bluuebunny/crossref_metadata_2025 huggingface dataset:
Beijing Consensus and Development Legitimacy: The Evolution of China’s Foreign Direct Investment (FDI) Regime from a Law & Development Perspective
Authors: GUAN Wenwei
Published: March 2017

The evolution of China’s trade and investment regime since the late 1970s has been a process of constant liberalization of FDI control with a special focus on national development and self-determination. This so-called Beijing Consensus presents a sharp contrast with the neo-liberalist Washington Consensus. A theoretical analysis of this contrast from the law and development critique reveals that, while setting forth itself as the development model and excluding other development alternatives, the legitimacy deficit of the Washington Consensus stems from a self-sufficient ontological myth of legal voluntarism. The Beijing Consensus, with its attention to local conditions and emphasis on self-determination, gains its legitimacy through the dynamic process of selective adaptation of limit-transgression through which it challenges and at the same time enriches international development legitimacy. This article suggests that the Beijing Consensus’ roots in the African Continent’s Agenda 2063 and its First Ten-year Implementation Plan offer positive future prospects.
Chemosymbiotic bivalves from Miocene methane-seep carbonates in Italy
Authors: Kiel Steffen , Taviani Marco
Published: March 2017

Eleven species of chemosymbiotic bivalves are reported from middle to late Miocene methane seep deposits (‘Calcari aLucina’) in the Italian Apennines, including seven new species and one new genus. The new species areBathymodiolus(s.l.)moroniaeandB. (s.l.)miomediterraneusamong the Bathymodiolinae andArchivesica aharoni,A.apenninica,A.strigarum, and ‘Pliocardia’italicaamong the Vesicomyidae; specimens from the middle Miocene of Deruta are reported asArchivesicaaff.aharoni.Samiolus iohannesbaptistaenew genus new species is introduced for an unusual mytilid with a commarginally ribbed surface, which might be the first non-bathymodiolin mytilid obligate to the seep environment. The two large lucinid species from which these deposits derived their informal name ‘Calcari aLucina’ are identified asMeganodontia hoernea(Des Moulins, 1868) andLucinoma perusina(Sacco, 1901). WithChanellaxinussp., we report the first thyasirid from a Neogene deep-water seep deposit in Italy and the first fossil occurrence of this genus.
A study on conserving invariants of the Vlasov equation in semi-Lagrangian computer simulations
Authors: Einkemmer L.
Published: March 2017

The semi-Lagrangian discontinuous Galerkin method, coupled with a splitting approach in time, has recently been introduced for the Vlasov–Poisson equation. Since these methods are conservative, local in space and able to limit numerical diffusion, they are considered a promising alternative to more traditional semi-Lagrangian schemes. In this paper we study the conservation of important physical invariants and the long-time behaviour of the semi-Lagrangian discontinuous Galerkin method. To that end we conduct a theoretical analysis and perform a number of numerical simulations. In particular, we find that the entropy is non-decreasing for the discontinuous Galerkin scheme, while unphysical oscillations in the entropy are observed for the traditional method based on cubic spline interpolation.
Deletion of Stk40 impairs definitive erythropoiesis in the mouse fetal liver
Authors: Wang Lina , Yu Hongyao , Cheng Hui , He Ke , Fang Zhuoqing , Ge Laixiang , Cheng Tao , Jin Ying
Published: March 2017

The serine threonine kinase Stk40 has been shown to involve in mouse embryonic stem cell differentiation, pulmonary maturation and adipocyte differentiation. Here we report that targeted deletion of Stk40 leads to fetal liver hypoplasia and anemia in the mouse embryo. The reduction of erythrocytes in the fetal liver is accompanied by increased apoptosis and compromised erythroid maturation. Stk40−/− fetal liver cells have significantly reduced colony-forming units (CFUs) capable of erythroid differentiation, including burst forming unit-erythroid, CFU-erythroid (CFU-E), and CFU-granulocyte, erythrocyte, megakaryocyte and macrophage, but not CFU-granulocyte/macrophages. Purified Stk40−/− megakaryocyte–erythrocyte progenitors produce substantially fewer CFU-E colonies compared to control cells. Moreover, Stk40−/− fetal liver erythroblasts fail to form normal erythroblastic islands in association with wild type or Stk40−/− macrophages, indicating an intrinsic defect of Stk40−/− erythroblasts. Furthermore, the hematopoietic stem and progenitor cell pool is reduced in Stk40−/− fetal livers but still retains the multi-lineage reconstitution capacity. Finally, comparison of microarray data between wild type and Stk40−/− E14.5 fetal liver cells reveals a potential role of aberrantly activated TNF-α signaling in Stk40 depletion induced dyserythropoiesis with a concomitant increase in cleaved caspase-3 and decrease in Gata1 proteins. Altogether, the identification of Stk40 as a regulator for fetal erythroid maturation and survival provides new clues to the molecular regulation of erythropoiesis and related diseases.
Erratum: Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp
Authors: Trivedi Vikas D. , Jangir Pramod Kumar , Sharma Rakesh , Phale Prashant S.
Published: March 2017

