ALBERT

Beschreibung: Article Superconductivity in the iron pnictides is believed to be related to quantum critical fluctuations. Putzke et al. observe unexpected anomalies in the critical fields of BaFe 2 (As 1−x P x ) 2 that emerge close to its magnetic critical point, which they argue is a generic feature of quantum critical superconductivity. Nature Communications doi: 10.1038/ncomms6679 Authors: C. Putzke, P. Walmsley, J. D. Fletcher, L. Malone, D. Vignolles, C. Proust, S. Badoux, P. See, H. E. Beere, D. A. Ritchie, S. Kasahara, Y. Mizukami, T. Shibauchi, Y. Matsuda, A. Carrington

Beschreibung: Article microRNAs are short non-coding RNAs that post-transcriptionally regulate gene expression for which the identification of promoter and primary transcripts (pri-miRNAs) has been difficult. Here the authors describe microTSS, an algorithm that supports the precise identification of intergenic pri-miRNA transcription start sites. Nature Communications doi: 10.1038/ncomms6700 Authors: Georgios Georgakilas, Ioannis S. Vlachos, Maria D. Paraskevopoulou, Peter Yang, Yuhong Zhang, Aris N. Economides, Artemis G. Hatzigeorgiou

Beschreibung: Article Autism spectrum disorder (ASD) is a common, highly heritable neurodevelopmental condition characterized by marked genetic heterogeneity. In this study, the authors use RNA sequencing analyses to characterize differences in the transcriptome between autistic and typically developing brains. Nature Communications doi: 10.1038/ncomms6748 Authors: Simone Gupta, Shannon E. Ellis, Foram N. Ashar, Anna Moes, Joel S. Bader, Jianan Zhan, Andrew B. West, Dan E. Arking

Beschreibung: Article Pulse oximetry is a non-invasive means for measuring blood oxygen saturation and pulse rate, with typical sensors based on rigid electronics. Here, the authors develop a pulse oximeter based solely on organic materials, allowing flexible devices and hence increasing the potential sensing locations on the body. Nature Communications doi: 10.1038/ncomms6745 Authors: Claire M. Lochner, Yasser Khan, Adrien Pierre, Ana C. Arias

Beschreibung: Article The straightforward and scalable synthesis and patterning of graphene-based nanomaterials remains a technological challenge. Here, the authors use a CO 2 infrared laser, under ambient conditions, to directly produce and pattern porous graphene films with three-dimensional networks from commercial polymer films. Nature Communications doi: 10.1038/ncomms6714 Authors: Jian Lin, Zhiwei Peng, Yuanyue Liu, Francisco Ruiz-Zepeda, Ruquan Ye, Errol L. G. Samuel, Miguel Jose Yacaman, Boris I. Yakobson, James M. Tour

Beschreibung: Article Plasmons in metallic nanostructures provide light enhancement that amplifies their nonlinear optical response. This study shows that graphene nanoislands also give rise to an amplified nonlinear polarizability that can be tuned electrically to surpass those of other nonlinear media by orders of magnitude. Nature Communications doi: 10.1038/ncomms6725 Authors: Joel D. Cox, F. Javier García de Abajo

Beschreibung: Article FAN1 is a structure-specific nuclease that plays a major role in eliminating highly cytotoxic interstrand DNA crosslinks. Here, Zhao et al . present several crystal structures of FAN1 in complex with DNA substrates and biochemical analyses that establish how FAN1 functions to resolve interstrand DNA crosslinks. Nature Communications doi: 10.1038/ncomms6726 Authors: Qi Zhao, Xiaoyu Xue, Simonne Longerich, Patrick Sung, Yong Xiong

Beschreibung: Article Spartan/DVC1 is a translesion synthesis regulator with important roles in cellular DNA damage tolerance. Here, the authors report that Spartan is essential for DNA lesion bypass and that Spartan insufficiency in mice causes chromosomal instability, cellular senescence and early onset of age-related phenotypes. Nature Communications doi: 10.1038/ncomms6744 Authors: Reeja S. Maskey, Myoung Shin Kim, Darren J. Baker, Bennett Childs, Liviu A. Malureanu, Karthik B. Jeganathan, Yuka Machida, Jan M. van Deursen, Yuichi J. Machida

Beschreibung: Article Carbon sequestration will be vital in mitigating future climate change, and understanding how CO 2 behaves in aquifers is important for developing technologies. Here, the authors suggest that silicate-rich rocks inhibit the transport of CO 2 , which may have consequences for future engineered storage facilities. Nature Communications doi: 10.1038/ncomms6743 Authors: S. S. S. Cardoso, J. T. H. Andres

Beschreibung: Article The Microrchidia (Morc) family of GHKL ATPases are important repressors of transposons and other DNA-methylated and silent genes in A. thaliana . Here, the authors show that MORC1 is responsible for repression and methylation of specific classes of transposons in the mouse male germline. Nature Communications doi: 10.1038/ncomms6795 Authors: William A. Pastor, Hume Stroud, Kevin Nee, Wanlu Liu, Dubravka Pezic, Sergei Manakov, Serena A. Lee, Guillaume Moissiard, Natasha Zamudio, Déborah Bourc’his, Alexei A. Aravin, Amander T. Clark, Steven E. Jacobsen

Beschreibung: Article The induction of autophagy under stress conditions such as chemotherapy is a contributing factor towards resistance to anticancer therapy. Here, Zhang et al . identify the molecular chaperone clusterin as an adaptor that facilitates lipidation of LC3 and autophagosome biogenesis. Nature Communications doi: 10.1038/ncomms6775 Authors: Fan Zhang, Masafumi Kumano, Eliana Beraldi, Ladan Fazli, Caigan Du, Susan Moore, Poul Sorensen, Amina Zoubeidi, Martin E. Gleave

Beschreibung: We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.

Beschreibung: In this paper, we report the existence of intervalence charge transfer (IVCT) luminescence in Yb-doped fluorite-type crystals associated with Yb 2+ –Yb 3+ mixed valence pairs. By means of embedded cluster, wave function theory ab initio calculations, we show that the widely studied, very broad band, anomalous emission of Yb 2+ -doped CaF 2 and SrF 2 , usually associated with impurity-trapped excitons, is, rather, an IVCT luminescence associated with Yb 2+ –Yb 3+ mixed valence pairs. The IVCT luminescence is very efficiently excited by a two-photon upconversion mechanism where each photon provokes the same strong 4 f 14 –1 A 1g → 4 f 13 ( 2 F 7/2 )5 de g –1 T 1u absorption in the Yb 2+ part of the pair: the first one, from the pair ground state; the second one, from an excited state of the pair whose Yb 3+ moiety is in the higher 4 f 13 ( 2 F 5/2 ) multiplet. The Yb 2+ –Yb 3+ → Yb 3+ –Yb 2+ IVCT emission consists of an Yb 2+ 5 de g → Yb 3+ 4 f 7/2 charge transfer accompanied by a 4 f 7/2 → 4 f 5/2 deexcitation within the Yb 2+ 4 f 13 subshell: [ 2 F 5/2 5 de g , 2 F 7/2 ] → [ 2 F 7/2 ,4 f 14 ]. The IVCT vertical transition leaves the oxidized and reduced moieties of the pair after electron transfer very far from their equilibrium structures; this explains the unexpectedly large band width of the emission band and its low peak energy, because the large reorganization energies are subtracted from the normal emission. The IVCT energy diagrams resulting from the quantum mechanical calculations explain the different luminescent properties of Yb-doped CaF 2 , SrF 2 , BaF 2 , and SrCl 2 : the presence of IVCT luminescence in Yb-doped CaF 2 and SrF 2 ; its coexistence with regular 5 d -4 f emission in SrF 2 ; its absence in BaF 2 and SrCl 2 ; the quenching of all emissions in BaF 2 ; and the presence of additional 5 d –4 f emissions in SrCl 2 which are absent in SrF 2 . They also allow to interpret and reproduce recent experiments on transient photoluminescence enhancement in Yb 2+ -doped CaF 2 and SrF 2 , the appearance of Yb 2+ 4 f –5 d absorption bands in the excitation spectra of the IR Yb 3+ emission in partly reduced CaF 2 :Yb 3+ samples, and to identify the broadband observed in the excitation spectrum of the so far called anomalous emission of SrF 2 :Yb 2+ as an IVCT absorption, which corresponds to an Yb 2+ 4 f 5/2 → Yb 3+ 4 f 7/2 electron transfer.

