TY - THES AB - Plants maintain the capacity to develop new organs e.g. lateral roots post-embryonically throughout their whole life and thereby flexibly adapt to ever-changing environmental conditions. Plant hormones auxin and cytokinin are the main regulators of the lateral root organogenesis. Additionally to their solo activities, the interaction between auxin and cytokinin plays crucial role in fine-tuning of lateral root development and growth. In particular, cytokinin modulates auxin distribution within the developing lateral root by affecting the endomembrane trafficking of auxin transporter PIN1 and promoting its vacuolar degradation (Marhavý et al., 2011, 2014). This effect is independent of transcription and translation. Therefore, it suggests novel, non-canonical cytokinin activity occuring possibly on the posttranslational level. Impact of cytokinin and other plant hormones on auxin transporters (including PIN1) on the posttranslational level is described in detail in the introduction part of this thesis in a form of a review (Semeradova et al., 2020). To gain insights into the molecular machinery underlying cytokinin effect on the endomembrane trafficking in the plant cell, in particular on the PIN1 degradation, we conducted two large proteomic screens: 1) Identification of cytokinin binding proteins using chemical proteomics. 2) Monitoring of proteomic and phosphoproteomic changes upon cytokinin treatment. In the first screen, we identified DYNAMIN RELATED PROTEIN 2A (DRP2A). We found that DRP2A plays a role in cytokinin regulated processes during the plant growth and that cytokinin treatment promotes destabilization of DRP2A protein. However, the role of DRP2A in the PIN1 degradation remains to be elucidated. In the second screen, we found VACUOLAR PROTEIN SORTING 9A (VPS9A). VPS9a plays crucial role in plant’s response to cytokin and in cytokinin mediated PIN1 degradation. Altogether, we identified proteins, which bind to cytokinin and proteins that in response to cytokinin exhibit significantly changed abundance or phosphorylation pattern. By combining information from these two screens, we can pave our way towards understanding of noncanonical cytokinin effects. AU - Semerádová, Hana ID - 10135 SN - 2663-337X TI - Molecular mechanisms of the cytokinin-regulated endomembrane trafficking to coordinate plant organogenesis ER - TY - THES AB - Most real-world flows are multiphase, yet we know little about them compared to their single-phase counterparts. Multiphase flows are more difficult to investigate as their dynamics occur in large parameter space and involve complex phenomena such as preferential concentration, turbulence modulation, non-Newtonian rheology, etc. Over the last few decades, experiments in particle-laden flows have taken a back seat in favour of ever-improving computational resources. However, computers are still not powerful enough to simulate a real-world fluid with millions of finite-size particles. Experiments are essential not only because they offer a reliable way to investigate real-world multiphase flows but also because they serve to validate numerical studies and steer the research in a relevant direction. In this work, we have experimentally investigated particle-laden flows in pipes, and in particular, examined the effect of particles on the laminar-turbulent transition and the drag scaling in turbulent flows. For particle-laden pipe flows, an earlier study [Matas et al., 2003] reported how the sub-critical (i.e., hysteretic) transition that occurs via localised turbulent structures called puffs is affected by the addition of particles. In this study, in addition to this known transition, we found a super-critical transition to a globally fluctuating state with increasing particle concentration. At the same time, the Newtonian-type transition via puffs is delayed to larger Reynolds numbers. At an even higher concentration, only the globally fluctuating state is found. The dynamics of particle-laden flows are hence determined by two competing instabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle-induced globally fluctuating state at high, and a coexistence state at intermediate concentrations. The effect of particles on turbulent drag is ambiguous, with