Scientific Reports 6: Article number: 38430; published online: 07 December 2016; updated: 30 March 2017 This Article contains an error in Figure 1, where panel A is a duplication of panel B. The correct Figure appears below; the Figure legend is correct in the published version.
Glass-ceramic optical fiber containing Ba2TiSi2O8 nanocrystals for frequency conversion of lasers
Authors: Fang Zaijin , Xiao Xusheng , Wang Xin , Ma Zhijun , Lewis Elfed , Farrell Gerald , Wang Pengfei , Ren Jing , Guo Haitao , Qiu Jianrong
Published: March 2017

A glass-ceramic optical fiber containing Ba2TiSi2O8 nanocrystals fabricated using a novel combination of the melt-in-tube method and successive heat treatment is reported for the first time. For the melt-in-tube method, fibers act as a precursor at the drawing temperature for which the cladding glass is softened while the core glass is melted. It is demonstrated experimentally that following heat treatment, Ba2TiSi2O8 nanocrystals with diameters below 10 nm are evenly distributed throughout the fiber core. Comparing to the conventional rod-in-tube method, the melt-in-tube method is superior in terms of controllability of crystallization to allow for the fabrication of low loss glass-ceramic fibers. When irradiated using a 1030 nm femtosecond laser, an enhanced green emission at a wavelength of 515 nm is observed in the glass-ceramic fiber, which demonstrates second harmonic generation of a laser action in the fabricated glass-ceramic fibers. Therefore, this new glass-ceramic fiber not only provides a highly promising development for frequency conversion of lasers in all optical fiber based networks, but the melt-in-tube fabrication method also offers excellent opportunities for fabricating a wide range of novel glass-ceramic optical fibers for multiple future applications including fiber telecommunications and lasers.
Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecology
Authors: Rouzé H. , Leray M. , Magalon H. , Penin L. , Gélin P. , Knowlton N. , Fauvelot C.
Published: March 2017

Several obligate associate crabs and shrimps species may co-occur and interact within a single coral host, leading to patterns of associations that can provide essential ecological services. However, knowledge of the dynamics of interactions in this system is limited, partly because identifying species involved in the network remains challenging. In this study, we assessed the diversity of the decapods involved in exosymbiotic assemblages for juvenile and adult Pocillopora damicornis types α and β on reefs of New Caledonia and Reunion Island. This approach revealed complex patterns of association at regional and local scales with a prevalence of assemblages involving crab-shrimp partnerships. Furthermore, the distinction of two lineages in the snapping shrimp Alpheus lottini complex, rarely recognized in ecological studies, reveals a key role for cryptic diversity in structuring communities of mutualists. The existence of partnerships between species that occurred more commonly than expected by chance suggests an increased advantage for the host or a better adaptation of associated species to local environmental conditions. The consideration of cryptic diversity helps to accurately describe the complexity of interaction webs for diverse systems such as coral reefs, as well as the functional roles of dominant associated species for the persistence of coral populations.
Correction: Corrigendum: Direct coupling: a possible strategy to control fruit production in alternate bearing
Authors: Prasad Awadhesh , Sakai Kenshi , Hoshino Yoshinobu
Published: March 2017

Scientific Reports 7: Article number: 39890; published online: 04 January 2017; updated: 30 March 2017 This Article contains a typographical error in the Results and Discussion section. In Equation (7), should read:
MiR-126 and miR-126* regulate shear-resistant firm leukocyte adhesion to human brain endothelium
Authors: Cerutti Camilla , Edwards Laura J. , de Vries Helga E. , Sharrack Basil , Male David K. , Romero Ignacio A.
Published: March 2017

Leukocyte adhesion to brain endothelial cells, the blood-brain barrier main component, is a critical step in the pathogenesis of neuroinflammatory diseases such as multiple sclerosis (MS). Leukocyte adhesion is mediated mainly by selectins, cell adhesion molecules and chemokines induced by pro-inflammatory cytokines such as TNFα and IFNγ, but the regulation of this process is not fully clear. This study investigated the regulation of firm leukocyte adhesion to human brain endothelium by two different brain endothelial microRNAs (miRs), miR-126 and miR-126*, that are downregulated by TNFα and IFNγ in a human brain endothelial cell line, hCMEC/D3. Using a leukocyte adhesion in vitro assay under shear forces mimicking blood flow, we observed that reduction of endothelial miR-126 and miR-126* enhanced firm monocyte and T cell adhesion to hCMEC/D3 cells, whereas their increased expression partially prevented THP1, Jurkat and primary MS patient-derived PBMC firm adhesion. Furthermore, we observed that miR-126* and miR-126 downregulation increased E-selectin and VCAM1, respectively, while miR-126 overexpression reduced VCAM1 and CCL2 expression by hCMEC/D3 cells, suggesting that these miRs regulate leukocyte adhesion by modulating the expression of adhesion-associated endothelial mRNA targets. Hence, human brain endothelial miR-126 and miR-126* could be used as a therapeutic tool to reduce leukocyte adhesion and thus reduce neuroinflammation.
Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase
Authors: Minges Alexander , Ciupka Daniel , Winkler Christian , Höppner Astrid , Gohlke Holger , Groth Georg
Published: March 2017