Beschreibung: A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction.

Beschreibung: Article The kinase LRRK2 is implicated in Parkinson’s disease progression and is known to be phosphorylated. Chia et al. show that this phosphorylation is mediated by the kinase CK1a, and is required for the recruitment of LRRK2 to Golgi-derived vesicles, suggesting a role for this protein in Golgi maintenance. Nature Communications doi: 10.1038/ncomms6827 Authors: Ruth Chia, Sara Haddock, Alexandra Beilina, Iakov N. Rudenko, Adamantios Mamais, Alice Kaganovich, Yan Li, Ravindran Kumaran, Michael A. Nalls, Mark R. Cookson

Beschreibung: Article Synaptotagmin-1 (syt-1) triggers fast synchronous neurotransmission mediated by fusion of synaptic vesicles with presynaptic membranes. Here Lin et al. use inter-membrane FRET combined with DNA rulers as calibration standards to quantify Ca 2+ -induced changes in membrane distances mediated by syt-1. Nature Communications doi: 10.1038/ncomms6859 Authors: Chao-Chen Lin, Jan Seikowski, Angel Pérez-Lara, Reinhard Jahn, Claudia Höbartner, Peter Jomo Walla

Beschreibung: Article Loss of olfactory function is one of the many symptoms of the ciliopathy Bardet–Biedl syndrome. Williams et al . show that Bardet–Biedl proteins are components of intraflagellar transport particles within cilia, and directly visualize their trafficking in native mammalian olfactory neurons. Nature Communications doi: 10.1038/ncomms6813 Authors: Corey L. Williams, Jeremy C. McIntyre, Stephen R. Norris, Paul M. Jenkins, Lian Zhang, Qinglin Pei, Kristen Verhey, Jeffrey R. Martens

Beschreibung: Article Immune cell pro-inflammatory gene expression is suppressed following prolonged stimulation. Using a chemoproteomic approach, the authors show that methyltransferase G9a forms a protein complex that promotes the transcriptional repressor activity of c-Myc to repress inflammation-induced gene expression. Nature Communications doi: 10.1038/ncomms6733 Authors: Cui Liu, Yanbao Yu, Feng Liu, Xin Wei, John A. Wrobel, Harsha P. Gunawardena, Li Zhou, Jian Jin, Xian Chen

Beschreibung: Article Increased expression of MITF transcription factor is thought to promote melanoma progression and kinase inhibitor resistance. Here Muller et al . show that MITF loss is also common in melanomas and confers kinase inhibitor resistance due to upregulation of AXL and other receptor tyrosine kinases. Nature Communications doi: 10.1038/ncomms6712 Authors: Judith Müller, Oscar Krijgsman, Jennifer Tsoi, Lidia Robert, Willy Hugo, Chunying Song, Xiangju Kong, Patricia A. Possik, Paulien D. M. Cornelissen-Steijger, Marnix H Geukes Foppen, Kristel Kemper, Colin R. Goding, Ultan McDermott, Christian Blank, John Haanen, Thomas G. Graeber, Antoni Ribas, Roger S. Lo, Daniel S. Peeper

Beschreibung: Excited states and the ground state of the diatomic molecule RbSr were calculated by post Hartree-Fock molecular orbital theory up to 22 000 cm −1 . We applied a multireference configuration interaction calculation based on multiconfigurational self-consistent field wave functions. Both methods made use of effective core potentials and core polarization potentials. Potential energy curves, transition dipole moments, and permanent electric dipole moments were determined for RbSr and could be compared with other recent calculations. We found a good agreement with experimental spectra, which have been obtained recently by helium nanodroplet isolation spectroscopy. For the lowest two asymptotes (Rb (5 s 2 S) + Sr (5 s 4 d 3 P°) and Rb (5 p 2 P°) + Sr (5 s 2 1 S)), which exhibit a significant spin-orbit coupling, we included relativistic effects by two approaches, one applying the Breit-Pauli Hamiltonian to the multireference configuration interaction wave functions, the other combining a spin-orbit Hamiltonian and multireference configuration interaction potential energy curves. Using the results for the relativistic potential energy curves that correspond to the Rb (5 s 2 S) + Sr (5 s 4 d 3 P°) asymptote, we have simulated dispersed fluorescence spectra as they were recently measured in our lab. The comparison with experimental data allows to benchmark both methods and demonstrate that spin-orbit coupling has to be included for the lowest states of RbSr.

Beschreibung: Ozonolysis of alkenes, a principle non-photolytic source of atmospheric OH radicals, proceeds through unimolecular decay of energized carbonyl oxide intermediates, known as Criegee intermediates. In this work, cold dimethyl-substituted Criegee intermediates are vibrationally activated in the CH stretch overtone region to drive the 1,4 hydrogen transfer reaction that leads to OH radical products. IR excitation of (CH 3 ) 2 COO reveals the vibrational states with sufficient oscillator strength, coupling to the reaction coordinate, and energy to surmount the effective barrier (≤ 16.0 kcal mol −1 ) to reaction. Insight on the dissociation dynamics is gleaned from homogeneous broadening of the spectral features, indicative of rapid intramolecular vibrational energy redistribution and/or reaction, as well as the quantum state distribution of the OH X 2 Π (v = 0) products. The experimental results are compared with complementary electronic structure calculations, which provide the IR absorption spectrum and geometric changes along the intrinsic reaction coordinate. Additional theoretical analysis reveals the vibrational modes and couplings that permit (CH 3 ) 2 COO to access to the transition state region for reaction. The experimental and theoretical results are compared with an analogous recent study of the IR activation of syn -CH 3 CHOO and its unimolecular decay to OH products [F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, Science345, 1596 (2014)].

Beschreibung: In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.

Beschreibung: The properties of dipolar cubic lattices are studied and the paradox of how to obtain a long range polarization in such lattices is resolved by choosing a proper shape of the total system. It has been shown that large but finite number of aligned dipoles prefer to exist as needle shaped macroscopic particles [M. Yoon and D. Tománek, J. Phys.: Condens. Matter22, 455105 (2010)]. The total energy for a particle in such a system has one short range contribution depending on the packing (the chosen lattice) and one long range term depending on the dipole density of the system. We show that the latter term corresponds exactly to the polarization term from a dielectric medium embedding a sphere of the considered system. There is no need to include a dielectric medium in this modeling and the “dielectric stabilization” is generated solely by the dipoles of the system.

Beschreibung: A practical hyperdynamics method is proposed to accelerate systems with highly endothermic and exothermic reactions such as hydrocarbon pyrolysis and oxidation reactions. In this method, referred to as the “adaptive hyperdynamics (AHD) method,” the bias potential parameters are adaptively updated according to the change in potential energy. The approach is intensively examined for JP-10 (exo-tetrahydrodicyclopentadiene) pyrolysis simulations using the ReaxFF reactive force field. Valid boost parameter ranges are clarified as a result. It is shown that AHD can be used to model pyrolysis at temperatures as low as 1000 K while achieving a boost factor of around 10 5 .

Beschreibung: E -crotonic acid was isolated in cryogenic solid N 2 and xenon matrices, and subjected to Laser ultraviolet (UV) and near-infrared (NIR) irradiations. In the deposited matrices, the two low-energy cis C–O E -cc and E -ct conformers, which are the only forms significantly populated in the gas phase, were observed. UV irradiation (λ= 250 nm) of the compound in N 2 matrix allows for experimental detection, not just of the two low-energy cis C–O isomers of Z -crotonic acid previously observed in the experiments carried out in argon matrix [ Z -cc and Z -ct; R. Fausto, A. Kulbida, and O. Schrems, J. Chem. Soc., Faraday Trans.91, 3755–3770 (1995)] but also of the never observed before high-energy forms of both E - and Z -crotonic acids bearing the carboxylic acid group in the trans arrangement ( E -tc and Z -tc conformers). In turn, NIR irradiation experiments in the N 2 matrix allow to produce the high-energy E -tc trans C–O conformer in a selective way, from the initially deposited E -cc form. The vibrational signatures of all the 6 rotameric structures of the crotonic acids experimentally observed, including those of the new trans C–O forms, were determined and the individual spectra fully assigned, also with support of theoretically obtained data. On the other hand, as found before for the compound isolated in argon matrix, the experiments performed in xenon matrix failed to experimental detection of the trans C–O forms. This demonstrates that in noble gas matrices these forms are not stable long enough to allow for their observation by steady state spectroscopy techniques. In these matrices, the trans C–O forms convert spontaneously into their cis C–O counterparts, by tunnelling. Some mechanistic details of the studied processes were extracted and discussed.