studies reporting drag reduction, no net change, and even drag increase. The ambiguity arises because, in addition to particle concentration, particle shape, size, and density also affect the net drag. Even similar particles might affect the flow dissimilarly in different Reynolds number and concentration ranges. In the present study, we explored a wide range of both Reynolds number and concentration, using spherical as well as cylindrical particles. We found that the spherical particles do not reduce drag while the cylindrical particles are drag-reducing within a specific Reynolds number interval. The interval strongly depends on the particle concentration and the relative size of the pipe and particles. Within this interval, the magnitude of drag reduction reaches a maximum. These drag reduction maxima appear to fall onto a distinct power-law curve irrespective of the pipe diameter and particle concentration, and this curve can be considered as the maximum drag reduction asymptote for a given fibre shape. Such an asymptote is well known for polymeric flows but had not been identified for particle-laden flows prior to this work. AU - Agrawal, Nishchal ID - 9728 KW - Drag Reduction KW - Transition to Turbulence KW - Multiphase Flows KW - particle Laden Flows KW - Complex Flows KW - Experiments KW - Fluid Dynamics SN - 2663-337X TI - Transition to turbulence and drag reduction in particle-laden pipe flows ER - TY - JOUR AB - Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context. AU - Krausser, Johannes AU - Knowles, Tuomas P. J. AU - Šarić, Anđela ID - 10336 IS - 52 JF - Proceedings of the National Academy of Sciences SN - 0027-8424 TI - Physical mechanisms of amyloid nucleation on fluid membranes VL - 117 ER - TY - JOUR AB - The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across. AU - Tian, Xiaohe AU - Leite, Diana M. AU - Scarpa, Edoardo AU - Nyberg, Sophie AU - Fullstone, Gavin AU - Forth, Joe AU - Matias, Diana AU - Apriceno, Azzurra AU - Poma, Alessandro AU - Duro-Castano, Aroa AU - Vuyyuru, Manish AU - Harker-Kirschneck, Lena AU - Šarić, Anđela AU - Zhang, Zhongping AU - Xiang, Pan AU - Fang, Bin AU - Tian, Yupeng AU - Luo, Lei AU - Rizzello, Loris AU - Battaglia, Giuseppe ID - 10342 IS - 48 JF - Science Advances KW - multidisciplinary SN - 2375-2548 TI - On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias VL - 6 ER - TY - JOUR AB - In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry. AU - Forster, Joel C. AU - Krausser, Johannes AU - Vuyyuru, Manish R. AU - Baum, Buzz AU - Šarić, Anđela ID - 10344 IS - 22 JF - Physical Review Letters SN - 0031-9007 TI - Exploring the design rules for efficient membrane-reshaping nanostructures VL - 125 ER - TY - JOUR AB - Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes. AU - Debets, V. E. AU - Janssen, L. M. C. AU - Šarić, Anđela ID - 10341 IS - 47 JF - Soft Matter KW - condensed matter physics KW - general chemistry SN - 1744-683X TI - Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes VL - 16 ER - TY - JOUR AB - One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications. AU - Hafner, Anne E. AU - Gyori, Noemi G. AU - Bench, Ciaran A. AU - Davis, Luke K. AU - Šarić, Anđela ID - 10346 IS - 9 JF - Biophysical Journal KW - biophysics SN - 0006-3495 TI - Modeling fibrillogenesis of collagen-mimetic molecules VL - 119 ER - TY - JOUR AB - The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation. AU - Dear, Alexander J. AU - Meisl, Georg AU - Šarić, Anđela AU - Michaels, Thomas C. T. AU - Kjaergaard, Magnus AU - Linse, Sara AU - Knowles, Tuomas P. J. ID - 10350 IS - 24 JF - Chemical Science KW - general chemistry SN - 2041-6520 TI - Identification of on- and off-pathway oligomers in amyloid fibril formation VL - 11 ER - TY - JOUR AB - Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control. AU - Tarrason Risa, Gabriel AU - Hurtig, Fredrik AU - Bray, Sian AU - Hafner, Anne E. AU - Harker-Kirschneck, Lena AU - Faull, Peter AU - Davis, Colin AU - Papatziamou, Dimitra AU - Mutavchiev, Delyan R. AU - Fan, Catherine AU - Meneguello, Leticia AU - Arashiro Pulschen, Andre AU - Dey, Gautam AU - Culley, Siân AU - Kilkenny, Mairi AU - Souza, Diorge P. AU - Pellegrini, Luca AU - de Bruin, Robertus A. M. AU - Henriques, Ricardo