bluuebunny/crossref_metadata_2025 huggingface dataset:
Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase
Authors: Bai Liping , Fujishiro Takashi , Huang Gangfeng , Koch Jürgen , Takabayashi Atsushi , Yokono Makio , Tanaka Ayumi , Xu Tao , Hu Xile , Ermler Ulrich , Shima Seigo
Published: October 2016

The greenhouse gas and energy carrier methane is produced on Earth mainly by methanogenic archaea. In the hydrogenotrophic methanogenic pathway the reduction of one CO2 to one methane molecule requires four molecules of H2 containing eight electrons. Four of the electrons from two H2 are supplied for reduction of an electron carrier F420, which is catalyzed by F420-reducing [NiFe]-hydrogenase under nickel-sufficient conditions. The same reaction is catalysed under nickel-limiting conditions by [Fe]-hydrogenase coupled with a reaction catalyzed by F420-dependent methylene tetrahydromethanopterin dehydrogenase. [Fe]-hydrogenase contains an iron-guanylylpyridinol (FeGP) cofactor for H2 activation at the active site. FeII of FeGP is coordinated to a pyridinol-nitrogen, an acyl-carbon, two CO and a cysteine-thiolate. We report here on comparative genomic analyses of biosynthetic genes of the FeGP cofactor, which are primarily located in a hmd-co-occurring (hcg) gene cluster. One of the gene products is HcgB which transfers the guanosine monophosphate (GMP) moiety from guanosine triphosphate (GTP) to a pyridinol precursor. Crystal structure analysis of HcgB from Methanococcus maripaludis and its complex with 6-carboxymethyl-3,5-dimethyl-4-hydroxy-2-pyridinol confirmed the physiological guanylyltransferase reaction. Furthermore, we tested the properties of semi-synthetic [Fe]-hydrogenases using the [Fe]-hydrogenase apoenzyme from several methanogenic archaea and a mimic of the FeGP cofactor. On the basis of the enzymatic reactions involved in the methanogenic pathway, we came up with an idea how the methanogenic pathway could be simplified to develop an artificial methanogenesis system.
Effective synthesis of dimethylhexane-1,6-dicarbamate from 1,6-hexanediamine and dimethyl carbonate using 3-amino-1,2,4-triazole potassium as a solid base catalyst at ambient temperature
Authors: Wang Peixue , Fei Yuqing , Li Qinghe , Deng Youquan
Published: October 2016

Efficient syntheses of N-substituted carbamates from linear amines and dimethyl carbonate over KATriz catalyst at ambient temperature.
Silver-initiated radical ring expansion/fluorination of ethynyl cyclobutanols: efficient synthesis of monofluoroethenyl cyclopentanones
Authors: Tian Qingshan , Chen Bin , Zhang Guozhu
Published: October 2016

A stereoselective synthesis of β-halogenated 2-methylenecyclopentanones via silver-catalyzed formal ring expansion using water as the cosolvent is described.
Impact of Laser-Induced Breakdown Spectroscopy data normalization on multivariate classification accuracy
Authors: Pořízka P. , Klus J. , Hrdlička A. , Vrábel J. , Škarková P. , Prochazka D. , Novotný J. , Novotný K. , Kaiser J.
Published: October 2016

Normalization of data is significant and should be chosen according to the sample matrix under investigation.
Simple and reusable off-the-shelf microfluidic devices for the versatile generation of droplets
Authors: Li Tianbao , Zhao Lei , Liu Wenming , Xu Juan , Wang Jinyi
Published: October 2016

We demonstrated a pragmatic and facile approach to assemble microfluidic droplet devices using off-the-shelf components.
Spatiotemporal control of kinesin motor protein by photoswitches enabling selective single microtubule regulations
Authors: Kumar K. R. Sunil , Amrutha Ammathnadu S. , Tamaoki Nobuyuki
Published: October 2016

Artificial control of bio-nanomachines should have a major impact on the development of controllable transport systems for specific cargo transport on chips.
Synthesis and pharmacological evaluation of novel selective MOR agonist 6β-pyridinyl amidomorphines exhibiting long-lasting antinociception
Authors: Urai Ákos , Váradi András , Szőcs Levente , Komjáti Balázs , Le Rouzic Valerie , Hunkele Amanda , Pasternak Gavril W. , Majumdar Susruta , Hosztafi Sándor
Published: October 2016

The synthesized novel 6β-pyridinyl amidomorphines exhibit long-lasting antinociception.
Synthetic methods for 1,3-diamines
Authors: Ji Xiaolei , Huang Hanmin
Published: October 2016

In this review, the synthetic methods for the preparation of 1,3-diamines and their applications in synthetic organic chemistry are summarized.
A metal-free cyclic iminium induced one-pot double annulation cascade: access to dihydroisoquinolinium (DHIQ) salts
Authors: Sagar A. , Nagarjuna Babu Venkata , Shinde Anand H. , Sharada Duddu S.
Published: October 2016

A reactive cyclic iminium induced one-pot Groebke–Blackburn–Bienayme (GBB) double annulation cascade (DAC) for the synthesis of skeletally diverse DHIQ salts has been described. The key features of this protocol are solvent-free, robust method, clean reaction profile and operational simplicity.
How to manipulate the upper critical solution temperature (UCST)?
Authors: Niskanen Jukka , Tenhu Heikki
Published: October 2016