Beschreibung: We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange–correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

Beschreibung: Article How volcanoes and the cryosphere interact is of interest for understanding hazard mitigation at ice-clad volcanoes and for paleoclimate studies. Here, the authors provide quantitative details from an eruption in Kamchatka, demonstrating that two kinds of lava, ′a′a and pahoehoe, produced different snowpack responses. Nature Communications doi: 10.1038/ncomms6666 Authors: B. R. Edwards, A. Belousov, M. Belousova

Beschreibung: Article Artificial atoms usually constitute an orbital structure for trapped charge carriers. Here, Hönig et al . demonstrate that polarization fields and large charge carrier masses can dilute the common orbital conception and find a hybrid-biexciton molecule that enables anomalous spin configurations. Nature Communications doi: 10.1038/ncomms6721 Authors: Gerald Hönig, Gordon Callsen, Andrei Schliwa, Stefan Kalinowski, Christian Kindel, Satoshi Kako, Yasuhiko Arakawa, Dieter Bimberg, Axel Hoffmann

Beschreibung: Article Certain soil fungi form specialized cellular structures or 'traps' to feed on nematodes, which in turn eat bacteria. Here, the authors show that urea released from bacteria induces trap formation in the fungi and this promotes nematode elimination. Nature Communications doi: 10.1038/ncomms6776 Authors: Xin Wang, Guo-Hong Li, Cheng-Gang Zou, Xing-Lai Ji, Tong Liu, Pei-Ji Zhao, Lian-Ming Liang, Jian-Ping Xu, Zhi-Qiang An, Xi Zheng, Yue-Ke Qin, Meng-Qing Tian, You-Yao Xu, Yi-Cheng Ma, Ze-Fen Yu, Xiao-Wei Huang, Shu-Qun Liu, Xue-Mei Niu, Jin-Kui Yang, Ying Huang, Ke-Qin Zhang

Beschreibung: Article BMP signalling is important in early post-implantation embryonic development. Here the authors perform mRNA sequencing of inside and outside cells of pre-implantation mouse embryos and show that BMP signalling is critical for the development of the two extra-embryonic lineages at this early stage. Nature Communications doi: 10.1038/ncomms6667 Authors: Sarah J. L. Graham, Krzysztof B. Wicher, Agnieszka Jedrusik, Guoji Guo, Wishva Herath, Paul Robson, Magdalena Zernicka-Goetz

Beschreibung: Article Single-crystal diamond is a promising material for applications in classical and quantum optics, but the lack of scalable fabrication remains an issue. Here, Burek et al . adapt angle-etching nanofabrication techniques to realize ring resonators and photonic crystal cavities in single crystal diamond with quality factors in excess of 10 5 . Nature Communications doi: 10.1038/ncomms6718 Authors: Michael J. Burek, Yiwen Chu, Madelaine S. Z. Liddy, Parth Patel, Jake Rochman, Srujan Meesala, Wooyoung Hong, Qimin Quan, Mikhail D. Lukin, Marko Lončar

Beschreibung: Article Interesting changes in physical and optical properties can result from the binding of small molecules to supramolecular polymers. Here, the authors present an ATP assay, using a supramolecular helix to switch between left- and right-handed conformations on binding different adenosine phosphates. Nature Communications doi: 10.1038/ncomms6793 Authors: Mohit Kumar, Patrick Brocorens, Claire Tonnelé, David Beljonne, Mathieu Surin, Subi J. George

Beschreibung: Article Genetic variation is key to species evolution. Here the authors sequence two phenotypically distinct populations of the ant Cardiocondyla obscurior , and find accumulations of transposable elements correlating with genetic variation that may have a role in differentiation, adaptation and speciation. Nature Communications doi: 10.1038/ncomms6495 Authors: Lukas Schrader, Jay W. Kim, Daniel Ence, Aleksey Zimin, Antonia Klein, Katharina Wyschetzki, Tobias Weichselgartner, Carsten Kemena, Johannes Stökl, Eva Schultner, Yannick Wurm, Christopher D. Smith, Mark Yandell, Jürgen Heinze, Jürgen Gadau, Jan Oettler

Beschreibung: Article A potential therapeutic strategy for spinal cord injury (SCI) is to maintain continuity of damaged axons after contusion, but the viability of such strategies depends on the degree to which initially injured axons can recover. Here the authors use morphological and molecular in vivo imaging after contusion SCI in mice, to show that injured axons persist in a metastable state for hours. Nature Communications doi: 10.1038/ncomms6683 Authors: Philip R. Williams, Bogdan-Nicolae Marincu, Catherine D. Sorbara, Christoph F. Mahler, Adrian-Minh Schumacher, Oliver Griesbeck, Martin Kerschensteiner, Thomas Misgeld

Beschreibung: Article The mammalian circadian clock is influenced by nuclear receptors such as Rev-Erb. Here Kumar et al . show that ecdysone-induced protein 75 (E75), a fly homologue of Rev-Erb, regulates circadian rhythms in Drosophila , and demonstrate that E75 protects the clock against environmental stressors. Nature Communications doi: 10.1038/ncomms6697 Authors: Shailesh Kumar, Dechun Chen, Christopher Jang, Alexandra Nall, Xiangzhong Zheng, Amita Sehgal

Beschreibung: Nature Materials 14, 13 (2015). doi:10.1038/nmat4189 Author: Pep Pàmies

Beschreibung: Nature Materials 14, 16 (2015). doi:10.1038/nmat4185 Author: Philip Ball

Beschreibung: Nature Materials 14, 43 (2015). doi:10.1038/nmat4088 Authors: Thomas C. Fitzgibbons, Malcolm Guthrie, En-shi Xu, Vincent H. Crespi, Stephen K. Davidowski, George D. Cody, Nasim Alem & John V. Badding Low-dimensional carbon nanomaterials such as fullerenes, nanotubes, graphene and diamondoids have extraordinary physical and chemical properties. Compression-induced polymerization of aromatic molecules could provide a viable synthetic route to ordered carbon nanomaterials, but despite almost a century of study this approach has produced only amorphous products. Here we report recovery to ambient pressure of macroscopic quantities of a crystalline one- dimensional sp3carbon nanomaterial formed by high-pressure solid-state reaction of benzene. X-ray and neutron diffraction, Raman spectroscopy, solid-state NMR, transmission electron microscopy and first-principles calculations reveal close- packed bundles of subnanometre-diameter sp3-bonded carbon threads capped with hydrogen, crystalline in two dimensions and short-range ordered in the third. These nanothreads promise extraordinary properties such as strength and stiffness higher than that of sp2carbon nanotubes or conven tional high-strength polymers. They may be the first member of a new class of ordered sp3 nanomaterials synthesized by kinetic control of high-pressure solid-state reactions.

Beschreibung: Nature Materials 14, 61 (2015). doi:10.1038/nmat4109 Authors: Lang Feng, Bezia Laderman, Stefano Sacanna & Paul Chaikin In polymer–colloid mixtures, non-adsorbing polymers dispersed with much larger colloids provide a universal yet specific entropic attraction between the colloids. Such so-called depletion interaction arises from an osmotic-pressure imbalance caused by the polymers and is considered to be independent of temperature. Here we show that, for the most commonly used polymer–colloid depletion systems, the polymer undergoes a crossover from non-adsorbing to adsorbing and that, consequently, the effective colloidal interactions depend on temperature. We also find that a combination of the enthalpic (polymer bridging) and entropic (polymer exclusion) interactions, both attractive, leads to a re-entrant regime where the colloids are dispersed and form solids both on heating and on cooling. We provide a simple model to explain the observed transitions and to fill the theoretical gap at the polymer-adsorption crossover. Our findings open possibilities for colloidal self-assembly, the formation of colloidal crystals and glasses, and the behaviour of temperature-controlled viscoelastic materials.

