@article{1292,
abstract = {We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds.},
author = {Durst, Sebastian and Kegel, Marc and Klukas, Mirko D},
journal = {Acta Mathematica Hungarica},
number = {2},
pages = {441 -- 455},
publisher = {Springer},
title = {{Computing the Thurston–Bennequin invariant in open books}},
doi = {10.1007/s10474-016-0648-4},
volume = {150},
year = {2016},
}
@article{1293,
abstract = {For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.},
author = {Solus, Liam T and Uhler, Caroline and Yoshida, Ruriko},
journal = {Linear Algebra and Its Applications},
pages = {247 -- 275},
publisher = {Elsevier},
title = {{Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors}},
doi = {10.1016/j.laa.2016.07.026},
volume = {509},
year = {2016},
}
@article{1318,
abstract = {We develop a large-scale regularity theory of higher order for divergence-form elliptic equations with heterogeneous coefficient fields a in the context of stochastic homogenization. The large-scale regularity of a-harmonic functions is encoded by Liouville principles: The space of a-harmonic functions that grow at most like a polynomial of degree k has the same dimension as in the constant-coefficient case. This result can be seen as the qualitative side of a large-scale Ck,α-regularity theory, which in the present work is developed in the form of a corresponding Ck,α-“excess decay” estimate: For a given a-harmonic function u on a ball BR, its energy distance on some ball Br to the above space of a-harmonic functions that grow at most like a polynomial of degree k has the natural decay in the radius r above some minimal radius r0. Though motivated by stochastic homogenization, the contribution of this paper is of purely deterministic nature: We work under the assumption that for the given realization a of the coefficient field, the couple (φ, σ) of scalar and vector potentials of the harmonic coordinates, where φ is the usual corrector, grows sublinearly in a mildly quantified way. We then construct “kth-order correctors” and thereby the space of a-harmonic functions that grow at most like a polynomial of degree k, establish the above excess decay, and then the corresponding Liouville principle.},
author = {Julian Fischer and Otto, Felix},
journal = {Communications in Partial Differential Equations},
number = {7},
pages = {1108 -- 1148},
publisher = {Taylor & Francis},
title = {{A higher-order large scale regularity theory for random elliptic operators}},
doi = {10.1080/03605302.2016.1179318},
volume = {41},
year = {2016},
}
@article{1322,
abstract = {Direct reciprocity is a major mechanism for the evolution of cooperation. Several classical studies have suggested that humans should quickly learn to adopt reciprocal strategies to establish mutual cooperation in repeated interactions. On the other hand, the recently discovered theory of ZD strategies has found that subjects who use extortionate strategies are able to exploit and subdue cooperators. Although such extortioners have been predicted to succeed in any population of adaptive opponents, theoretical follow-up studies questioned whether extortion can evolve in reality. However, most of these studies presumed that individuals have similar strategic possibilities and comparable outside options, whereas asymmetries are ubiquitous in real world applications. Here we show with a model and an economic experiment that extortionate strategies readily emerge once subjects differ in their strategic power. Our experiment combines a repeated social dilemma with asymmetric partner choice. In our main treatment there is one randomly chosen group member who is unilaterally allowed to exchange one of the other group members after every ten rounds of the social dilemma. We find that this asymmetric replacement opportunity generally promotes cooperation, but often the resulting payoff distribution reflects the underlying power structure. Almost half of the subjects in a better strategic position turn into extortioners, who quickly proceed to exploit their peers. By adapting their cooperation probabilities consistent with ZD theory, extortioners force their co-players to cooperate without being similarly cooperative themselves. Comparison to non-extortionate players under the same conditions indicates a substantial net gain to extortion. Our results thus highlight how power asymmetries can endanger mutually beneficial interactions, and transform them into exploitative relationships. In particular, our results indicate that the extortionate strategies predicted from ZD theory could play a more prominent role in our daily interactions than previously thought.},
author = {Hilbe, Christian and Hagel, Kristin and Milinski, Manfred},
journal = {PLoS One},
number = {10},
publisher = {Public Library of Science},
title = {{Asymmetric power boosts extortion in an economic experiment}},
doi = {10.1371/journal.pone.0163867},
volume = {11},
year = {2016},
}
@article{1323,
