@article{8746, abstract = {Research in the field of colloidal semiconductor nanocrystals (NCs) has progressed tremendously, mostly because of their exceptional optoelectronic properties. Core@shell NCs, in which one or more inorganic layers overcoat individual NCs, recently received significant attention due to their remarkable optical characteristics. Reduced Auger recombination, suppressed blinking, and enhanced carrier multiplication are among the merits of core@shell NCs. Despite their importance in device development, the influence of the shell and the surface modification of the core@shell NC assemblies on the charge carrier transport remains a pertinent research objective. Type-II PbTe@PbS core@shell NCs, in which exclusive electron transport was demonstrated, still exhibit instability of their electron ransport. Here, we demonstrate the enhancement of electron transport and stability in PbTe@PbS core@shell NC assemblies using iodide as a surface passivating ligand. The combination of the PbS shelling and the use of the iodide ligand contributes to the addition of one mobile electron for each core@shell NC. Furthermore, both electron mobility and on/off current modulation ratio values of the core@shell NC field-effect transistor are steady with the usage of iodide. Excellent stability in these exclusively electron-transporting core@shell NCs paves the way for their utilization in electronic devices. }, author = {Miranti, Retno and Septianto, Ricky Dwi and Ibáñez, Maria and Kovalenko, Maksym V. and Matsushita, Nobuhiro and Iwasa, Yoshihiro and Bisri, Satria Zulkarnaen}, issn = {1077-3118}, journal = {Applied Physics Letters}, number = {17}, publisher = {AIP Publishing}, title = {{Electron transport in iodide-capped core@shell PbTe@PbS colloidal nanocrystal solids}}, doi = {10.1063/5.0025965}, volume = {117}, year = {2020}, } @article{7985, abstract = {The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.}, author = {Kwak, WJ and Sharon, D and Xia, C and Kim, H and Johnson, LR and Bruce, PG and Nazar, LF and Sun, YK and Frimer, AA and Noked, M and Freunberger, Stefan Alexander and Aurbach, D}, issn = {1520-6890}, journal = {Chemical Reviews}, number = {14}, pages = {6626--6683}, publisher = {American Chemical Society}, title = {{Lithium-oxygen batteries and related systems: Potential, status, and future}}, doi = {10.1021/acs.chemrev.9b00609}, volume = {120}, year = {2020}, } @article{8721, abstract = {Spontaneously arising channels that transport the phytohormone auxin provide positional cues for self-organizing aspects of plant development such as flexible vasculature regeneration or its patterning during leaf venation. The auxin canalization hypothesis proposes a feedback between auxin signaling and transport as the underlying mechanism, but molecular players await discovery. We identified part of the machinery that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like kinase) interact with and phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization, which macroscopically manifests as defects in leaf venation and vasculature regeneration after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback that coordinates polarization of individual cells during auxin canalization.}, author = {Hajny, Jakub and Prat, Tomas and Rydza, N and Rodriguez Solovey, Lesia and Tan, Shutang and Verstraeten, Inge and Domjan, David and Mazur, E and Smakowska-Luzan, E and Smet, W and Mor, E and Nolf, J and Yang, B and Grunewald, W and Molnar, Gergely and Belkhadir, Y and De Rybel, B and Friml, Jiří}, issn = {1095-9203}, journal = {Science}, number = {6516}, pages = {550--557}, publisher = {American Association for the Advancement of Science}, title = {{Receptor kinase module targets PIN-dependent auxin transport during canalization}}, doi = {10.1126/science.aba3178}, volume = {370}, year = {2020}, } @article{7968, abstract = {Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role.}, author = {Ghazaryan, Areg and Paltiel, Yossi and Lemeshko, Mikhail}, issn = {1932-7455}, journal = {The Journal of Physical Chemistry C}, number = {21}, pages = {11716--11721}, publisher = {American Chemical Society}, title = {{Analytic model of chiral-induced spin selectivity}}, doi = {10.1021/acs.jpcc.0c02584}, volume = {124}, year = {2020}, } @article{10866, abstract = {Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management.}, author = {Duan, Jiahua and Capote-Robayna, Nathaniel and Taboada-Gutiérrez, Javier and Álvarez-Pérez, Gonzalo and Prieto Gonzalez, Ivan and Martín-Sánchez, Javier and Nikitin, Alexey Y. and Alonso-González, Pablo}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Mechanical Engineering, Condensed Matter Physics, General Materials Science, General Chemistry, Bioengineering}, number = {7}, pages = {5323--5329}, publisher = {American Chemical Society}, title = {{Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs}}, doi = {10.1021/acs.nanolett.0c01673}, volume = {20}, year = {2020}, } @article{8588, abstract = {Dipolar (or spatially indirect) excitons (IXs) in semiconductor double quantum well (DQW) subjected to an electric field are neutral species with a dipole moment oriented perpendicular