Beschreibung: Nature Materials 14, 73 (2015). doi:10.1038/nmat4117 Authors: Daichi Matsunami, Asaya Fujita, Koshi Takenaka & Mika Kano

Beschreibung: The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding – a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.

Beschreibung: We investigate the performance of Stieltjes Imaging applied to Lanczos pseudo-spectra generated at the coupled cluster singles and doubles, coupled cluster singles and approximate iterative doubles and coupled cluster singles levels of theory in modeling the photodetachment cross sections of the closed shell anions H − , Li − , Na − , F − , Cl − , and OH − . The accurate description of double excitations is found to play a much more important role than in the case of photoionization of neutral species.

Beschreibung: For conical intersections of two states ( I,J = I + 1) the vectors defining the branching or g-h plane, the energy difference gradient vector g I,J , and the interstate coupling vector h I,J , can be made orthogonal by a one parameter rotation of the degenerate electronic eigenstates. The representation obtained from this rotation is used to construct the parameters that describe the vicinity of the conical intersection seam, the conical parameters, s I,J x ( R ), s I,J y ( R ), g I,J ( R ), and h I,J ( R ). As a result of the orthogonalization these parameters can be made continuous functions of R , the internuclear coordinates. In this work we generalize this notion to construct continuous parametrizations of conical intersection seams of three or more states. The generalization derives from a recently introduced procedure for using non-degenerate electronic states to construct coupled diabatic states that represent adiabatic states coupled by conical intersections. The procedure is illustrated using the seam of conical intersections of three states in parazolyl as an example.

Beschreibung: State averaged complete active space self-consistent field (SA-CASSCF) is a workhorse for determining the excited-state electronic structure of molecules, particularly for states with multireference character; however, the method suffers from known issues that have prevented its wider adoption. One issue is the presence of discontinuities in potential energy surfaces when a state that is not included in the state averaging crosses with one that is. In this communication I introduce a new dynamical weight with spline (DWS) scheme that mimics SA-CASSCF while removing energy discontinuities due to unweighted state crossings. In addition, analytical gradients for DWS-CASSCF (and other dynamically weighted schemes) are derived for the first time, enabling energy-conserving excited-state ab initio molecular dynamics in instances where SA-CASSCF fails.

Beschreibung: Modern materials processing applications and technologies often occur far from equilibrium. To this end, the processing of complex materials such as polymer melts and nanocomposites generally occurs under strong deformations and flows, conditions under which equilibrium thermodynamics does not apply. As a result, the ability to determine the nonequilibrium thermodynamic properties of polymeric materials from measurable quantities such as heat and work is a major challenge in the field. Here, we use work relations to show that nonequilibrium thermodynamic quantities such as free energy and entropy can be determined for dilute polymer solutions in flow. In this way, we determine the thermodynamic properties of DNA molecules in strong flows using a combination of simulations, kinetic theory, and single molecule experiments. We show that it is possible to calculate polymer relaxation timescales purely from polymer stretching dynamics in flow. We further observe a thermodynamic equivalence between nonequilibrium and equilibrium steady-states for polymeric systems. In this way, our results provide an improved understanding of the energetics of flowing polymer solutions.

Beschreibung: Cohesive interactions between filamentous molecules have broad implications for a range of biological and synthetic materials. While long-standing theoretical approaches have addressed the problem of inter-filament forces from the limit of infinitely rigid rods, the ability of flexible filaments to deform intra-filament shape in response to changes in inter-filament geometry has a profound affect on the nature of cohesive interactions. In this paper, we study two theoretical models of inter-filament cohesion in the opposite limit, in which filaments are sufficiently flexible to maintain cohesive contact along their contours, and address, in particular, the role played by helical-interfilament geometry in defining interactions. Specifically, we study models of featureless, tubular filaments interacting via: (1) pair-wise Lennard-Jones (LJ) interactions between surface elements and (2) depletion-induced filament binding stabilized by electrostatic surface repulsion. Analysis of these models reveals a universal preference for cohesive filament interactions for non-zero helical skew, and further, that in the asymptotic limit of vanishing interaction range relative to filament diameter, the skew-dependence of cohesion approaches a geometrically defined limit described purely by the close-packing geometry of twisted tubular filaments. We further analyze non-universal features of the skew-dependence of cohesion at small-twist for both potentials, and argue that in the LJ model the pair-wise surface attraction generically destabilizes parallel filaments, while in the second model, pair-wise electrostatic repulsion in combination with non-pairwise additivity of depletion leads to a meta-stable parallel state.

Beschreibung: The effect of strong intermolecular hydrogen bonding on torsional degrees of freedom is investigated by far-infrared absorption spectroscopy for different methanol dimer isotopologues isolated in supersonic jet expansions or embedded in inert neon matrices at low temperatures. For the vacuum-isolated and Ne-embedded methanol dimer, the hydrogen bond OH librational mode of the donor subunit is finally observed at ∼560 cm −1 , blue-shifted by more than 300 cm −1 relative to the OH torsional fundamental of the free methanol monomer. The OH torsional mode of the acceptor embedded in neon is observed at ∼286 cm −1 . The experimental findings are held against harmonic predictions from local coupled-cluster methods with single and double excitations and a perturbative treatment of triple excitations [LCCSD(T)] and anharmonic. VPT2 corrections at canonical MP2 and density functional theory (DFT) levels in order to quantify the contribution of vibrational anharmonicity for this important class of intermolecular hydrogen bond vibrational motion.

Beschreibung: Extensive numerical solutions of the hypernetted-chain (HNC) and Rogers-Young (RY) integral equations are presented for the pair structure of a system of two coupled replicae (1 and 2) of a “soft-sphere” fluid of atoms interacting via an inverse-12 pair potential. In the limit of vanishing inter-replica coupling ɛ 12 , both integral equations predict the existence of three branches of solutions: (1) A high temperature liquid branch ( L ), which extends to a supercooled regime upon cooling when the two replicae are kept at ɛ 12 = 0 throughout; upon separating the configurational and vibrational contributions to the free energy and entropy of the L branch, the Kauzmann temperature is located where the configurational entropy vanishes. (2) Starting with an initial finite coupling ɛ 12 , two “glass” branches G 1 and G 2 are found below some critical temperature, which are characterized by a strong remnant spatial inter-replica correlation upon taking the limit ɛ 12 → 0. Branch G 2 is characterized by an increasing overlap order parameter upon cooling, and may hence be identified with the hypothetical “ideal glass” phase. Branch G 1 exhibits the opposite trend of increasing order parameter upon heating; its free energy lies consistently below that of the L branch and above that of the G 2 branch. The free energies of the L and G 2 branches are found to intersect at an alleged “random first-order transition” (RFOT) characterized by weak discontinuities of the volume and entropy. The Kauzmann and RFOT temperatures predicted by RY differ significantly from their HNC counterparts.

Beschreibung: We present a continuum solvent model (CSM) with a smooth cavity for the application in grid-based electronic structure methods. The cavity is identified with the inherently smooth distribution function of a binary mixture at infinite dilution. We obtain a cavity model based on atomic van der Waals radii and one free parameter controlling the overall size. This single parameter is sufficient to adequately reproduce experimental partial molar volumes. The CSM based on this cavity is of similar accuracy in the prediction of aqueous solvation Gibbs energies of small neutral molecules and ions as other CSMs with a smooth cavity. We apply the model to systems in non-aqueous solution, i.e., spiropyran/merocyanin energetics, a proton transfer reaction in dimethyl sulfoxide, and the electrostatic screening of charged gold clusters in an ionic liquid.