abstract = {Mossy fiber synapses on CA3 pyramidal cells are 'conditional detonators' that reliably discharge postsynaptic targets. The 'conditional' nature implies that burst activity in dentate gyrus granule cells is required for detonation. Whether single unitary excitatory postsynaptic potentials (EPSPs) trigger spikes in CA3 neurons remains unknown. Mossy fiber synapses exhibit both pronounced short-term facilitation and uniquely large post-tetanic potentiation (PTP). We tested whether PTP could convert mossy fiber synapses from subdetonator into detonator mode, using a recently developed method to selectively and noninvasively stimulate individual presynaptic terminals in rat brain slices. Unitary EPSPs failed to initiate a spike in CA3 neurons under control conditions, but reliably discharged them after induction of presynaptic short-term plasticity. Remarkably, PTP switched mossy fiber synapses into full detonators for tens of seconds. Plasticity-dependent detonation may be critical for efficient coding, storage, and recall of information in the granule cell–CA3 cell network.},
author = {Vyleta, Nicholas and Borges Merjane, Carolina and Jonas, Peter M},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses}},
doi = {10.7554/eLife.17977},
volume = {5},
year = {2016},
}
@inproceedings{1325,
abstract = {We study graphs and two-player games in which rewards are assigned to states, and the goal of the players is to satisfy or dissatisfy certain property of the generated outcome, given as a mean payoff property. Since the notion of mean-payoff does not reflect possible fluctuations from the mean-payoff along a run, we propose definitions and algorithms for capturing the stability of the system, and give algorithms for deciding if a given mean payoff and stability objective can be ensured in the system.},
author = {Brázdil, Tomáš and Forejt, Vojtěch and Kučera, Antonín and Novotny, Petr},
location = {Quebec City, Canada},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Stability in graphs and games}},
doi = {10.4230/LIPIcs.CONCUR.2016.10},
volume = {59},
year = {2016},
}
@inproceedings{1326,
abstract = {Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. },
author = {Brázdil, Tomáš and Kučera, Antonín and Novotny, Petr},
location = {Chiba, Japan},
pages = {32 -- 49},
publisher = {Springer},
title = {{Optimizing the expected mean payoff in Energy Markov Decision Processes}},
doi = {10.1007/978-3-319-46520-3_3},
volume = {9938},
year = {2016},
}
@inproceedings{1327,
abstract = {We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. },
author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Chmelik, Martin and Gupta, Anchit and Novotny, Petr},
booktitle = {Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems},
location = {Singapore},
pages = {1465 -- 1466},
publisher = {ACM},
title = {{Stochastic shortest path with energy constraints in POMDPs}},
year = {2016},
}
@article{1329,
abstract = {Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.},
author = {Huylmans, Ann K and López Ezquerra, Alberto and Parsch, John and Cordellier, Mathilde},
journal = {Genome Biology and Evolution},
number = {10},
pages = {3120 -- 3139},
publisher = {Oxford University Press},
title = {{De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata}},
doi = {10.1093/gbe/evw221},
volume = {8},
year = {2016},
}
@article{1330,
abstract = {In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K.},
author = {Akopyan, Arseniy and Balitskiy, Alexey},
journal = {Israel Journal of Mathematics},
number = {2},
pages = {833 -- 845},
publisher = {Springer},
title = {{Billiards in convex bodies with acute angles}},
doi = {10.1007/s11856-016-1429-z},
volume = {216},
year = {2016},
}
@article{1332,
abstract = {Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.},
author = {Chait, Remy P and Palmer, Adam and Yelin, Idan and Kishony, Roy},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments}},
doi = {10.1038/ncomms10333},
volume = {7},
year = {2016},
}
@article{1333,
abstract = {Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most.},
author = {Milinski, Manfred and Hilbe, Christian and Semmann, Dirk and Sommerfeld, Ralf and Marotzke, Jochem},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Humans choose representatives who enforce cooperation in social dilemmas through extortion}},
doi = {10.1038/ncomms10915},
volume = {7},
year = {2016},
}
@article{1334,
abstract = {Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping.},
author = {Schönenberger, Philipp and O'Neill, Joseph and Csicsvari, Jozsef L},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Activity dependent plasticity of hippocampal place maps}},
doi = {10.1038/ncomms11824},
volume = {7},
year = {2016},
}
@inproceedings{1335,
abstract = {In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
location = {Edinburgh, United Kingdom},
pages = {23 -- 38},
publisher = {Springer},
title = {{Quantitative monitor automata}},
doi = {10.1007/978-3-662-53413-7_2},
volume = {9837},