to the DQW plane. Here, we theoretically study interactions between IXs in stacked DQW bilayers, where the dipolar coupling can be either attractive or repulsive depending on the relative positions of the particles. By using microscopic band structure calculations to determine the electronic states forming the excitons, we show that the attractive dipolar interaction between stacked IXs deforms their electronic wave function, thereby increasing the inter-DQW interaction energy and making the IX even more electrically polarizable. Many-particle interaction effects are addressed by considering the coupling between a single IX in one of the DQWs to a cloud of IXs in the other DQW, which is modeled either as a closed-packed lattice or as a continuum IX fluid. We find that the lattice model yields IX interlayer binding energies decreasing with increasing lattice density. This behavior is due to the dominating role of the intra-DQW dipolar repulsion, which prevents more than one exciton from entering the attractive region of the inter-DQW coupling. Finally, both models shows that the single IX distorts the distribution of IXs in the adjacent DQW, thus inducing the formation of an IX dipolar polaron (dipolaron). While the interlayer binding energy reduces with IX density for lattice dipolarons, the continuous polaron model predicts a nonmonotonous dependence on density in semiquantitative agreement with a recent experimental study [cf. Hubert et al., Phys. Rev. X 9, 021026 (2019)].}, author = {Hubert, C. and Cohen, K. and Ghazaryan, Areg and Lemeshko, Mikhail and Rapaport, R. and Santos, P. V.}, issn = {2469-9969}, journal = {Physical Review B}, number = {4}, publisher = {American Physical Society}, title = {{Attractive interactions, molecular complexes, and polarons in coupled dipolar exciton fluids}}, doi = {10.1103/physrevb.102.045307}, volume = {102}, year = {2020}, } @article{8769, abstract = {One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas.}, author = {Yakaboylu, Enderalp and Ghazaryan, Areg and Lundholm, D. and Rougerie, N. and Lemeshko, Mikhail and Seiringer, Robert}, issn = {2469-9969}, journal = {Physical Review B}, number = {14}, publisher = {American Physical Society}, title = {{Quantum impurity model for anyons}}, doi = {10.1103/physrevb.102.144109}, volume = {102}, year = {2020}, } @article{7971, abstract = {Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state.}, author = {Rao, Peng and Serbyn, Maksym}, issn = {2469-9969}, journal = {Physical Review B}, number = {24}, publisher = {American Physical Society}, title = {{Gully quantum Hall ferromagnetism in biased trilayer graphene}}, doi = {10.1103/physrevb.101.245411}, volume = {101}, year = {2020}, } @article{8634, abstract = {In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent.}, author = {Suri, Balachandra and Kageorge, Logan and Grigoriev, Roman O. and Schatz, Michael F.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {6}, publisher = {American Physical Society}, title = {{Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits}}, doi = {10.1103/physrevlett.125.064501}, volume = {125}, year = {2020}, } @article{7949, abstract = {Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-terminally encoded peptide 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.}, author = {Smith, S and Zhu, S and Joos, L and Roberts, I and Nikonorova, N and Vu, LD and Stes, E and Cho, H and Larrieu, A and Xuan, W and Goodall, B and van de Cotte, B and Waite, JM and Rigal, A and R Harborough, SR and Persiau, G and Vanneste, S and Kirschner, GK and Vandermarliere, E and Martens, L and Stahl, Y and Audenaert, D and Friml, Jiří and Felix, G and Simon, R and Bennett, M and Bishopp, A and De Jaeger, G and Ljung, K and Kepinski, S and Robert, S and Nemhauser, J and Hwang, I and Gevaert, K and Beeckman, T and De Smet, I}, issn = {1535-9484}, journal = {Molecular & Cellular Proteomics}, number = {8}, pages = {1248--1262}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis}}, doi = {10.1074/mcp.ra119.001826}, volume = {19}, year = {2020}, } @article{7619, abstract = {Cell polarity is a fundamental feature of all multicellular organisms. In plants, prominent cell polarity markers are PIN auxin transporters crucial for plant development. To identify novel components involved in cell polarity establishment and maintenance, we carried out a forward genetic screening with PIN2:PIN1-HA;pin2 Arabidopsis plants, which ectopically express predominantly basally localized PIN1 in the root epidermal cells leading to agravitropic root growth. From the screen, we identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused PIN1-HA polarity switch from basal to apical side of root epidermal cells. Complementation experiments established the repp12 causative mutation as an amino acid substitution in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase with predicted function in vesicle formation. ala3 T-DNA mutants show defects in many auxin-regulated processes, in asymmetric auxin distribution and in PIN trafficking. Analysis of quintuple and sextuple mutants confirmed a crucial role of ALA proteins in regulating plant development and in PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with GNOM and BIG3 ARF GEFs. Taken together, our results identified ALA3 flippase as an important interactor and regulator of ARF GEF functioning in PIN polarity, trafficking and auxin-mediated development.