Beschreibung: Article The Sonic hedgehog (Shh) signalling pathway plays important roles during development and its abnormal activation has been implicated in cancer. Here the authors uncover an epigenetic switch in the Shh pathway that involves the PRC2, Jmjd3/Kdm6b and Set1/MLL complexes in regulating signalling induced gene activation. Nature Communications doi: 10.1038/ncomms6425 Authors: Xuanming Shi, Zilai Zhang, Xiaoming Zhan, Mou Cao, Takashi Satoh, Shizuo Akira, Karl Shpargel, Terry Magnuson, Qingtian Li, Rongfu Wang, Chaochen Wang, Kai Ge, Jiang Wu

Beschreibung: Article Despite the technological relevance of molecular thin films, there is limited understanding of their growth on a molecular level. Here, the authors characterize the relevant processes in real time and determine energy parameters using a combination of X-ray techniques and kinetic Monte Carlo simulations. Nature Communications doi: 10.1038/ncomms6388 Authors: S. Bommel, N. Kleppmann, C. Weber, H. Spranger, P. Schäfer, J. Novak, S.V. Roth, F. Schreiber, S.H.L. Klapp, S. Kowarik

Beschreibung: Article The upregulation of TRP ion channels is implicated in pain processing. In this study, the authors show that the zinc-finger protein ZBTB20 is responsible for TRP channel upregulation, and eliminating ZBTB20 from pain-sensing neurons in mouse models of pain results in the reduction of pain-like sensation. Nature Communications doi: 10.1038/ncomms5984 Authors: An-Jing Ren, Kai Wang, Huan Zhang, Anjun Liu, Xianhua Ma, Qing Liang, Dongmei Cao, John N. Wood, David Z. He, Yu-Qiang Ding, Wen-Jun Yuan, Zhifang Xie, Weiping J. Zhang

Beschreibung: Article Metal nanostructures strongly influence fluorescence of nearby molecules, ranging from significant enhancement to total quenching. To decode the precise interactions taking place, Holzmeister et al . present a method that distinguishes the contributions to excitation, radiative and non-radiative rates. Nature Communications doi: 10.1038/ncomms6356 Authors: Phil Holzmeister, Enrico Pibiri, Jürgen J. Schmied, Tapasi Sen, Guillermo P. Acuna, Philip Tinnefeld

Beschreibung: Article Relaxor ferroelectrics are important materials that are used in electronic capacitors and other devices, although the origin of their unusual properties remains poorly understood. Here, the authors predict that Fano resonances between phonon modes could explain some properties of lead-free relaxors. Nature Communications doi: 10.1038/ncomms6100 Authors: D. Wang, J. Hlinka, A. A. Bokov, Z. -G. Ye, P. Ondrejkovic, J. Petzelt, L. Bellaiche

Beschreibung: Article A longstanding question in quantum information is the validity of the disputed Peres conjecture stating that bound entangled state can never lead to Bell inequality violation. Here Vértesi and Brunner prove that the Peres conjecture is false by providing an explicit counter example. Nature Communications doi: 10.1038/ncomms6297 Authors: Tamás Vértesi, Nicolas Brunner

Beschreibung: Article Oxylipin signalling is known to play important roles in plant growth, development and defence against pathogens. Here Sun et al. identify a novel cytochrome P450 in cotton and show that its suppression leads to activation of plant defence responses and alteration of oxylipin metabolism. Nature Communications doi: 10.1038/ncomms6372 Authors: Longqing Sun, Longfu Zhu, Li Xu, Daojun Yuan, Ling Min, Xianlong Zhang

Beschreibung: Article There is substantial research into new catalysts for oxygen reduction. Here, the authors report a structurally ordered gold–palladium–cobalt intermetallic catalyst which exhibits comparable activity to platinum/carbon in both acid and alkaline media, and probe its structure-activity behaviour. Nature Communications doi: 10.1038/ncomms6185 Authors: Kurian A. Kuttiyiel, Kotaro Sasaki, Dong Su, Lijun Wu, Yimei Zhu, Radoslav R. Adzic

Beschreibung: Article Cell migration is regulated by spatial and temporal information, but how the two are integrated is not well understood. Here, Nakajima et al . use dynamic microfluidics gradients to show that Ras activation at the leading edge of Dictyostelium is suppressed when chemoattractant concentration decreases over time. Nature Communications doi: 10.1038/ncomms6367 Authors: Akihiko Nakajima, Shuji Ishihara, Daisuke Imoto, Satoshi Sawai

Beschreibung: Article Thermodynamics typically favour the formation of crystals with flat facets. Here, the authors report an approach for the synthesis of curved boundaries in titania single crystals, composed of high index microfacets. Nature Communications doi: 10.1038/ncomms6355 Authors: Shuang Yang, Bing Xing Yang, Long Wu, Yu Hang Li, Porun Liu, Huijun Zhao, Yan Yan Yu, Xue Qing Gong, Hua Gui Yang

Beschreibung: Article Asian speleothem δ 18 O records are widely used as a proxy for summer monsoon intensity, but their validity has been questioned. Here, the authors evaluate their validity using a 150,000-year transient simulation from an isotope-enabled global climate model. Nature Communications doi: 10.1038/ncomms6371 Authors: Thibaut Caley, Didier M. Roche, Hans Renssen

Beschreibung: Article Tools derived from synthetic biology offer powerful means to refine drug delivery and disease detection. Liu et al . engineer a logical AND gate using CRISPR-Cas9 to drive gene expression only cells in which two promoters are active, and use it to selectively inhibit the growth of bladder cancer cells in vitro . Nature Communications doi: 10.1038/ncomms6393 Authors: Yuchen Liu, Yayue Zeng, Li Liu, Chengle Zhuang, Xing Fu, Weiren Huang, Zhiming Cai

Beschreibung: Article If photonics and electronics are to form hybrid information processing systems, it will be necessary to manipulate and isolate light electrically, over short distances. Davoyan and Engheta propose a route to achieve this in plasmonic waveguides by exploiting the magnetic field induced by a direct current. Nature Communications doi: 10.1038/ncomms6250 Authors: Artur Davoyan, Nader Engheta

Beschreibung: Article The use of chalcogenide glasses in simple electronic devices, such as a p-n junction, is hindered by the lack of n-type material. Here, Hughes et al. demonstrate n-type doping of GeTe and GaLaSO amorphous films using bismuth-ion implantation. Nature Communications doi: 10.1038/ncomms6346 Authors: Mark A. Hughes, Yanina Fedorenko, Behrad Gholipour, Jin Yao, Tae-Hoon Lee, Russell M. Gwilliam, Kevin P. Homewood, Steven Hinder, Daniel W. Hewak, Stephen R. Elliott, Richard J. Curry

Beschreibung: Article It is generally accepted that Polynesian settlers were directly responsible for the extinction of New Zealand moa. Here, the authors present three series of radiocarbon ages that define the brief period of interaction between Polynesians and moa, and show that high human population densities are not a prerequisite for the extinction of megafauna populations. Nature Communications doi: 10.1038/ncomms6436 Authors: Richard N. Holdaway, Morten E. Allentoft, Christopher Jacomb, Charlotte L. Oskam, Nancy R. Beavan, Michael Bunce

Beschreibung: Article The genetic basis of sex chromosome pseudoautosomal regions (PAR) in organisms with female heterogamety is largely unknown. Smeds et al. provide the first molecular characterization of the PAR in birds with differentiated sex chromosomes and show a potential recombination hotspot and no evidence for strong sexual antagonism in this region. Nature Communications doi: 10.1038/ncomms6448 Authors: Linnéa Smeds, Takeshi Kawakami, Reto Burri, Paulina Bolivar, Arild Husby, Anna Qvarnström, Severin Uebbing, Hans Ellegren

Beschreibung: Article Spin–orbit coupling gives rise to a plethora of rich phenomena in many condensed matter and atomic systems. Syzranov et al. study the role of dipole–dipole interactions in ultracold polar molecule gases and show that they produce an effective spin–orbit coupling that generates chiral excitations. Nature Communications doi: 10.1038/ncomms6391 Authors: Sergey V. Syzranov, Michael L. Wall, Victor Gurarie, Ana Maria Rey

Beschreibung: Article The origin of the unique turtle lung ventilatory apparatus is poorly understood. Here the authors show an increase in body wall rigidity early in evolution that allowed the abdominal muscles to become specialized for breathing and the ribs to eventually form the iconic turtle shell. Nature Communications doi: 10.1038/ncomms6211 Authors: Tyler R. Lyson, Emma R. Schachner, Jennifer Botha-Brink, Torsten M. Scheyer, Markus Lambertz, G. S. Bever, Bruce S. Rubidge, Kevin de Queiroz