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and P i -dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.
Modified SJH alleviates FFAs-induced hepatic steatosis through leptin signaling pathways
Authors: Lim Dong-Woo , Bose Shambhunath , Wang Jing-Hua , Choi Han Seok , Kim Young-Mi , Chin Young-Won , Jeon Song-Hee , Kim Jai-Eun , Kim Hojun
Published: March 2017

Samjunghwan (SJH) is an herbal formula used in traditional Korean medicine. This prescription has long been used in treatment of aging and lifestyle diseases. The current study showed the effect and mechanisms of anti-hepatic steatosis action of modified SJH (mSJH)in vitroandin vivo. Treatment with mSJH resulted in significantly decreased intracellular lipid accumulation in steatosis-induced cells. Furthermore, mSJH triggered the phosphorylation of AMP-activated protein kinase andacetyl-CoA carboxylaseas well as increased the expression of leptin at both protein and gene levels. In addition, C57BL6 mice fed high-fat diet (HFD) showed significant improvements in body, liver weights and fat weights; and serum, hepatic and fecal lipid parameters in response to the treatment with mSJH. Furthermore, mSJH showed favorable effects on the hepatic expression of several genes related to lipid metabolism. Betaine, one of constituents of mSJH exerted fundamental beneficial impact on FFAs-induced cells. However, the beneficial effects of mSJH were diminished upon blocking of leptin signaling by dexamethasone, suggesting the leptin signaling as a key component in mSJH-mediated modulation of lipid homeostasis. Our results suggest that mSJH exerts an anti-hepatic steatosis effect via activation of leptin and associated signaling cascades related to lipid metabolism.
ATHB17 enhances stress tolerance by coordinating photosynthesis associated nuclear gene and ATSIG5 expression in response to abiotic stress
Authors: Zhao Ping , Cui Rong , Xu Ping , Wu Jie , Mao Jie-Li , Chen Yu , Zhou Cong-Zhao , Yu Lin-Hui , Xiang Cheng-Bin
Published: March 2017

Photosynthesis is sensitive to environmental stress and must be efficiently modulated in response to abiotic stress. However, the underlying mechanisms are not well understood. Here we report that ARABIDOPSIS THALIANA HOMEOBOX 17 (ATHB17), an Arabidopsis HD-Zip transcription factor, regulated the expression of a number of photosynthesis associated nuclear genes (PhANGs) involved in the light reaction and ATSIG5 in response to abiotic stress. ATHB17 was responsive to ABA and multiple stress treatments. ATHB17-overexpressing plants displayed enhanced stress tolerance, whereas its knockout mutant was more sensitive compared to the wild type. Through RNA-seq and quantitative real-time reverse transcription PCR (qRT-PCR) analysis, we found that ATHB17 did not affect the expression of many known stress-responsive marker genes. Interestingly, we found that ATHB17 down-regulated many PhANGs and could directly modulate the expression of several PhANGs by binding to their promoters. Moreover, we identified ATSIG5, encoding a plastid sigma factor, as one of the target genes of ATHB17. Loss of ATSIG5 reduced salt tolerance while overexpression of ATSIG5 enhanced salt tolerance, similar to that of ATHB17. ATHB17 can positively modulate the expression of many plastid encoded genes (PEGs) through regulation of ATSIG5. Taken together, our results suggest that ATHB17 may play an important role in protecting plants by adjusting expression of PhANGs and PEGs in response to abiotic stresses.
HLA-B*15:21 and carbamazepine-induced Stevens-Johnson syndrome: pooled-data and in silico analysis
Authors: Jaruthamsophon Kanoot , Tipmanee Varomyalin , Sangiemchoey Antida , Sukasem Chonlaphat , Limprasert Pornprot
Published: March 2017

HLA-B*15:02 screening before carbamazepine (CBZ) prescription in Asian populations is the recommended practice to prevent CBZ-induced Stevens-Johnson syndrome (CBZ-SJS). However, a number of patients have developed CBZ-SJS even having no HLA-B*15:02. Herein, we present the case of a Thai patient who had a negative HLA-B*15:02 screening result but later developed CBZ-SJS. Further HLA typing revealed HLA-B*15:21/B*13:01. HLA-B*15:21 is a member of the HLA-B75 serotype and is commonly found in Southeast Asian populations. Based on this case, we hypothesised that if all HLA-B*15:02 carriers were prevented from CBZ prescription, another common HLA-B75 serotype marker would show its association with CBZ-SJS. To test this hypothesis, we pooled data from previous association studies in Asian populations, excluded all cases with HLA-B*15:02, and analysed the association significance of HLA-B75 serotype markers. A significant association was found between CBZ-SJS and HLA-B*15:21 and HLA-B*15:11. We also applied an in silico analysis and found that all HLA-B75 serotype molecules shared similar capability in binding the CBZ molecule. In summary, this report provides the first evidence of a positive association between HLA-B*15:21 and CBZ-SJS and the first in silico analysis of CBZ binding sites and details of the molecular behaviour of HLA-B75 molecule to explain its molecular action.
Relevance of secretor status genotype and microbiota composition in susceptibility to rotavirus and norovirus infections in humans
Authors: Rodríguez-Díaz Jesús , García-Mantrana Izaskun , Vila-Vicent Susana , Gozalbo-Rovira Roberto , Buesa Javier , Monedero Vicente , Collado Maria Carmen
Published: March 2017

