@inproceedings{1421, abstract = {Hybridization methods enable the analysis of hybrid automata with complex, nonlinear dynamics through a sound abstraction process. Complex dynamics are converted to simpler ones with added noise, and then analysis is done using a reachability method for the simpler dynamics. Several such recent approaches advocate that only "dynamic" hybridization techniquesi.e., those where the dynamics are abstracted on-The-fly during a reachability computation are effective. In this paper, we demonstrate this is not the case, and create static hybridization methods that are more scalable than earlier approaches. The main insight in our approach is that quick, numeric simulations can be used to guide the process, eliminating the need for an exponential number of hybridization domains. Transitions between domains are generally timetriggered, avoiding accumulated error from geometric intersections. We enhance our static technique by combining time-Triggered transitions with occasional space-Triggered transitions, and demonstrate the benefits of the combined approach in what we call mixed-Triggered hybridization. Finally, error modes are inserted to confirm that the reachable states stay within the hybridized regions. The developed techniques can scale to higher dimensions than previous static approaches, while enabling the parallelization of the main performance bottleneck for many dynamic hybridization approaches: The nonlinear optimization required for sound dynamics abstraction. We implement our method as a model transformation pass in the HYST tool, and perform reachability analysis and evaluation using an unmodified version of SpaceEx on nonlinear models with up to six dimensions.}, author = {Bak, Stanley and Bogomolov, Sergiy and Henzinger, Thomas A and Johnson, Taylor and Prakash, Pradyot}, location = {Vienna, Austria}, pages = {155 -- 164}, publisher = {Springer}, title = {{Scalable static hybridization methods for analysis of nonlinear systems}}, doi = {10.1145/2883817.2883837}, year = {2016}, } @article{1422, abstract = {We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior.}, author = {Frank, Rupert and Hainzl, Christian and Schlein, Benjamin and Seiringer, Robert}, journal = {Letters in Mathematical Physics}, number = {7}, pages = {913 -- 923}, publisher = {Springer}, title = {{Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations}}, doi = {10.1007/s11005-016-0847-5}, volume = {106}, year = {2016}, } @article{1423, abstract = {Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation.}, author = {Baek, Seung and Jeong, Hyeongchai and Hilbe, Christian and Nowak, Martin}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Comparing reactive and memory-one strategies of direct reciprocity}}, doi = {10.1038/srep25676}, volume = {6}, year = {2016}, } @article{1427, abstract = {Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.}, author = {Lagator, Mato and Igler, Claudia and Moreno, Anaisa and Guet, Calin C and Bollback, Jonathan P}, journal = {Molecular Biology and Evolution}, number = {3}, pages = {761 -- 769}, publisher = {Oxford University Press}, title = {{Epistatic interactions in the arabinose cis-regulatory element}}, doi = {10.1093/molbev/msv269}, volume = {33}, year = {2016}, } @inproceedings{1428, abstract = {We report on a mathematically rigorous analysis of the superfluid properties of a Bose- Einstein condensate in the many-body ground state of a one-dimensional model of interacting bosons in a random potential.}, author = {Könenberg, Martin and Moser, Thomas and Seiringer, Robert and Yngvason, Jakob}, booktitle = {Journal of Physics: Conference Series}, location = {Shanghai, China}, number = {1}, publisher = {IOP Publishing}, title = {{Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential}}, doi = {10.1088/1742-6596/691/1/012016}, volume = {691}, year = {2016}, } @article{1429, abstract = {Solitons are localized waves formed by a balance of focusing and defocusing effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar properties including stability, periodic recurrence and particle-like trajectories. One important property is soliton fission, a process by which an energetic higher-order soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate through both experiment and theory that nonlinear photocarrier generation can induce soliton fission. Using near-field measurements, we directly observe the nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic semiconductor waveguide. We develop an analytic formalism describing the free-carrier dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold by an order of magnitude. We confirm these observations with a numerical nonlinear Schrödinger equation model. These results provide a fundamental explanation and physical scaling of optical pulse evolution in free-carrier media and could enable improved supercontinuum sources in gas based and integrated semiconductor waveguides.}, author = {Husko, Chad and Wulf, Matthias and Lefrançois, Simon and Combrié, Sylvain and Lehoucq, Gaëlle and De Rossi, Alfredo and Eggleton, Benjamin and Kuipers, Laurens}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides}}, doi = {10.1038/ncomms11332}, volume = {7}, year = {2016}, } @article{1431, abstract = {The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow.}, author = {Tartally, András and Kelager, Andreas and Fürst, Matthias and Nash, David}, journal = {PeerJ}, number = {3}, publisher = {PeerJ}, title = {{Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon}}, doi = {10.7717/peerj.1865}, volume = {2016}, year = {2016}, } @article{1434, abstract = {We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B on scales down to N−2/3N−2/3.}, author = {Bao, Zhigang and Erdös, László and Schnelli, Kevin}, journal = {Journal of Functional Analysis}, number = {3}, pages = {672 -- 719}, publisher = {Academic Press}, title = {{Local stability of the free additive convolution}}, doi = {10.1016/j.jfa.2016.04.006}, volume = {271}, year = {2016}, } @article{1435, abstract = {ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.}, author = {Guzmán, José and Gerevich, Zoltan}, journal = {Neural Plasticity}, publisher = {Hindawi Publishing Corporation}, title = {{P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction}}, doi = {10.1155/2016/1207393}, volume = {2016}, year = {2016}, } @article{1436, abstract = {We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system.}, author = {Bach, Volker and Breteaux, Sébastien and Petrat, Sören P and Pickl, Peter and Tzaneteas, Tim}, journal = {Journal de Mathématiques Pures et Appliquées}, number = {1}, pages = {1 -- 30}, publisher = {Elsevier}, title = {{Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction}}, doi = {10.1016/j.matpur.2015.09.003}, volume = {105}, year = {2016}, } @inproceedings{1438, abstract = {In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.}, author = {Chatterjee, Krishnendu and Fu, Hongfei and Novotny, Petr and Hasheminezhad, Rouzbeh}, location = {St. Petersburg, FL, USA}, pages = {327 -- 342}, publisher = {ACM}, title = {{Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs}}, doi = {10.1145/2837614.2837639}, volume = {20-22}, year = {2016}, } @inproceedings{1439, abstract = {Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification.}, author = {Dragoi, Cezara and Henzinger, Thomas A and Zufferey, Damien}, location = {St. Petersburg, FL, USA}, pages = {400 -- 415}, publisher = {ACM}, title = {{PSYNC: A partially synchronous language for fault-tolerant distributed algorithms}}, doi = {10.1145/2837614.2837650}, volume = {20-22}, year = {2016}, } @article{1440, author = {Janovjak, Harald L}, journal = {Structure}, number = {2}, pages = {213 -- 215}, publisher = {Cell Press}, title = {{Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain}}, doi = {10.1016/j.str.2016.01.002}, volume = {24}, year = {2016}, } @article{1446, abstract = {The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index.}, author = {Calatrava Moreno, Maria and Auzinger, Thomas and Werthner, Hannes}, journal = {Scientometrics}, number = {1}, pages = {213 -- 232}, publisher = {Springer}, title = {{On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data}}, doi = {10.1007/s11192-016-1842-4}, volume = {107}, year = {2016}, } @article{1448, abstract = {We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.}, author = {Fathi, Max and Maas, Jan}, journal = {The Annals of Applied Probability}, number = {3}, pages = {1774 -- 1806}, publisher = {Institute of Mathematical Statistics}, title = {{Entropic Ricci curvature bounds for discrete interacting systems}}, doi = {10.1214/15-AAP1133}, volume = {26}, year = {2016}, } @article{1475, abstract = {The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.}, author = {Toshima, Junko and Furuya, Eri and Nagano, Makoto and Kanno, Chisa and Sakamoto, Yuta and Ebihara, Masashi and Siekhaus, Daria E and Toshima, Jiro}, journal = {eLife}, number = {February 2016}, publisher = {eLife Sciences Publications}, title = {{Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton}}, doi = {10.7554/eLife.10276}, volume = {5}, year = {2016}, } @article{1476, abstract = {The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis}, author = {Toshima, Junko and Horikomi, Chika and Okada, Asuka and Hatori, Makiko and Nagano, Makoto and Masuda, Atsushi and Yamamoto, Wataru and Siekhaus, Daria E and Toshima, Jiro}, journal = {Journal of Cell Science}, number = {2}, pages = {367 -- 379}, publisher = {Company of Biologists}, title = {{Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis}}, doi = {10.1242/jcs.176651}, volume = {129}, year = {2016}, } @article{1477, abstract = {We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples.}, author = {Chatterjee, Krishnendu and Chmelik, Martin and Tracol, Mathieu}, journal = {Journal of Computer and System Sciences}, number = {5}, pages = {878 -- 911}, publisher = {Elsevier}, title = {{What is decidable about partially observable Markov decision processes with ω-regular objectives}}, doi = {10.1016/j.jcss.2016.02.009}, volume = {82}, year = {2016}, } @article{1478, abstract = {We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.}, author = {Seiringer, Robert and Warzel, Simone}, journal = {New Journal of Physics}, number = {3}, publisher = {IOP Publishing}, title = {{Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas}}, doi = {10.1088/1367-2630/18/3/035002}, volume = {18}, year = {2016}, } @article{1479, abstract = {Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero. Our counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable. Finally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.}, author = {Krenn, Stephan and Pietrzak, Krzysztof Z and Wadia, Akshay and Wichs, Daniel}, journal = {Computational Complexity}, number = {3}, pages = {567 -- 605}, publisher = {Springer}, title = {{A counterexample to the chain rule for conditional HILL entropy}}, doi = {10.1007/s00037-015-0120-9}, volume = {25}, year = {2016}, }