Beschreibung: Article ABC systems are an important class of transporters involved in human pathologies for which the basis for transport remains poorly understood. Here the authors suggest a molecular basis for ATP-powered vectorial peptide export by the human transporter associated with antigen processing (TAP). Nature Communications doi: 10.1038/ncomms6419 Authors: Nina Grossmann, Ahmet S. Vakkasoglu, Sabine Hulpke, Rupert Abele, Rachelle Gaudet, Robert Tampé

Beschreibung: Article Interfacial charge transport determines the performance of organic semiconductors, yet the surface influence is poorly understood. Here, Morisaki et al. observe surface relaxation and its resulting transport properties in the first monolayer of tetracene, which are dissimilar to those of the bulk. Nature Communications doi: 10.1038/ncomms6400 Authors: Hazuki Morisaki, Takashi Koretsune, Chisa Hotta, Jun Takeya, Tsuyoshi Kimura, Yusuke Wakabayashi

Beschreibung: Article Difluoromethylation of organic molecules typically requires stoichiometric metal salts or harsh conditions. Here, the authors report a dual metal catalytic system for difluoromethylation allowing mild and direct functionalization of aryl halides, including highly functionalized molecules. Nature Communications doi: 10.1038/ncomms6405 Authors: Yang Gu, Xuebing Leng, Qilong Shen

Beschreibung: Article During translation, several ribosomes assemble on an mRNA strand to form polyribosomes. Here the authors describe—using cryo electron tomography—a compact state of the eukaryotic polysome where individual ribosomes contact each other and form a tight helical assembly that creates a continuous inner channel for the mRNA. Nature Communications doi: 10.1038/ncomms6294 Authors: Alexander G. Myasnikov, Zhanna A. Afonina, Jean-François Ménétret, Vladimir A. Shirokov, Alexander S. Spirin, Bruno P. Klaholz

Beschreibung: Article N -alpha-acetyltransferase 10 (NAA10) regulates cell growth and proliferation. Here the authors show that NAA10 also has a role in osteogenesis, by fine-tuning the activity of the osteogenic transcription factor Runx2. Nature Communications doi: 10.1038/ncomms6176 Authors: Haejin Yoon, Hye-Lim Kim, Yang-Sook Chun, Dong Hoon Shin, Kyoung-Hwa Lee, Chan Soo Shin, Dong Yeon Lee, Hong-Hee Kim, Zang Hee Lee, Hyun-Mo Ryoo, Mi-Ni Lee, Goo Taeg Oh, Jong-Wan Park

Beschreibung: Article Understanding the structural relationship and electronic states between incommensurate/commensurate phases remains an ongoing challenge. Here, the authors report incommensurate structures and electronic roughness on the surface of cleaved IrTe 2 . Nature Communications doi: 10.1038/ncomms6358 Authors: Qing Li, Wenzhi Lin, Jiaqiang Yan, Xin Chen, Anthony G. Gianfrancesco, David J. Singh, David Mandrus, Sergei V. Kalinin, Minghu Pan

Beschreibung: In this paper, we examine the behaviour of basic autocatalytic feedback modules involving a species catalyzing its own production, either directly or indirectly. We first perform a systematic study of the autocatalytic feedback module in isolation, examining the effect of different factors, showing how this module is capable of exhibiting monostable threshold and bistable switch-like behaviour. We then study the behaviour of this module embedded in different kinds of basic networks including (essentially) irreversible cycles, open and closed reversible chains, and networks with additional feedback. We study the behaviour of the networks deterministically and also stochastically, using simulations, analytical work, and bifurcation analysis. We find that (i) there are significant differences between the behaviour of this module in isolation and in a network: thresholds may be altered or destroyed and bistability may be destroyed or even induced, even when the ambient network is simple. The global characteristics and topology of this network and the position of the module in the ambient network can play important and unexpected roles. (ii) There can be important differences between the deterministic and stochastic dynamics of the module embedded in networks, which may be accentuated by the ambient network. This provides new insights into the functioning of such enzymatic modules individually and as part of networks, with relevance to other enzymatic signalling modules as well.

Beschreibung: Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β -peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two A β -peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.

Beschreibung: We study the distribution of multivalent counterions next to a dielectric slab, bearing a quenched, random distribution of charges on one of its solution interfaces, with a given mean and variance, both in the absence and in the presence of a bathing monovalent salt solution. We use the previously derived approach based on the dressed multivalent-ion theory that combines aspects of the strong and weak coupling of multivalent and monovalent ions in a single framework. The presence of quenched charge disorder on the charged surface of the dielectric slab is shown to substantially increase the density of multivalent counterions in its vicinity. In the counterion-only model (with no monovalent salt ions), the surface disorder generates an additional logarithmic attraction potential and thus an algebraically singular counterion density profile at the surface. This behavior persists also in the presence of a monovalent salt bath and results in significant violation of the contact-value theorem, reflecting the anti-fragility effects of the disorder that drive the system towards a more “ordered” state. In the presence of an interfacial dielectric discontinuity, depleting the counterion layer at the surface, the charge disorder still generates a much enhanced counterion density further away from the surface. Likewise, the charge inversion and/or overcharging of the surface occur more strongly and at smaller bulk concentrations of multivalent counterions when the surface carries quenched charge disorder. Overall, the presence of quenched surface charge disorder leads to sizable effects in the distribution of multivalent counterions in a wide range of realistic parameters and typically within a distance of a few nanometers from the charged surface.

Beschreibung: The reaction free energy for dehydrogenation of phenol, aniline, thiophenol, benzoic acid, and 1,4-benzenediol on the close packed copper, silver, and gold surfaces has been studied by density functional theory calculations. Dehydrogenation of thiophenol is found to be favourable on all three surfaces while aniline does not dehydrogenate on any of them. For phenol, benzenediol and benzoic acid dehydrogenation is favourable on copper and silver only, following the general trend of an increasing reaction free energy when going form gold to silver to copper. This trend can be correlated with the changes in bond lengths within the molecule upon dehydrogenation. While copper is able to replace hydrogen, leaving small changes in the bond lengths of the aromatic ring, the metal-molecule bond is weaker for silver and gold, resulting in a partial loss of aromaticity. This difference in bond strength leads to pronounced differences in adsorption geometries upon multiple dehydrogenations.

Beschreibung: Confinement can modify the dynamics, the thermodynamics, and the structural properties of liquid water, the prototypical anomalous liquid. By considering a generic model for anomalous liquids, suitable for describing solutions of globular proteins, colloids, or liquid metals, we study by molecular dynamics simulations the effect that an attractive wall with structure and a repulsive wall without structure have on the phases, the crystal nucleation, and the dynamics of the fluid. We find that at low temperatures the large density of the attractive wall induces a high-density, high-energy structure in the first layer (“templating” effect). In turn, the first layer induces a “molding” effect on the second layer determining a structure with reduced energy and density, closer to the average density of the system. This low-density, low-energy structure propagates further through the layers by templating effect and can involve all the existing layers at the lowest temperatures investigated. Therefore, although the high-density, high-energy structure does not self-reproduce further than the first layer, the structured wall can have a long-range influence thanks to a sequence of templating, molding, and templating effects through the layers. We find that the walls also have an influence on the dynamics of the liquid, with a stronger effect near the attractive wall. In particular, we observe that the dynamics is largely heterogeneous (i) among the layers, as a consequence of the sequence of structures caused by the walls presence, and (ii) within the same layer, due to superdiffusive liquid veins within a frozen matrix of particles near the walls at low temperature and high density. Hence, the partial freezing of the first layer does not correspond necessarily to an effective reduction of the channel's section in terms of transport properties, as suggested by other authors.

Beschreibung: We propose a novel quantum chemical method, called the harmonic solvation model (HSM), for calculating thermochemical parameters in the condensed phase, particularly in the liquid phase. The HSM represents translational and rotational motions of a solute as vibrations interacting with a cavity wall of solvent molecules. As examples, the HSM and the ideal-gas model (IGM) were used for the standard formation reaction of liquid water, combustion reactions of liquid formic acid, methanol, and ethanol, vapor–liquid equilibration of water and ethanol, and dissolution of gaseous CO 2 in water. The numerical results confirmed the reliability and applicability of the HSM. In particular, the temperature dependence of the Gibbs energy of liquid molecules was accurately reproduced by the HSM; for example, the boiling point of water was reasonably determined using the HSM, whereas the conventional IGM treatment failed to obtain a crossing of the two Gibbs energy curves for gaseous and liquid water.

