TY - JOUR AB - Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes. Results: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group. Conclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei. AU - Bochkareva, Olga AU - Moroz, Elena V. AU - Davydov, Iakov I. AU - Gelfand, Mikhail S. ID - 8262 JF - BMC Genomics SN - 1471-2164 TI - Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. VL - 19 ER - TY - JOUR AB - Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content. AU - Bochkareva, Olga AU - Dranenko, Natalia O. AU - Ocheredko, Elena S. AU - Kanevsky, German M. AU - Lozinsky, Yaroslav N. AU - Khalaycheva, Vera A. AU - Artamonova, Irena I. AU - Gelfand, Mikhail S. ID - 8265 JF - PeerJ SN - 2167-8359 TI - Genome rearrangements and phylogeny reconstruction in Yersinia pestis VL - 6 ER - TY - JOUR AB - Background/Aim: Our aim was to investigate the crosstalk between tumor and immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes (dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2 overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages, was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29 human colon cancer cells and reduced production of COX2 in BT474 human mammary cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion: Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape a tolerogenic tumor microenvironment in CMT. AU - Carvalho, Maria Isabel AU - Bianchini, Rodolfo AU - Fazekas-Singer, Judit AU - Herrmann, Ina AU - Flickinger, Irene AU - Thalhammer, Johann G. AU - Pires, Isabel AU - Jensen-Jarolim, Erika AU - Queiroga, Felisbina L. ID - 8274 IS - 5 JF - Anticancer Research SN - 0250-7005 TI - Bidirectional regulation of COX-2 expression between cancer cells and macrophages VL - 38 ER - TY - CONF AB - Sharding, or partitioning the system’s state so that different subsets of participants handle it, is a proven approach to building distributed systems whose total capacity scales horizontally with the number of participants. Many distributed ledgers have adopted this approach to increase their performance, however, they focus on the permissionless setting that assumes the existence of a strong adversary. In this paper, we deploy channels for permissioned blockchains. Our first contribution is to adapt sharding on asset-management applications for the permissioned setting, while preserving liveness and safety even on transactions spanning across-channels. Our second contribution is to leverage channels as a confidentiality boundary, enabling different organizations and consortia to preserve their privacy within their channels and still be part of a bigger collaborative ecosystem. To make our system concrete we map it on top of Hyperledger Fabric. AU - Androulaki, Elli AU - Cachin, Christian AU - De Caro, Angelo AU - Kokoris Kogias, Eleftherios ID - 8298 SN - 0302-9743 T2 - Computer Security TI - Channels: Horizontal scaling and confidentiality on permissioned blockchains VL - 11098 ER - TY - CONF AB - Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment processors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify” validation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput scales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds. AU - Kokoris Kogias, Eleftherios AU - Jovanovic, Philipp AU - Gasser, Linus AU - Gailly, Nicolas AU - Syta, Ewa AU - Ford, Bryan ID - 8297 SN - 2375-1207 T2 - 2018 IEEE Symposium on Security and Privacy TI - OmniLedger: A secure, scale-out, decentralized ledger via sharding ER - TY - JOUR AB - Characterizing the structure of membrane proteins (MPs) generally requires extraction from their native environment, most commonly with detergents. Yet, the physicochemical properties of detergent micelles and lipid bilayers differ markedly and could alter the structural organization of MPs, albeit without general rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure determination by NMR, but the physiological relevance of several prominent structures has been questioned, though indirectly, by other biophysical techniques, e.g., functional/thermostability assay (TSA) and molecular dynamics (MD) simulations. Here, we resolve unambiguously this controversy by probing the functional relevance of three different mitochondrial carriers (MCs) in DPC at the atomic level, using an exhaustive set of solution-NMR experiments, complemented by functional/TSA and MD data. Our results provide atomic-level insight into the structure, substrate interaction and dynamics of the detergent–membrane protein complexes and demonstrates cogently that, while high-resolution NMR signals can be obtained for MCs in DPC, they systematically correspond to nonfunctional states. AU - Kurauskas, Vilius AU - Hessel, Audrey AU - Ma, Peixiang AU - Lunetti, Paola AU - Weinhäupl, Katharina AU - Imbert, Lionel AU - Brutscher, Bernhard AU - King, Martin S. AU - Sounier, Rémy AU - Dolce, Vincenza AU - Kunji, Edmund R. S. AU - Capobianco, Loredana AU - Chipot, Christophe AU - Dehez, François AU - Bersch, Beate AU - Schanda, Paul ID - 8443 IS - 5 JF - The Journal of Physical Chemistry Letters KW - General Materials Science SN - 1948-7185 TI - How detergent impacts membrane proteins: Atomic-level views of mitochondrial carriers in dodecylphosphocholine VL - 9 ER - TY - JOUR AB - Mycobacterium tuberculosis can remain dormant in the host, an ability that explains the failure of many current tuberculosis treatments. Recently, the natural products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein substrates, such as proteins containing phosphorylated arginine residues, to the ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these dynamics are caused by conformational changes and do not result from unfolding or oligomerization of this domain. Cyclomarin binding to this domain specifically blocked these N-terminal dynamics. On the basis of these results, we propose a mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics, which modulates the chaperone enzymatic activity leading eventually to cell death. AU - Weinhäupl, Katharina AU - Brennich, Martha AU - Kazmaier, Uli AU - Lelievre, Joel AU - Ballell, Lluis AU - Goldberg, Alfred AU - Schanda, Paul AU - Fraga, Hugo ID - 8440 IS - 22 JF - Journal of Biological Chemistry KW - Cell Biology KW - Biochemistry KW - Molecular Biology SN - 0021-9258 TI - The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis VL - 293 ER - TY - JOUR AB - Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. AU - Chipot, Christophe AU - Dehez, François AU - Schnell, Jason R. AU - Zitzmann, Nicole AU - Pebay-Peyroula, Eva AU - Catoire, Laurent J. AU - Miroux, Bruno AU - Kunji, Edmund R. S. AU - Veglia, Gianluigi AU - Cross, Timothy A. AU - Schanda, Paul ID - 8442 IS - 7 JF - Chemical Reviews KW - General Chemistry SN - 0009-2665 TI - Perturbations of native membrane protein structure in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical studies VL - 118 ER - TY - JOUR AB - Solid-state near-rotary-resonance measurements of the spin–lattice relaxation rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1ρ data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, “dead time” in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1ρ measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30–50 μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process. AU - Krushelnitsky, Alexey AU - Gauto, Diego AU - Rodriguez Camargo, Diana C. AU - Schanda, Paul AU - Saalwächter, Kay ID - 8441 IS - 1 JF - Journal of Biomolecular NMR SN - 0925-2738 TI - Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments: The model case of protein overall-rocking in crystals VL - 71 ER - TY - JOUR AB - Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly hampers their structural study in an environment similar to the bacterial surface. We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long O-antigen polysaccharides assembled in solution as vesicles or elongated micelles. Solid-state NMR with magic-angle spinning permitted the identification of NMR signals arising from regions with different flexibilities in the LPS, from the lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa LPS, for which we could confirm that a specific oligosaccharide is involved in the antibiotic binding. The possibility to study LPS alone and bound to a ligand when it is assembled in membrane-like structures opens great prospects for the investigation of proteins and antibiotics that specifically target such an important molecule at the surface of Gram-negative bacteria. AU - Laguri, Cedric AU - Silipo, Alba AU - Martorana, Alessandra M. AU - Schanda, Paul AU - Marchetti, Roberta AU - Polissi, Alessandra AU - Molinaro, Antonio AU - Simorre, Jean-Pierre ID - 8439 IS - 8 JF - ACS Chemical Biology KW - Molecular Medicine KW - Biochemistry KW - General Medicine SN - 1554-8929 TI - Solid state NMR studies of intact lipopolysaccharide endotoxin VL - 13 ER - TY - GEN AB - The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex. AU - Llorca, Alfredo AU - Ciceri, Gabriele AU - Beattie, Robert J AU - Wong, Fong K. AU - Diana, Giovanni AU - Serafeimidou, Eleni AU - Fernández-Otero, Marian AU - Streicher, Carmen AU - Arnold, Sebastian J. AU - Meyer, Martin AU - Hippenmeyer, Simon AU - Maravall, Miguel AU - Marín, Oscar ID - 8547 T2 - bioRxiv TI - Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture ER - TY - CHAP AB - Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms. AU - Chatterjee, Krishnendu AU - Henzinger, Thomas A AU - Otop, Jan ED - Lohstroh, Marten ED - Derler, Patricia ED - Sirjani, Marjan ID - 86 T2 - Principles of Modeling TI - Computing average response time VL - 10760 ER - TY - JOUR AB - Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery. AU - Aubret, Antoine AU - Youssef, Mena AU - Sacanna, Stefano AU - Palacci, Jérémie A ID - 9062 IS - 11 JF - Nature Physics SN - 1745-2473 TI - Targeted assembly and synchronization of self-spinning microgears VL - 14 ER - TY - JOUR AU - Danzl, Johann G ID - 9229 IS - S1 JF - Opera Medica et Physiologica SN - 2500-2287 TI - Diffraction-unlimited optical imaging for synaptic physiology VL - 4 ER - TY - CONF AB - Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting. AU - Avni, Guy AU - Guha, Shibashis AU - Kupferman, Orna ID - 6005 SN - 1868-8969 TI - Timed network games with clocks VL - 117 ER - TY - JOUR AB - Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods. AU - Cheng, Bingqing AU - Dellago, Christoph AU - Ceriotti, Michele ID - 9668 IS - 45 JF - Physical Chemistry Chemical Physics SN - 1463-9076 TI - Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics VL - 20 ER - TY - JOUR AB - The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures. AU - Cheng, Bingqing AU - Ceriotti, Michele ID - 9687 IS - 5 JF - Physical Review B SN - 2469-9950 TI - Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids VL - 97 ER - TY - JOUR AB - More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range. AU - Polechova, Jitka ID - 315 IS - 6 JF - PLoS Biology SN - 15449173 TI - Is the sky the limit? On the expansion threshold of a species’ range VL - 16 ER - TY - JOUR AB - The restricted planar elliptic three body problem (RPETBP) describes the motion of a massless particle (a comet or an asteroid) under the gravitational field of two massive bodies (the primaries, say the Sun and Jupiter) revolving around their center of mass on elliptic orbits with some positive eccentricity. The aim of this paper is to show the existence of orbits whose angular momentum performs arbitrary excursions in a large region. In particular, there exist diffusive orbits, that is, with a large variation of angular momentum. The leading idea of the proof consists in analyzing parabolic motions of the comet. By a well-known result of McGehee, the union of future (resp. past) parabolic orbits is an analytic manifold P+ (resp. P−). In a properly chosen coordinate system these manifolds are stable (resp. unstable) manifolds of a manifold at infinity P∞, which we call the manifold at parabolic infinity. On P∞ it is possible to define two scattering maps, which contain the map structure of the homoclinic trajectories to it, i.e. orbits parabolic both in the future and the past. Since the inner dynamics inside P∞ is trivial, two different scattering maps are used. The combination of these two scattering maps permits the design of the desired diffusive pseudo-orbits. Using shadowing techniques and these pseudo orbits we show the existence of true trajectories of the RPETBP whose angular momentum varies in any predetermined fashion. AU - Delshams, Amadeu AU - Kaloshin, Vadim AU - de la Rosa, Abraham AU - Seara, Tere M. ID - 8417 IS - 3 JF - Communications