year = {2016},
}
@article{1347,
abstract = {During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem's constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.},
author = {Schmidt, Richard and Lemeshko, Mikhail},
journal = {Physical Review X},
number = {1},
publisher = {American Physical Society},
title = {{Deformation of a quantum many-particle system by a rotating impurity}},
doi = {10.1103/PhysRevX.6.011012},
volume = {6},
year = {2016},
}
@inproceedings{1348,
abstract = {A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest.},
author = {Fulek, Radoslav},
location = {Helsinki, Finland},
pages = {31 -- 42},
publisher = {Springer},
title = {{Bounded embeddings of graphs in the plane}},
doi = {10.1007/978-3-319-44543-4_3},
volume = {9843},
year = {2016},
}
@inproceedings{1349,
abstract = {Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.},
author = {Oliveto, Pietro and Paixao, Tiago and Heredia, Jorge and Sudholt, Dirk and Trubenova, Barbora},
booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference 2016 },
location = {Denver, CO, USA},
pages = {1163 -- 1170},
publisher = {ACM},
title = {{When non-elitism outperforms elitism for crossing fitness valleys}},
doi = {10.1145/2908812.2908909},
year = {2016},
}
@article{1350,
abstract = {The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3
synapses are thought to be the subcellular substrate of pattern completion. However, the
synaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.
Simultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient
memory storage and retrieval in hippocampal networks.},
author = {Guzmán, José and Schlögl, Alois and Frotscher, Michael and Jonas, Peter M},
journal = {Science},
number = {6304},
pages = {1117 -- 1123},
publisher = {American Association for the Advancement of Science},
title = {{Synaptic mechanisms of pattern completion in the hippocampal CA3 network}},
doi = {10.1126/science.aaf1836},
volume = {353},
year = {2016},
}
@article{1342,
abstract = {A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics.},
author = {Baym, Michael and Lieberman, Tami and Kelsic, Eric and Chait, Remy P and Gross, Rotem and Yelin, Idan and Kishony, Roy},
journal = {Science},
number = {6304},
pages = {1147 -- 1151},
publisher = {American Association for the Advancement of Science},
title = {{Spatiotemporal microbial evolution on antibiotic landscapes}},
doi = {10.1126/science.aag0822},
volume = {353},
year = {2016},
}
@article{1343,
abstract = {The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a
potential for explaining the mystery of high-temperature superconductivity. Recent progress in
ultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using
the tools of quantum simulation, which emerged as a promising alternative to the numerical
calculations plagued by the infamous sign problem. However, the temperatures achieved using
elaborate laser cooling protocols so far have been too high to show the appearance of
antiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate
that using the machinery of dissipative quantum state engineering, one can observe the emergence of
the AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach
is to add incoherent laser scattering in such a way that the AF state emerges as the dark state of
the driven-dissipative dynamics. The proposed controlled dissipation channels described in this work
are straightforward to add to already existing experimental setups.},
author = {Kaczmarczyk, Jan and Weimer, Hendrik and Lemeshko, Mikhail},
journal = {New Journal of Physics},
number = {9},
publisher = {IOP Publishing Ltd.},
title = {{Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model}},
doi = {10.1088/1367-2630/18/9/093042},
volume = {18},
year = {2016},
}
@article{1344,
abstract = {Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.},
author = {Fendrych, Matyas and Leung, Jeffrey and Friml, Jirí},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls}},
doi = {10.7554/eLife.19048},
volume = {5},
year = {2016},
}
@article{1345,
abstract = {The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components.},
author = {Molnar, Gergely and Fendrych, Matyas and Friml, Jirí},
journal = {Nature Plants},
publisher = {Nature Publishing Group},
title = {{Plasma membrane: Negative attraction}},
doi = {10.1038/nplants.2016.102},
volume = {2},
year = {2016},
}
@article{1339,
abstract = {We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive
actuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By
measuring the resonance frequencies of the system, we show that the comb-drive actuator and the
silicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate
(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)
placed close to the silicon beam. In contrast, the effective spring constant of the system is insensitive
to either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator
can be used to switch between different coupling rates with a frequency of at least 10 kHz.