AU - Snijders, Ambrosius P. AU - Šarić, Anđela AU - Lindås, Ann-Christin AU - Robinson, Nicholas P. AU - Baum, Buzz ID - 10349 IS - 6504 JF - Science KW - multidisciplinary SN - 0036-8075 TI - The proteasome controls ESCRT-III–mediated cell division in an archaeon VL - 369 ER - TY - JOUR AB - Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors. AU - Michaels, Thomas C. T. AU - Šarić, Anđela AU - Meisl, Georg AU - Heller, Gabriella T. AU - Curk, Samo AU - Arosio, Paolo AU - Linse, Sara AU - Dobson, Christopher M. AU - Vendruscolo, Michele AU - Knowles, Tuomas P. J. ID - 10347 IS - 39 JF - Proceedings of the National Academy of Sciences KW - multidisciplinary SN - 0027-8424 TI - Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors VL - 117 ER - TY - JOUR AB - Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases. AU - Michaels, Thomas C. T. AU - Šarić, Anđela AU - Curk, Samo AU - Bernfur, Katja AU - Arosio, Paolo AU - Meisl, Georg AU - Dear, Alexander J. AU - Cohen, Samuel I. A. AU - Dobson, Christopher M. AU - Vendruscolo, Michele AU - Linse, Sara AU - Knowles, Tuomas P. J. ID - 10351 IS - 5 JF - Nature Chemistry KW - general chemical engineering KW - general chemistry SN - 1755-4330 TI - Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide VL - 12 ER - TY - JOUR AB - The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity. AU - Pfitzner, Anna-Katharina AU - Mercier, Vincent AU - Jiang, Xiuyun AU - Moser von Filseck, Joachim AU - Baum, Buzz AU - Šarić, Anđela AU - Roux, Aurélien ID - 10348 IS - 5 JF - Cell KW - general biochemistry KW - genetics and molecular biology SN - 0092-8674 TI - An ESCRT-III polymerization sequence drives membrane deformation and fission VL - 182 ER - TY - JOUR AB - In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events. AU - Davis, Luke K. AU - Ford, Ian J. AU - Šarić, Anđela AU - Hoogenboom, Bart W. ID - 10352 IS - 2 JF - Physical Review E SN - 2470-0045 TI - Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics VL - 101 ER - TY - JOUR AB - Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content. AU - Paraschiv, Alexandru AU - Hegde, Smitha AU - Ganti, Raman AU - Pilizota, Teuta AU - Šarić, Anđela ID - 10353 IS - 4 JF - Physical Review Letters KW - general physics and astronomy SN - 0031-9007 TI - Dynamic clustering regulates activity of mechanosensitive membrane channels VL - 124 ER - TY - GEN AB - Data storage and retrieval systems, methods, and computer-readable media utilize a cryptographically verifiable data structure that facilitates verification of a transaction in a decentralized peer-to-peer environment using multi-hop backwards and forwards links. Backward links are cryptographic hashes of past records. Forward links are cryptographic signatures of future records that are added retroactively to records once the target block has been appended to the data structure. AU - Ford, Bryan AU - Gasse, Linus AU - Kokoris Kogias, Eleftherios AU - Jovanovic, Philipp ID - 10557 TI - Cryptographically verifiable data structure having multi-hop forward and backwards links and associated systems and methods ER - TY - JOUR AB - Magnetism typically arises from the joint effect of Fermi statistics and repulsive Coulomb interactions, which favours ground states with non-zero electron spin. As a result, controlling spin magnetism with electric fields—a longstanding technological goal in spintronics and multiferroics1,2—can be achieved only indirectly. Here we experimentally demonstrate direct electric-field control of magnetic states in an orbital Chern insulator3,4,5,6, a magnetic system in which non-trivial band topology favours long-range order of orbital angular momentum but the spins are thought to remain disordered7,8,9,10,11,12,13,14. We use van der Waals heterostructures consisting of a graphene monolayer rotationally faulted with respect to a Bernal-stacked bilayer to realize narrow and topologically non-trivial valley-projected moiré minibands15,16,17. At fillings of one and three electrons per moiré unit cell within these bands, we observe quantized anomalous Hall effects18 with transverse resistance approximately equal to h/2e2 (where h is Planck’s constant and e is the charge on the electron), which is indicative of spontaneous polarization