}, author = {Zhang, Xixi and Adamowski, Maciek and Marhavá, Petra and Tan, Shutang and Zhang, Yuzhou and Rodriguez Solovey, Lesia and Zwiewka, Marta and Pukyšová, Vendula and Sánchez, Adrià Sans and Raxwal, Vivek Kumar and Hardtke, Christian S. and Nodzynski, Tomasz and Friml, Jiří}, issn = {1532-298X}, journal = {The Plant Cell}, number = {5}, pages = {1644--1664}, publisher = {American Society of Plant Biologists}, title = {{Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters}}, doi = {10.1105/tpc.19.00869}, volume = {32}, year = {2020}, } @article{8607, abstract = {Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants.}, author = {Liu, D and Kumar, R and LAN, Claus and Johnson, Alexander J and Siao, W and Vanhoutte, I and Wang, P and Bender, KW and Yperman, K and Martins, S and Zhao, X and Vert, G and Van Damme, D and Friml, Jiří and Russinova, E}, issn = {1532-298x}, journal = {Plant Cell}, number = {11}, pages = {3598--3612}, publisher = {American Society of Plant Biologists}, title = {{Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif}}, doi = {10.1105/tpc.20.00384}, volume = {32}, year = {2020}, } @article{7695, abstract = {The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex.}, author = {Wang, J and Mylle, E and Johnson, Alexander J and Besbrugge, N and De Jaeger, G and Friml, Jiří and Pleskot, R and van Damme, D}, issn = {1532-2548}, journal = {Plant Physiology}, number = {3}, pages = {986--997}, publisher = {American Society of Plant Biologists}, title = {{High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits}}, doi = {10.1104/pp.20.00178}, volume = {183}, year = {2020}, } @article{9197, abstract = {In this paper we introduce and study all-pay bidding games, a class of two player, zero-sum games on graphs. The game proceeds as follows. We place a token on some vertex in the graph and assign budgets to the two players. Each turn, each player submits a sealed legal bid (non-negative and below their remaining budget), which is deducted from their budget and the highest bidder moves the token onto an adjacent vertex. The game ends once a sink is reached, and Player 1 pays Player 2 the outcome that is associated with the sink. The players attempt to maximize their expected outcome. Our games model settings where effort (of no inherent value) needs to be invested in an ongoing and stateful manner. On the negative side, we show that even in simple games on DAGs, optimal strategies may require a distribution over bids with infinite support. A central quantity in bidding games is the ratio of the players budgets. On the positive side, we show a simple FPTAS for DAGs, that, for each budget ratio, outputs an approximation for the optimal strategy for that ratio. We also implement it, show that it performs well, and suggests interesting properties of these games. Then, given an outcome c, we show an algorithm for finding the necessary and sufficient initial ratio for guaranteeing outcome c with probability 1 and a strategy ensuring such. Finally, while the general case has not previously been studied, solving the specific game in which Player 1 wins iff he wins the first two auctions, has been long stated as an open question, which we solve.}, author = {Avni, Guy and Ibsen-Jensen, Rasmus and Tkadlec, Josef}, isbn = {9781577358350}, issn = {2374-3468}, journal = {Proceedings of the AAAI Conference on Artificial Intelligence}, location = {New York, NY, United States}, number = {02}, pages = {1798--1805}, publisher = {Association for the Advancement of Artificial Intelligence}, title = {{All-pay bidding games on graphs}}, doi = {10.1609/aaai.v34i02.5546}, volume = {34}, year = {2020}, } @article{8142, abstract = {Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.}, author = {Montesinos López, Juan C and Abuzeineh, A and Kopf, Aglaja and Juanes Garcia, Alba and Ötvös, Krisztina and Petrášek, J and Sixt, Michael K and Benková, Eva}, issn = {1460-2075}, journal = {The Embo Journal}, number = {17}, publisher = {Embo Press}, title = {{Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage}}, doi = {10.15252/embj.2019104238}, volume = {39}, year = {2020}, } @article{8084, abstract = {Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.}, author = {Lombardi, Fabrizio and Gómez-Extremera, Manuel and Bernaola-Galván, Pedro and Vetrivelan, Ramalingam and Saper, Clifford B. and Scammell, Thomas E. and Ivanov, Plamen Ch.