Beschreibung: In this paper, we examine the behaviour of basic autocatalytic feedback modules involving a species catalyzing its own production, either directly or indirectly. We first perform a systematic study of the autocatalytic feedback module in isolation, examining the effect of different factors, showing how this module is capable of exhibiting monostable threshold and bistable switch-like behaviour. We then study the behaviour of this module embedded in different kinds of basic networks including (essentially) irreversible cycles, open and closed reversible chains, and networks with additional feedback. We study the behaviour of the networks deterministically and also stochastically, using simulations, analytical work, and bifurcation analysis. We find that (i) there are significant differences between the behaviour of this module in isolation and in a network: thresholds may be altered or destroyed and bistability may be destroyed or even induced, even when the ambient network is simple. The global characteristics and topology of this network and the position of the module in the ambient network can play important and unexpected roles. (ii) There can be important differences between the deterministic and stochastic dynamics of the module embedded in networks, which may be accentuated by the ambient network. This provides new insights into the functioning of such enzymatic modules individually and as part of networks, with relevance to other enzymatic signalling modules as well.

Beschreibung: We report high-resolution photoelectron spectra of the transition metal suboxide clusters Fe 3 O − and Co 3 O − . The combination of slow electron velocity-map imaging and cryogenic cooling yields vibrationally well-resolved spectra, from which we obtain precise values of 1.4408(3) and 1.3951(4) eV for the electron affinities of Fe 3 O and Co 3 O. Several vibrational frequencies of the neutral ground state Fe 3 O and Co 3 O clusters are assigned for the first time, and a low-lying excited state of Fe 3 O is observed. The experimental results are compared with density functional electronic structure calculations and Franck-Condon spectral simulations, enabling identification of the structural isomer and electronic states. As has been found in photoelectron spectra of other trimetal oxo species, Fe 3 O 0/− and Co 3 O 0/− are assigned to a μ 2 -oxo isomer with planar C 2 v symmetry. We identify the ground states of Fe 3 O – and Co 3 O – as 12 A 1 and 9 B 2 states, respectively. From these states we observe photodetachment to the 11 B 2 ground and 13 A 1 excited states of Fe 3 O, as well as to the 8 A 1 ground state of Co 3 O.

Beschreibung: Liquid helium nanodroplets, consisting of on average 2 × 10 6 atoms, are examined using femtosecond time-resolved photoelectron imaging. The droplets are excited by an extreme ultraviolet light pulse centered at 23.7 eV photon energy, leading to states within a band that is associated with the 1 s 3 p and 1 s 4 p Rydberg levels of free helium atoms. The initially excited states and subsequent relaxation dynamics are probed by photoionizing transient species with a 3.2 eV pulse and using velocity map imaging to measure time-dependent photoelectron kinetic energy distributions. Significant differences are seen compared to previous studies with a lower energy (1.6 eV) probe pulse. Three distinct time-dependent signals are analyzed by global fitting. A broad intense signal, centered at an electron kinetic energy (eKE) of 2.3 eV, grows in faster than the experimental time resolution and decays in ∼100 fs. This feature is attributed to the initially excited droplet state. A second broad transient feature, with eKE ranging from 0.5 to 4 eV, appears at a rate similar to the decay of the initially excited state and is attributed to rapid atomic reconfiguration resulting in Franck-Condon overlap with a broader range of cation geometries, possibly involving formation of a Rydberg-excited (He n )* core within the droplet. An additional relaxation pathway leads to another short-lived feature with vertical binding energies ≳2.4 eV, which is identified as a transient population within the lower-lying 1 s 2 p Rydberg band. Ionization at 3.2 eV shows an enhanced contribution from electronically excited droplet states compared to ejected Rydberg atoms, which dominate at 1.6 eV. This is possibly the result of increased photoelectron generation from the bulk of the droplet by the more energetic probe photons.

Beschreibung: Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β -peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two A β -peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.

Beschreibung: Using the recently developed explicitly correlated coupled cluster method in connection with the aug-cc-pVTZ basis set, we generated the three-dimensional potential energy surface (3D-PES) of the ground state of the Ar–BeO complex. This PES covers the regions of the global and local minima, the saddle point, and the dissociation of the complex. The PES is also used for the calculation of the rovibrational spectrum up to the dissociation limit. The high density of levels which is observed favors the mixing of the states and hence the occurrence of anharmonic resonances. The wavefunctions of the high rovibrational levels exhibit large amplitude motions in addition to strong anharmonic resonances. Our theoretical spectrum should be helpful in identifying the van der Waals modes of this complex in laboratory.

Beschreibung: Fluctuating hydrodynamics (FHD) is a general framework of mesoscopic modeling and simulation based on conservational laws and constitutive equations of linear and nonlinear responses. However, explicit representation of electrical forces in FHD has yet to appear. In this work, we devised an Ansatz for the dynamics of dipole moment densities that is linked with the Poisson equation of the electrical potential ϕ in coupling to the other equations of FHD. The resulting ϕ-FHD equations then serve as a platform for integrating the essential forces, including electrostatics in addition to hydrodynamics, pressure-volume equation of state, surface tension, and solvent-particle interactions that govern the emergent behaviors of molecular systems at an intermediate scale. This unique merit of ϕ-FHD is illustrated by showing that the water dielectric function and ion hydration free energies in homogeneous and heterogenous systems can be captured accurately via the mesoscopic simulation. Furthermore, we show that the field variables of ϕ-FHD can be mapped from the trajectory of an all-atom molecular dynamics simulation such that model development and parametrization can be based on the information obtained at a finer-grained scale. With the aforementioned multiscale capabilities and a spatial resolution as high as 5 Å, the ϕ-FHD equations represent a useful semi-explicit solvent model for the modeling and simulation of complex systems, such as biomolecular machines and nanofluidics.

Beschreibung: The atomic structure and the electron transfer properties of hydrogen bonds formed between two carboxylated alkanethiol molecules connected to gold electrodes are investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Three types of molecular junctions are constructed, in which one carboxyl alkanethiol molecule contains two methylene, –CH 2 , groups and the other one is composed of one, two, or three –CH 2 groups. Our calculations show that, similarly to the cases of isolated carboxylic acid dimers, in these molecular junctions the two carboxyl, –COOH, groups form two H-bonds resulting in a cyclic structure. When self-interaction corrections are explicitly considered, the calculated transmission coefficients of these three H-bonded molecular junctions at the Fermi level are in good agreement with the experimental values. The analysis of the projected density of states confirms that the covalent Au–S bonds localized at the molecule-electrode interfaces and the electronic coupling between –COOH and S dominate the low-bias junction conductance. Following the increase of the number of the –CH 2 groups, the coupling between –COOH and S decreases deeply. As a result, the junction conductance decays rapidly as the length of the H-bonded molecules increases. These findings not only provide an explanation to the observed distance dependence of the electron transfer properties of H-bonds, but also help the design of molecular devices constructed through H-bonds.

Beschreibung: The treatment of bending and buckling of stiff biopolymer filaments by the popular worm-like chain model does not provide adequate understanding of these processes at the microscopic level. Thus, we have used the atomistic molecular-dynamic simulations and the Amber03 force field to examine the compression buckling of α-helix (AH) filaments at room temperature. It was found that the buckling instability occurs in AHs at the critical force f c in the range of tens of pN depending on the AH length. The decrease of the force f c with the contour length follows the prediction of the classic thin rod theory. At the force f c the helical filament undergoes the swift and irreversible transition from the smoothly bent structure to the buckled one. A sharp kink in the AH contour arises at the transition, accompanied by the disruption of the hydrogen bonds in its vicinity. The kink defect brings in an effective softening of the AH molecule at buckling. Nonbonded interactions between helical branches drive the rearrangement of a kinked AH into the ultimate buckled structure of a compact helical hairpin described earlier in the literature.

