TY - CONF
AB - 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.
AU - Miguel Villalba, Eder
AU - Lepoutre, Mathias
AU - Bickel, Bernd
ID - 1364
IS - 4
TI - Computational design of stable planar-rod structures
VL - 35
ER -
TY - CONF
AB - 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.
AU - Alwen, Joel F
AU - Blocki, Jeremiah
ID - 1365
TI - Efficiently computing data-independent memory-hard functions
VL - 9815
ER -
TY - CONF
AB - 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.
AU - Gazi, Peter
AU - Tessaro, Stefano
ID - 1366
TI - Provably robust sponge-based PRNGs and KDFs
VL - 9665
ER -
TY - JOUR
AB - 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.
AU - Wysokiński, Marcin
AU - Kaczmarczyk, Jan
AU - Spałek, Jozef
ID - 1368
IS - 2
JF - Physical Review B - Condensed Matter and Materials Physics
TI - Correlation driven d wave superconductivity in Anderson lattice model: Two gaps
VL - 94
ER -
TY - CONF
AB - 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.
AU - Kolesnikov, Alexander
AU - Lampert, Christoph
ID - 1369
TI - Seed, expand and constrain: Three principles for weakly-supervised image segmentation
VL - 9908
ER -
TY - JOUR
AB - 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.
AU - Barzanjeh, Shabir
AU - Vitali, David
ID - 1370
IS - 3
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Phonon Josephson junction with nanomechanical resonators
VL - 93
ER -
TY - JOUR
AB - 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.
AU - Pernisová, Markéta
AU - Prat, Tomas
AU - Grones, Peter
AU - Haruštiaková, Danka
AU - Matonohova, Martina
AU - Spíchal, Lukáš
AU - Nodzyński, Tomasz
AU - Friml, Jirí
AU - Hejátko, Jan
ID - 1372
IS - 2
JF - New Phytologist
TI - Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis
VL - 212
ER -
TY - JOUR
AU - Martin, Olivier
AU - Zagórski, Marcin P
ID - 1373
JF - Physics of Life Reviews
TI - Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"
VL - 17
ER -
TY - JOUR
AB - 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.
AU - Kolmogorov, Vladimir
AU - Pock, Thomas
AU - Rolinek, Michal
ID - 1377
IS - 2
JF - SIAM Journal on Imaging Sciences
TI - Total variation on a tree
VL - 9
ER -
TY - CONF
AB - We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M.
AU - Dotterrer, Dominic
AU - Kaufman, Tali
AU - Wagner, Uli
ID - 1378
TI - On expansion and topological overlap
VL - 51
ER -
TY - CONF
AB - We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.
AU - Burton, Benjamin
AU - De Mesmay, Arnaud N
AU - Wagner, Uli
ID - 1379
TI - Finding non-orientable surfaces in 3-manifolds
VL - 51
ER -
TY - JOUR
AB - 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.
AU - Chonev, Ventsislav K
AU - Ouaknine, Joël
AU - Worrell, James
ID - 1380
IS - 3
JF - Journal of the ACM
TI - On the complexity of the orbit problem
VL - 63
ER -
TY - CONF
AB - 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.
AU - Mabillard, Isaac
AU - Wagner, Uli
ID - 1381
TI - Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range
VL - 51
ER -
TY - CONF
AB - 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.
AU - Chonev, Ventsislav K
AU - Ouaknine, Joël
AU - Worrell, James
ID - 1389
T2 - LICS '16
TI - On recurrent reachability for continuous linear dynamical systems
ER -
TY - CONF
AB - 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.
AU - Daca, Przemyslaw
AU - Henzinger, Thomas A
AU - Kupriyanov, Andrey
ID - 1391
TI - Array folds logic
VL - 9780
ER -
TY - JOUR
AB - 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.
AU - De Martino, Daniele
AU - Capuani, Fabrizio
AU - De Martino, Andrea
ID - 1394
IS - 3
JF - Physical Biology
TI - Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli
VL - 13
ER -
TY - THES
AB - Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.