}, issn = {1529-2401}, journal = {Journal of Neuroscience}, number = {1}, pages = {171--190}, publisher = {Society for Neuroscience}, title = {{Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake}}, doi = {10.1523/jneurosci.1278-19.2019}, volume = {40}, year = {2020}, } @article{7650, abstract = {We consider a dilute, homogeneous Bose gas at positive temperature. The system is investigated in the Gross–Pitaevskii limit, where the scattering length a is so small that the interaction energy is of the same order of magnitude as the spectral gap of the Laplacian, and for temperatures that are comparable to the critical temperature of the ideal gas. We show that the difference between the specific free energy of the interacting system and the one of the ideal gas is to leading order given by 4πa(2ϱ2−ϱ20). Here ϱ denotes the density of the system and ϱ0 is the expected condensate density of the ideal gas. Additionally, we show that the one-particle density matrix of any approximate minimizer of the Gibbs free energy functional is to leading order given by the one of the ideal gas. This in particular proves Bose–Einstein condensation with critical temperature given by the one of the ideal gas to leading order. One key ingredient of our proof is a novel use of the Gibbs variational principle that goes hand in hand with the c-number substitution.}, author = {Deuchert, Andreas and Seiringer, Robert}, issn = {1432-0673}, journal = {Archive for Rational Mechanics and Analysis}, number = {6}, pages = {1217--1271}, publisher = {Springer Nature}, title = {{Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature}}, doi = {10.1007/s00205-020-01489-4}, volume = {236}, year = {2020}, } @article{8130, abstract = {We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.}, author = {Bossmann, Lea}, issn = {1432-0673}, journal = {Archive for Rational Mechanics and Analysis}, number = {11}, pages = {541--606}, publisher = {Springer Nature}, title = {{Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons}}, doi = {10.1007/s00205-020-01548-w}, volume = {238}, year = {2020}, } @article{7235, abstract = {We consider the Fröhlich model of a polaron, and show that its effective mass diverges in thestrong coupling limit.}, author = {Lieb, Elliott H. and Seiringer, Robert}, issn = {1572-9613}, journal = {Journal of Statistical Physics}, pages = {23--33}, publisher = {Springer Nature}, title = {{Divergence of the effective mass of a polaron in the strong coupling limit}}, doi = {10.1007/s10955-019-02322-3}, volume = {180}, year = {2020}, } @inproceedings{7966, abstract = {For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters). For Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario. As our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem.}, author = {Auerbach, Benedikt and Giacon, Federico and Kiltz, Eike}, booktitle = {Advances in Cryptology – EUROCRYPT 2020}, isbn = {9783030457266}, issn = {1611-3349}, pages = {475--506}, publisher = {Springer Nature}, title = {{Everybody’s a target: Scalability in public-key encryption}}, doi = {10.1007/978-3-030-45727-3_16}, volume = {12107}, year = {2020}, } @inproceedings{8623, abstract = {We introduce the monitoring of trace properties under assumptions. An assumption limits the space of possible traces that the monitor may encounter. An assumption may result from knowledge about the system that is being monitored, about the environment, or about another, connected monitor. We define monitorability under assumptions and study its theoretical properties. In particular, we show that for every assumption A, the boolean combinations of properties that are safe or co-safe relative to A are monitorable under A. We give several examples and constructions on how an assumption can make a non-monitorable property monitorable, and how an assumption can make a monitorable property monitorable with fewer resources, such as integer registers.}, author = {Henzinger, Thomas A and Sarac, Naci E}, booktitle = {Runtime Verification}, isbn = {9783030605070}, issn = {1611-3349}, location = {Los Angeles, CA, United States}, pages = {3--18}, publisher = {Springer Nature}, title = {{Monitorability under assumptions}}, doi = {10.1007/978-3-030-60508-7_1}, volume = {12399}, year = {2020}, } @inproceedings{8732, abstract = {A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP -complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ , it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.}, author = {Arroyo Guevara, Alan M and Klute, Fabian and Parada, Irene and Seidel, Raimund and Vogtenhuber, Birgit and Wiedera, Tilo}, booktitle = {Graph-Theoretic Concepts in Computer Science}, isbn = {9783030604394}, issn = {1611-3349}, location = {Leeds, United Kingdom}, pages = {325--338}, publisher = {Springer Nature}, title = {{Inserting one edge into a simple drawing is hard}}, doi = {10.1007/978-3-030-60440-0_26}, volume = {12301}, year = {2020}, } @inbook{10865, abstract = {We introduce the notion of Witness Maps as a cryptographic notion of a proof system. A Unique Witness Map (UWM) deterministically maps all witnesses for an NP statement to a single representative witness, resulting in a computationally sound, deterministic-prover, non-interactive witness independent proof system. A relaxation of UWM, called Compact Witness Map (CWM), maps all the witnesses to a small number of witnesses, resulting in a “lossy” deterministic-prover, non-interactive proof-system. We also define a Dual Mode Witness Map (DMWM) which adds an “extractable” mode to a CWM. Our main construction is a DMWM for all NP relations, assuming sub-exponentially secure indistinguishability obfuscation ( iO ), along with standard cryptographic