in Mathematical Physics KW - Mathematical Physics KW - Statistical and Nonlinear Physics SN - 0010-3616 TI - Global instability in the restricted planar elliptic three body problem VL - 366 ER - TY - JOUR AB - The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of an ellipse of small eccentricity which preserves integrability near the boundary, is itself an ellipse. This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability was assumed on a larger set. In particular, it shows that (local) integrability near the boundary implies global integrability. One of the crucial ideas in the proof consists in analyzing Taylor expansion of the corresponding action-angle coordinates with respect to the eccentricity parameter, deriving and studying higher order conditions for the preservation of integrable rational caustics. AU - Huang, Guan AU - Kaloshin, Vadim AU - Sorrentino, Alfonso ID - 8422 IS - 2 JF - Geometric and Functional Analysis KW - Geometry and Topology KW - Analysis SN - 1016-443X TI - Nearly circular domains which are integrable close to the boundary are ellipses VL - 28 ER - TY - JOUR AB - The classical Birkhoff conjecture claims that the boundary of a strictly convex integrable billiard table is necessarily an ellipse (or a circle as a special case). In this article we prove a complete local version of this conjecture: a small integrable perturbation of an ellipse must be an ellipse. This extends and completes the result in Avila-De Simoi-Kaloshin, where nearly circular domains were considered. One of the crucial ideas in the proof is to extend action-angle coordinates for elliptic billiards into complex domains (with respect to the angle), and to thoroughly analyze the nature of their complex singularities. As an application, we are able to prove some spectral rigidity results for elliptic domains. AU - Kaloshin, Vadim AU - Sorrentino, Alfonso ID - 8421 IS - 1 JF - Annals of Mathematics KW - Statistics KW - Probability and Uncertainty KW - Statistics and Probability SN - 0003-486X TI - On the local Birkhoff conjecture for convex billiards VL - 188 ER - TY - JOUR AB - In this survey, we provide a concise introduction to convex billiards and describe some recent results, obtained by the authors and collaborators, on the classification of integrable billiards, namely the so-called Birkhoff conjecture. This article is part of the theme issue ‘Finite dimensional integrable systems: new trends and methods’. AU - Kaloshin, Vadim AU - Sorrentino, Alfonso ID - 8419 IS - 2131 JF - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences KW - General Engineering KW - General Physics and Astronomy KW - General Mathematics SN - 1364-503X TI - On the integrability of Birkhoff billiards VL - 376 ER - TY - JOUR AB - We show that in the space of all convex billiard boundaries, the set of boundaries with rational caustics is dense. More precisely, the set of billiard boundaries with caustics of rotation number 1/q is polynomially sense in the smooth case, and exponentially dense in the analytic case. AU - Kaloshin, Vadim AU - Zhang, Ke ID - 8420 IS - 11 JF - Nonlinearity KW - Mathematical Physics KW - General Physics and Astronomy KW - Applied Mathematics KW - Statistical and Nonlinear Physics SN - 0951-7715 TI - Density of convex billiards with rational caustics VL - 31 ER - TY - JOUR AB - Chaperonins are ubiquitous protein assemblies present in bacteria, eukaryota, and archaea, facilitating the folding of proteins, preventing protein aggregation, and thus participating in maintaining protein homeostasis in the cell. During their functional cycle, they bind unfolded client proteins inside their double ring structure and promote protein folding by closing the ring chamber in an adenosine 5′-triphosphate (ATP)–dependent manner. Although the static structures of fully open and closed forms of chaperonins were solved by x-ray crystallography or electron microscopy, elucidating the mechanisms of such ATP-driven molecular events requires studying the proteins at the structural level under working conditions. We introduce an approach that combines site-specific nuclear magnetic resonance observation of very large proteins, enabled by advanced isotope labeling methods, with an in situ ATP regeneration system. Using this method, we provide functional insight into the 1-MDa large hsp60 chaperonin while processing client proteins and reveal how nucleotide binding, hydrolysis, and release control switching between closed and open states. While the open conformation stabilizes the unfolded state of client proteins, the internalization of the client protein inside the chaperonin cavity speeds up its functional cycle. This approach opens new perspectives to study structures and mechanisms of various ATP-driven biological machineries in the heat of action. AU - Mas, Guillaume AU - Guan, Jia-Ying AU - Crublet, Elodie AU - Debled, Elisa Colas AU - Moriscot, Christine AU - Gans, Pierre AU - Schoehn, Guy AU - Macek, Pavel AU - Schanda, Paul AU - Boisbouvier, Jerome ID - 8437 IS - 9 JF - Science Advances SN - 2375-2548 TI - Structural investigation of a chaperonin in action reveals how nucleotide binding regulates the functional cycle VL - 4 ER - TY - JOUR AB - The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial “transfer-chaperone” system is able to guide α-helical and β-barrel membrane proteins in a “nascent chain-like” conformation through a ribosome-free compartment. AU - Weinhäupl, Katharina AU - Lindau, Caroline AU - Hessel, Audrey AU - Wang, Yong AU - Schütze, Conny AU - Jores, Tobias AU - Melchionda, Laura AU - Schönfisch, Birgit AU - Kalbacher, Hubert AU - Bersch, Beate AU - Rapaport, Doron AU - Brennich, Martha AU - Lindorff-Larsen, Kresten AU - Wiedemann, Nils AU - Schanda, Paul ID - 8436 IS - 5 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Structural basis of membrane protein chaperoning through the mitochondrial intermembrane space VL - 175 ER - TY - JOUR AB - For any strictly convex planar domain Ω ⊂ R2 with a C∞ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi–Merlose [5]. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine Ω up to isometry. In this paper we give a counterexample, namely, we present two nonisometric domains Ω and Ω¯ with the same collection of Marvizi–Melrose invariants. Moreover, each domain has countably many periodic orbits {Sn}n≥1 (resp. {S¯n}n⩾1) of period going to infinity such that Sn and S¯n have the same period and perimeter for each n. AU - Buhovsky, Lev AU - Kaloshin, Vadim ID - 8426 JF - Regular and Chaotic Dynamics SN - 1560-3547 TI - Nonisometric domains with the same Marvizi-Melrose invariants VL - 23 ER - TY - JOUR AU - Kurauskas, Vilius AU - Hessel, Audrey AU - Dehez, François AU - Chipot, Christophe AU - Bersch, Beate AU - Schanda, Paul ID - 8438 IS - 9 JF - Nature Structural & Molecular Biology KW - Molecular Biology KW - Structural Biology SN - 1545-9993 TI - Dynamics and interactions of AAC3 in DPC are not functionally relevant VL - 25 ER - TY - JOUR AB - The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We recently demonstrated the hierarchical self-assembly of phoretic microswimmers into self-spinning microgears and their synchronization by diffusiophoretic interactions [Aubret et al., Nat. Phys., 2018]. In this paper, we adopt a pedagogical approach and expose our strategy to control self-assembly and build machines using phoretic phenomena. We notably introduce Highly Inclined Laminated Optical sheets microscopy (HILO) to image and characterize anisotropic and dynamic diffusiophoretic interactions, which cannot be performed by conventional fluorescence microscopy. The dynamics of a (haematite) photocatalytic material immersed in (hydrogen peroxide) fuel under various illumination patterns is first described and quantitatively rationalized by a model of diffusiophoresis, the migration of a colloidal particle in a concentration gradient. It is further exploited to design phototactic microswimmers that direct towards the high intensity of light, as a result of the reorientation of the haematite in a light gradient. We finally show the assembly of self-spinning microgears from colloidal microswimmers and carefully characterize the interactions using HILO techniques. The results are compared with analytical and numerical predictions and agree quantitatively, stressing the important role played by concentration gradients induced by chemical activity to control and design interactions. Because the approach described hereby is generic, this works paves the way for the rational design of machines by controlling phoretic phenomena. AU - Aubret, Antoine AU - Palacci, Jérémie A ID - 9053 IS - 47 JF - Soft Matter KW - General Chemistry KW - Condensed Matter Physics SN - 1744-683X TI - Diffusiophoretic design of self-spinning microgears from colloidal microswimmers VL - 14 ER - TY - JOUR AB - The novel electronic state of the canted antiferromagnetic (AFM) insulator, strontium iridate (Sr2IrO4) has been well described by the spin-orbit-entangled isospin Jeff = 1/2, but the role of isospin in transport phenomena remains poorly understood. In this study, antiferromagnet-based spintronic functionality is demonstrated by combining unique characteristics of the isospin state in Sr2IrO4. Based on magnetic and transport measurements, large and highly anisotropic magnetoresistance (AMR) is obtained by manipulating the antiferromagnetic isospin domains. First-principles calculations suggest that electrons whose isospin directions are strongly coupled to in-plane net magnetic moment encounter the isospin mismatch when moving across antiferromagnetic domain boundaries, which generates a high resistance state. By rotating a magnetic field that aligns in-plane net moments and removes domain boundaries, the macroscopically-ordered isospins govern dynamic transport through the system, which leads to the extremely angle-sensitive AMR. As with this work that establishes a link between isospins and magnetotransport in strongly spin-orbit-coupled AFM Sr2IrO4, the peculiar AMR effect provides a beneficial foundation for fundamental and applied research on AFM spintronics. AU - Lee, Nara AU - Ko, Eunjung AU - Choi, Hwan Young AU - Hong, Yun Jeong AU - Nauman, Muhammad AU - Kang, Woun AU - Choi, Hyoung Joon AU - Choi, Young Jai AU - Jo, Younjung ID - 9066 IS - 52 JF - Advanced Materials KW - Mechanical Engineering KW - General Materials Science KW - Mechanics of Materials SN - 0935-9648 TI - Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate VL - 30 ER - TY - JOUR AB - We report the temperature-dependent resistivity ρ(T) of chalcogenide NiS2-xSex (x = 0.1) using hydrostatic pressure as a control parameter in the temperature range of 4–300 K. The insulating behavior of ρ(T) survives at low temperatures in the pressure regime below 7.5 kbar, whereas a clear insulator-to-metallic transition is observed above 7.5 kbar. Two types of magnetic transitions, from the paramagnetic (PM) to the antiferromagnetic (AFM) state and from the AFM state to the weak ferromagnetic (WF) state, were evaluated and confirmed by magnetization measurement. According to the temperature–pressure phase diagram, the WF phase survives up to 7.5 kbar, and the transition temperature of the WF transition decreases as the pressure increases, whereas the metal–insulator transition temperature increases up to 9.4 kbar. We analyzed the metallic behavior and proposed Fermi-liquid behavior of NiS1.9Se0.1. AU - Hussain, Tayyaba AU - Oh, Myeong-jun AU - Nauman, Muhammad AU - Jo, Younjung AU - Han, Garam AU - Kim, Changyoung AU - Kang, Woun ID - 9068 JF - Physica B: Condensed Matter SN - 0921-4526 TI - Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se VL - 536 ER - TY - JOUR AB - In this study we investigate the scaling of precipitation extremes with temperature in the Mediterranean region by assessing against observations the present day and future regional climate simulations performed in the frame of the HyMeX and MED-CORDEX programs. Over the 1979–2008 period, despite differences in quantitative precipitation simulation across the various models, the change in precipitation extremes with respect to temperature is robust and consistent. The spatial variability of the temperature–precipitation extremes relationship displays a hook shape across the Mediterranean, with negative slope at high temperatures and a slope following Clausius–Clapeyron (CC)-scaling at low temperatures. The temperature at which the slope of the temperature–precipitation extreme relation sharply changes (or temperature break), ranges from about 20 °C in the western Mediterranean to <10 °C in Greece. In addition, this slope is always