},
author = {Verbiest, Gerard and Xu, Duo and Goldsche, Matthias and Khodkov, Timofiy and Barzanjeh, Shabir and Von Den Driesch, Nils and Buca, Dan and Stampfer, Christoph},
journal = {Applied Physics Letter},
publisher = {American Institute of Physics},
title = {{Tunable mechanical coupling between driven microelectromechanical resonators}},
doi = {10.1063/1.4964122},
volume = {109},
year = {2016},
}
@inproceedings{1340,
abstract = {We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11].},
author = {Hansen, Kristoffer and Ibsen-Jensen, Rasmus and Koucký, Michal},
location = {Liverpool, United Kingdom},
pages = {64 -- 76},
publisher = {Springer},
title = {{The big match in small space}},
doi = {10.1007/978-3-662-53354-3_6},
volume = {9928},
year = {2016},
}
@inproceedings{1363,
abstract = {When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special "non-reflecting" boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation.},
author = {Bojsen-Hansen, Morten and Wojtan, Christopher J},
location = {Anaheim, CA, USA},
number = {4},
publisher = {ACM},
title = {{Generalized non-reflecting boundaries for fluid re-simulation}},
doi = {10.1145/2897824.2925963},
volume = {35},
year = {2016},
}
@inproceedings{1364,
abstract = {We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated.},
author = {Miguel Villalba, Eder and Lepoutre, Mathias and Bickel, Bernd},
location = {Anaheim, CA, USA},
number = {4},
publisher = {ACM},
title = {{Computational design of stable planar-rod structures}},
doi = {10.1145/2897824.2925978},
volume = {35},
year = {2016},
}
@inproceedings{1365,
abstract = {A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest.},
author = {Alwen, Joel F and Blocki, Jeremiah},
location = {Santa Barbara, CA, USA},
pages = {241 -- 271},
publisher = {Springer},
title = {{Efficiently computing data-independent memory-hard functions}},
doi = {10.1007/978-3-662-53008-5_9},
volume = {9815},
year = {2016},
}
@inproceedings{1366,
abstract = {We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions.},
author = {Gazi, Peter and Tessaro, Stefano},
location = {Vienna, Austria},
pages = {87 -- 116},
publisher = {Springer},
title = {{Provably robust sponge-based PRNGs and KDFs}},
doi = {10.1007/978-3-662-49890-3_4},
volume = {9665},
year = {2016},
}
@article{1368,
abstract = {Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.},
author = {Wysokiński, Marcin and Kaczmarczyk, Jan and Spałek, Jozef},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {2},
publisher = {American Physical Society},
title = {{Correlation driven d wave superconductivity in Anderson lattice model: Two gaps}},
doi = {10.1103/PhysRevB.94.024517},
volume = {94},
year = {2016},
}
@inproceedings{1369,
abstract = {We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations.},
author = {Kolesnikov, Alexander and Lampert, Christoph},
location = {Amsterdam, The Netherlands},
pages = {695 -- 711},
publisher = {Springer},
title = {{Seed, expand and constrain: Three principles for weakly-supervised image segmentation}},
doi = {10.1007/978-3-319-46493-0_42},
volume = {9908},
year = {2016},
}
@article{1370,
abstract = {We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction.},
author = {Barzanjeh, Shabir and Vitali, David},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {3},
publisher = {American Physical Society},
title = {{Phonon Josephson junction with nanomechanical resonators}},
doi = {10.1103/PhysRevA.93.033846},
volume = {93},
year = {2016},
}
@article{1372,
abstract = {Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism.},
author = {Pernisová, Markéta and Prat, Tomas and Grones, Peter and Haruštiaková, Danka and Matonohova, Martina and Spíchal, Lukáš and Nodzyński, Tomasz and Friml, Jirí and Hejátko, Jan},
journal = {New Phytologist},
number = {2},
pages = {497 -- 509},
publisher = {Wiley-Blackwell},
title = {{Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis}},
doi = {10.1111/nph.14049},
volume = {212},
year = {2016},
}
@article{1373,
author = {Martin, Olivier and Zagórski, Marcin P},
journal = {Physics of Life Reviews},
pages = {168 -- 171},
publisher = {Elsevier},
title = {{Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"}},