AU - Ellis, Thomas
ID - 1398
TI - The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone
ER -
TY - JOUR
AB - The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status.
AU - Franek, Peter
AU - Krcál, Marek
ID - 1408
IS - 1
JF - Discrete & Computational Geometry
TI - On computability and triviality of well groups
VL - 56
ER -
TY - JOUR
AU - Abbott, Richard
AU - Barton, Nicholas H
AU - Good, Jeffrey
ID - 1409
IS - 11
JF - Molecular Ecology
TI - Genomics of hybridization and its evolutionary consequences
VL - 25
ER -
TY - JOUR
AB - The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.
AU - Ugalde, José
AU - Rodríguez Furlán, Cecilia
AU - De Rycke, Riet
AU - Norambuena, Lorena
AU - Friml, Jirí
AU - León, Gabriel
AU - Tejos, Ricardo
ID - 1410
JF - Plant Science
TI - Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development
VL - 250
ER -
TY - JOUR
AB - We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn on a compact two-dimensional surface M with boundary. Each αi and each βj is either an arc meeting the boundary of M at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise such that the total number of crossings of the ai with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. The proofs rely, among other things, on a result concerning simultaneous planar drawings of graphs by Erten and Kobourov.
AU - Matoušek, Jiří
AU - Sedgwick, Eric
AU - Tancer, Martin
AU - Wagner, Uli
ID - 1411
IS - 1
JF - Israel Journal of Mathematics
TI - Untangling two systems of noncrossing curves
VL - 212
ER -
TY - JOUR
AB - 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.
AU - Goldade, Ryan
AU - Batty, Christopher
AU - Wojtan, Christopher J
ID - 1412
IS - 2
JF - Computer Graphics Forum
TI - A practical method for high-resolution embedded liquid surfaces
VL - 35
ER -
TY - JOUR
AB - 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.
AU - Ferstl, Florian
AU - Ando, Ryoichi
AU - Wojtan, Christopher J
AU - Westermann, Rüdiger
AU - Thuerey, Nils
ID - 1415
IS - 2
JF - Computer Graphics Forum
TI - Narrow band FLIP for liquid simulations
VL - 35
ER -
TY - JOUR
AB - Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven.
AU - Van Loon, Erik
AU - Katsnelson, Mikhail
AU - Chomaz, Lauriane
AU - Lemeshko, Mikhail
ID - 1416
IS - 19
JF - Physical Review B - Condensed Matter and Materials Physics
TI - Interaction-driven Lifshitz transition with dipolar fermions in optical lattices
VL - 93
ER -
TY - JOUR
AB - Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.
AU - Simon, Sibu
AU - Skůpa, Petr
AU - Viaene, Tom
AU - Zwiewka, Marta
AU - Tejos, Ricardo
AU - Klíma, Petr
AU - Čarná, Mária
AU - Rolčík, Jakub
AU - De Rycke, Riet
AU - Moreno, Ignacio
AU - Dobrev, Petre
AU - Orellana, Ariel
AU - Zažímalová, Eva
AU - Friml, Jirí
ID - 1417
IS - 1
JF - New Phytologist
TI - PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis
VL - 211
ER -
TY - JOUR
AB - Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly.
AU - Bod'ová, Katarína
AU - Tkacik, Gasper
AU - Barton, Nicholas H
ID - 1420
IS - 4
JF - Genetics
TI - A general approximation for the dynamics of quantitative traits
VL - 202
ER -
TY - JOUR
AB - 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.
AU - Frank, Rupert
AU - Hainzl, Christian
AU - Schlein, Benjamin
AU - Seiringer, Robert
ID - 1422
IS - 7
JF - Letters in Mathematical Physics
TI - Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations
VL - 106
ER -
TY - JOUR
AB - 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.