Beschreibung: The strong field ionization rates for ethylene, trans 1,3-butadiene, and trans,trans 1,3,5-hexatriene have been calculated using time-dependent configuration interaction with single excitations and a complex absorbing potential (TDCIS-CAP). The calculations used the aug-cc-pVTZ basis set with a large set of diffuse functions (3 s , 2 p , 3 d , and 1 f ) on each atom. The absorbing boundary was placed 3.5 times the van der Waals radius from each atom. The simulations employed a seven-cycle cosine squared pulse with a wavelength of 800 nm. Ionization rates were calculated for intensities ranging from 0.3 × 10 14 W/cm 2 to 3.5 × 10 14 W/cm 2 . Ionization rates along the molecular axis increased markedly with increasing conjugation length. By contrast, ionization rates perpendicular to the molecular axis were almost independent of the conjugation length.

Beschreibung: During the dissociative adsorption on a solid surface, the substrate usually participates in a passive manner to accommodate fragments produced upon the cleavage of the internal bond(s) of a (transient) molecular adsorbate. This simple picture, however, neglects the flexibility of surface atoms. Here, we report a Density Functional Theory study to revisit our early studies of the dissociative adsorption of CH 3 X (X = Br and Cl) on Si(100). We have identified a new reaction pathway, which involves a flip of a silicon dimer; this new pathway agrees better with experiments. For our main exemplar of CH 3 Br, insights have been gained using a simple model that involves a three-atom reactive center, Br-C-Si. When the silicon dimer flips, the interaction between C and Si in the Br-C-Si center is enhanced, evident in the increased energy-split of the frontier orbitals. We also examine how the dissociation dynamics of CH 3 Br is altered on a heterodimer (Si-Al, Si-P, and Si-Ge) in a Si(100) surface. In each case, we conclude, on the basis of computed reaction pathways, that no heterodimer flipping is involved before the system transverses the transition state to dissociative adsorption.

Beschreibung: Hemoprotein mimics, cobalt picket fence porphyrins have been prepared in the gas phase as neutral molecules for the first time. Their ligation properties have been studied with 1-methylimidazole and compared with those of other cobalt porphyrins, tetraphenyl porphyrin, and cobalt protoporphyrin IX chloride, in view of studying the sterical properties of the ligation. It is shown that the cobalt picket fence porphyrin can only accept one 1-methylimidazole ligand in contrast to less sterically crowded porphyrins like cobalt tetraphenylporphyrin that present two accessible ligation sites. The femtosecond dynamics of these ligated systems have been studied after excitation at 400 nm, in comparison with the unligated ones. The observed transients are formed in much shorter times, 30 fs for the ligated species, as compared to free species (100 fs), supporting the porphyrin to metal charge transfer nature of these transients. The similar decays of the ligated transients

Beschreibung: The interface between Ru(tcterpy)(NCS) 3 TBA 2 [black dye (BD); tcterpy = 4,4 ′ ,4 ″ -tricarboxy-2,2 ′ :6 ′ ,2 ″ -terpyridine, NCS = thiocyanato, TBA = tetrabutylammonium cation] and nanocrystalline TiO 2 , as found in dye-sensitized solar cells, is investigated by soft-X-ray synchrotron radiation and compared with the adsorption structure of cis -Ru(Hdcbpy) 2 (NCS) 2 TBA 2 (N719; dcbpy = 4,4 ′ -dicarboxy-2,2 ′ -bipyridine) on TiO 2 to elucidate the relationship between the adsorption mode of BD and the photocurrent with and without coadsorbed indoline dye D131. The depth profile is characterized with X-ray photoelectron spectroscopy and S K -edge X-ray absorption fine structure using synchrotron radiation. Both datasets indicate that one of the isothiocyanate groups of BD interacts with TiO 2 via its S atom when the dye is adsorbed from a single-component solution. In contrast, the interaction is slightly suppressed when D131 is coadsorbed, indicated by the fact that the presence of D131 changes the adsorption mode of BD. Based upon these results, the number of BD dye molecules interacting with the substrate is shown to decrease by 10% when D131 is coadsorbed, and the dissociation is shown to be related to the short-circuit photocurrent in the 600–800 nm region. The design of a procedure to promote the preferential adsorption of D131 therefore leads to an improvement of the short-circuit current and conversion efficiency.

Beschreibung: We demonstrate that the Hadwiger form of the free energy of a fluid in contact with a wall is insufficient to describe the low-density behavior of a hard-sphere fluid. This implies that morphological thermodynamics of the hard-sphere fluid is an approximate theory if only four geometric measures are included. In order to quantify deviations from the Hadwiger form we extend standard fundamental measure theory of the bulk fluid by introducing additional scaled-particle variables which allow for the description of non-Hadwiger coefficients. The theory is in excellent agreement with recent computer simulations. The fact that the leading non-Hadwiger coefficient is one order of magnitude smaller than the smallest Hadwiger coefficient lends confidence to the numerous results that have been previously obtained within standard morphological thermodynamics.

Beschreibung: Article Plasmonic nanostructures enable control over the spatial and spectral dependence of scattered light. Here, the authors use pixels formed of nanoellipse or nanosquare dimers to show polarization-dependent full-colour scattering in reflection, and build 3D stereoscopic colour microprints from them. Nature Communications doi: 10.1038/ncomms6361 Authors: Xiao Ming Goh, Yihan Zheng, Shawn J. Tan, Lei Zhang, Karthik Kumar, Cheng-Wei Qiu, Joel K. W. Yang

Beschreibung: Article Operating devices that can navigate biomedical fluids and tissues is one of the ultimate goals of microrobotics. Whilst the current designs are restricted to non-reciprocal actuations, Qiu et al . report swimming via simple reciprocal motion by exploiting the non-Newtonian rheology of viscous fluids. Nature Communications doi: 10.1038/ncomms6119 Authors: Tian Qiu, Tung-Chun Lee, Andrew G. Mark, Konstantin I. Morozov, Raphael Münster, Otto Mierka, Stefan Turek, Alexander M. Leshansky, Peer Fischer

Beschreibung: Article The death receptor CD95/Fas induces apoptosis of many normal cells but prevents necrotic death of cancer cells. Here the authors demonstrate that CD95 activation promotes a cancer stem cell (CSC) phenotype, and that CSCs but not differentiated cancer cells are resistant to CD95-mediated apoptosis and depend on CD95 signalling to prevent necrosis. Nature Communications doi: 10.1038/ncomms6238 Authors: Paolo Ceppi, Abbas Hadji, Frederick J. Kohlhapp, Abhinandan Pattanayak, Annika Hau, Xia Liu, Huiping Liu, Andrea E. Murmann, Marcus E. Peter

Beschreibung: Article AUF1 is an RNA-binding protein believed to function mostly by regulating the decay of its target transcripts. Here, Yoon et al. systematically identify the targets of AUF1 and provide insights into how AUF1 functions to regulate various cellular processes by enhancing the decay, stability or translation of specific RNAs. Nature Communications doi: 10.1038/ncomms6248 Authors: Je-Hyun Yoon, Supriyo De, Subramanya Srikantan, Kotb Abdelmohsen, Ioannis Grammatikakis, Jiyoung Kim, Kyoung Mi Kim, Ji Heon Noh, Elizabeth J. F. White, Jennifer L. Martindale, Xiaoling Yang, Min-Ju Kang, William H. Wood 3rd, Nicole Noren Hooten, Michele K. Evans, Kevin G. Becker, Vidisha Tripathi, Kannanganattu V. Prasanth, Gerald M. Wilson, Thomas Tuschl, Nicholas T. Ingolia, Markus Hafner, Myriam Gorospe

Beschreibung: Article Individual emitters of light in close proximity, such as atoms, can couple together via the light they create leading to a concentrated burst of radiation. Here Mlynek et al. experminetally explore the fundamental origin of this superradiance by studying two superconducting qubits coupled to a microwave cavity. Nature Communications doi: 10.1038/ncomms6186 Authors: J. A. Mlynek, A. A. Abdumalikov, C. Eichler, A. Wallraff

Beschreibung: Article In chiral helimagnets, the Dzyaloshinskii–Moriya interaction is known to stabilize skyrmions, but the microscopic roots remain enigmatic. Here, Janson et al. apply a multi-scale approach to Cu 2 OSeO 3 and show that its skyrmions can be traced back to magnetic tetrahedra of a quantum nature. Nature Communications doi: 10.1038/ncomms6376 Authors: Oleg Janson, Ioannis Rousochatzakis, Alexander A. Tsirlin, Marilena Belesi, Andrei A. Leonov, Ulrich K. Rößler, Jeroen van den Brink, Helge Rosner