Host genetic factors, such as histo-blood group antigens (HBGAs), are associated with susceptibility to norovirus (NoV) and rotavirus (RV) infections. Recent advances point to the gut microbiome as a key player necessary for a viral pathogen to cause infection. In vitro NoV attachment to host cells and resulting infections have been linked to interactions with certain bacterial types in the gut microbiota. We investigated the relationship between host genotype, gut microbiota, and viral infections. Saliva and fecal samples from 35 adult volunteers were analysed for secretor status genotype, the gut microbiota composition by 16S rRNA gene sequencing, and salivary IgA titers to NoV and RV. Higher levels of IgA against NoV and RV were related to secretor-positive status. No significant differences were found between the FUT2 genotype groups, although the multivariate analysis showed a significant impact of host genotype on specific viral susceptibilities in the microbiome composition. A specific link was found between the abundance of certain bacterial groups, such as Faecalibacterium and Ruminococcus spp., and lower IgA titers against NoV and RV. As a conclusion, we can state that there is a link between host genetics, gut microbiota, and susceptibility to viral infections in humans.
Chemical interaction mechanism of 10-MDP with zirconia
Authors: Nagaoka Noriyuki , Yoshihara Kumiko , Feitosa Victor Pinheiro , Tamada Yoshiyuki , Irie Masao , Yoshida Yasuhiro , Van Meerbeek Bart , Hayakawa Satoshi
Published: March 2017

Currently, the functional monomer 10-methacryloyloxy-decyl-dihydrogen-phosphate (10-MDP) was documented to chemically bond to zirconia ceramics. However, little research has been conducted to unravel the underlying mechanisms. This study aimed to assess the chemical interaction and to demonstrate the mechanisms of coordination between 10-MDP and zirconium oxide using 1H and 31P magic angle spinning (MAS) nuclear magnetic resonance (NMR) and two dimensional (2D) 1H → 31P heteronuclear correlation (HETCOR) NMR. In addition, shear bond-strength (SBS) tests were conducted to determine the effect of 10-MDP concentration on the bonding effectiveness to zirconia. These SBS tests revealed a 10-MDP concentration-dependent SBS with a minimum of 1-ppb 10-MDP needed. 31P-NMR revealed that one P-OH non-deprotonated of the PO3H2 group from 10-MDP chemically bonded strongly to zirconia. 1H-31P HETCOR NMR indicated that the 10-MDP monomer can be adsorbed onto the zirconia particles by hydrogen bonding between the P=O and Zr-OH groups or via ionic interactions between partially positive Zr and deprotonated 10-MDP (P-O−). The combination of 1H NMR and 2D 1H-31P HETCOR NMR enabled to describe the different chemical states of the 10-MDP bonds with zirconia; they not only revealed ionic but also hydrogen bonding between 10-MDP and zirconia.
End-to-end assembly and disassembly of gold nanorods based on photo-responsive host–guest interaction
Authors: Wu Jie , Xu Yun , Li Dengfeng , Ma Xiang , Tian He
Published: March 2017

The end-to-end assembly and disassembly of gold nanorods were realized via HS-β-CD recognition and controllable by both UV light irradiation and guest competition.
Non-symmetrical, potentially redox non-innocent imino NHC pyridine ‘pincers’ via a zinc ion template-assisted synthesis
Authors: Simler Thomas , Danopoulos Andreas A. , Braunstein Pierre
Published: March 2017

A ZnII-promoted modular synthesis allows access to new non-symmetrical, redox-active imino NHC pyridine pincer ligands. Radical anionic and dianionic redox states of the ligand are involved in its FeII complexes obtained from FeBr2/KC8.
Water-controlled selective preparation of α-mono or α,α′-dihalo ketones via catalytic cascade reaction of unactivated alkynes with 1,3-dihalo-5,5-dimethylhydantoin
Authors: Wu Chao , Xin Xiu , Fu Zhi-Min , Xie Long-Yong , Liu Kai-Jian , Wang Zheng , Li Wenyi , Yuan Zhi-Hui , He Wei-Min
Published: March 2017

An efficient protocol for the selective synthesis of α-mono or α,α′-dihalo ketones via a water-controlled chemodivergent and regiospecific cascade reaction has been developed.
Stereoselective, solvent free, highly efficient synthesis of aldo- and keto-N-acylhydrazones applying grindstone chemistry
Authors: dos Santos Filho José Maurício , Pinheiro Savio Moita
Published: March 2017

An efficient and stereoselective methodology for the synthesis ofN-acylhydrazones is disclosed, based on grindstone chemistry. The method tolerates a broad variety of substrates, as demonstrated by the 51 examples, 21 of them unpublished.
The biochemical properties of the twoArabidopsis thalianaisochorismate synthases
Authors: Macaulay Keith M. , Heath Geraldine A. , Ciulli Alessio , Murphy Alex M. , Abell Chris , Carr John P. , Smith Alison G.
Published: March 2017

