@article{9674, abstract = {The coalescence of nano-crystals during sintering is often found to result in interesting crystalline structures such as multi-fold twins, and yet the plasticity mechanism accompanying their formation is unclear. In this work, the sintering behavior of two unsupported copper nanoparticles initially at room temperature is investigated by molecular dynamics simulations under the constant-energy ensemble. The results reveal that once the two nanoparticles are brought into contact, they often go through drastic structural changes with the inter-particle grain boundary quickly eliminated, and single- and multi-fold twinning occurs frequently in the coalesced product. Whereas the formation of single twins is found to be via the more usual mechanism of emission of Shockley partials on {1 1 1} planes, the formation of fivefold twins, however, takes place via a novel dislocation-free mechanism involving a series of shear and rigid-body rotation processes caused by elastic waves with amplitudes not corresponding to any allowable Burgers vector in the fcc lattice. Such a lattice-wave, dislocation-free twinning mechanism has never been reported before.}, author = {Cheng, Bingqing and Ngan, Alfonso H.W.}, issn = {0749-6419}, journal = {International Journal of Plasticity}, pages = {65--79}, publisher = {Elsevier}, title = {{The crystal structures of sintered copper nanoparticles: A molecular dynamics study}}, doi = {10.1016/j.ijplas.2013.01.006}, volume = {47}, year = {2013}, } @article{9676, abstract = {Despite its relevance to a range of technological applications including nanocrystalline material fabrication, the sintering mechanisms of nanoparticles have not been well understood. It has been recognized that extrapolation from understanding of macro-particle sintering is unreliable for the nano-particle size regime. In this work, the sintering behaviour of copper nanoparticles under periodic boundary conditions at different temperatures and pressures was investigated by Molecular Dynamics simulations. It was found that smaller particle sizes, higher temperature and higher external pressure facilitate densification. Through a comparison with a two-sphere model, the governing mechanisms for many nanoparticles sintered at low temperature (T⩽900K) were identified to be a variety of plasticity processes including dislocation, twinning and even amorphization at the contact neck regions, due to the presence of high stresses.}, author = {Cheng, Bingqing and Ngan, Alfonso H.W.}, issn = {0927-0256}, journal = {Computational Materials Science}, pages = {1--11}, publisher = {Elsevier}, title = {{The sintering and densification behaviour of many copper nanoparticles: A molecular dynamics study}}, doi = {10.1016/j.commatsci.2013.03.014}, volume = {74}, year = {2013}, } @article{9682, abstract = {In this work, we simulate the response of two Cu nanoparticles colliding at different approaching rates at room temperature by MD. For small nanospheres, the formation of single twins is favored at high approach rates, whereas larger nanospheres mainly deform by dislocation slip. For small nanocubes with large {100} flat surfaces, however, a dislocation-free direct geometrical conversion process that leads to five-fold twinning dominates except at highly retarded approaching rates. For larger nanocubes, single twin formation is the governing plasticity mechanism. The probability for plastic deformation by dislocation slip or twinning is attributed to the abundance of surface steps, which act as sites for dislocation nucleation.}, author = {Cheng, Bingqing and Ngan, Alfonso H.W.}, issn = {0921-5093}, journal = {Materials Science and Engineering: A}, pages = {326--334}, publisher = {Elsevier}, title = {{Crystal plasticity of Cu nanocrystals during collision}}, doi = {10.1016/j.msea.2013.07.065}, volume = {585}, year = {2013}, } @article{970, abstract = {Recently a new high-mobility Dirac material, trilayer graphene, was realized experimentally. The band structure of ABA-stacked trilayer graphene consists of a monolayer-like and a bilayer-like pair of bands. Here we study electronic properties of ABA-stacked trilayer graphene biased by a perpendicular electric field. We find that the combination of the bias and trigonal warping gives rise to a set of new Dirac points: In each valley, seven species of Dirac fermions with small masses of order of a few meV emerge. The positions and masses of the emergent Dirac fermions are tunable by bias, and one group of Dirac fermions becomes massless at a certain bias value. Therefore, in contrast to bilayer graphene, the conductivity at the neutrality point is expected to show nonmonotonic behavior, becoming of the order of a few e2/h when some Dirac masses vanish. Further, we analyze the evolution of the Landau level spectrum as a function of bias. The emergence of new Dirac points in the band structure translates into new threefold-degenerate groups of Landau levels. This leads to an anomalous quantum Hall effect, in which some quantum Hall steps have a height of 3e2/h. At an intermediate bias, the degeneracies of all Landau levels get lifted, and in this regime all quantum Hall plateaus are spaced by e2/h. Finally, we show that the pattern of Landau level crossings is very sensitive to certain band structure parameters, and can therefore provide a useful tool for determining their precise values.