Agarwal Anuradha
Published: June 2013

Integrated mid-infrared devices including (i) straight/bent waveguides and (ii) directional couplers are demonstrated on silicon nitride (SiN) thin films prepared by optimized low-pressure chemical vapor deposition. The deposited SiN film has a broad spectral transparency from visible up to a wavelength of λ = 8.5 μm (as seen from Fourier transform infrared spectroscopy). Our SiN waveguide shows a dominant fundamental mode with an optical loss of 2.1 dB/cm at λ = 3.7 μm. In addition, we demonstrate an efficient SiN directional coupler between λ = 3.55 μm to λ = 3.75 μm where an 8 dB extinction ratio is achieved within each channel upon wavelength scanning. With the inherent advantage of complementary metal–oxide–semiconductor compatibility, our SiN platform paves the way to create sophisticated photonic circuits that are desired for mid-infrared nonlinear light generation and chip-scale biochemical sensors.
Electromagnon excitations in canted-spin multiferroics
Authors: Chen Hong-Bo , Li You-Quan
Published: June 2013

The dynamical interplay between magnetism and electric polarization in a multiferroic with a canted-spin order is investigated by extending the conventional spin-current mechanism. We unravel the magnetic and magnetoelectric excitations of the system and manifest the existence of two species of electromagnon excitations exhibiting unique selection rules. Our results suggest a route to accurately identify the underlying magnetoelectric coupling of a multiferroic via an optical probe, which is essential for controlling the electromagnons in future magnonic devices.