In this mini-review, we discuss multi-stimuli-responsive polymers, which exhibit upper critical solution temperature (UCST) behavior mainly in aqueous solutions, and focus on examples where counter ions, electricity, light, or pH influence the thermoresponsiveness of these polymers.
Synthesis of poly(methyl methacrylate) and block copolymers by semi-batch nitroxide mediated polymerization
Authors: Ballard N. , Simula A. , Aguirre M. , Leiza J. R. , van Es S. , Asua J. M.
Published: October 2016

The limits of control of the molecular weight and polymer structure in the semi-batch solution polymerization of methyl methacrylate by NMP are explored.
A highly efficient synthesis of the DEFG-ring system of rubriflordilactone B
Authors: Wang Yong , Zhang Yuhan , Li Zhongle , Yang Zhenjie , Xie Zhixiang
Published: October 2016

A highly efficient synthesis of the DEFG-ring system of rubriflordilactone B via polar-radical-crossover cycloaddition and carbonyl allylation/lactonization is described.
Use of network model to explore dynamic and allosteric properties of three GPCR homodimers
Authors: Jiang Yuanyuan , Yuan Yuan , Zhang Xi , Liang Tao , Guo Yanzhi , Li Menglong , Pu Xumei
Published: October 2016

We used an elastic network model and protein structure network to study three class A GPCR homodimers.
A novel diagnostic method of Raman spectroscopy for malignant pheochromocytoma/paraganglioma
Authors: Du Yiqing , Huang Zhixin , Wang Lei , Huang Liqing , Cao Peilong , He Dalin , zhang Yue , Wu Dapeng , Yang Zhishang , Fan Jinhai
Published: October 2016

Raman spectroscopy, a potential tool in diagnosis of malignant pheochromocytoma/paraganglioma.
Nitrogen-doped porous carbon with a hierarchical structure prepared for a high performance symmetric supercapacitor
Authors: Lei Ze-Kun , Li Ying , Zhang Lin-Qun , Zhou Zhi-Xin , Liu An-Ran , Zhang Yuan-Jian , Liu Song-Qin
Published: October 2016

The synthesis of nitrogen-doped hierarchical porous carbon materials for high performance supercapacitors through carbonization of PoPD by using molten-salt as a template.
CRANAD-1 as a cyanide sensor in aqueous media: a theoretical study
Authors: Sherin D. R. , Manojkumar T. K. , Rajasekharan K. N.
Published: October 2016

The lethal toxicity of cyanide ions to animals and the environment has led to considerable research into the development of methods for rapid and sensitive cyanide detection.
A numerical study of the photothermal behaviour of near-infrared plasmonic colloids
Authors: Liu Kai , Xue Xiaozheng , Furlani Edward P.
Published: October 2016

3D computational analysis is performed to investigate and compare plasmonic and photothermal behavior of silica@Au core–shell nanoparticles and Au nanocages.
Induction of smectic polymorphism in bent-core derivatives of the 6-oxoverdazyl by partial fluorination of alkyl chains
Authors: Ciastek Sylwia , Kaszyński Piotr , Pociecha Damian , Jasiński Marcin
Published: October 2016

A series of bent-core mesogens 2[m,n] derived from the 6-oxoverdazyl radical and containing partially fluorinated alkyl tails was prepared and investigated by thermal, optical, XRD and EPR methods.
Non-stoichiometric Co(ii), Ni(ii), Zn(ii)-ferrite nanospheres: size controllable synthesis, excellent gas-sensing and magnetic properties
Authors: Xu Yanyan , Sun Dandan , Hao Hongying , Gao Dongzhao , Sun Yaqiu
Published: October 2016

Non-stoichiometric Co(ii), Ni(ii), Zn(ii)-ferrite nanospheres with controllable size, superior magnetic property and gas-sensing behavior were synthesized and characterized thoroughly.
Ultrathin-nanosheet-assembled Bi2MoO6 mesoporous hollow framework for realizing optimized sunlight-driven photocatalytic water oxidation
Authors: Hao Yuchen , Dong Xiaoli , Wang Xiuying , Ma Hongchao , Zhang Xiufang
Published: October 2016

A Bi2MoO6 mesoporous hollow framework composed of atomically-thin nanosheets was fabricated for the first time using a one-step solvothermal route and exhibited improved photocatalytic performance for water oxidation.
One-step solvothermal synthesis of Al-promoted Fe3O4 magnetic catalysts for the selective oxidation of benzyl alcohol to benzaldehyde with H2O2 in water
Authors: Xiong Leisha , Chen Rong , Chen Fengxi
Published: October 2016

The in situ modification of Fe3O4 by aluminium introduced new active sites besides the primary iron sites. Their synergistic effect contributes to much better catalytic activity of Al-promoted Fe3O4 in the title reaction.
Bio-based elastomer nanoparticles with controllable biodegradability
Authors: Wang Qingguo , Zai Yingying , Yang Dejing , Qiu Liyan , Niu Chengqun
Published: October 2016

Using melt polycondensation of bio-derived dicarboxylic acids and diols, followed by polyester emulsification and radiation, we fabricate the bio-based elastomer nanoparticles with controllable biodegradability, which can be used in biomedical fields.
The structural assembly switch of cell division protein FtsZ probed with fluorescent allosteric inhibitors
Authors: Artola Marta , Ruíz-Avila Laura B. , Ramírez-Aportela Erney , Martínez R. Fernando , Araujo-Bazán Lidia , Vázquez-Villa Henar , Martín-Fontecha Mar , Oliva María A. , Martín-Galiano A. Javier , Chacón Pablo , López-Rodríguez María L. , Andreu José M. , Huecas Sonia
Published: October 2016