}, author = {Maksym Serbyn and Abanin, Dmitry A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {11}, publisher = {American Physical Society}, title = {{New Dirac points and multiple Landau level crossings in biased trilayer graphene}}, doi = {10.1103/PhysRevB.87.115422}, volume = {87}, year = {2013}, } @article{971, abstract = {We study the stability of the normal state in a mesoscopic NSN junction biased by a constant voltage V with respect to the formation of the superconducting order. Using the linearized time-dependent Ginzburg-Landau equation, we obtain the temperature dependence of the instability line, V inst(T), where nucleation of superconductivity takes place. For sufficiently low biases, a stationary symmetric superconducting state emerges below the instability line. For higher biases, the normal phase is destroyed by the formation of a nonstationary bimodal state with two superconducting nuclei localized near the opposite terminals. The low-temperature and large-voltage behavior of the instability line is highly sensitive to the details of the inelastic relaxation mechanism in the wire. Therefore, experimental studies of Vinst(T) in NSN junctions may be used as an effective tool to access the parameters of the inelastic relaxation in the normal state.}, author = {Maksym Serbyn and Skvortsov, Mikhail A}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {2}, publisher = {American Physical Society}, title = {{Onset of superconductivity in a voltage-biased normal-superconducting-normal microbridge}}, doi = {10.1103/PhysRevB.87.020501}, volume = {87}, year = {2013}, } @article{972, abstract = {In topological crystalline insulators (TCIs), topology and crystal symmetry intertwine to create surface states with distinct characteristics. The breaking of crystal symmetry in TCIs is predicted to impart mass to the massless Dirac fermions. Here, we report high-resolution scanning tunneling microscopy studies of a TCI, Pb1-xSnxSe that reveal the coexistence of zero-mass Dirac fermions protected by crystal symmetry with massive Dirac fermions consistent with crystal symmetry breaking. In addition, we show two distinct regimes of the Fermi surface topology separated by a Van-Hove singularity at the Lifshitz transition point. Our work paves the way for engineering the Dirac band gap and realizing interaction-driven topological quantum phenomena in TCIs.}, author = {Okada, Yoshinori and Serbyn, Maksym and Lin, Hsin and Walkup, Daniel and Zhou, Wenwen and Dhital, Chetan and Neupane, Madhab and Xu, Suyang and Wang, Yungjui and Sankar, Raman and Chou, Fangcheng and Bansil, Arun and Hasan, Md and Wilson, Stephen and Fu, Liang and Madhavan, Vidya}, journal = {Science}, number = {6153}, pages = {1496 -- 1499}, publisher = {American Association for the Advancement of Science}, title = {{Observation of dirac node formation and mass acquisition in a topological crystalline insulator}}, doi = {10.1126/science.1239451}, volume = {341}, year = {2013}, } @article{973, abstract = {We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion.}, author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A}, journal = {Physical Review Letters}, number = {12}, publisher = {American Physical Society}, title = {{Local conservation laws and the structure of the many body localized states}}, doi = {10.1103/PhysRevLett.111.127201}, volume = {111}, year = {2013}, } @article{974, abstract = {We propose a possible realization of the overscreened Kondo impurity problem by a magnetic s=1/2 impurity embedded in a two-dimensional S=1 U(1) spin liquid with a Fermi surface. This problem contains an interesting interplay between non-Fermi-liquid behavior induced by a U(1) gauge field coupled to fermions and a non-Fermi-liquid fixed point in the overscreened Kondo problem. Using a large-N expansion together with an expansion in the dynamical exponent of the gauge field, we find that the coupling to the gauge field leads to weak but observable changes in the physical properties of the system at the overscreened Kondo fixed point. We discuss the extrapolation of this result to a physical case and argue that the realization of overscreened Kondo physics could lead to observations of effects due to gauge fields.}, author = {Serbyn, Maksym and Senthil, Todadri and Lee, Patrick}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {2}, publisher = {American Physical Society}, title = {{Overscreened Kondo fixed point in S=1 spin liquid}}, doi = {10.1103/PhysRevB.88.024419}, volume = {88}, year = {2013}, } @misc{9749, abstract = {Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise.}, author = {Zagorsky, Benjamin and Reiter, Johannes and Chatterjee, Krishnendu and Nowak, Martin}, publisher = {Public Library of Science}, title = {{Forgiver triumphs in alternating prisoner's dilemma }}, doi = {10.1371/journal.pone.0080814.s001}, year = {2013}, } @article{975, abstract = {Recent numerical work by Bardarson, Pollmann, and Moore revealed a slow, logarithmic in time, growth of the entanglement entropy for initial product states in a putative many-body localized phase. We show that this surprising phenomenon results from the dephasing due to exponentially small interaction-induced corrections to the eigenenergies of different states. For weak interactions, we find that the entanglement entropy grows as ξln (Vt/), where V is the interaction strength, and ξ is the single-particle localization length. The saturated value of the entanglement entropy at long times is determined by the participation ratios of the initial state over the eigenstates of the subsystem. Our work shows that the logarithmic entanglement growth is a universal phenomenon characteristic of the many-body localized phase in any number of spatial dimensions, and reveals a broad hierarchy of dephasing time scales present in such a phase.