assumptions. The DMWM construction relies on a CWM and a new primitive called Cumulative All-Lossy-But-One Trapdoor Functions (C-ALBO-TDF), both of which are in turn instantiated based on iO and other primitives. Our instantiation of a CWM is in fact a UWM; in turn, we show that a UWM implies Witness Encryption. Along the way to constructing UWM and C-ALBO-TDF, we also construct, from standard assumptions, Puncturable Digital Signatures and a new primitive called Cumulative Lossy Trapdoor Functions (C-LTDF). The former improves up on a construction of Bellare et al. (Eurocrypt 2016), who relied on sub-exponentially secure iO and sub-exponentially secure OWF. As an application of our constructions, we show how to use a DMWM to construct the first leakage and tamper-resilient signatures with a deterministic signer, thereby solving a decade old open problem posed by Katz and Vaikunthanathan (Asiacrypt 2009), by Boyle, Segev and Wichs (Eurocrypt 2011), as well as by Faonio and Venturi (Asiacrypt 2016). Our construction achieves the optimal leakage rate of 1−o(1) .}, author = {Chakraborty, Suvradip and Prabhakaran, Manoj and Wichs, Daniel}, booktitle = {Public-Key Cryptography}, editor = {Kiayias, A}, isbn = {9783030453732}, issn = {1611-3349}, pages = {220--246}, publisher = {Springer Nature}, title = {{Witness maps and applications}}, doi = {10.1007/978-3-030-45374-9_8}, volume = {12110}, year = {2020}, } @article{7611, abstract = {We consider a system of N bosons in the limit N→∞, interacting through singular potentials. For initial data exhibiting Bose–Einstein condensation, the many-body time evolution is well approximated through a quadratic fluctuation dynamics around a cubic nonlinear Schrödinger equation of the condensate wave function. We show that these fluctuations satisfy a (multi-variate) central limit theorem.}, author = {Rademacher, Simone Anna Elvira}, issn = {1573-0530}, journal = {Letters in Mathematical Physics}, pages = {2143--2174}, publisher = {Springer Nature}, title = {{Central limit theorem for Bose gases interacting through singular potentials}}, doi = {10.1007/s11005-020-01286-w}, volume = {110}, 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 = {1557-7015}, 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}, } @article{7697, abstract = {* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown. * In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells. * Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization. * These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants.}, author = {Zhang, Yuzhou and Hartinger, Corinna and Wang, Xiaojuan and Friml, Jiří}, issn = {1469-8137}, journal = {New Phytologist}, number = {5}, pages = {1406--1416}, publisher = {Wiley}, title = {{Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters}}, doi = {10.1111/nph.16629}, volume = {227}, year = {2020}, } @article{8765, abstract = {This paper introduces a simple method for simulating highly anisotropic elastoplastic material behaviors like the dissolution of fibrous phenomena (splintering wood, shredding bales of hay) and materials composed of large numbers of irregularly‐shaped bodies (piles of twigs, pencils, or cards). We introduce a simple transformation of the anisotropic problem into an equivalent isotropic one, and we solve this new “fictitious” isotropic problem using an existing simulator based on the material point method. Our approach results in minimal changes to existing simulators, and it allows us to re‐use popular isotropic plasticity models like the Drucker‐Prager yield criterion instead of inventing new anisotropic plasticity models for every phenomenon we wish to simulate.}, author = {Schreck, Camille and Wojtan, Christopher J}, issn = {1467-8659}, journal = {Computer Graphics Forum}, keywords = {Computer Networks and Communications}, number = {2}, pages = {89--99}, publisher = {Wiley}, title = {{A practical method for animating anisotropic elastoplastic materials}}, doi = {10.1111/cgf.13914}, volume = {39}, year = {2020}, } @article{8057, abstract = {Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability.}, author = {Bouchal, Roza and Li, Zhujie and Bongu, Chandra and Le Vot, Steven and Berthelot, Romain and Rotenberg, Benjamin and Favier, Frederic and Freunberger, Stefan Alexander and Salanne, Mathieu and Fontaine, Olivier}, issn = {1521-3757}, journal = {Angewandte Chemie}, number = {37}, pages = {16047--16051}, publisher = {Wiley}, title = {{Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte}}, doi = {10.1002/ange.202005378}, volume = {132}, year = {2020}, } @article{7343, abstract = {Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level.}, author = {Milutinovic, Barbara and Stock, Miriam and Grasse, Anna V and Naderlinger, Elisabeth and Hilbe, Christian and Cremer, Sylvia}, issn = {1461-0248}, journal = {Ecology Letters}, number = {3}, pages = {565--574}, publisher = {Wiley}, title = {{Social immunity modulates competition between coinfecting pathogens}}, doi = {10.1111/ele.13458}, volume = {23}, year = {2020}, } @article{8099, abstract = {Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.