The assembly switch of cell division protein FtsZ monitored with a fluorescent probe targeting the cleft between domains.
Intramolecular-initiating photopolymerization behavior of nanogels with the capability of reducing shrinkage
Authors: Han Junyi , Jiang Shengling , Gao Yanjing , Sun Fang
Published: October 2016

Multifunctional nanogels are successfully synthesized to initiate photopolymerization and to reduce polymerization shrinkage under UV irradiation.
The zebrafish homologs of SET/I2PP2A oncoprotein: expression patterns and insights into their physiological roles during development
Authors: Serifi Iliana , Tzima Eleni , Soupsana Katerina , Karetsou Zoe , Beis Dimitris , Papamarcaki Thomais
Published: October 2016

The oncoprotein SET/I2PP2A (protein phosphatase 2A inhibitor 2) participates in various cellular mechanisms such as transcription, cell cycle regulation and cell migration. SET is also an inhibitor of the serine/threonine phosphatase PP2A, which is involved in the regulation of cell homeostasis. In zebrafish, there are two paralogous set genes that encode Seta (269 amino acids) and Setb (275 amino acids) proteins which share 94% identity. We show here that seta and setb are similarly expressed in the eye, the otic vesicle, the brain and the lateral line system, as indicated by in situ hybridization labeling. Whole-mount immunofluorescence analysis revealed the expression of Seta/b proteins in the eye retina, the olfactory pit and the lateral line neuromasts. Loss-of-function studies using antisense morpholino oligonucleotides targeting both seta and setb genes (MOab) resulted in increased apoptosis, reduced cell proliferation and morphological defects. The morphant phenotypes were partially rescued when MOab was co-injected with human SET mRNA. Knockdown of setb with a transcription-blocking morpholino oligonucleotide (MOb) resulted in phenotypic defects comparable with those induced by setb gRNA (guide RNA)/Cas9 [CRISPR (clustered regularly interspaced short palindromic repeats)-associated 9] injections. In vivo labeling of hair cells showed a significantly decreased number of neuromasts in MOab-, MOb- and gRNA/Cas9-injected embryos. Microarray analysis of MOab morphant transcriptome revealed differential expression in gene networks controlling transcription in the sensory organs, including the eye retina, the ear and the lateral line. Collectively, our results suggest that seta and setb are required during embryogenesis and play roles in the zebrafish sensory system development.
Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans
Authors: Agapov Aleksei , Esyunina Daria , Pupov Danil , Kulbachinskiy Andrey
Published: October 2016

Transcription factors of the Gre family bind within the secondary channel of bacterial RNA polymerase (RNAP) directly modulating its catalytic activities. Universally conserved Gre factors activate RNA cleavage by RNAP, by chelating catalytic metal ions in the RNAP active site, and facilitate both promoter escape and transcription elongation. Gfh factors are Deinococcus/Thermus-specific homologues of Gre factors whose transcription functions remain poorly understood. Recently, we found that Gfh1 and Gfh2 proteins from Deinococcus radiodurans dramatically stimulate RNAP pausing during transcription elongation in the presence of Mn2+, but not Mg2+, ions. In contrast, we show that Gfh1 and Gfh2 moderately inhibit transcription initiation in the presence of either Mg2+ or Mn2+ ions. By using a molecular beacon assay, we demonstrate that Gfh1 and Gfh2 do not significantly change promoter complex stability or the rate of promoter escape by D. radiodurans RNAP. At the same time, Gfh factors significantly increase the apparent KM value for the 5′-initiating nucleotide, without having major effects on the affinity of metal ions for the RNAP active site. Similar inhibitory effects of Gfh factors are observed for transcription initiation on promoters recognized by the principal and an alternative σ factor. In summary, our data suggest that D. radiodurans Gfh factors impair the binding of initiating substrates independently of the metal ions bound in the RNAP active site, but have only mild overall effects on transcription initiation. Thus the mechanisms of modulation of RNAP activity by these factors are different for various steps of transcription.
2D single snapshot imaging using MIMO radar based on SR
Authors: Chen Chunhui , Zhang Qun , Gu Fufei , Luo Ying
Published: October 2016

To overcome the disadvantages of the required motion compensation in the traditional inverse synthetic aperture radar imaging of moving targets, a 2D single snapshot imaging method using a MIMO radar based on the sparse representation (SR) is proposed. It can simultaneously recover a real‐time 2D image and avoid motion compensation. By exploiting the sparsity and data structure of the echo signals, a 2D SR model is established. The SR problem is solved based on the compressed sensing theory and the 2D smoothed L0 algorithm. Finally, the 2D image of the target can be reconstructed at low signal‐to‐noise ratio and high compressed ratio, which is advantageous for target recognition and classification. Compared with the existing 1D methods, the proposed method can directly recover 2D images and has lower computational complexity. Simulations are performed to verify the effectiveness of the method.
Robust DED based on bad scenario set considering wind, EV and battery switching station
Authors: Zhi‐gang Lu , Hao Zhao , Hai‐feng Xiao , Jiang‐feng Zhang , Xue‐ping Li , Xiao‐feng Sun
Published: October 2016