of the system into a single-valley-projected band with a Chern number equal to two. At a filling of three electrons per moiré unit cell, we find that the sign of the quantum anomalous Hall effect can be reversed via field-effect control of the chemical potential; moreover, this transition is hysteretic, which we use to demonstrate non-volatile electric-field-induced reversal of the magnetic state. A theoretical analysis19 indicates that the effect arises from the topological edge states, which drive a change in sign of the magnetization and thus a reversal in the favoured magnetic state. Voltage control of magnetic states can be used to electrically pattern non-volatile magnetic-domain structures hosting chiral edge states, with applications ranging from reconfigurable microwave circuit elements to ultralow-power magnetic memories. AU - Polshyn, Hryhoriy AU - Zhu, J. AU - Kumar, M. A. AU - Zhang, Y. AU - Yang, F. AU - Tschirhart, C. L. AU - Serlin, M. AU - Watanabe, K. AU - Taniguchi, T. AU - MacDonald, A. H. AU - Young, A. F. ID - 10618 IS - 7836 JF - Nature KW - multidisciplinary SN - 0028-0836 TI - Electrical switching of magnetic order in an orbital Chern insulator VL - 588 ER - TY - GEN AB - The understanding of material systems with strong electron-electron interactions is the central problem in modern condensed matter physics. Despite this, the essential physics of many of these materials is still not understood and we have no overall perspective on their properties. Moreover, we have very little ability to make predictions in this class of systems. In this manuscript we share our personal views of what the major open problems are in correlated electron systems and we discuss some possible routes to make progress in this rich and fascinating field. This manuscript is the result of the vigorous discussions and deliberations that took place at Johns Hopkins University during a three-day workshop January 27, 28, and 29, 2020 that brought together six senior scientists and 46 more junior scientists. Our hope, is that the topics we have presented will provide inspiration for others working in this field and motivation for the idea that significant progress can be made on very hard problems if we focus our collective energies. AU - Alexandradinata, A AU - Armitage, N.P. AU - Baydin, Andrey AU - Bi, Wenli AU - Cao, Yue AU - Changlani, Hitesh J. AU - Chertkov, Eli AU - da Silva Neto, Eduardo H. AU - Delacretaz, Luca AU - El Baggari, Ismail AU - Ferguson, G.M. AU - Gannon, William J. AU - Ghorashi, Sayed Ali Akbar AU - Goodge, Berit H. AU - Goulko, Olga AU - Grissonnache, G. AU - Hallas, Alannah AU - Hayes, Ian M. AU - He, Yu AU - Huang, Edwin W. AU - Kogar, Anshu AU - Kumah, Divine AU - Lee, Jong Yeon AU - Legros, A. AU - Mahmood, Fahad AU - Maximenko, Yulia AU - Pellatz, Nick AU - Polshyn, Hryhoriy AU - Sarkar, Tarapada AU - Scheie, Allen AU - Seyler, Kyle L. AU - Shi, Zhenzhong AU - Skinner, Brian AU - Steinke, Lucia AU - Thirunavukkuarasu, K. AU - Trevisan, Thaís Victa AU - Vogl, Michael AU - Volkov, Pavel A. AU - Wang, Yao AU - Wang, Yishu AU - Wei, Di AU - Wei, Kaya AU - Yang, Shuolong AU - Zhang, Xian AU - Zhang, Ya-Hui AU - Zhao, Liuyan AU - Zong, Alfred ID - 10650 T2 - arXiv TI - The future of the correlated electron problem ER - TY - CONF AB - We propose a neural information processing system obtained by re-purposing the function of a biological neural circuit model to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce ordinary neural circuits (ONCs), defined as the model of biological neural circuits reparameterized for the control of alternative tasks. We first demonstrate that ONCs realize networks with higher maximum flow compared to arbitrary wired networks. We then learn instances of ONCs to control a series of robotic tasks, including the autonomous parking of a real-world rover robot. For reconfiguration of the purpose of the neural circuit, we adopt a search-based optimization algorithm. Ordinary neural circuits perform on par and, in some cases, significantly surpass the performance of contemporary deep learning models. ONC networks are compact, 77% sparser than their counterpart neural controllers, and their neural dynamics are fully interpretable at the cell-level. AU - Hasani, Ramin