negative in the arid regions of the Mediterranean. The scaling of the simulated precipitation extremes is insensitive to ocean–atmosphere coupling, while it depends very weakly on the resolution at high temperatures for short precipitation accumulation times. In future climate scenario simulations covering the 2070–2100 period, the temperature break shifts to higher temperatures by a value which is on average the mean regional temperature change due to global warming. The slope of the simulated future temperature–precipitation extremes relationship is close to CC-scaling at temperatures below the temperature break, while at high temperatures, the negative slope is close, but somewhat flatter or steeper, than in the current climate depending on the model. Overall, models predict more intense precipitation extremes in the future. Adjusting the temperature–precipitation extremes relationship in the present climate using the CC law and the temperature shift in the future allows the recovery of the temperature–precipitation extremes relationship in the future climate. This implies negligible regional changes of relative humidity in the future despite the large warming and drying over the Mediterranean. This suggests that the Mediterranean Sea is the primary source of moisture which counteracts the drying and warming impacts on relative humidity in parts of the Mediterranean region. AU - Drobinski, Philippe AU - Silva, Nicolas Da AU - Panthou, Gérémy AU - Bastin, Sophie AU - Muller, Caroline J AU - Ahrens, Bodo AU - Borga, Marco AU - Conte, Dario AU - Fosser, Giorgia AU - Giorgi, Filippo AU - Güttler, Ivan AU - Kotroni, Vassiliki AU - Li, Laurent AU - Morin, Efrat AU - Önol, Bariş AU - Quintana-Segui, Pere AU - Romera, Raquel AU - Torma, Csaba Zsolt ID - 9136 IS - 3 JF - Climate Dynamics KW - Atmospheric Science SN - 0930-7575 TI - Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios VL - 51 ER - TY - JOUR AB - Several studies have shown the existence of a critical latitude where the dissipation of internal tides is strongly enhanced. Internal tides are internal waves generated by barotropic tidal currents impinging rough topography at the seafloor. Their dissipation and concomitant diapycnal mixing are believed to be important for water masses and the large‐scale ocean circulation. The purpose of this study is to clarify the physical processes at the origin of this strong latitudinal dependence of tidal energy dissipation. We find that different mechanisms are involved equatorward and poleward of the critical latitude. Triadic resonant instabilities are responsible for the dissipation of internal tides equatorward of the critical latitude. In particular, a dominant triad involving the primary internal tide and near‐inertial waves is key. At the critical latitude, the peak of energy dissipation is explained by both increased instability growth rates, and smaller scales of secondary waves thus more prone to break and dissipate their energy. Surprisingly, poleward of the critical latitude, the generation of evanescent waves appears to be crucial. Triadic instabilities have been widely studied, but the transfer of energy to evanescent waves has received comparatively little attention. Our work suggests that the nonlinear transfer of energy from the internal tide to evanescent waves (corresponding to the 2f‐pump mechanism described by Young et al., 2008, https://doi.org/10.1017/S0022112008001742) is an efficient mechanism to dissipate internal tide energy near and poleward of the critical latitude. The theoretical results are confirmed in idealized high‐resolution numerical simulations of a barotropic M2 tide impinging sinusoidal topography in a linearly stratified fluid. AU - Richet, O. AU - Chomaz, J.-M. AU - Muller, Caroline J ID - 9134 IS - 9 JF - Journal of Geophysical Research: Oceans SN - 2169-9275 TI - Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude VL - 123 ER - TY - JOUR AB - Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone. AU - Muller, Caroline J AU - Romps, David M. ID - 9135 IS - 12 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Acceleration of tropical cyclogenesis by self-aggregation feedbacks VL - 115 ER - TY - JOUR AB - The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin. AU - Frost, Jennifer M. AU - Kim, M. Yvonne AU - Park, Guen Tae AU - Hsieh, Ping-Hung AU - Nakamura, Miyuki AU - Lin, Samuel J. H. AU - Yoo, Hyunjin AU - Choi, Jaemyung AU - Ikeda, Yoko AU - Kinoshita, Tetsu AU - Choi, Yeonhee AU - Zilberman, Daniel AU - Fischer, Robert L. ID - 9471 IS - 20 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis VL - 115 ER - TY - JOUR AB - Electrostatic charging of insulating fine particles can be responsible for numerous phenomena ranging from lightning in volcanic plumes to dust explosions. However, even basic aspects of how fine particles become charged are still unclear. Studying particle charging is challenging because it usually involves the complexities associated with many-particle collisions. To address these issues, we introduce a method based on acoustic levitation, which makes it possible to initiate sequences of repeated collisions of a single submillimeter particle with a flat plate, and to precisely measure the particle charge in situ after each collision. We show that collisional charge transfer between insulators is dependent on the hydrophobicity of the contacting surfaces. We use glass, which we modify by attaching nonpolar molecules to the particle, the plate, or both. We find that hydrophilic surfaces develop significant positive charges after contacting hydrophobic surfaces. Moreover, we demonstrate that charging between a hydrophilic and a hydrophobic surface is suppressed in an acidic environment and enhanced in a basic one. Application of an electric field during each collision is found to modify the charge transfer, again depending on surface hydrophobicity. We discuss these results within the context of contact charging due to ion transfer, and we show that they lend strong support to OH− ions as the charge carriers. AU - Lee, Victor AU - James, Nicole AU - Waitukaitis, Scott R AU - Jaeger, Heinrich ID - 95 IS - 3 JF - Physical Review Materials TI - Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer VL - 2 ER - TY - JOUR AB - Let P be a graph property which is preserved by removal