With the increasing penetration of wind power and electric vehicle (EV) into the power system, system operators face new challenges for system reliability and generation cost due to the intermittent of wind power. Furthermore, the randomly connected EVs at different time periods and locations add more uncertainty to the power system. In this study, uncertainties in wind power generation and EV charging load are modelled into the day‐ahead dynamic economic dispatch (DED) problem, solution feasibility and robustness are discussed, and the bad scenario set is formulated for the day‐ahead DED problem. In the obtained model, parameters can be used to adjust the positive bias or conservative bias, charging/discharging power of battery switch stations are also controlled to optimise the total cost of power system. To solve the optimisation problem, the multi‐agent bacterial colony chemotaxis algorithm and a mutation strategy based on the cloud theory are developed. The simulation results show that the proposed method is effective, and battery switching station can help to reduce total cost by charging and discharging batteries.
Mixed AC high‐voltage direct current benchmark test system for security constrained optimal power flow calculation
Authors: Sass Florian , Sennewald Tom , Marten Anne‐Katrin , Westermann Dirk
Published: October 2016

Mixed AC‐HVDC systems enable new perspectives in the fields of operation, control and security of AC transmission systems. Although a promising vision, meshed HVDC grids do not exist in a real setting. Research on HVDC grid operation is therefore in need of valid test systems for static and dynamic aspects. Besides the CIGRÉ test system, which focuses on offshore factors and which is consequently not an overlay HVDC grid, a publically available test system does not currently exist. Recent publications in this field adapt established standard AC test systems to their case‐related requirements of an HVDC extension. This work introduces and provides a mixed AC‐HVDC test system enabling the evaluation of optimal power flow and security constrained OPF algorithms. State‐of‐the‐art literature for HVDC‐OPF applications is assessed, applied AC standard test systems are evaluated and key indices are derived from the findings. With respect to this, the proposed test system's validity and the AC grid's reference to reality is ensured. The proposed system, comprising 67 AC nodes, 102 AC branches, 9 VSCs and 11 HVDC branches, contains 13 critical contingencies which can be removed by either preventive or corrective measures. The data describing the proposed system is provided.
Wave-front error breakdown in laser guide star multi-object adaptive optics validated on-sky by Canary
Authors: Martin O. A. , Gendron É. , Rousset G. , Gratadour D. , Vidal F. , Morris T. J. , Basden A. G. , Myers R. M. , Correia C. M. , Henry D.
Published: October 2016

Context. Canary is the multi-object adaptive optics (MOAO) on-sky pathfinder developed in the perspective of multi-object spectrograph on extremely large telescopes (ELTs). In 2013, Canary was operated on-sky at the William Herschel telescope (WHT), using three off-axis natural guide stars (NGS) and four off-axis Rayleigh laser guide stars (LGS), in open-loop, with the on-axis compensated turbulence observed with a H-band imaging camera and a Truth wave-front sensor (TS) for diagnostic purposes.

Aims. Our purpose is to establish a reliable and accurate wave-front error breakdown for LGS MOAO. This will enable a comprehensive analysis of Canary on-sky results and provide tools for validating simulations of MOAO systems for ELTs.

Methods. To evaluate the MOAO performance, we compared the Canary on-sky results running in MOAO, in single conjugated adaptive optics (SCAO) and in ground layer adaptive optics (GLAO) modes, over a large set of data acquired in 2013. We provide a statistical study of the seeing. We also evaluated the wave-front error breakdown from both analytic computations, one based on a MOAO system modelling and the other on the measurements from the Canary TS. We have focussed especially on the tomographic error and we detail its vertical error decomposition.

Results. We show that Canary obtained 30.1%, 21.4% and 17.1% H-band Strehl ratios in SCAO, MOAO and GLAO respectively, for median seeing conditions with 0.66′′ of total seeing including 0.59′′ at the ground. Moreover, we get 99% of correlation over 4500 samples, for any AO modes, between two analytic computations of residual phase variance. Based on these variances, we obtain a reasonable Strehl-ratio (SR) estimation when compared to the measured IR image SR. We evaluate the gain in compensation for the altitude turbulence brought by MOAO when compared to GLAO.
Operative Strategies during Awake Surgery Affect Deterioration of Paresis a Month after Surgery for Brain Lesions in the Primary Motor Area
Authors: Midorikawa Akira , Yamada Ryoji , Hiromitsu Kentaro , Itoi Chihiro , Saito Shoko , Yagi Kazuo , Shinoura Nobusada
Published: October 2016

Introduction We analyzed factors associated with worsened paresis at 1-month follow-up in patients with brain tumors located in the primary motor area (M1) to establish protocols for safe awake craniotomy for M1 lesions.

Methods Patients with M1 brain tumors who underwent awake surgery in our hospital (n = 61) were evaluated before, during, and immediately and 1 month after surgery for severity of paresis, tumor location, extent of resection, complications, preoperative motor strength, histology, and operative strategies (surgery stopped or continued after deterioration of motor function).

Results Worsened paresis at 1-month follow-up was significantly associated with worsened paresis immediately after surgery and also with operative strategy. Specifically, when motor function deteriorated during awake surgery and did not recover within 5 to 10 minutes, no deterioration was observed at 1-month follow-up in cases where we stopped surgery, whereas 6 of 13 cases showed deteriorated motor function at 1-month follow-up in cases where we continued surgery.