AU - Lechner, Mathias AU - Amini, Alexander AU - Rus, Daniela AU - Grosu, Radu ID - 10673 SN - 2640-3498 T2 - Proceedings of the 37th International Conference on Machine Learning TI - A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits ER - TY - CONF AB - High quality graphene heterostructures host an array of fractional quantum Hall isospin ferromagnets with diverse spin and valley orders. While a variety of phase transitions have been observed, disentangling the isospin phase diagram of these states is hampered by the absence of direct probes of spin and valley order. I will describe nonlocal transport measurements based on launching spin waves from a gate defined lateral heterojunction, performed in ultra-clean Corbino geometry graphene devices. At high magnetic fields, we find that the spin-wave transport signal is detected in all FQH states between ν = 0 and 1; however, between ν = 1 and 2 only odd numerator FQH states show finite nonlocal transport, despite the identical ground state spin polarizations in odd- and even numerator states. The results reveal that the neutral spin-waves are both spin and sublattice polarized making them a sensitive probe of ground state sublattice structure. Armed with this understanding, we use nonlocal transport signal to a magnetic field tuned isospin phase transition, showing that the emergent even denominator state at ν = 1/2 in monolayer graphene is indeed a multicomponent state featuring equal populations on each sublattice. AU - Zhou, Haoxin AU - Polshyn, Hryhoriy AU - Tanaguchi, Takashi AU - Watanabe, Kenji AU - Young, Andrea ID - 10693 IS - 1 SN - 0003-0503 T2 - APS March Meeting 2020 TI - Sublattice resolved spin wave transport through graphene fractional quantum Hall states as a probe of isospin order VL - 65 ER - TY - CONF AB - This is the second of three talks describing the observation and characterization of a ferromagnetic moiré heterostructure based on twisted bilayer graphene aligned to hexagonal boron nitride. I will compare the qualitative and quantitative features of this observed quantum anomalous Hall state to traditional systems engineered from thin film (Bi,Sb)2Te3 topological insulators. In particular, we find that the measured electronic energy gap of ~30K is several times higher than the Curie temperature, consistent with a lack of disorder associated with magnetic dopants. In this system, the quantization arises from spontaneous ferromagnetic polarization into a single spin and valley moiré subband, which is topological despite the lack of spin orbit coupling. I will also discuss the observation of current induced switching, which allows the magnetic state of the heterostructure to be controllably reversed with currents as small as a few nanoamperes. AU - Serlin, Marec AU - Tschirhart, Charles AU - Polshyn, Hryhoriy AU - Zhang, Yuxuan AU - Zhu, Jiacheng AU - Huber, Martin E. AU - Balents, Leon AU - Watanabe, Kenji AU - Tanaguchi, Takashi AU - Young, Andrea ID - 10698 IS - 1 T2 - APS March Meeting 2020 TI - Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part II: Temperature dependence and current switching VL - 65 ER - TY - CONF AB - This is the third of three talks describing the observation and characterization of a ferromagnetic moiré heterostructure based on twisted bilayer graphene aligned to hexagonal boron nitride. In this segment I will present scanning probe magnetometry data acquired using a nanoSQUID-on-tip microscope, which provides ~150 nm spatial resolution and a field sensitivity of ~10 nT/rtHz. We study the distribution of magnetic domains within the device as a function of density, magnetic field training, and DC current. Our data allow us to constrain the magnitude of the orbital magnetic moment of the electrons in the QAH state. Comparison with simultaneously acquired transport data allows us to precisely correlate single domain dynamics with discrete jumps in the observed anomalous Hall signal. AU - Tschirhart, Charles AU - Serlin, Marec AU - Polshyn, Hryhoriy AU - Zhang, Yuxuan AU - Zhu, Jiacheng AU - Balents, Leon AU - Huber, Martin E. AU - Watanabe, Kenji AU - Tanaguchi, Takashi AU - Young, Andrea ID - 10699 IS - 1 SN - 0003-0503 T2 - APS March Meeting 2020 TI - Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part