doi = {10.1016/j.plrev.2016.06.006},
volume = {17},
year = {2016},
}
@article{1352,
abstract = {We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking.},
author = {Kaczmarczyk, Jan and Schickling, Tobias and Bünemann, Jörg},
journal = {Physical Review B - Condensed Matter and Materials Physics},
number = {8},
publisher = {American Physical Society},
title = {{Coexistence of nematic order and superconductivity in the Hubbard model}},
doi = {10.1103/PhysRevB.94.085152},
volume = {94},
year = {2016},
}
@article{1353,
abstract = {We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations.},
author = {Barto, Libor and Kazda, Alexandr},
journal = {International Journal of Algebra and Computation},
number = {5},
pages = {1033 -- 1060},
publisher = {World Scientific Publishing},
title = {{Deciding absorption}},
doi = {10.1142/S0218196716500430},
volume = {26},
year = {2016},
}
@article{1354,
abstract = {Fabrication processes involving anhydrous hydrofluoric vapor etching are developed to create high-Q aluminum superconducting microwave resonators on free-standing silicon membranes formed from a silicon-on-insulator wafer. Using this fabrication process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave spectroscopy and radiation pressure backaction are used to characterize the coupled system in a dilution refrigerator down to temperatures of Tf=11 mK, yielding a measured electromechanical vacuum coupling rate of g0/2π=24.6 Hz and a mechanical resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being realized at an elevated fridge temperature of Tf=211 mK.},
author = {Dieterle, Paul and Kalaee, Mahmoud and Fink, Johannes M and Painter, Oskar},
journal = {Physical Review Applied},
number = {1},
publisher = {American Physical Society},
title = {{Superconducting cavity electromechanics on a silicon-on-insulator platform}},
doi = {10.1103/PhysRevApplied.6.014013},
volume = {6},
year = {2016},
}
@article{1355,
abstract = {Radiation pressure has recently been used to effectively couple the quantum motion of mechanical elements to the fields of optical or microwave light. Integration of all three degrees of freedom—mechanical, optical and microwave—would enable a quantum interconnect between microwave and optical quantum systems. We present a platform based on silicon nitride nanomembranes for integrating superconducting microwave circuits with planar acoustic and optical devices such as phononic and photonic crystals. Using planar capacitors with vacuum gaps of 60 nm and spiral inductor coils of micron pitch we realize microwave resonant circuits with large electromechanical coupling to planar acoustic structures of nanoscale dimensions and femtoFarad motional capacitance. Using this enhanced coupling, we demonstrate microwave backaction cooling of the 4.48 MHz mechanical resonance of a nanobeam to an occupancy as low as 0.32. These results indicate the viability of silicon nitride nanomembranes as an all-in-one substrate for quantum electro-opto-mechanical experiments.},
author = {Fink, Johannes M and Kalaee, Mahmoud and Pitanti, Alessandro and Norte, Richard and Heinzle, Lukas and Davanço, Marcelo and Srinivasan, Kartik and Painter, Oskar},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Quantum electromechanics on silicon nitride nanomembranes}},
doi = {10.1038/ncomms12396},
volume = {7},
year = {2016},
}
@article{1356,
author = {Barton, Nicholas H},
journal = {Genetics},
number = {1},
pages = {3 -- 4},
publisher = {Genetics Society of America},
title = {{Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”}},
doi = {10.1534/genetics.115.184796},
volume = {202},
year = {2016},
}
@article{1357,
author = {Barton, Nicholas H},
journal = {Genetics},
number = {3},
pages = {865 -- 866},
publisher = {Genetics Society of America},
title = {{Richard Hudson and Norman Kaplan on the coalescent process}},
doi = {10.1534/genetics.116.187542},
volume = {202},
year = {2016},
}
@article{1359,
abstract = {The role of gene interactions in the evolutionary process has long
been controversial. Although some argue that they are not of
importance, because most variation is additive, others claim that