}, author = {Gammerdinger, William J and Toups, Melissa A and Vicoso, Beatriz}, issn = {1755-0998}, journal = {Molecular Ecology Resources}, number = {6}, pages = {1517--1525}, publisher = {Wiley}, title = {{Disagreement in FST estimators: A case study from sex chromosomes}}, doi = {10.1111/1755-0998.13210}, volume = {20}, year = {2020}, } @article{7847, abstract = {Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities nearing 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of 'free' and 'bound' water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability. }, author = {Bouchal, Roza and Li, Zhujie and Bongu, Chandra and Le Vot, Steven and Berthelot, Romain and Rotenberg, Benjamin and Favier, Fréderic and Freunberger, Stefan Alexander and Salanne, Mathieu and Fontaine, Olivier}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, number = {37}, pages = {15913--1591}, publisher = {Wiley}, title = {{Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte}}, doi = {10.1002/anie.202005378}, volume = {59}, 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 = {1461-0248}, 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{8329, abstract = {We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles.}, author = {Schlemmer, Werner and Nothdurft, Philipp and Petzold, Alina and Frühwirt, Philipp and Schmallegger, Max and Gescheidt-Demner, Georg and Fischer, Roland and Freunberger, Stefan Alexander and Kern, Wolfgang and Spirk, Stefan}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, number = {51}, pages = {22943--22946}, publisher = {Wiley}, title = {{2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries}}, doi = {10.1002/anie.202008253}, volume = {59}, year = {2020}, } @misc{13060, abstract = {Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity ­– influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level.}, author = {Milutinovic, Barbara and Stock, Miriam and Grasse, Anna V and Naderlinger, Elisabeth and Hilbe, Christian and Cremer, Sylvia}, publisher = {Dryad}, title = {{Social immunity modulates competition between coinfecting pathogens}}, doi = {10.5061/DRYAD.CRJDFN318}, year = {2020}, } @misc{9780, abstract = {PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol Space Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°}, author = {Schlemmer, Werner and Nothdurft, Philipp and Petzold, Alina and Riess, Gisbert and Frühwirt, Philipp and Schmallegger, Max and Gescheidt-Demner, Georg and Fischer, Roland and Freunberger, Stefan Alexander and Kern, Wolfgang and Spirk, Stefan}, publisher = {CCDC}, title = {{CCDC 1991959: Experimental Crystal Structure Determination}}, doi = {10.5517/ccdc.csd.cc24vsrk}, year = {2020}, } @article{7207, abstract = {The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD.}, author = {Martín-Belmonte, Alejandro and Aguado, Carolina and Alfaro-Ruíz, Rocío and Moreno-Martínez, Ana Esther and De La Ossa, Luis and Martínez-Hernández, José and Buisson, Alain and Früh, Simon and Bettler, Bernhard and Shigemoto, Ryuichi and Fukazawa, Yugo and Luján, Rafael}, issn = {17503639}, journal = {Brain Pathology}, number = {3}, pages = {554--575}, publisher = {Wiley}, title = {{Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease}}, doi = {10.1111/bpa.12802}, volume = {30}, year = {2020}, } @article{7205, abstract = {Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.}, author = {Johannesson, Kerstin and Zagrodzka, Zuzanna and Faria, Rui and Westram, Anja M and Butlin, Roger K.}, issn = {14209101}, journal = {Journal of Evolutionary Biology}, number = {3}, pages = {342--351}, publisher = {Wiley}, title = {{Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?}}, doi = {10.1111/jeb.13570}, volume = {33}, year = {2020}, } @inbook{7227, abstract = {Gastrulation entails specification and formation of three embryonic germ layers—ectoderm, mesoderm and endoderm—thereby establishing the basis for the future body plan. In zebrafish embryos, germ layer specification occurs during blastula and early gastrula stages (Ho & Kimmel, 1993), a period when the main morphogenetic movements underlying gastrulation are initiated. Hence, the signals driving progenitor cell fate specification, such as Nodal ligands from the TGF-β family, also play key roles in regulating germ layer progenitor cell segregation (Carmany-Rampey & Schier, 2001; David & Rosa, 2001; Feldman et al., 2000; Gritsman et al., 1999; Keller et al., 2008). In this review, we summarize and discuss the main signaling pathways involved in germ layer progenitor cell fate specification and segregation, specifically focusing on recent advances in understanding the interplay between mesoderm and endoderm specification and the internalization movements at the onset of zebrafish gastrulation.}, author = {Nunes Pinheiro, Diana C and Heisenberg, Carl-Philipp J}, booktitle = {Gastrulation: From Embryonic Pattern to Form}, issn = {00702153}, pages = {343--375}, publisher = {Elsevier}, title = {{Zebrafish gastrulation: Putting fate in motion}}, doi = {10.1016/bs.ctdb.2019.10.009}, volume = {136}, year = {2020}, } @article{7417, abstract = {Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development.}, author = {Sinclair, Scott A and Gille, S. and Pauly, M. and Krämer, U.