III: Scanning probe magnetometry VL - 65 ER - TY - CONF AB - We report the observation of a quantized anomalous Hall effect in a moiré heterostructure consisting of twisted bilayer graphene aligned to an encapsulating hBN substrate. The effect occurs at a density of 3 electrons per superlattice unit cell, where we observe magnetic hysteresis and a Hall resistance quantized to within 0.1% of the resistance quantum at temperatures as high as 3K. In this first of 3 talks, I will describe the fabrication procedure for our device as well as basic transport characterization measurements. I will introduce the phenomenology of twisted bilayer graphene and present evidence for hBN alignment as manifested in the hierarchy of symmetry-breaking gaps and anomalous magnetoresistance. AU - Zhang, Yuxuan AU - Serlin, Marec AU - Tschirhart, Charles AU - Polshyn, Hryhoriy AU - Zhu, Jiacheng AU - Balents, Leon AU - Huber, Martin E. AU - Taniguchi, Takashi AU - Watanabe, Kenji AU - Young, Andrea ID - 10697 IS - 1 T2 - APS March Meeting 2020 TI - Intrinsic quantized anomalous Hall effect in a moiré heterostructure, part I: Device fabrication and transport VL - 65 ER - TY - CONF AB - We experimentally investigate twisted van der Waals heterostructures of monolayer graphene rotated with respect to a bernal stacked graphene bilayer. We report transport measurements for devices with twist angles between 0.9 and 1.4°. The electric field allows efficient tuning of the width, isolation and the topology of the moiré bands in this system. By comparing magnetoresistance measurements to numerical simulations, we develop an understanding of the band structure. Finally, we observe correlated states at half- and quarter-fillings, which arise when narrow moire sublattice band is isolated by energy gaps from dispersive bands. We investigate the effects of in-plane and out-of-plane magnetic field on these states and discuss the implication for their spin- and valley- polarization. AU - Polshyn, Hryhoriy AU - Zhu, Jihang AU - Kumar, Manish AU - Taniguchi, Takashi AU - Watanabe, Kenji AU - MacDonald, Allan AU - Young, Andrea ID - 10696 IS - 1 SN - 0003-0503 T2 - APS March Meeting 2020 TI - Correlated states and tunable topological bands in twisted monolayer-bilayer graphene heterostructures VL - 65 ER - TY - JOUR AB - Partially filled Landau levels host competing electronic orders. For example, electron solids may prevail close to integer filling of the Landau levels before giving way to fractional quantum Hall liquids at higher carrier density1,2. Here, we report the observation of an electron solid with non-collinear spin texture in monolayer graphene, consistent with solidification of skyrmions3—topological spin textures characterized by quantized electrical charge4,5. We probe the spin texture of the solids using a modified Corbino geometry that allows ferromagnetic magnons to be launched and detected6,7. We find that magnon transport is highly efficient when one Landau level is filled (ν=1), consistent with quantum Hall ferromagnetic spin polarization. However, even minimal doping immediately quenches the magnon signal while leaving the vanishing low-temperature charge conductivity unchanged. Our results can be understood by the formation of a solid of charged skyrmions near ν=1, whose non-collinear spin texture leads to rapid magnon decay. Data near fractional fillings show evidence of several fractional skyrmion solids, suggesting that graphene hosts a highly tunable landscape of coupled spin and charge orders. AU - Zhou, Haoxin AU - Polshyn, Hryhoriy AU - Taniguchi, Takashi AU - Watanabe, Kenji AU - Young, Andrea F. ID - 10701 IS - 2 JF - Nature Physics SN - 1745-2473 TI - Skyrmion solids in monolayer graphene VL - 16 ER - TY - JOUR AB - Aging of the circulatory system correlates with the pathogenesis of a large spectrum of diseases. However, it is largely unknown which factors drive the age-dependent or pathological decline of the vasculature and how vascular defects relate to tissue aging. The goal of the study is to design a multianalytical approach to identify how the cellular microenvironment (i.e., fibroblasts) and serum from healthy donors of different ages or Alzheimer disease (AD) patients can modulate the