Conclusion Stopping tumor resection on deterioration of motor function during awake surgery may help prevent worsened paresis at 1-month follow-up.
Knots and black holes: why we’re all prone to madness and what we can do about it
Authors: Kinderman Peter
Published: October 2016

People from all walks of life can suffer from mental health problems such as low mood, anxiety, obsessive-compulsive problems, even hearing voices. In extreme circumstances, people can begin to fear that other people are plotting to harm them, and some of us even take our own lives. While it is overwhelmingly true that traumatic experiences or on-going deprivation or abuse are possible factors that contribute to psychological problems, there remains an apparent capriciousness to mental health problems. Some people seem to rise above trauma; other people are plagued by great misery without obvious external causes. There is a tendency to explain these differences as reflecting personal, even biological, vulnerabilities. This article is published as part of a collection entitled “On balance: lifestyle, mental health and wellbeing”.
On balance: lifestyle, mental health and wellbeing
Authors: Haggett Ali
Published: October 2016

Given the supremacy of the biomedical model in defining our understanding and treatment of a wide range of physcial and psychological disorders, it is perhaps curious that simultaneously, scientists, clinicians, governments and patients routinely employ the concepts of “lifestyle” and “balance” to try to explain the causes of bodily disease and psychological disorder. Concurrently, the health advantages that are assumed to be inherent in a “balanced life” have been exploited by a rapidly expanding consumer market in “wellbeing”—by companies and individuals promoting food supplements, “wearable fitness”, diet trends and the self-help material. Exploring the tension between the biomedical doctrine and the parallel preoccupation with balance and lifestyle has provided the impetus for this special issue. Emerging originally from papers presented at an interdisciplinary conference held at the University of Exeter in June 2015, and augmented by two further comment pieces, the collection of articles aims to explore the ways in which changing notions of “balance” have been used to understand the causes of mental illness; to rationalise new approaches to its treatment; and to validate advice relating to balance in work and family life.
“Not to come near our person by ten mile”: London, plague and spatial relations in 2 Henry IV
Authors: Knowles Katie
Published: October 2016

Unlike many of his contemporaries, Shakespeare rarely set his plays in London and those of his plays that are partially set in the capital do not seem particularly interested in their location. Consequently studies of early modern London in Renaissance drama have tended to focus on the city comedies, or on those of Shakespeare’s plays where another city (Rome, Athens, Venice and so on), might be argued to “stand in” for or shadow early modern London and its concerns. Shakespeare’s histories, therefore, have not featured as prominently in discussions of dramatic presentations of early modern London as they deserve to. This article suggests that2 Henry IVis deeply concerned with what Henri Lefebvre termed “the production of space”, but that it is not in its location of scenes in Eastcheap or Westminster that this play reveals its immersion in the early modern London of its production, but in its discourse of disease, its imagery of boundaries and containment, and its repeated evocation of fluid and equivocal spaces, including the tavern, the battlefield and the crown itself. It reads the play’s imagery of contradictory, ambiguous and transformative spaces, and of boundaries being set up and broken, as implicitly engaged with contemporary preoccupations with London’s shifting cultural and geographical identity, the growth and character of the suburbs, and particularly with fears about plague and its transmission across city spaces. It concludes that the fluid nature of urban space, and the artificial nature of boundaries are brought into focus by crises such as plague, and that the play’s discourse of contagion can be read as an illuminating backdrop to its emphasis on changeable and disorienting spaces. This article is published as part of a collection to commemorate the 400th anniversary of Shakespeare’s death.
From paradox to principles: where next for scientific advice to governments?
Authors: Gluckman Peter , Wilsdon James
Published: October 2016

Scientific advice to governments has never been in greater demand; nor has it been more contested. From climate change to cyber-security, poverty to pandemics, food technologies to fracking, the questions being asked of scientists, engineers and other experts by policymakers, the media and the wider public continue to multiply and increase in complexity. At the same time, the authority and legitimacy of experts are under increasing scrutiny. This thematic article collection (‘special issue’) brings together perspectives on the theory, practice and politics of scientific advice that build on the conclusions of the landmark conference in Auckland in August 2014, which led to the creation of the International Network for Government Science Advice (INGSA). We hope that new papers will continue to be added to this collection over the next year and beyond, making it a living, fully open access repository for new scholarship and policy thinking—and an important contribution to the emerging science and art of scientific advice.
Experimental investigation of energy localization in line-defect resonator based on silicon locally resonant phononic crystal
Authors: Jiang Wanli , Feng Duan , Xu Dehui , Xiong Bin , Wang Yuelin
Published: October 2016

In this paper, energy localization in line-defect resonator based on locally resonant phononic crystal (PnC) is experimentally studied. The defected resonator is realized by creating line defects on a two-dimension (2-D) silicon PnC. The silicon resonator was fabricated by micro machining process and tested by a combination of the fluid coupling method and Laser Doppler Vibrometer (LDV). Acoustic waves with frequency range from 7.19 MHz to 7.50 MHz are trapped in the cavity, and the corresponding resonant modes are observed in-situ. The measured quality (Q) factor of the resonator, which is 427 at its resonant frequency of 7.3 MHz, is smaller than the simulated ones (666 and 5135). The experimental results agree well with the simulation results that frequencies of the trapped acoustic waves of are mostly in the range of the phononic bandgaps. The locally resonant based PnC resonator in paper with 17 dB magnitude amplification, which is normalized with respect to the transmission of a freestanding silicon slab in the same frequency range, has great potential in energy harvesting or sound concentration.
Why many polymers are so fragile: A new perspective
Authors: Dalle-Ferrier C. , Kisliuk A. , Hong L. , Carini G. , Carini G. , D’Angelo G. , Alba-Simionesco C. , Novikov V. N. , Sokolov A. P.
Published: October 2016