The important plant hormone salicylic acid (SA; 2-hydroxybenzoic acid) regulates several key plant responses including, most notably, defence against pathogens. A key enzyme for SA biosynthesis is isochorismate synthase (ICS), which converts chorismate into isochorismate, and for which there are two genes in Arabidopsis thaliana. One (AtICS1) has been shown to be required for increased SA biosynthesis in response to pathogens and its expression can be stimulated throughout the leaf by virus infection and exogenous SA. The other (AtICS2) appears to be expressed constitutively, predominantly in the plant vasculature. Here, we characterise the enzymatic activity of both isozymes expressed as hexahistidine fusion proteins in Escherichia coli. We show for the first time that recombinant AtICS2 is enzymatically active. Both isozymes are Mg2+-dependent with similar temperature optima (ca. 33°C) and similar Km values for chorismate of 34.3 ± 3.7 and 28.8 ± 6.9 µM for ICS1 and ICS2, respectively, but reaction rates were greater for ICS1 than for ICS2, with respective values for Vmax of 63.5 ± 2.4 and 28.3 ± 2.0 nM s−1 and for kcat of 38.1 ± 1.5 and 17.0 ± 1.2 min−1. However, neither enzyme displayed isochorismate pyruvate lyase (IPL) activity, which would enable these proteins to act as bifunctional SA synthases, i.e. to convert chorismate into SA. These results show that although Arabidopsis has two functional ICS enzymes, it must possess one or more IPL enzymes to complete biosynthesis of SA starting from chorismate.
Noise characteristics of the new converter transformer under DC bias
Authors: Liu Junhua , Luo Longfu
Published: March 2017

Harmonic magnetic fluxes in transformer's core and harmonic currents in grid‐side winding can be restrained via the inductive filtering technology, and running noise of the transformer is reduced at the source. The A‐weighted sound levels of the measuring points are measured under DC bias. The noise test results verify this theory. When the fully‐tuned filters matched with the new converter transformer are inputted and not inputted, the noise response curves of the measured points are compared. The fitting coefficients of the noise values at 1250 and 1600 Hz with the unbalance degrees of the trigger angle are obtained.
Regularity of spectral residual for reduced reference image quality assessment
Authors: Liu Delei , Li Fuzhong , Song Houbing
Published: March 2017

Inspired by the facts that visual saliency captures more attention and spectral residual (SR) can indicate the saliency of the image, a novel reduced‐reference image quality assessment metric is proposed based on the regularity of the SR. The orientation and frequency components of an image are first extracted in wavelet domain. Then SR is obtained to represent the saliency of the component. Next fractal dimension is adopted to encode SR and concatenated as the image features. Finally, the feature differences between reference image and distorted one are pooled as the quality score. The proposed metric is evaluated on four largest image databases (TID2013, TID2008, CSIQ, and LIVE databases), and experimental results confirm that the proposed metric has a good performance.
Markov state models from short non-equilibrium simulations—Analysis and correction of estimation bias
Authors: Nüske Feliks , Wu Hao , Prinz Jan-Hendrik , Wehmeyer Christoph , Clementi Cecilia , Noé Frank
Published: March 2017

Many state-of-the-art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are integrated. In this context, Markov state models (MSMs) are extremely popular because they can be used to compute stationary quantities and long-time kinetics from ensembles of short simulations, provided that these short simulations are in “local equilibrium” within the MSM states. However, over the last 15 years since the inception of MSMs, it has been controversially discussed and not yet been answered how deviations from local equilibrium can be detected, whether these deviations induce a practical bias in MSM estimation, and how to correct for them. In this paper, we address these issues: We systematically analyze the estimation of MSMs from short non-equilibrium simulations, and we provide an expression for the error between unbiased transition probabilities and the expected estimate from many short simulations. We show that the unbiased MSM estimate can be obtained even from relatively short non-equilibrium simulations in the limit of long lag times and good discretization. Further, we exploit observable operator model (OOM) theory to derive an unbiased estimator for the MSM transition matrix that corrects for the effect of starting out of equilibrium, even when short lag times are used. Finally, we show how the OOM framework can be used to estimate the exact eigenvalues or relaxation time scales of the system without estimating an MSM transition matrix, which allows us to practically assess the discretization quality of the MSM. Applications to model systems and molecular dynamics simulation data of alanine dipeptide are included for illustration. The improved MSM estimator is implemented in PyEMMA of version 2.3.
Effects of translational and rotational degrees of freedom on properties of the Mercedes–Benz water model
Authors: Urbic T. , Mohoric T.
Published: March 2017

Non–equilibrium Monte Carlo and molecular dynamics simulations are used to study the effect of translational and rotational degrees of freedom on the structural and thermodynamic properties of the simple Mercedes–Benz water model. We establish a non–equilibrium steady state where rotational and translational temperatures can be tuned. We separately show that Monte Carlo simulations can be used to study non-equilibrium properties if sampling is performed correctly. By holding one of the temperatures constant and varying the other one, we investigate the effect of faster motion in the corresponding degrees of freedom on the properties of the simple water model. In particular, the situation where the rotational temperature exceeded the translational one is mimicking the effects of microwaves on the water model. A decrease of rotational temperature leads to the higher structural order while an increase causes the structure to be more Lennard–Jones fluid like.
Influence of resonant collisions on the self-broadening of acetylene
Authors: Lehmann Kevin K.
Published: March 2017