functionality of organ-specific vascular endothelial cells (VECs). Long-living human microvascular networks embedding VECs and fibroblasts from skin biopsies are generated. RNA-seq, secretome analyses, and microfluidic assays demonstrate that fibroblasts from young donors restore the functionality of aged endothelial cells, an effect also achieved by serum from young donors. New biomarkers of vascular aging are validated in human biopsies and it is shown that young serum induces angiopoietin-like-4, which can restore compromised vascular barriers. This strategy is then employed to characterize transcriptional/functional changes induced on the blood–brain barrier by AD serum, demonstrating the importance of PTP4A3 in the regulation of permeability. Features of vascular degeneration during aging and AD are recapitulated, and a tool to identify novel biomarkers that can be exploited to develop future therapeutics modulating vascular function is established. AU - Bersini, Simone AU - Arrojo e Drigo, Rafael AU - Huang, Ling AU - Shokhirev, Maxim N. AU - HETZER, Martin W ID - 11056 IS - 5 JF - Advanced Biosystems KW - General Biochemistry KW - Genetics and Molecular Biology KW - Biomedical Engineering KW - Biomaterials SN - 2366-7478 TI - Transcriptional and functional changes of the human microvasculature during physiological aging and Alzheimer disease VL - 4 ER - TY - JOUR AB - Vascular dysfunctions are a common feature of multiple age-related diseases. However, modeling healthy and pathological aging of the human vasculature represents an unresolved experimental challenge. Here, we generated induced vascular endothelial cells (iVECs) and smooth muscle cells (iSMCs) by direct reprogramming of healthy human fibroblasts from donors of different ages and Hutchinson-Gilford Progeria Syndrome (HGPS) patients. iVECs induced from old donors revealed upregulation of GSTM1 and PALD1, genes linked to oxidative stress, inflammation and endothelial junction stability, as vascular aging markers. A functional assay performed on PALD1 KD VECs demonstrated a recovery in vascular permeability. We found that iSMCs from HGPS donors overexpressed bone morphogenetic protein (BMP)−4, which plays a key role in both vascular calcification and endothelial barrier damage observed in HGPS. Strikingly, BMP4 concentrations are higher in serum from HGPS vs. age-matched mice. Furthermore, targeting BMP4 with blocking antibody recovered the functionality of the vascular barrier in vitro, hence representing a potential future therapeutic strategy to limit cardiovascular dysfunction in HGPS. These results show that iVECs and iSMCs retain disease-related signatures, allowing modeling of vascular aging and HGPS in vitro. AU - Bersini, Simone AU - Schulte, Roberta AU - Huang, Ling AU - Tsai, Hannah AU - HETZER, Martin W ID - 11055 JF - eLife KW - General Immunology and Microbiology KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Medicine KW - General Neuroscience SN - 2050-084X TI - Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome VL - 9 ER - TY - JOUR AB - In recent years, the nuclear pore complex (NPC) has emerged as a key player in genome regulation and cellular homeostasis. New discoveries have revealed that the NPC has multiple cellular functions besides mediating the molecular exchange between the nucleus and the cytoplasm. In this review, we discuss non-transport aspects of the NPC focusing on the NPC-genome interaction, the extreme longevity of the NPC proteins, and NPC dysfunction in age-related diseases. The examples summarized herein demonstrate that the NPC, which first evolved to enable the biochemical communication between the nucleus and the cytoplasm, now doubles as the gatekeeper of cellular identity and aging. AU - Cho, Ukrae H. AU - HETZER, Martin W ID - 11054 IS - 6 JF - Neuron KW - General Neuroscience SN - 0896-6273 TI - Nuclear periphery takes center stage: The role of nuclear pore complexes in cell identity and aging VL - 106 ER - TY - JOUR AB - During mitosis, transcription of genomic DNA is dramatically reduced, before it is reactivated during nuclear reformation in anaphase/telophase. Many aspects of the underlying principles that mediate transcriptional memory and reactivation in the daughter cells