@inproceedings{10796, abstract = {We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).}, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus}, booktitle = {Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms}, isbn = {978-161197374-7}, location = {San Diego, CA, United States}, number = {1}, pages = {1018--1029}, publisher = {SIAM}, title = {{The value 1 problem under finite-memory strategies for concurrent mean-payoff games}}, doi = {10.1137/1.9781611973730.69}, volume = {2015}, year = {2015}, } @article{9532, abstract = {Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.}, author = {Rodrigues, Jessica A. and Zilberman, Daniel}, issn = {1549-5477}, journal = {Genes and Development}, number = {24}, pages = {2517–2531}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Evolution and function of genomic imprinting in plants}}, doi = {10.1101/gad.269902.115}, volume = {29}, year = {2015}, } @article{9575, abstract = {We give several results showing that different discrete structures typically gain certain spanning substructures (in particular, Hamilton cycles) after a modest random perturbation. First, we prove that adding linearly many random edges to a dense k-uniform hypergraph ensures the (asymptotically almost sure) existence of a perfect matching or a loose Hamilton cycle. The proof involves an interesting application of Szemerédi's Regularity Lemma, which might be independently useful. We next prove that digraphs with certain strong expansion properties are pancyclic, and use this to show that adding a linear number of random edges typically makes a dense digraph pancyclic. Finally, we prove that perturbing a certain (minimum-degree-dependent) number of random edges in a tournament typically ensures the existence of multiple edge-disjoint Hamilton cycles. All our results are tight.}, author = {Krivelevich, Michael and Kwan, Matthew Alan and Sudakov, Benny}, issn = {1571-0653}, journal = {Electronic Notes in Discrete Mathematics}, pages = {181--187}, publisher = {Elsevier}, title = {{Cycles and matchings in randomly perturbed digraphs and hypergraphs}}, doi = {10.1016/j.endm.2015.06.027}, volume = {49}, year = {2015}, } @article{9673, abstract = {Current strategies of computational crystal plasticity that focus on individual atoms or dislocations are impractical for real-scale, large-strain problems even with today’s computing power. Dislocation-density based approaches are a way forward but a critical issue to address is a realistic description of the interactions between dislocations. In this paper, a new scheme for computational dynamics of dislocation-density functions is proposed, which takes full consideration of the mutual elastic interactions between dislocations based on the Hirth–Lothe formulation. Other features considered include (i) the continuity nature of the movements of dislocation densities, (ii) forest hardening, (iii) generation according to high spatial gradients in dislocation densities, and (iv) annihilation. Numerical implementation by the finite-volume method, which is well suited for flow problems with high gradients, is discussed. Numerical examples performed for a single-crystal aluminum model show typical strength anisotropy behavior comparable to experimental observations. Furthermore, a detailed case study on small-scale crystal plasticity successfully captures a number of key experimental features, including power-law relation between strength and size, low dislocation storage and jerky deformation.}, author = {Leung, H.S. and Leung, P.S.S. and Cheng, Bingqing and Ngan, A.H.W.}, issn = {0749-6419}, journal = {International Journal of Plasticity}, pages = {1--25}, publisher = {Elsevier}, title = {{A new dislocation-density-function dynamics scheme for computational crystal plasticity by explicit consideration of dislocation elastic interactions}}, doi = {10.1016/j.ijplas.2014.09.009}, volume = {67}, year = {2015}, } @article{9684, abstract = {The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept.}, author = {Leung, P S S and Leung, H S and Cheng, Bingqing and Ngan, A H W}, issn = {1361-651X}, journal = {Modelling and Simulation in Materials Science and Engineering}, number = {3}, publisher = {IOP Publishing}, title = {{Size dependence of yield strength simulated by a dislocation-density function dynamics approach}}, doi = {10.1088/0965-0393/23/3/035001}, volume = {23}, year = {2015}, } @article{9688, abstract = {The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.