}, issn = {1559-2324}, journal = {Plant Signaling & Behavior}, number = {1}, publisher = {Informa UK Limited}, title = {{Regulation of acetylation of plant cell wall components is complex and responds to external stimuli}}, doi = {10.1080/15592324.2019.1687185}, volume = {15}, year = {2020}, } @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 = {1203--1278}, publisher = {Springer Nature}, title = {{Cusp universality for random matrices I: Local law and the complex Hermitian case}}, doi = {10.1007/s00220-019-03657-4}, volume = {378}, year = {2020}, } @phdthesis{7629, abstract = {This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck equation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces. The second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation. In the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of corresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals.}, author = {Forkert, Dominik L}, issn = {2663-337X}, pages = {154}, publisher = {Institute of Science and Technology Austria}, title = {{Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains}}, doi = {10.15479/AT:ISTA:7629}, year = {2020}, } @phdthesis{8574, abstract = {This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes leave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. In Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful tool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real behavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments. In Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model. We give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both drift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. In Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare the results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. In the last chapter, we give a brief outlook to further research. }, author = {Szep, Eniko}, issn = {2663-337X}, pages = {158}, publisher = {Institute of Science and Technology Austria}, title = {{Local adaptation in metapopulations}}, doi = {10.15479/AT:ISTA:8574}, year = {2020}, } @phdthesis{7514, abstract = {We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case. We motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.}, author = {Mayer, Simon}, issn = {2663-337X}, pages = {148}, publisher = {Institute of Science and Technology Austria}, title = {{The free energy of a dilute two-dimensional Bose gas}}, doi = {10.15479/AT:ISTA:7514}, year = {2020}, } @phdthesis{8353, abstract = {Mrp (Multi resistance and pH adaptation) are broadly distributed secondary active antiporters that catalyze the transport of monovalent ions such as sodium and potassium outside of the cell coupled to the inward translocation of protons. Mrp antiporters are unique in a way that they are composed of seven subunits (MrpABCDEFG) encoded in a single operon, whereas other antiporters catalyzing the same reaction are mostly encoded by a single gene. Mrp exchangers are crucial for intracellular pH homeostasis and Na+ efflux, essential mechanisms for H+ uptake under alkaline environments and for reduction of the intracellular concentration of toxic cations. Mrp displays no homology to any other monovalent Na+(K+)/H+ antiporters but Mrp subunits have primary sequence similarity to essential redox-driven proton pumps, such as respiratory complex I and membrane-bound hydrogenases. This similarity reinforces the hypothesis that these present day redox-driven proton pumps are descended from the Mrp antiporter. The Mrp structure serves as a model to understand the yet obscure coupling mechanism between ion or electron transfer and proton translocation in this large group of proteins. In the thesis, I am presenting the purification, biochemical analysis, cryo-EM analysis and molecular structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. Numerous conditions were screened to purify Mrp to high homogeneity and to obtain an appropriate distribution of single particles on cryo-EM grids covered with a continuous layer of ultrathin carbon. A preferred particle orientation problem was solved by performing a tilted data collection. The activity assays showed the specific pH-dependent profile of secondary active antiporters. The molecular structure shows that Mrp is a dimer of seven-subunit protomers with 50 trans-membrane helices each. The dimer interface is built by many short and tilted transmembrane helices, probably causing a thinning of the bacterial membrane. The surface charge distribution shows an extraordinary asymmetry within each monomer, revealing presumable proton and sodium translocation pathways. The two largest and homologous Mrp subunits MrpA and MrpD probably translocate one proton each into the cell. The sodium ion is likely being translocated in the opposite direction within the small subunits along a ladder of charged and conserved residues. Based on the structure, we propose a mechanism were the antiport activity is accomplished via electrostatic interactions between the charged cations and key charged residues. The flexible key TM helices coordinate these electrostatic interactions, while the membrane thinning between the monomers enables the translocation of sodium across the charged membrane. The entire family of redox-driven proton pumps is likely to perform their mechanism in a likewise manner.