@article{6185,
abstract = {For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).},
author = {Erdös, László and Krüger, Torben H and Schröder, Dominik J},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
pages = {50},
publisher = {Springer Nature},
title = {{Cusp universality for random matrices I: Local law and the complex hermitian case}},
doi = {10.1007/s00220-019-03657-4},
year = {2020},
}
@article{6358,
abstract = {We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras. Our settingcovers arbitrary skew-derivations and it provides a unified framework that simultaneously generalizes recently constructed transport metrics for Markov chains, Lindblad equations, and the Fermi Ornstein–Uhlenbeck semigroup. We develop a non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature bounds, logarithmic Sobolev inequalities, transport-entropy inequalities, andspectral gap estimates.},
author = {Carlen, Eric A. and Maas, Jan},
issn = {15729613},
journal = {Journal of Statistical Physics},
number = {2},
pages = {319--378},
publisher = {Springer Nature},
title = {{Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems}},
doi = {10.1007/s10955-019-02434-w},
volume = {178},
year = {2020},
}
@article{6563,
abstract = {This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋.},
author = {Filakovský, Marek and Vokřínek, Lukas},
issn = {16153383},
journal = {Foundations of Computational Mathematics},
pages = {311--330},
publisher = {Springer Nature},
title = {{Are two given maps homotopic? An algorithmic viewpoint}},
doi = {10.1007/s10208-019-09419-x},
volume = {20},
year = {2020},
}
@article{6593,
abstract = {We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising.},
author = {Shehu, Yekini and Li, Xiao-Huan and Dong, Qiao-Li},
issn = {1017-1398},
journal = {Numerical Algorithms},
pages = {365--388},
publisher = {Springer Nature},
title = {{An efficient projection-type method for monotone variational inequalities in Hilbert spaces}},
doi = {10.1007/s11075-019-00758-y},
volume = {84},
year = {2020},
}
@article{6649,
abstract = {While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.
},
author = {Benedikter, Niels P and Nam, Phan Thành and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert},
issn = {1432-0916},
journal = {Communications in Mathematical Physics},
pages = {2097–2150},
publisher = {Springer Nature},
title = {{Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime}},
doi = {10.1007/s00220-019-03505-5},
volume = {374},
year = {2020},
}
@article{6761,
abstract = {In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.},
author = {Avni, Guy and Henzinger, Thomas A and Kupferman, Orna},
issn = {03043975},
journal = {Theoretical Computer Science},
pages = {42--55},
publisher = {Elsevier},
title = {{Dynamic resource allocation games}},
doi = {10.1016/j.tcs.2019.06.031},
volume = {807},
year = {2020},
}
@article{6796,
abstract = {Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.},
author = {Stella, Federico and Urdapilleta, Eugenio and Luo, Yifan and Treves, Alessandro},
issn = {10981063},
journal = {Hippocampus},
number = {4},
pages = {302--313},
publisher = {Wiley},
title = {{Partial coherence and frustration in self-organizing spherical grids}},
doi = {10.1002/hipo.23144},
volume = {30},
year = {2020},
}
@article{6808,
abstract = {Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.},
author = {Jahr, Wiebke and Velicky, Philipp and Danzl, Johann G},
issn = {1046-2023},
journal = {Methods},
number = {3},
pages = {27--41},
publisher = {Elsevier},
title = {{Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens}},
doi = {10.1016/j.ymeth.2019.07.019},
volume = {174},
year = {2020},
}
@article{6918,
abstract = {We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.
We provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem.},
author = {Goharshady, Amir Kafshdar and Mohammadi, Fatemeh},
issn = {09518320},
journal = {Reliability Engineering and System Safety},
publisher = {Elsevier},
title = {{An efficient algorithm for computing network reliability in small treewidth}},
doi = {10.1016/j.ress.2019.106665},
volume = {193},
year = {2020},
}
@article{6997,
author = {Zhang, Yuzhou and Friml, Jiří},
issn = {1469-8137},
journal = {New Phytologist},
number = {3},
pages = {1049--1052},
publisher = {Wiley},
title = {{Auxin guides roots to avoid obstacles during gravitropic growth}},
doi = {10.1111/nph.16203},
volume = {225},
year = {2020},
}
@article{7142,
abstract = {The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin.},
author = {Gallei, Michelle C and Luschnig, C and Friml, Jiří},
issn = {1879-0356},
journal = {Current Opinion in Plant Biology},
pages = {43--49},
publisher = {Elsevier},
title = {{Auxin signalling in growth: Schrödinger's cat out of the bag}},
doi = {10.1016/j.pbi.2019.10.003},
volume = {53},
year = {2020},
}
@article{7149,
abstract = {In recent years, many genes have been associated with chromatinopathies classified as “Cornelia de Lange Syndrome‐like.” It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that “CdLS‐like syndromes” are part of a larger “rare disease family” sharing multiple clinical features and common disrupted molecular pathways.},
author = {Avagliano, Laura and Parenti, Ilaria and Grazioli, Paolo and Di Fede, Elisabetta and Parodi, Chiara and Mariani, Milena and Kaiser, Frank J. and Selicorni, Angelo and Gervasini, Cristina and Massa, Valentina},
issn = {1399-0004},
journal = {Clinical Genetics},
number = {1},
pages = {3--11},
publisher = {Wiley},
title = {{Chromatinopathies: A focus on Cornelia de Lange syndrome}},
doi = {10.1111/cge.13674},
volume = {97},
year = {2020},
}
@article{7166,
abstract = {In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.},
author = {Ucar, Mehmet C and Lipowsky, Reinhard},
issn = {1530-6992},
journal = {Nano Letters},
number = {1},
pages = {669--676},
publisher = {ACS},
title = {{Collective force generation by molecular motors is determined by strain-induced unbinding}},
doi = {10.1021/acs.nanolett.9b04445},
volume = {20},
year = {2020},
}
@phdthesis{7196,
abstract = {In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.},
author = {Tkadlec, Josef},
issn = {2663-337X},
pages = {144},
publisher = {IST Austria},
title = {{A role of graphs in evolutionary processes}},
doi = {10.15479/AT:ISTA:7196},
year = {2020},
}
@article{7204,
abstract = {Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin.},
author = {Li, Yang and Wang, Yaping and Tan, Shutang and Li, Zhen and Yuan, Zhi and Glanc, Matous and Domjan, David and Wang, Kai and Xuan, Wei and Guo, Yan and Gong, Zhizhong and Friml, Jiří and Zhang, Jing},
issn = {2198-3844},
journal = {Advanced Science},
number = {3},
publisher = {Wiley},
title = {{Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex}},
doi = {10.1002/advs.201901455},
volume = {7},
year = {2020},
}
@article{7212,
abstract = {The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process.},
author = {Tkadlec, Josef and Pavlogiannis, Andreas and Chatterjee, Krishnendu and Nowak, Martin A.},
issn = {15537358},
journal = {PLoS computational biology},
publisher = {PLoS},
title = {{Limits on amplifiers of natural selection under death-Birth updating}},
doi = {10.1371/journal.pcbi.1007494},
volume = {16},
year = {2020},
}
@article{7219,
abstract = {Root system architecture (RSA), governed by the phytohormone auxin, endows plants with an adaptive advantage in particular environments. Using geographically representative arabidopsis (Arabidopsis thaliana) accessions as a resource for GWA mapping, Waidmann et al. and Ogura et al. recently identified two novel components involved in modulating auxin-mediated RSA and conferring plant fitness in particular habitats.},
author = {Xiao, Guanghui and Zhang, Yuzhou},
issn = {13601385},
journal = {Trends in Plant Science},
number = {2},
pages = {121--123},
publisher = {Elsevier},
title = {{Adaptive growth: Shaping auxin-mediated root system architecture}},
doi = {10.1016/j.tplants.2019.12.001},
volume = {25},
year = {2020},
}
@article{7224,
abstract = {Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity.},
author = {Rybicki, Joel and Abrego, Nerea and Ovaskainen, Otso},
issn = {1461-023X},
journal = {Ecology Letters},
number = {3},
pages = {506--517},
publisher = {Wiley},
title = {{Habitat fragmentation and species diversity in competitive communities}},
doi = {10.1111/ele.13450},
volume = {23},
year = {2020},
}
@article{7236,
abstract = {The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.},
author = {Baskett, Carina and Schroeder, Lucy and Weber, Marjorie G. and Schemske, Douglas W.},
issn = {0012-9615},
journal = {Ecological Monographs},
number = {1},
publisher = {Wiley},
title = {{Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair}},
doi = {10.1002/ecm.1397},
volume = {90},
year = {2020},
}
@phdthesis{7258,
abstract = {Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings.},
author = {Scarselli, Davide},
issn = {2663-337X},
pages = {174},
publisher = {IST Austria},
title = {{New approaches to reduce friction in turbulent pipe flow}},
doi = {10.15479/AT:ISTA:7258},
year = {2020},
}