Many polymers exhibit much steeper temperature dependence of their structural relaxation time (higher fragility) than liquids of small molecules, and the mechanism of this unusually high fragility in polymers remains a puzzle. To reveal additional hints for understanding the underlying mechanism, we analyzed correlation of many properties of polymers to their fragility on example of model polymer polystyrene with various molecular weights (MWs). We demonstrate that these correlations work for short chains (oligomers), but fail progressively with increase in MW. Our surprising discovery is that the steepness of the temperature dependence (fragility) of the viscosity that is determined by chain relaxation follows the correlations at all molecular weights. These results suggest that the molecular level relaxation still follows the behavior usual for small molecules even in polymers, and its fragility (chain fragility) falls in the range usual for molecular liquids. It is the segmental relaxation that has this unusually high fragility. We speculate that many polymers cannot reach an ergodic state on the time scale of segmental dynamics due to chain connectivity and rigidity. This leads to sharper decrease in accessible configurational entropy upon cooling and results in steeper temperature dependence of segmental relaxation. The proposed scenario provides a new important insight into the specifics of polymer dynamics: the role of ergodicity time and length scale. At the end, we suggest that a similar scenario can be applicable also to other molecular systems with slow intra-molecular degrees of freedom and to chemically complex systems where the time scale of chemical fluctuations can be longer than the time scale of structural relaxation.
Approach for removing ghost-images in remote field eddy current testing of ferromagnetic pipes
Authors: Luo Q. W. , Shi Y. B. , Wang Z. G. , Zhang W. , Zhang Y.
Published: October 2016

In the non-destructive testing of ferromagnetic pipes based on remote field eddy currents, an array of sensing coils is often used to detect local defects. While testing, the image that is obtained by sensing coils exhibits a ghost-image, which originates from both the transmitter and sensing coils passing over the same defects in pipes. Ghost-images are caused by transmitters and lead to undesirable assessments of defects. In order to remove ghost-images, two pickup coils are coaxially set to each other in remote field. Due to the time delay between differential signals tested by the two pickup coils, a Wiener deconvolution filter is used to identify the artificial peaks that lead to ghost-images. Because the sensing coils and two pickup coils all receive the same signal from one transmitter, they all contain the same artificial peaks. By subtracting the artificial peak values obtained by the two pickup coils from the imaging data, the ghost-image caused by the transmitter is eliminated. Finally, a relatively highly accurate image of local defects is obtained by these sensing coils. With proposed method, there is no need to subtract the average value of the sensing coils, and it is sensitive to ringed defects.
Solution-processed organic ferroelectric field-effect transistors on ultra-flexible substrates
Authors: Kim Min Gee , Han Dae Hee , Park Kyung Eun , Park Byung-Eun
Published: October 2016

We fabricated ultra-flexible organic non-volatile ferroelectric field-effect transistors (FeFETs) with poly(vinylidene fluoride-trifluoroethylene) [P(VDF-TrFE)] on polyimide substrates, which adopted a solution-based top-contact/bottom-gate structure for low cost process without patterning. P(VDF-TrFE) gate dielectric layers and regioregular poly(3-hexylthiophene) active layers were formed by the spin-coating method. The field-effect mobility (μFE) was ∼0.28 cm2/V s, the on/off ratio was approximately 5.6 × 103, and the memory window (threshold voltage shift) was approximately 7 V. In addition, FeFETs were operated even at small bend radii without considerable changes in these values.
Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations
Authors: Yin Shi , Bernstein Elliot R.
Published: October 2016

A new magnetic-bottle time-of-flight photoelectron spectroscopy (PES) apparatus is constructed in our laboratory. The PES spectra of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide [FeSm(SH)n−; m, n = 0–3, 0 < (m + n) ≤ 3] cluster anions, obtained at 2.331 eV (532 nm) and 3.492 eV (355 nm) photon energies, are reported. The electronic structure and bonding properties of these clusters are additionally investigated at different levels of density functional theory. The most probable structures and ground state spin multiplicity for these cluster anions are tentatively assigned by comparing their theoretical first vertical detachment energies (VDEs) with their respective experiment values. The behavior of S and (SH) as ligands in these iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions is investigated and compared. The experimental first VDEs for Fe(SH)1−3− cluster anions are lower than those found for their respective FeS1−3− cluster anions. The experimental first VDEs for FeS1−3− clusters are observed to increase for the first two S atoms bound to Fe−; however, due to the formation of an S–S bond for the FeS3− cluster, its first VDE is found to be ∼0.41 eV lower than the first VDE for the FeS2− cluster. The first VDEs of Fe(SH)1−3− cluster anions are observed to increase with the increasing numbers of SH groups. The calculated partial charges of the Fe atom for ground state FeS1−3− and Fe(SH)1−3− clusters are apparently related to and correlated with their determined first VDEs. The higher first VDE is correlated with a higher, more positive partial charge for the Fe atom of these cluster anions. Iron sulfide/hydrosulfide mixed cluster anions are also explored in this work: the first VDE for FeS(SH)− is lower than that for FeS2−, but higher than that for Fe(SH)2−; the first VDEs for FeS2(SH)− and FeS(SH)2− are close to that for FeS3−, but higher than that for Fe(SH)3−. The first VDEs of general iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide clusters [FeSm(SH)n−; m, n = 0–3, 0 < (m + n) ≤ 3] are dependent on three properties of these anions: 1. the partial charge on the Fe atom, 2. disulfide bond formation (S–S) in the cluster, and 3. the number of hydrosulfide ligands in the cluster. The higher the partial charge on the Fe atom of these clusters, the larger the first VDE; however, cluster S–S bonding and more (SH) ligands in the cluster lower the cluster anion first VDE.
Accelerating the search for global minima on potential energy surfaces using machine learning
Authors: Carr S. F. , Garnett R. , Lo C. S.
Published: October 2016