Iwakuni et al. [Phys. Rev. Lett. 117, 143902 (2016)] have reported an ortho-para alternation of ∼10% in the self pressure broadening coefficients for ro-vibrational lines of the C2H2 transitions in the ν1+ν3 C–H (local mode) overtone band near 197 THz (1.52 μm). These authors attributed this effect to the contribution of resonant collisions, where the rotational energy change of one molecule is exactly compensated by the rotational energy change of its collision partner. Resonant collisions are known to be important in the case of self pressure broadening of highly polar molecules, such as HCN, but have not previously been invoked in the case of nonpolar molecules, such as acetylene, where the long range potential is dominated by the quadrupole-quadrupole electrostatic interaction. In the present work, the simple semiclassical Anderson-theory approach is used to estimate the rates of C2H2–C2H2 rotationally inelastic collisions and these used to predict pressure broadening rates, ignoring other contributions to the broadening, which should not have resonant enhancements. It is found that exactly resonant collisions do not make a major contribution to the broadening and these calculations predict an ortho-para alternation of the pressure broadening coefficients far below what was inferred by Iwakuni et al. The present results are consistent with a large body of published work that reported self-broadening coefficients of C2H2 ro-vibrational transitions that found negligible dependence on the vibrational transition and no even-odd alternation, even for Q and S branch transitions where any such effect is predicted to be much larger than for the P and R branch transitions studied by Iwakuni et al.
A simple resonance enhanced laser ionization scheme for CO via the A1Π state
Authors: Sun Z. F. , von Zastrow A. D. , Parker D. H.
Published: March 2017

We investigate the laser ionization process taking place when the CO molecule is exposed to vacuum ultraviolet (VUV) radiation resonant with the CO A1Π(v = 0) ← X1Σ+(v = 0) transition around 154 nm, along with the ultraviolet (UV) and visible (Red) radiation used to generate VUV by four-wave difference-frequency mixing. By measuring the CO+ ion recoil and a room temperature gas spectrum, it is possible to assign the ionization process as 1 + 1’ + 1’’ REMPI where the one-photon steps refer to the VUV, UV, and Red radiation, respectively. Resonance enhanced ionization of rotational states around J = 12 arise due to the overlap of the fixed wavelength UV (∼250 nm) with the R band-head of a transition assigned to CO E1Π(v = 6) ← A1Π(v = 0) with a term value of 104 787.5 cm−1. The REMPI process is efficient and polarization sensitive and should be useful in a wide range of studies involving nascent CO.
Focus: Structure and dynamics of the interfacial layer in polymer nanocomposites with attractive interactions
Authors: Cheng Shiwang , Carroll Bobby , Bocharova Vera , Carrillo Jan-Michael , Sumpter Bobby G. , Sokolov Alexei P.
Published: March 2017

In recent years it has become clear that the interfacial layer formed around nanoparticles in polymer nanocomposites (PNCs) is critical for controlling their macroscopic properties. The interfacial layer occupies a significant volume fraction of the polymer matrix in PNCs and creates strong intrinsic heterogeneity in their structure and dynamics. Here, we focus on analysis of the structure and dynamics of the interfacial region in model PNCs with well-dispersed, spherical nanoparticles with attractive interactions. First, we discuss several experimental techniques that provide structural and dynamic information on the interfacial region in PNCs. Then, we discuss the role of various microscopic parameters in controlling structure and dynamics of the interfacial layer. The analysis presented emphasizes the importance of the polymer-nanoparticle interactions for the slowing down dynamics in the interfacial region, while the thickness of the interfacial layer appears to be dependent on chain rigidity, and has been shown to increase with cooling upon approaching the glass transition. Aside from chain rigidity and polymer-nanoparticle interactions, the interfacial layer properties are also affected by the molecular weight of the polymer and the size of the nanoparticles. In the final part of this focus article, we emphasize the important challenges in the field of polymer nanocomposites and a potential analogy with the behavior observed in thin films.
Mercury cadmium telluride surface passivation by the thin alumina film atomic-layer deposition
Authors: Kovchavtsev A. P. , Sidorov G. Yu. , Nastovjak A. E. , Tsarenko A. V. , Sabinina I. V. , Vasilyev V. V.
Published: March 2017

We analyzed the C-V curves of CdхHg1-хTe-based (x ∼ 0.22) MIS structures with Al2O3 as an insulator. Alumina films were deposited on p and n type CdхHg1-хTe by atomic layer deposition. C-V curve specific features at high and low frequencies were found to be a result of the semiconductor-dielectric interface surface state influence. The surface state density was derived from the fitting experimental C-V curves at high and low frequencies with the theoretical model. The calculated curves were obtained by solving Poisson and continuity equations within the drift-diffusion model. The charge exchange between the surface states and permitted bands was supposed to be conducted using the Shockley-Read-Hall mechanism.
Photo-assisted adsorption of gold nanoparticles onto a silicon substrate
Authors: Malyar Ivan V. , Gorin Dmitry A. , Santer Svetlana , Stetsyura Svetlana V.
Published: March 2017