}, author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A}, journal = {Physical Review Letters}, number = {26}, publisher = {American Physical Society}, title = {{Universal slow growth of entanglement in interacting strongly disordered systems}}, doi = {10.1103/PhysRevLett.110.260601}, volume = {110}, year = {2013}, } @misc{9751, abstract = {High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.}, author = {Refardt, Dominik and Bergmiller, Tobias and Kümmerli, Rolf}, publisher = {Dryad}, title = {{Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection}}, doi = {10.5061/dryad.b1q2n}, year = {2013}, } @misc{9754, abstract = {Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.}, author = {Hearn, Jack and Stone, Graham and Barton, Nicholas H and Lohse, Konrad and Bunnefeld, Lynsey}, publisher = {Dryad}, title = {{Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies}}, doi = {10.5061/dryad.r3r60}, year = {2013}, } @article{976, abstract = {Motivated by a search for experimental probes to access the physics of fractionalized excitations called spinons in spin liquids, we study the interaction of spinons with lattice vibrations. We consider the case of algebraic spin liquid, when spinons have fermionic statistics and a Dirac-like dispersion. We establish the general procedure for deriving spinon-phonon interactions, which is based on symmetry considerations. The procedure is illustrated for four different algebraic spin liquids: π-flux and staggered-flux phases on a square lattice, π-flux phase on a kagome lattice, and zero-flux phase on a honeycomb lattice. Although the low-energy description is similar for all these phases, different underlying symmetry groups lead to a distinct form of spinon-phonon interaction Hamiltonian. The explicit form of the spinon-phonon interaction is used to estimate the attenuation of ultrasound in an algebraic spin liquid. The prospects of the sound attenuation as a probe of spinons are discussed.}, author = {Maksym Serbyn and Lee, Patrick}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {17}, publisher = {American Physical Society}, title = {{Spinon-phonon interaction in algebraic spin liquids}}, doi = {10.1103/PhysRevB.87.174424}, volume = {87}, year = {2013}, } @article{2443, abstract = {The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.}, author = {Simon, Sibu and Kubeš, Martin and Baster, Pawel and Robert, Stéphanie and Dobrev, Petre and Friml, Jirí and Petrášek, Jan and Zažímalová, Eva}, journal = {New Phytologist}, number = {4}, pages = {1034 -- 1048}, publisher = {Wiley}, title = {{Defining the selectivity of processes along the auxin response chain: A study using auxin analogues}}, doi = {10.1111/nph.12437}, volume = {200}, year = {2013}, } @inproceedings{2444, abstract = {We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.}, author = {Chatterjee, Krishnendu and Ła̧Cki, Jakub}, location = {St. Petersburg, Russia}, pages = {543 -- 558}, publisher = {Springer}, title = {{Faster algorithms for Markov decision processes with low treewidth}}, doi = {10.1007/978-3-642-39799-8_36}, volume = {8044}, year = {2013}, } @article{10895, abstract = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. }, author = {Vanneste, Steffen and Friml, Jiří}, issn = {2223-7747}, journal = {Plants}, keywords = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics}, number = {4}, pages = {650--675}, publisher = {MDPI}, title = {{Calcium: The missing link in auxin action}}, doi = {10.3390/plants2040650}, volume = {2}, year = {2013}, } @inproceedings{10897, abstract = {Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.}, author = {Edelsbrunner, Herbert}, booktitle = {Graph-Based Representations in Pattern Recognition}, isbn = {9783642382208}, issn = {1611-3349}, location = {Vienna, Austria}, pages = {182--183}, publisher = {Springer Nature}, title = {{Persistent homology in image processing}}, doi = {10.1007/978-3-642-38221-5_19}, volume = {7877}, year = {2013}, } @inproceedings{10898, abstract = {A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered.}, author = {Haas, Andreas and Lippautz, Michael and Henzinger, Thomas A and Payer, Hannes and Sokolova, Ana and Kirsch, Christoph M. and Sezgin, Ali}, booktitle = {Proceedings of the ACM International Conference on Computing Frontiers - CF '13}, isbn = {978-145032053-5}, location = {Ischia, Italy}, number = {5}, publisher = {ACM Press}, title = {{Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation}}, doi = {10.1145/2482767.2482789}, year = {2013}, } @inbook{10899, author = {Barton, Nicholas H}, booktitle = {Encyclopedia of Biodiversity}, isbn = {978-0-12-384720-1}, keywords = {Adaptive landscape, Cline, Coalescent process, Gene flow, Hybrid zone, Local adaptation, Natural selection, Neutral theory, Population structure, Speciation}, pages = {508--515}, publisher = {Elsevier}, title = {{Differentiation}}, doi = {10.1016/b978-0-12-384719-5.00031-9}, year = {2013}, } @inbook{10900, abstract = {Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays.}, author = {Weber, Michele and Sixt, Michael K}, booktitle = {Chemokines}, editor = {Cardona, Astrid and Ubogu, Eroboghene}, isbn = {9781627034258}, issn = {1940-6029}, pages = {215--226}, publisher = {Humana Press}, title = {{Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations}}, doi = {10.1007/978-1-62703-426-5_14}, volume = {1013}, year = {2013}, }