Controlling molecule-surface interactions is key for chemical applications ranging from catalysis to gas sensing. We present a framework for accelerating the search for the global minimum on potential surfaces, corresponding to stable adsorbate-surface structures. We present a technique using Bayesian inference that enables us to predict converged density functional theory potential energies with fewer self-consistent field iterations. We then discuss how this technique fits in with the Bayesian Active Site Calculator, which applies Bayesian optimization to the problem. We demonstrate the performance of our framework using a hematite (Fe2O3) surface and present the adsorption sites found by our global optimization method for various simple hydrocarbons on the rutile TiO2 (110) surface.
Similarity transformation approach for ferromagnetic mixed convection flow in the presence of chemically reactive magnetic dipole
Authors: Hayat Tasawar , Ijaz Khan Muhammad , Imtiaz Maria , Alsaedi Ahmed , Waqas Muhammad
Published: October 2016

A simple model of chemical reactions for two dimensional ferrofluid flows is constructed. The impact of magnetic dipole and mixed convection is further analyzed. Flow is caused by linear stretching of the sheet. Similarity transformation is adopted to convert the partial differential equations into ordinary differential equations and then solved by Euler’s explicit method. The characteristics of sundry parameters on the velocity, temperature, and concentration fields are graphically elaborated. It is noted that the impact of magneto-thermomechanical interaction is to slow down the fluid motion. The skin friction coefficient enhances and affects the rate of heat transfer. For higher values of ferrohydrodynamics, the interaction velocity shows decreasing behavior. Further the Prandtl number on temperature has opposite behavior when compared with thermal radiation and ferrohydrodynamics interaction.
Direct numerical simulation of heat transfer in a spatially developing turbulent boundary layer
Authors: Li Dong , Luo Kun , Fan Jianren
Published: October 2016

Direct numerical simulation has been performed to investigate heat transfer in a zero-pressure-gradient spatially developing turbulent boundary layer with realistic thermal inflow boundary conditions. The temperature is considered as a passive scalar and the molecular Prandtl number is set to be 0.71. The turbulence statistics for both the velocity and temperature fields show good agreement with previous numerical and experimental data in the literature. The present study provides a valuable database for the spatially developing turbulent thermal boundary layer over a wide range of Reynolds numbers from Reθ = 1100 to 1940. The simulation results indicate that both the peak value and peak location of the streamwise velocity fluctuation grow slightly with increasing Reynolds number, same as those of the temperature fluctuation. The relationship between the streamwise velocity and temperature fluctuations has been examined and a strong correlation is observed in the vicinity of the wall. With increasing distance from the wall, however, the degree of correlation significantly decreases. In addition, the difference between the turbulent velocity and temperature fields is also analysed by investigating the mechanisms of heat and momentum transport in boundary layer flow.
Domain overlap matrices from plane-wave-based methods of electronic structure calculation
Authors: Golub Pavlo , Baranov Alexey I.
Published: October 2016

Plane waves are one of the most popular and efficient basis sets for electronic structure calculations of solids; however, their delocalized nature makes it difficult to employ for them classical orbital-based methods of chemical bonding analysis. The quantum chemical topology approach, introducing chemical concepts via partitioning of real space into chemically meaningful domains, has no difficulties with plane-wave-based basis sets. Many popular tools employed within this approach, for instance delocalization indices, need overlap integrals over these domains—the elements of the so called domain overlap matrices. This article reports an efficient algorithm for evaluation of domain overlap matrix elements for plane-wave-based calculations as well as evaluation of its implementation for one of the most popular projector augmented wave (PAW) methods on the small set of simple and complex solids. The stability of the obtained results with respect to PAW calculation parameters has been investigated, and the comparison of the results with the results from other calculation methods has also been made.
Early evolution of electron cyclotron driven current during suppression of tearing modes in a circular tokamak
Authors: Pratt J. , Huijsmans G. T. A. , Westerhof E.
Published: October 2016

When electron cyclotron (EC) driven current is first applied to the inside of a magnetic island, the current spreads throughout the island and after a short period achieves a steady level. Using a two equation fluid model for the EC current that allows us to examine this early evolution in detail, we analyze high-resolution simulations of a 2/1 classical tearing mode in a low-beta large aspect-ratio circular tokamak. These simulations use a nonlinear 3D reduced-MHD fluid model and the JOREK code. During the initial period where the EC driven current grows and spreads throughout the magnetic island, it is not a function of the magnetic flux. However, once it has reached a steady-state, it should be a flux function. We demonstrate numerically that if sufficiently resolved toroidally, the steady-state EC driven current becomes approximately a flux function. We discuss the physics of this early period of EC evolution and its impact on the size of the magnetic island.
On the threshold of magnetic island width in nonlinear mutual destabilization of tearing mode and ion temperature gradient mode
Authors: Liu T. , Wang Z. X. , Hu Z. Q. , Wei L. , Li J. Q. , Kishimoto Y.
Published: October 2016