}, author = {Cheng, Bingqing and Tribello, Gareth A. and Ceriotti, Michele}, issn = {1550-235X}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {18}, publisher = {American Physical Society}, title = {{Solid-liquid interfacial free energy out of equilibrium}}, doi = {10.1103/physrevb.92.180102}, volume = {92}, year = {2015}, } @misc{9711, author = {Chevereau, Guillaume and Lukacisinova, Marta and Batur, Tugce and Guvenek, Aysegul and Ayhan, Dilay Hazal and Toprak, Erdal and Bollenbach, Mark Tobias}, publisher = {Public Library of Science}, title = {{Excel file containing the raw data for all figures}}, doi = {10.1371/journal.pbio.1002299.s001}, year = {2015}, } @misc{9712, author = {Tugrul, Murat and Paixao, Tiago and Barton, Nicholas H and Tkačik, Gašper}, publisher = {Public Library of Science}, title = {{Other fitness models for comparison & for interacting TFBSs}}, doi = {10.1371/journal.pgen.1005639.s001}, year = {2015}, } @misc{9714, author = {Gómez Sicilia, Àngel and Sikora, Mateusz K and Cieplak, Marek and Carrión Vázquez, Mariano}, publisher = {Public Library of Science }, title = {{An exploration of the universe of polyglutamine structures - submission to PLOS journals}}, doi = {10.1371/journal.pcbi.1004541.s001}, year = {2015}, } @misc{9715, author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar}, publisher = {Public Library of Science}, title = {{Mathematical inference of the results}}, doi = {10.1371/journal.pone.0126907.s001}, year = {2015}, } @misc{9718, author = {Friedlander, Tamar and Mayo, Avraham E. and Tlusty, Tsvi and Alon, Uri}, publisher = {Public Library of Science}, title = {{Supporting information text}}, doi = {10.1371/journal.pcbi.1004055.s001}, year = {2015}, } @misc{9719, abstract = {Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.}, author = {Wielgoss, Sébastien and Bergmiller, Tobias and Bischofberger, Anna M. and Hall, Alex R.}, publisher = {Dryad}, title = {{Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria}}, doi = {10.5061/dryad.cj910}, year = {2015}, } @misc{9721, abstract = {To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.}, author = {Theis, Fabian and Ugelvig, Line V and Marr, Carsten and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Opposing effects of allogrooming on disease transmission in ant societies}}, doi = {10.5061/dryad.dj2bf}, year = {2015}, } @misc{9737, author = {Symonova, Olga and Topp, Christopher and Edelsbrunner, Herbert}, publisher = {Public Library of Science}, title = {{Root traits computed by DynamicRoots for the maize root shown in fig 2}}, doi = {10.1371/journal.pone.0127657.s001}, year = {2015}, } @misc{9742, abstract = {Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects.}, author = {Westhus, Claudia and Ugelvig, Line V and Tourdot, Edouard and Heinze, Jürgen and Doums, Claudie and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant}}, doi = {10.5061/dryad.7kc79}, year = {2015}, } @misc{9765, author = {Chevereau, Guillaume and Lukacisinova, Marta and Batur, Tugce and Guvenek, Aysegul and Ayhan, Dilay Hazal and Toprak, Erdal and Bollenbach, Mark Tobias}, publisher = {Public Library of Science}, title = {{Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs}}, doi = {10.1371/journal.pbio.1002299.s008}, year = {2015}, } @misc{9772, author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar}, publisher = {Public Library of Science}, title = {{Description of the agent based simulations}}, doi = {10.1371/journal.pone.0126907.s003}, year = {2015}, } @misc{9773, author = {Friedlander, Tamar and Mayo, Avraham E. and Tlusty, Tsvi and Alon, Uri}, publisher = {Public Library of Science}, title = {{Evolutionary simulation code}}, doi = {10.1371/journal.pcbi.1004055.s002}, year = {2015}, } @article{981, abstract = {The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials.}, author = {Zeljkovic, Ilija and Okada, Yoshinori and Maksym Serbyn and Sankar, Raman and Walkup, Daniel and Zhou, Wenwen and Liu, Junwei and Chang, Guoqing and Wang, Yungjui and Hasan, Md Z and Chou, Fangcheng and Lin, Hsin and Bansil, Arun and Fu, Liang and Madhavan, Vidya}, journal = {Nature Materials}, number = {3}, pages = {318 -- 324}, publisher = {Nature Publishing Group}, title = {{Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators}}, doi = {10.1038/nmat4215}, volume = {14}, year = {2015}, } @article{982, abstract = {We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.}, author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A}, journal = {Physical Review X}, number = {4}, publisher = {American Physical Society}, title = {{Criterion for many-body localization-delocalization phase transition}}, doi = {10.1103/PhysRevX.5.041047}, volume = {5}, year = {2015}, }