We report on a photo-assisted adsorption of gold nanoparticles on a silicon substrate studied using atomic-force microscopy and secondary ion mass-spectrometry. Depending on a silicon conductivity type (n-Si or p-Si), the amount of photo-assisted adsorbed gold nanoparticles either increases (n-Si) or decreases (p-Si) on irradiation. In addition, the impacts of a cationic polyelectrolyte monolayer and adsorption time were also revealed. The polyelectrolyte layer enhances the adsorption of the gold nanoparticles but decreases the influence of light. The results of the photo-assisted adsorption on two types of silicon wafer were explained by electron processes at the substrate/solution interface.
An experimental investigation of wing-tip vortex decay in turbulence
Authors: Ghimire Hari C. , Bailey Sean C. C.
Published: March 2017

Particle image velocimetry measurements were conducted for a wing-tip vortex decaying in free-stream turbulence. The vortex exhibited stochastic collapse with free-stream turbulence present, with the breakdown initiating earlier for higher levels of turbulence. An increased rate of decay of the vortex tangential velocity was also observed, increasing with increasing free-stream turbulence. The decay of the vortex tangential velocity without the free-stream turbulence was well represented by viscous diffusion, resulting in an increase in the core radius and decrease in the peak tangential velocity. With the addition of free-stream turbulence, the rate of decay of the peak tangential velocity of the vortex increases, whereas the rate of increase of core radius remains unchanged. The circulation of the vortex decayed in time when immersed in free-stream turbulence, whereas it remained approximately constant when free-stream turbulence was not present. This decay in circulation was found to be almost entirely due to a decrease in circulation of the vortex core, caused by the relative decrease in the peak tangential velocity without a corresponding increase in the core radius. The scaling of the radial profiles of velocity and circulation was also examined, and it was found that, regardless of the free-stream condition, the core was scaled by the peak tangential velocity and core radius. The region outside the core did not scale with these quantities, and an alternative scaling for circulation is proposed which results in improved collapse of the profiles.
Particle resolved simulations of liquid/solid and gas/solid fluidized beds
Authors: Esteghamatian Amir , Hammouti Abdelkader , Lance Michel , Wachs Anthony
Published: March 2017

The present work studies particle resolved simulations of liquid/solid and gas/solid fluidization in a cuboid domain with periodic lateral boundary conditions. The focus is on investigating particles’ dynamics, while a particular care is devoted to the spatial grid resolution and statistical time convergence of the results. A statistical analysis of particles’ motion and fluid fluctuations asserts the intrinsic differences in the flow characteristics and mixing properties of these two configurations. Results reveal anisotropic mechanisms driving particles’ motion and highlight the dominance of diffusive and convective mechanisms in liquid/solid and gas/solid regimes, respectively. Following a framework similar to that of Nicolai et al. [“Particle velocity fluctuations and hydrodynamic self-diffusion of sedimenting non-Brownian spheres,” Phys. Fluids 7(1), 12–23 (1995)], we estimate the correlation time and the fluctuation length of particles’ motion. A force budget analysis is discussed to gain more insight into the role of collision in isotropization of the system. Owing to the wide range of employed grid resolutions and accurate error analysis, the present dataset is also deemed to be useful in calibrating the grid resolution for a desired accuracy of the solution in a fluidization configuration.
Three-dimensional hydrodynamic simulations of OMEGA implosions
Authors: Igumenshchev I. V. , Michel D. T. , Shah R. C. , Campbell E. M. , Epstein R. , Forrest C. J. , Glebov V. Yu. , Goncharov V. N. , Knauer J. P. , Marshall F. J. , McCrory R. L. , Regan S. P. , Sangster T. C. , Stoeckl C. , Schmitt A. J. , Obenschain S.
Published: March 2017

The effects of large-scale (with Legendre modes ≲10) asymmetries in OMEGA direct-drive implosions caused by laser illumination nonuniformities (beam-power imbalance and beam mispointing and mistiming), target offset, and variation in target-layer thickness were investigated using the low-noise, three-dimensional Eulerian hydrodynamic code ASTER. Simulations indicate that these asymmetries can significantly degrade the implosion performance. The most important sources of the asymmetries are the target offsets (∼10 to 20 μm), beam-power imbalance (σrms∼10%), and variations (∼5%) in target-layer thickness. Large-scale asymmetries distort implosion cores, resulting in a reduced hot-spot confinement and an increased residual kinetic energy of implosion targets. The ion temperature inferred from the width of simulated neutron spectra is influenced by bulk fuel motion in the distorted hot spot and can result in up to an ∼1-keV increase in apparent temperature. Similar temperature variations along different lines of sight are observed. Demonstrating hydrodynamic equivalence to ignition designs on OMEGA requires a reduction in large-scale target and laser-imposed nonuniformities, minimizing target offset, and employing highly efficient mid-adiabat (α = 4) implosion designs, which mitigate cross-beam energy transfer and suppress short-wavelength Rayleigh–Taylor growth.
Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red
Authors: Zuehlsdorff T. J. , Haynes P. D. , Payne M. C. , Hine N. D. M.
Published: March 2017