Nonlinear multi-scale interactions between the tearing mode and the ion temperature gradient (ITG) mode are investigated by means of numerical simulations in a self-consistent 5-field Landau-fluid model. It is observed that there exists a threshold of magnetic island width in the nonlinear evolution of interaction, above which the ITG turbulence can enhance the island growth significantly. Dependence of the threshold on basic plasma parameters is deeply analyzed. It is found that the higher ion viscosity may raise the threshold through its effect on the E×B drift and the diamagnetic drift of electron density gradient in different ways, both of which play a synergetic role in determining the threshold. Moreover, the effects of plasma resistivity, gradient length of equilibrium current sheet as well as magnetic shear of field line on the threshold are discussed based on the analyses of the initial growth rate of islands.
Self-guiding of electromagnetic beams in degenerate relativistic electron-positron plasma
Authors: Berezhiani V. I. , Shatashvili N. L.
Published: October 2016

The possibility of self-trapped propagation of electromagnetic beams in the fully degenerate relativistic electron-positron plasma has been studied applying the Fluid-Maxwell model; it is shown that dynamics of such beams can be described by the generalized nonlinear Schrödinger equation with specific type of saturating nonlinearity. Existence of radially symmetric localized solitary structures is demonstrated. It is found that stable solitary structures exist for the arbitrary level of degeneracy.
Anomalous ferroelectric switching dynamics in single crystalline SrTiO3
Authors: Shukla Vinay Kumar , Mukhopadhyay Soumik
Published: October 2016

Pure SrTiO3 in bulk form is known to be an “incipient ferroelectric” where the quantum fluctuations of lattice positions prevent long range ferroelectric ordering at a finite temperature. We show evidence and identify the origin of ferroelectric relaxation up to nearly room temperature in single crystalline SrTiO3. Strikingly, the origin of the observed ferroelectric switching is intrinsic which is the coherent switching of surface nanopolar regions and not due to the nucleation and growth of domains, as described by the Kolmogorov-Avrami-Ishibashi Model.
Electrical transport properties of La1−xSrxCoO3 thin films
Authors: Liu Bin , Wang Yiqian , Liu Guiju , Feng Honglei , Yang Huaiwen , Sun Jirong
Published: October 2016

The electrical transport properties of La1−xSrxCoO3 (LSCO) thin films were investigated in this paper. As x increased up to 0.3, the electrical transport mechanism transferred from variable range hopping to double-exchange and the film simultaneously turned from an insulator into a conductor. Different from the bulk materials, the maximum conductivity of the film appeared at x = 0.3. A novel electrical transport model was proposed to explain this unconventional phenomenon. Besides, the effects of doped Sr and oxygen vacancies on the electrical transport properties were clarified by investigated the transport behaviors of the LaCoO3, La0.7S0.3CoO3, and La0.7S0.3CoO3−δ films. We found that, when Sr was doped into the LaCoO3 film, the insulating film turns into a conductor; when oxygen atoms were removed from the La0.7S0.3CoO3 film, the conducting film goes back to an insulator. Our work could shed light on the electrical transport mechanism of the LSCO films.
Electronic transport properties of graphene channel with metal electrodes or insulating substrates in 10 nm-scale devices
Authors: Jippo H. , Ozaki T. , Okada S. , Ohfuchi M.
Published: October 2016

We have studied the electronic transport properties of armchair graphene nanoribbons (AGNRs) bridged between two metal electrodes or supported on insulating substrates in 10 nm-scale devices using the first-principles calculations. The two metal species of Ti and Au are examined as metal electrodes and are compared. The current densities through the AGNR-Ti contact are about 10 times greater than those through the AGNR-Au contact, even though the AGNR width reaches 12 nm. For the insulating substrates, we have investigated the dependence of the channel length on the transport properties using models with two channel lengths of 15.1 and 9.91 nm. Regardless of the channel length, the on/off current ratio is 105 for the AGNRs on an O-terminated surface. This ratio is consistent with the recent experiments and is less by factors of 1016 for the 15.1 nm channel length and 108 for the 9.91 nm channel length compared to the freestanding AGNR.
Temperature-dependent recombination coefficients in InGaN light-emitting diodes: Hole localization, Auger processes, and the green gap
Authors: Nippert Felix , Karpov Sergey Yu. , Callsen Gordon , Galler Bastian , Kure Thomas , Nenstiel Christian , Wagner Markus R. , Straßburg Martin , Lugauer Hans-Jürgen , Hoffmann Axel
Published: October 2016

We obtain temperature-dependent recombination coefficients by measuring the quantum efficiency and differential carrier lifetimes in the state-of-the-art InGaN light-emitting diodes. This allows us to gain insight into the physical processes limiting the quantum efficiency of such devices. In the green spectral range, the efficiency deteriorates, which we assign to a combination of diminishing electron-hole wave function overlap and enhanced Auger processes, while a significant reduction in material quality with increased In content can be precluded. Here, we analyze and quantify the entire balance of all loss mechanisms and highlight the particular role of hole localization.