of edges, and consider the random graph process that starts with the empty n-vertex graph and then adds edges one-by-one, each chosen uniformly at random subject to the constraint that P is not violated. These types of random processes have been the subject of extensive research over the last 20 years, having striking applications in extremal combinatorics, and leading to the discovery of important probabilistic tools. In this paper we consider the k-matching-free process, where P is the property of not containing a matching of size k. We are able to analyse the behaviour of this process for a wide range of values of k; in particular we prove that if k=o(n) or if n−2k=o(n−−√/logn) then this process is likely to terminate in a k-matching-free graph with the maximum possible number of edges, as characterised by Erdős and Gallai. We also show that these bounds on k are essentially best possible, and we make a first step towards understanding the behaviour of the process in the intermediate regime. AU - Krivelevich, Michael AU - Kwan, Matthew Alan AU - Loh, Po‐Shen AU - Sudakov, Benny ID - 9567 IS - 4 JF - Random Structures and Algorithms SN - 1042-9832 TI - The random k‐matching‐free process VL - 53 ER - TY - JOUR AB - Let D(n,p) be the random directed graph on n vertices where each of the n(n-1) possible arcs is present independently with probability p. A celebrated result of Frieze shows that if p≥(logn+ω(1))/n then D(n,p) typically has a directed Hamilton cycle, and this is best possible. In this paper, we obtain a strengthening of this result, showing that under the same condition, the number of directed Hamilton cycles in D(n,p) is typically n!(p(1+o(1)))n. We also prove a hitting-time version of this statement, showing that in the random directed graph process, as soon as every vertex has in-/out-degrees at least 1, there are typically n!(logn/n(1+o(1)))n directed Hamilton cycles. AU - Ferber, Asaf AU - Kwan, Matthew Alan AU - Sudakov, Benny ID - 9565 IS - 4 JF - Random Structures and Algorithms SN - 1042-9832 TI - Counting Hamilton cycles in sparse random directed graphs VL - 53 ER - TY - JOUR AB - An intercalate in a Latin square is a 2×2 Latin subsquare. Let N be the number of intercalates in a uniformly random n×n Latin square. We prove that asymptotically almost surely N≥(1−o(1))n2/4, and that EN≤(1+o(1))n2/2 (therefore asymptotically almost surely N≤fn2 for any f→∞). This significantly improves the previous best lower and upper bounds. We also give an upper tail bound for the number of intercalates in two fixed rows of a random Latin square. In addition, we discuss a problem of Linial and Luria on low-discrepancy Latin squares. AU - Kwan, Matthew Alan AU - Sudakov, Benny ID - 9568 IS - 2 JF - Random Structures and Algorithms SN - 1042-9832 TI - Intercalates and discrepancy in random Latin squares VL - 52 ER - TY - JOUR AB - We say a family of sets is intersecting if any two of its sets intersect, and we say it is trivially intersecting if there is an element which appears in every set of the family. In this paper we study the maximum size of a non-trivially intersecting family in a natural “multi-part” setting. Here the ground set is divided into parts, and one considers families of sets whose intersection with each part is of a prescribed size. Our work is motivated by classical results in the single-part setting due to Erdős, Ko and Rado, and Hilton and Milner, and by a theorem of Frankl concerning intersecting families in this multi-part setting. In the case where the part sizes are sufficiently large we determine the maximum size of a non-trivially intersecting multi-part family, disproving a conjecture of Alon and Katona. AU - Kwan, Matthew Alan AU - Sudakov, Benny AU - Vieira, Pedro ID - 9587 JF - Journal of Combinatorial Theory Series A SN - 0097-3165 TI - Non-trivially intersecting multi-part families VL - 156 ER - TY - JOUR AB - We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic α-iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect. By a sequence of steps in a thought experiment, each involving a thermodynamic integration, we are able to separate out the binding free energy of a proton to a defect into harmonic and anharmonic, and classical and quantum contributions. We find that about 30% of a typical binding free energy of hydrogen to a lattice defect in iron is accounted for by finite temperature effects, and about half of these arise from quantum proton fluctuations. This has huge implications for the comparison between thermal desorption and permeation experiments and standard electronic structure theory. The implications are even greater for the interpretation of muon spin resonance experiments. AU - Cheng, Bingqing AU - Paxton, Anthony T. AU - Ceriotti, Michele ID - 9665 IS - 22 JF - Physical Review Letters SN - 0031-9007 TI - Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations VL - 120 ER - TY - JOUR AB - The curvature dependence of interfacial free energy, which is crucial in quantitatively predicting nucleation kinetics and the stability of bubbles and droplets, is quantified by the Tolman length δ. For solid-liquid interfaces, however, δ has never been computed directly due to various theoretical and practical challenges. Here we perform a direct evaluation of the Tolman length from atomistic simulations of a solid-liquid planar interface in out-of-equilibrium conditions, by first computing the surface tension from the amplitude of thermal capillary fluctuations of a localized version of the Gibbs dividing surface and by then calculating how much the surface energy changes when it is defined relative to the equimolar dividing surface. We computed δ for a model potential, and found a good agreement with the values indirectly inferred from nucleation simulations. The agreement not only validates our approach but also suggests that the nucleation free energy of the system can be perfectly described using classical nucleation theory if the Tolman length is taken into account. AU - Cheng, Bingqing AU - Ceriotti, Michele ID - 9659 IS - 23 JF - The Journal of Chemical Physics SN - 0021-9606 TI - Communication: Computing the Tolman length for solid-liquid interfaces VL - 148 ER - TY - JOUR AB - We present a field-data rich modelling analysis to reconstruct the climatic forcing, glacier response, and runoff