their effect in the long term can be substantial. Here, we focus on
the long-term effects of genetic interactions under directional
selection assuming no mutation or dominance, and that epistasis is
symmetrical overall. We ask by how much the mean of a complex
trait can be increased by selection and analyze two extreme
regimes, in which either drift or selection dominate the dynamics
of allele frequencies. In both scenarios, epistatic interactions affect
the long-term response to selection by modulating the additive
genetic variance. When drift dominates, we extend Robertson
’
s
[Robertson A (1960)
Proc R Soc Lond B Biol Sci
153(951):234
−
249]
argument to show that, for any form of epistasis, the total response
of a haploid population is proportional to the initial total genotypic
variance. In contrast, the total response of a diploid population is
increased by epistasis, for a given initial genotypic variance. When
selection dominates, we show that the total selection response can
only be increased by epistasis when s
ome initially deleterious alleles
become favored as the genetic background changes. We find a sim-
ple approximation for this effect and show that, in this regime, it is
the structure of the genotype - phenotype map that matters and not
the variance components of the population.},
author = {Paixao, Tiago and Barton, Nicholas H},
journal = {PNAS},
number = {16},
pages = {4422 -- 4427},
publisher = {National Academy of Sciences},
title = {{The effect of gene interactions on the long-term response to selection}},
doi = {10.1073/pnas.1518830113},
volume = {113},
year = {2016},
}
@article{1360,
abstract = {We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. },
author = {Akopyan, Arseniy and Balitskiy, Alexey and Karasev, Roman and Sharipova, Anastasia},
journal = {Proceedings of the American Mathematical Society},
number = {10},
pages = {4501 -- 4513},
publisher = {American Mathematical Society},
title = {{Elementary approach to closed billiard trajectories in asymmetric normed spaces}},
doi = {10.1090/proc/13062},
volume = {144},
year = {2016},
}
@inproceedings{1361,
abstract = {We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes.},
author = {Da, Fang and Hahn, David and Batty, Christopher and Wojtan, Christopher J and Grinspun, Eitan},
location = {Anaheim, CA, USA},
number = {4},
publisher = {ACM},
title = {{Surface only liquids}},
doi = {10.1145/2897824.2925899},
volume = {35},
year = {2016},
}
@article{1377,
abstract = {We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.},
author = {Kolmogorov, Vladimir and Pock, Thomas and Rolinek, Michal},
journal = {SIAM Journal on Imaging Sciences},
number = {2},
pages = {605 -- 636},
publisher = {Society for Industrial and Applied Mathematics },
title = {{Total variation on a tree}},
doi = {10.1137/15M1010257},
volume = {9},
year = {2016},
}
@inproceedings{1389,
abstract = {The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be
described in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can
equivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear
differential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision.},
author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James},
booktitle = {LICS '16},
location = {New York, NY, USA},
pages = {515 -- 524},
publisher = {IEEE},
title = {{On recurrent reachability for continuous linear dynamical systems}},
doi = {10.1145/2933575.2934548},
year = {2016},
}
@inproceedings{1391,
abstract = {We present an extension to the quantifier-free theory of integer arrays which allows us to express counting. The properties expressible in Array Folds Logic (AFL) include statements such as "the first array cell contains the array length," and "the array contains equally many minimal and maximal elements." These properties cannot be expressed in quantified fragments of the theory of arrays, nor in the theory of concatenation. Using reduction to counter machines, we show that the satisfiability problem of AFL is PSPACE-complete, and with a natural restriction the complexity decreases to NP. We also show that adding either universal quantifiers or concatenation leads to undecidability.