AU - Baek, Seung
AU - Jeong, Hyeongchai
AU - Hilbe, Christian
AU - Nowak, Martin
ID - 1423
JF - Scientific Reports
TI - Comparing reactive and memory-one strategies of direct reciprocity
VL - 6
ER -
TY - JOUR
AB - Brood parasites exploit their host in order to increase their own fitness. Typically, this results in an arms race between parasite trickery and host defence. Thus, it is puzzling to observe hosts that accept parasitism without any resistance. The ‘mafia’ hypothesis suggests that these hosts accept parasitism to avoid retaliation. Retaliation has been shown to evolve when the hosts condition their response to mafia parasites, who use depredation as a targeted response to rejection. However, it is unclear if acceptance would also emerge when ‘farming’ parasites are present in the population. Farming parasites use depredation to synchronize the timing with the host, destroying mature clutches to force the host to re-nest. Herein, we develop an evolutionary model to analyse the interaction between depredatory parasites and their hosts. We show that coevolutionary cycles between farmers and mafia can still induce host acceptance of brood parasites. However, this equilibrium is unstable and in the long-run the dynamics of this host–parasite interaction exhibits strong oscillations: when farmers are the majority, accepters conditional to mafia (the host will reject first and only accept after retaliation by the parasite) have a higher fitness than unconditional accepters (the host always accepts parasitism). This leads to an increase in mafia parasites’ fitness and in turn induce an optimal environment for accepter hosts.
AU - Chakra, Maria
AU - Hilbe, Christian
AU - Traulsen, Arne
ID - 1426
IS - 5
JF - Royal Society Open Science
TI - Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites
VL - 3
ER -
TY - JOUR
AB - 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.
AU - Lagator, Mato
AU - Igler, Claudia
AU - Moreno, Anaisa
AU - Guet, Calin C
AU - Bollback, Jonathan P
ID - 1427
IS - 3
JF - Molecular Biology and Evolution
TI - Epistatic interactions in the arabinose cis-regulatory element
VL - 33
ER -
TY - CONF
AB - 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.
AU - Könenberg, Martin
AU - Moser, Thomas
AU - Seiringer, Robert
AU - Yngvason, Jakob
ID - 1428
IS - 1
T2 - Journal of Physics: Conference Series
TI - Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential
VL - 691
ER -
TY - JOUR
AB - 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.
AU - Husko, Chad
AU - Wulf, Matthias
AU - Lefrançois, Simon
AU - Combrié, Sylvain
AU - Lehoucq, Gaëlle
AU - De Rossi, Alfredo
AU - Eggleton, Benjamin
AU - Kuipers, Laurens
ID - 1429
JF - Nature Communications
TI - Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides
VL - 7
ER -
TY - JOUR
AB - 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.
AU - Tartally, András
AU - Kelager, Andreas
AU - Fürst, Matthias
AU - Nash, David
ID - 1431
IS - 3
JF - PeerJ
TI - Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon
VL - 2016
ER -
TY - JOUR
AB - 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.
AU - Bao, Zhigang
AU - Erdös, László
AU - Schnelli, Kevin
ID - 1434
IS - 3
JF - Journal of Functional Analysis
TI - Local stability of the free additive convolution
VL - 271
ER -
TY - JOUR
AB - 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.
AU - Guzmán, José
AU - Gerevich, Zoltan
ID - 1435
JF - Neural Plasticity
TI - P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction
VL - 2016
ER -
TY - JOUR
AB - 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.
AU - Bach, Volker
AU - Breteaux, Sébastien
AU - Petrat, Sören P
AU - Pickl, Peter
AU - Tzaneteas, Tim
ID - 1436
IS - 1
JF - Journal de Mathématiques Pures et Appliquées
TI - Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction
VL - 105
ER -
TY - CONF
AB - 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.
AU - Chatterjee, Krishnendu
AU - Fu, Hongfei
AU - Novotny, Petr
AU - Hasheminezhad, Rouzbeh
ID - 1438
TI - Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs
VL - 20-22
ER -
TY - CONF
AB - 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.