}, author = {Steiner, Julia}, issn = {2663-337X}, pages = {191}, publisher = {Institute of Science and Technology Austria}, title = {{Biochemical and structural investigation of the Mrp antiporter, an ancestor of complex I}}, doi = {10.15479/AT:ISTA:8353}, year = {2020}, } @phdthesis{8589, abstract = {The plant hormone auxin plays indispensable roles in plant growth and development. An essential level of regulation in auxin action is the directional auxin transport within cells. The establishment of auxin gradient in plant tissue has been attributed to local auxin biosynthesis and directional intercellular auxin transport, which both are controlled by various environmental and developmental signals. It is well established that asymmetric auxin distribution in cells is achieved by polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the initial insights into cellular mechanisms of PIN polarization obtained from the last decades, the molecular mechanism and specific regulators mediating PIN polarization remains elusive. In this thesis, we aim to find novel players in PIN subcellular polarity regulation during Arabidopsis development. We first characterize the physiological effect of piperonylic acid (PA) on Arabidopsis hypocotyl gravitropic bending and PIN polarization. Secondly, we reveal the importance of SCFTIR1/AFB auxin signaling pathway in shoot gravitropism bending termination. In addition, we also explore the role of myosin XI complex, and actin cytoskeleton in auxin feedback regulation on PIN polarity. In Chapter 1, we give an overview of the current knowledge about PIN-mediated auxin fluxes in various plant tropic responses. In Chapter 2, we study the physiological effect of PA on shoot gravitropic bending. Our results show that PA treatment inhibits auxin-mediated PIN3 repolarization by interfering with PINOID and PIN3 phosphorylation status, ultimately leading to hyperbending hypocotyls. In Chapter 3, we provide evidence to show that the SCFTIR1/AFB nuclear auxin signaling pathway is crucial and required for auxin-mediated PIN3 repolarization and shoot gravitropic bending termination. In Chapter 4, we perform a phosphoproteomics approach and identify the motor protein Myosin XI and its binding protein, the MadB2 family, as an essential regulator of PIN polarity for auxin-canalization related developmental processes. In Chapter 5, we demonstrate the vital role of actin cytoskeleton in auxin feedback on PIN polarity by regulating PIN subcellular trafficking. Overall, the data presented in this PhD thesis brings novel insights into the PIN polar localization regulation that resulted in the (re)establishment of the polar auxin flow and gradient in response to environmental stimuli during plant development.}, author = {Han, Huibin}, issn = {2663-337X}, pages = {164}, publisher = {Institute of Science and Technology Austria}, title = {{Novel insights into PIN polarity regulation during Arabidopsis development}}, doi = {10.15479/AT:ISTA:8589}, year = {2020}, } @article{8284, abstract = {Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.}, author = {Steiner, Julia and Sazanov, Leonid A}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter}}, doi = {10.7554/eLife.59407}, volume = {9}, year = {2020}, } @phdthesis{8155, abstract = {In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as transcriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal non-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters. In the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are hard to evolve or maintain. }, author = {Grah, Rok}, issn = {2663-337X}, pages = {310}, publisher = {Institute of Science and Technology Austria}, title = {{Gene regulation across scales – how biophysical constraints shape evolution}}, doi = {10.15479/AT:ISTA:8155}, year = {2020}, } @article{7643, author = {Han, Huibin and Rakusova, Hana and Verstraeten, Inge and Zhang, Yuzhou and Friml, Jiří}, issn = {1532-2548}, journal = {Plant Physiology}, number = {5}, pages = {37--40}, publisher = {American Society of Plant Biologists}, title = {{SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism}}, doi = {10.1104/pp.20.00212}, volume = {183}, year = {2020}, } @unpublished{7675, abstract = {In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.}, author = {Grah, Rok and Zoller, Benjamin and Tkačik, Gašper}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{Normative models of enhancer function}}, doi = {10.1101/2020.04.08.029405}, year = {2020}, } @phdthesis{7460, abstract = {Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications. For the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries.}, author = {Ölsböck, Katharina}, issn = {2663-337X}, keywords = {shape reconstruction, hole manipulation, ordered complexes, Alpha complex, Wrap complex, computational topology, Bregman geometry}, pages = {155}, publisher = {Institute of Science and Technology Austria}, title = {{The hole system of triangulated shapes}}, doi = {10.15479/AT:ISTA:7460}, year = {2020}, }