generation from a high-elevation catchment in central Chile over the period 2000–2015 to provide insights into the differing contributions of debris-covered and debris-free glaciers under current and future changing climatic conditions. Model simulations with the physically based glacio-hydrological model TOPKAPI-ETH reveal a period of neutral or slightly positive mass balance between 2000 and 2010, followed by a transition to increasingly large annual mass losses, associated with a recent mega drought. Mass losses commence earlier, and are more severe, for a heavily debris-covered glacier, most likely due to its strong dependence on snow avalanche accumulation, which has declined in recent years. Catchment runoff shows a marked decreasing trend over the study period, but with high interannual variability directly linked to winter snow accumulation, and high contribution from ice melt in dry periods and drought conditions. The study demonstrates the importance of incorporating local-scale processes such as snow avalanche accumulation and spatially variable debris thickness, in understanding the responses of different glacier types to climate change. We highlight the increased dependency of runoff from high Andean catchments on the diminishing resource of glacier ice during dry years. AU - Burger, Flavia AU - Ayala, Alvaro AU - Farias, David AU - Shaw, Thomas E. AU - MacDonell, Shelley AU - Brock, Ben AU - McPhee, James AU - Pellicciotti, Francesca ID - 12603 IS - 2 JF - Hydrological Processes KW - Water Science and Technology SN - 0885-6087 TI - Interannual variability in glacier contribution to runoff from a high‐elevation Andean catchment: Understanding the role of debris cover in glacier hydrology VL - 33 ER - TY - JOUR AB - Snow depth patterns over glaciers are controlled by precipitation, snow redistribution due to wind and avalanches, and the exchange of energy with the atmosphere that determines snow ablation. While many studies have advanced the understanding of ablation processes, less is known about winter snow patterns and their variability over glaciers. We analyze snow depth on Haut Glacier d'Arolla, Switzerland, in the two winter seasons 2006–2007 and 2010–2011 to (1) understand whether snow depth over an alpine glacier at the end of the accumulation season exhibits a behavior similar to the one observed on single slopes and vegetated areas; and (2) investigate the snow pattern consistency over the two accumulation seasons. We perform this analysis on a data set of high-resolution lidar-derived snow depth using variograms and fractal parameters. Our first main result is that snow depth patterns on the glacier exhibit a multiscale behavior, with a scale break around 20 m after which the fractal dimension increases, indicating more autocorrelated structure before the scale break than after. Second, this behavior is consistent over the two years, with fractal parameters and their spatial variability almost constant in the two seasons. We also show that snow depth patterns exhibit a distinct behavior in the glacier tongue and the upper catchment, with longer correlation distances on the tongue in the direction of the main winds, suggesting spatial distinctions that are likely induced by different processes and that should be taken into account when extrapolating snow depth from limited samples. AU - Clemenzi, I. AU - Pellicciotti, Francesca AU - Burlando, P. ID - 12605 IS - 10 JF - Water Resources Research KW - Water Science and Technology SN - 0043-1397 TI - Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d'Arolla, Switzerland VL - 54 ER - TY - JOUR AB - Glaciers in the high mountains of Asia provide an important water resource for millions of people. Many of these glaciers are partially covered by rocky debris, which protects the ice from solar radiation and warm air. However, studies have found that the surface of these debris-covered glaciers is actually lowering as fast as glaciers without debris. Water ponded on the surface of the glaciers may be partially responsible, as water can absorb atmospheric energy very efficiently. However, the overall effect of these ponds has not been thoroughly assessed yet. We study a valley in Nepal for which we have extensive weather measurements, and we use a numerical model to calculate the energy absorbed by ponds on the surface of the glaciers over 6 months. As we have not observed each individual pond thoroughly, we run the model 5,000 times with different setups. We find that ponds are extremely important for glacier melt and absorb energy 14 times as quickly as the debris-covered ice. Although the ponds account for 1% of the glacier area covered by rocks, and only 0.3% of the total glacier area, they absorb enough energy to account for one eighth of the whole valley's ice loss. AU - Miles, Evan S. AU - Willis, Ian AU - Buri, Pascal AU - Steiner, Jakob F. AU - Arnold, Neil S. AU - Pellicciotti, Francesca ID - 12604 IS - 19 JF - Geophysical Research Letters KW - General Earth and Planetary Sciences KW - Geophysics SN - 0094-8276 TI - Surface pond energy absorption across four Himalayan Glaciers accounts for 1/8 of total catchment ice loss VL - 45 ER - TY - JOUR AB - Supraglacial ice cliffs exist on debris-covered glaciers worldwide, but despite their importance as melt hot spots, their life cycle is little understood. Early field observations had advanced a hypothesis of survival of north-facing and disappearance of south-facing cliffs, which is central for predicting the contribution of cliffs to total glacier mass losses. Their role as windows of energy transfer suggests they may explain the anomalously high mass losses of debris-covered glaciers in High Mountain Asia (HMA) despite the insulating debris, currently at the center of a debated controversy. We use a 3D model of cliff evolution coupled to very high-resolution topographic data to demonstrate that ice cliffs facing south (in the Northern Hemisphere) disappear within a few months due to enhanced solar radiation receipts and that aspect is the key control on cliffs evolution. We reproduce continuous flattening of south-facing cliffs, a result of their vertical gradient of incoming solar radiation and sky view factor. Our results establish that only north-facing cliffs are recurrent features and thus stable contributors to the melting of