AU - Dragoi, Cezara
AU - Henzinger, Thomas A
AU - Zufferey, Damien
ID - 1439
TI - PSYNC: A partially synchronous language for fault-tolerant distributed algorithms
VL - 20-22
ER -
TY - JOUR
AB - Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.
AU - Gschaider-Reichhart, Eva
AU - Inglés Prieto, Álvaro
AU - Tichy, Alexandra-Madelaine
AU - Mckenzie, Catherine
AU - Janovjak, Harald L
ID - 1441
IS - 21
JF - Angewandte Chemie - International Edition
TI - A phytochrome sensory domain permits receptor activation by red light
VL - 55
ER -
TY - JOUR
AB - 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.
AU - Calatrava Moreno, Maria
AU - Auzinger, Thomas
AU - Werthner, Hannes
ID - 1446
IS - 1
JF - Scientometrics
TI - On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data
VL - 107
ER -
TY - JOUR
AB - 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.
AU - Fathi, Max
AU - Maas, Jan
ID - 1448
IS - 3
JF - The Annals of Applied Probability
TI - Entropic Ricci curvature bounds for discrete interacting systems
VL - 26
ER -
TY - JOUR
AB - 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.
AU - Toshima, Junko
AU - Furuya, Eri
AU - Nagano, Makoto
AU - Kanno, Chisa
AU - Sakamoto, Yuta
AU - Ebihara, Masashi
AU - Siekhaus, Daria E
AU - Toshima, Jiro
ID - 1475
IS - February 2016
JF - eLife
TI - Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton
VL - 5
ER -
TY - JOUR
AB - 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
AU - Toshima, Junko
AU - Horikomi, Chika
AU - Okada, Asuka
AU - Hatori, Makiko
AU - Nagano, Makoto
AU - Masuda, Atsushi
AU - Yamamoto, Wataru
AU - Siekhaus, Daria E
AU - Toshima, Jiro
ID - 1476
IS - 2
JF - Journal of Cell Science
TI - Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis
VL - 129
ER -
TY - JOUR
AB - 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.
AU - Chatterjee, Krishnendu
AU - Chmelik, Martin
AU - Tracol, Mathieu
ID - 1477
IS - 5
JF - Journal of Computer and System Sciences
TI - What is decidable about partially observable Markov decision processes with ω-regular objectives
VL - 82
ER -
TY - JOUR
AB - 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.
AU - Seiringer, Robert
AU - Warzel, Simone
ID - 1478
IS - 3
JF - New Journal of Physics
TI - Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas
VL - 18
ER -
TY - JOUR
AB - 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.
AU - Krenn, Stephan
AU - Pietrzak, Krzysztof Z
AU - Wadia, Akshay
AU - Wichs, Daniel
ID - 1479
IS - 3
JF - Computational Complexity
TI - A counterexample to the chain rule for conditional HILL entropy
VL - 25
ER -
TY - JOUR
AB - Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials.
AU - Michałek, Mateusz
AU - Sturmfels, Bernd
AU - Uhler, Caroline
AU - Zwiernik, Piotr
ID - 1480
IS - 1
JF - Proceedings of the London Mathematical Society
TI - Exponential varieties
VL - 112
ER -
TY - JOUR
AB - Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.
AU - Adibi, Milad
AU - Yoshida, Saiko
AU - Weijers, Dolf
AU - Fleck, Christian
ID - 1482
IS - 2
JF - PLoS One
TI - Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization
VL - 11
ER -
TY - JOUR
AU - Chen, Xu
AU - Wu, Shuang
AU - Liu, Zengyu
AU - Friml, Jiřĺ
ID - 1484
IS - 6
JF - Trends in Cell Biology
TI - Environmental and endogenous control of cortical microtubule orientation
VL - 26
ER -
TY - JOUR
AB - In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.
AU - De Martino, Daniele
ID - 1485
IS - 1
JF - Physical Biology
TI - Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis
VL - 13
ER -