The solvatochromic shift, as well as the change in colour of the simple organic dye nile red, is studied in two polar and two non-polar solvents in the context of large-scale time-dependent density-functional theory (TDDFT) calculations treating large parts of the solvent environment from first principles. We show that an explicit solvent representation is vital to resolve absorption peak shifts between nile red in n-hexane and toluene, as well as acetone and ethanol. The origin of the failure of implicit solvent models for these solvents is identified as being due to the strong solute-solvent interactions in form of π-stacking and hydrogen bonding in the case of toluene and ethanol. We furthermore demonstrate that the failures of the computationally inexpensive Perdew-Burke-Ernzerhof (PBE) functional in describing some features of the excited state potential energy surface of the S1 state of nile red can be corrected for in a straightforward fashion, relying only on a small number of calculations making use of more sophisticated range-separated hybrid functionals. The resulting solvatochromic shifts and predicted colours are in excellent agreement with experiment, showing the computational approach outlined in this work to yield very robust predictions of optical properties of dyes in solution.
Optimizing isotope substitution in graphene for thermal conductivity minimization by genetic algorithm driven molecular simulations
Authors: Davies Michael , Ganapathysubramanian Baskar , Balasubramanian Ganesh
Published: March 2017

We present results from a computational framework integrating genetic algorithm and molecular dynamics simulations to systematically design isotope engineered graphene structures for reduced thermal conductivity. In addition to the effect of mass disorder, our results reveal the importance of atomic distribution on thermal conductivity for the same isotopic concentration. Distinct groups of isotope-substituted graphene sheets are identified based on the atomic composition and distribution. Our results show that in structures with equiatomic compositions, the enhanced scattering by lattice vibrations results in lower thermal conductivities due to the absence of isotopic clusters.
Radiation-induced alloy rearrangement in InxGa1−xN
Authors: Prozheeva V. , Makkonen I. , Cuscó R. , Artús L. , Dadgar A. , Plazaola F. , Tuomisto F.
Published: March 2017

The effect of radiation damage on the defect and alloy structure in InxGa1−xN thin films grown on Si substrates was studied using positron annihilation spectroscopy. Prior to the measurements, the samples were subjected to double He+ implantation at 40 and 100 keV. The results show the presence of cation vacancy-like defects in high concentrations (>1018 cm−3) already in the as-grown samples. The evolution of the annihilation characteristics after the implantation suggests strong alloy disorder rearrangement under irradiation.
Poisson effect driven anomalous lattice expansion in metal nanoshells
Authors: Iyer Ganesh , Shervani Suboohi , Mishra Gargi , De Deb , Kumar Arun , Sivakumar Sri , Balani Kantesh , Pala Raj , Subramaniam Anandh
Published: March 2017

Surface stress can have profound effects on nanoscale materials and can lead to a contraction of the lattice in nanoparticles to compensate for the under-coordination of the surface atoms. The effect of elastic properties like Poisson's ratio can be accentuated in lower dimensional systems. The current study focuses on hollow metal nanoshells (MNSs), wherein there is interplay between the surface stresses existing in the inner and outer surfaces. Using a two scale computational method and transmission electron microscopy, we not only show a lattice expansion (in the radial direction) due to purely surface stress effects in a metallic system but also discover anomalous lattice expansion in the case of very thin walled MNSs. We argue that this effect, wherein the stress in the outer surface causes expansion in the radial lattice parameter (instead of compression), is a Poisson effect driven phenomenon. Although Ni nanoshells are used as an illustrative system for the studies, we generalize this effect for all metal nanoshells.
Self-reference line-dispersion interferometric microscopy
Authors: Hosseini Poorya , Lue Niyom , Yaqoob Zahid , Dasari Ramachandra R. , So Peter T. C.
Published: March 2017

We have developed a line-scanning interferometric microscope capable of measuring the quantitative phase over a wide continuous spectrum. The sample is illuminated with a spatially coherent broadband light source shaped into a line beam that interferes with itself in a Michelson configuration, coupled with a grating-based spectrometer. The spatial modulation of the interference pattern in the direction orthogonal to the wavelength axis in the spectrograph image plane allows obtaining the spectral quantitative phase along the line illumination in a single measurement. We show the feasibility of the technique by quantifying the refractive index of polystyrene beads immersed in oil and the dispersive properties of live cells over the visible spectrum.
Effect of inserting a non-metal C layer on the spin-orbit torque induced magnetization switching in Pt/Co/Ta structures with perpendicular magnetic anisotropy
Authors: Li Dong , Cui Baoshan , Wang Tao , Yun Jijun , Guo Xiaobin , Wu Kai , Zuo Yalu , Wang Jianbo , Yang Dezheng , Xi Li
Published: March 2017

Magnetization switching via charge current induced spin-orbit torques (SOTs) in heavy metal/ferromagnetic metal/heavy metal heterostructures has become an important issue due to its potential applications in high stability and low energy dissipation spintronic devices. In this work, based on a Pt/Co/Ta structure with perpendicular magnetic anisotropy (PMA), we report the effect of inserting a non-metal C interlayer between Co and Ta on the current-induced magnetization switching. A series of measurements based on the extraordinary Hall effect were carried out to investigate the difference of the anisotropy field, switching field, and damping-like and field-like SOT-induced effective fields as well as the current-induced spin Hall effect (SHE) torque after C decoration. The results show that PMA can be reduced by C decoration and the ratio of the effective SHE torque per unit current density and anisotropy field plays an essential role in the switching efficiency. In addition, the obtained switching current density has a quite low value around the order of 106 A/cm2. Our study could provide a way for achieving the low switching current density by manipulating PMA in SOT-based spintronic devices through interface decoration.