debris-covered glaciers. Satellite observations and mass balance modeling confirms that few south-facing cliffs of small size exist on the glaciers of Langtang, and their contribution to the glacier volume losses is very small (∼1%). This has major implications for the mass balance of HMA debris-covered glaciers as it provides the basis for new parameterizations of cliff evolution and distribution to constrain volume losses in a region where glaciers are highly relevant as water sources for millions of people. AU - Buri, Pascal AU - Pellicciotti, Francesca ID - 12607 IS - 17 JF - PNAS SN - 0027-8424 TI - Aspect controls the survival of ice cliffs on debris-covered glaciers VL - 115 ER - TY - JOUR AB - Ice cliffs within a supraglacial debris cover have been identified as a source for high ablation relative to the surrounding debris-covered area. Due to their small relative size and steep orientation, ice cliffs are difficult to detect using nadir-looking space borne sensors. The method presented here uses surface slopes calculated from digital elevation model (DEM) data to map ice cliff geometry and produce an ice cliff probability map. Surface slope thresholds, which can be sensitive to geographic location and/or data quality, are selected automatically. The method also attempts to include area at the (often narrowing) ends of ice cliffs which could otherwise be neglected due to signal saturation in surface slope data. The method was calibrated in the eastern Alaska Range, Alaska, USA, against a control ice cliff dataset derived from high-resolution visible and thermal data. Using the same input parameter set that performed best in Alaska, the method was tested against ice cliffs manually mapped in the Khumbu Himal, Nepal. Our results suggest the method can accommodate different glaciological settings and different DEM data sources without a data intensive (high-resolution, multi-data source) recalibration. AU - Herreid, Sam AU - Pellicciotti, Francesca ID - 12606 IS - 5 JF - The Cryosphere KW - Earth-Surface Processes KW - Water Science and Technology SN - 1994-0424 TI - Automated detection of ice cliffs within supraglacial debris cover VL - 12 ER - TY - JOUR AB - Focused ion beams perfectly suit for patterning two-dimensional (2D) materials, but the optimization of irradiation parameters requires full microscopic understanding of defect production mechanisms. In contrast to freestanding 2D systems, the details of damage creation in supported 2D materials are not fully understood, whereas the majority of experiments have been carried out for 2D targets deposited on substrates. Here, we suggest a universal and computationally efficient scheme to model the irradiation of supported 2D materials, which combines analytical potential molecular dynamics with Monte Carlo simulations and makes it possible to independently assess the contributions to the damage from backscattered ions and atoms sputtered from the substrate. Using the scheme, we study the defect production in graphene and MoS2 sheets, which are the two most important and wide-spread 2D materials, deposited on a SiO2 substrate. For helium and neon ions with a wide range of initial ion energies including those used in a commercial helium ion microscope (HIM), we demonstrate that depending on the ion energy and mass, the defect production in 2D systems can be dominated by backscattered ions and sputtered substrate atoms rather than by the direct ion impacts and that the amount of damage in 2D materials heavily depends on whether a substrate is present or not. We also study the factors which limit the spatial resolution of the patterning process. Our results, which agree well with the available experimental data, provide not only insights into defect production but also quantitative information, which can be used for the minimization of damage during imaging in HIM or optimization of the patterning process. AU - Kretschmer, Silvan AU - Maslov, Mikhail AU - Ghaderzadeh, Sadegh AU - Ghorbani-Asl, Mahdi AU - Hlawacek, Gregor AU - Krasheninnikov, Arkady V. ID - 13255 IS - 36 JF - ACS Applied Materials & Interfaces KW - General Materials Science SN - 1944-8244 TI - Supported two-dimensional materials under ion irradiation: The substrate governs defect production VL - 10 ER - TY - JOUR AB - Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light. AU - Samanta, Dipak AU - Gemen, Julius AU - Chu, Zonglin AU - Diskin-Posner, Yael AU - Shimon, Linda J. W. AU - Klajn, Rafal ID - 13376 IS - 38 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Reversible photoswitching of encapsulated azobenzenes in water VL - 115 ER - TY - JOUR AB - Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments. AU - Samanta, Dipak AU - Galaktionova, Daria AU - Gemen, Julius AU - Shimon, Linda J. W. AU - Diskin-Posner, Yael AU - Avram, Liat AU - Král, Petr AU - Klajn, Rafal ID - 13374 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Reversible chromism of spiropyran in the cavity of a flexible coordination cage VL - 9 ER - TY - JOUR AB - Confining organic molecules to the surfaces of inorganic nanoparticles can induce intermolecular interactions between them, which can affect the composition of the mixed self-assembled monolayers obtained by co-adsorption from solution of two different molecules. Two thiolated ligands (a dialkylviologen and a zwitterionic sulfobetaine) that can interact with each other electrostatically were coadsorbed onto gold nanoparticles. The nanoparticles favor a narrow range of ratios of these two molecules that is largely independent of the molar ratio in solution. Changing the solution molar ratio of the two ligands by a factor of 5 000 affects the on-nanoparticle ratio of these ligands by only threefold. This behavior is reminiscent of the formation of insoluble inorganic salts (such as AgCl), which similarly compensate positive and negative charges upon crystallizing. Our results pave the way towards developing well-defined hybrid organic–inorganic nanostructures. AU - Chu, Zonglin AU - Han, Yanxiao AU - Král, Petr AU - Klajn, Rafal ID - 13377 IS - 24 JF - Angewandte Chemie International Edition KW - General Chemistry KW - Catalysis SN - 1433-7851 TI - “Precipitation on nanoparticles”: Attractive intermolecular interactions stabilize specific ligand ratios on the surfaces of nanoparticles VL - 57 ER -