AFL contains terms that fold a function over an array. We demonstrate that folding, a well-known concept from functional languages, allows us to concisely summarize loops that count over arrays, which occurs frequently in real-life programs. We provide a tool that can discharge proof obligations in AFL, and we demonstrate on practical examples that our decision procedure can solve a broad range of problems in symbolic testing and program verification.},
author = {Daca, Przemyslaw and Henzinger, Thomas A and Kupriyanov, Andrey},
location = {Toronto, Canada},
pages = {230 -- 248},
publisher = {Springer},
title = {{Array folds logic}},
doi = {10.1007/978-3-319-41540-6_13},
volume = {9780},
year = {2016},
}
@article{1394,
abstract = {The solution space of genome-scale models of cellular metabolism provides a map between physically
viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the
corresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show
that empirical growth rate distributions recently obtained in experiments at single-cell resolution can
be explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the
higher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of
a large bacterial population that captures this trade-off. The scaling relationships observed in
experiments encode, in such frameworks, for the same distance from the maximum achievable growth
rate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being
grounded on genome-scale metabolic network reconstructions, these results allow for multiple
implications and extensions in spite of the underlying conceptual simplicity.},
author = {De Martino, Daniele and Capuani, Fabrizio and De Martino, Andrea},
journal = {Physical Biology},
number = {3},
publisher = {IOP Publishing Ltd.},
title = {{Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli}},
doi = {10.1088/1478-3975/13/3/036005},
volume = {13},
year = {2016},
}
@article{1380,
abstract = {We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP.},
author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James},
journal = {Journal of the ACM},
number = {3},
publisher = {ACM},
title = {{On the complexity of the orbit problem}},
doi = {10.1145/2857050},
volume = {63},
year = {2016},
}
@inproceedings{1381,
abstract = {Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there.},
author = {Mabillard, Isaac and Wagner, Uli},
location = {Medford, MA, USA},
pages = {51.1 -- 51.12},
publisher = {Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH},
title = {{Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range}},
doi = {10.4230/LIPIcs.SoCG.2016.51},
volume = {51},
year = {2016},
}
@article{1412,
abstract = {Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods.},
author = {Goldade, Ryan and Batty, Christopher and Wojtan, Christopher J},
journal = {Computer Graphics Forum},
number = {2},
pages = {233 -- 242},
publisher = {Wiley-Blackwell},
title = {{A practical method for high-resolution embedded liquid surfaces}},
doi = {10.1111/cgf.12826},
volume = {35},
year = {2016},
}
@article{1415,
abstract = {The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation.},
author = {Ferstl, Florian and Ando, Ryoichi and Wojtan, Christopher J and Westermann, Rüdiger and Thuerey, Nils},
journal = {Computer Graphics Forum},
number = {2},
pages = {225 -- 232},
publisher = {Wiley-Blackwell},
title = {{Narrow band FLIP for liquid simulations}},
doi = {10.1111/cgf.12825},
volume = {35},
year = {2016},
}