remain unclear. Here, we used ChIP-seq on synchronized cells at different stages after mitosis to generate genome-wide maps of histone modifications. Combined with EU-RNA-seq and Hi-C analyses, we found that during prometaphase, promoters, enhancers, and insulators retain H3K4me3 and H3K4me1, while losing H3K27ac. Enhancers globally retaining mitotic H3K4me1 or locally retaining mitotic H3K27ac are associated with cell type-specific genes and their transcription factors for rapid transcriptional activation. As cells exit mitosis, promoters regain H3K27ac, which correlates with transcriptional reactivation. Insulators also gain H3K27ac and CCCTC-binding factor (CTCF) in anaphase/telophase. This increase of H3K27ac in anaphase/telophase is required for posttranscriptional activation and may play a role in the establishment of topologically associating domains (TADs). Together, our results suggest that the genome is reorganized in a sequential order, in which histone methylations occur first in prometaphase, histone acetylation, and CTCF in anaphase/telophase, transcription in cytokinesis, and long-range chromatin interactions in early G1. We thus provide insights into the histone modification landscape that allows faithful reestablishment of the transcriptional program and TADs during cell division. AU - Kang, Hyeseon AU - Shokhirev, Maxim N. AU - Xu, Zhichao AU - Chandran, Sahaana AU - Dixon, Jesse R. AU - HETZER, Martin W ID - 11057 IS - 13-14 JF - Genes & Development KW - Developmental Biology KW - Genetics SN - 0890-9369 TI - Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation VL - 34 ER - TY - JOUR AB - Nucleoporin 93 (Nup93) expression inversely correlates with the survival of triple-negative breast cancer patients. However, our knowledge of Nup93 function in breast cancer besides its role as structural component of the nuclear pore complex is not understood. Combination of functional assays and genetic analyses suggested that chromatin interaction of Nup93 partially modulates the expression of genes associated with actin cytoskeleton remodeling and epithelial to mesenchymal transition, resulting in impaired invasion of triple-negative, claudin-low breast cancer cells. Nup93 depletion induced stress fiber formation associated with reduced cell migration/proliferation and impaired expression of mesenchymal-like genes. Silencing LIMCH1, a gene responsible for actin cytoskeleton remodeling and up-regulated upon Nup93 depletion, partially restored the invasive phenotype of cancer cells. Loss of Nup93 led to significant defects in tumor establishment/propagation in vivo, whereas patient samples revealed that high Nup93 and low LIMCH1 expression correlate with late tumor stage. Our approach identified Nup93 as contributor of triple-negative, claudin-low breast cancer cell invasion and paves the way to study the role of nuclear envelope proteins during breast cancer tumorigenesis. AU - Bersini, Simone AU - Lytle, Nikki K AU - Schulte, Roberta AU - Huang, Ling AU - Wahl, Geoffrey M AU - HETZER, Martin W ID - 11058 IS - 1 JF - Life Science Alliance KW - Health KW - Toxicology and Mutagenesis KW - Plant Science KW - Biochemistry KW - Genetics and Molecular Biology (miscellaneous) KW - Ecology SN - 2575-1077 TI - Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling VL - 3 ER - TY - JOUR AB - Context. The Lyα emitter (LAE) fraction, XLAE, is a potentially powerful probe of the evolution of the intergalactic neutral hydrogen gas fraction. However, uncertainties in the measurement of XLAE are still under debate. Aims. Thanks to deep data obtained with the integral field spectrograph Multi Unit Spectroscopic Explorer (MUSE), we can measure the evolution of the LAE fraction homogeneously over a wide redshift range of z ≈ 3–6 for UV-faint galaxies (down to UV magnitudes of M1500 ≈ −17.75). This is a significantly fainter range than in former studies (M1500 ≤ −18.75) and it allows us to probe the bulk of the population of high-redshift star-forming galaxies. Methods. We constructed a UV-complete photometric-redshift sample following UV luminosity functions and measured the Lyα emission with MUSE using the latest (second) data release from the MUSE Hubble Ultra Deep Field Survey. Results. We derived the redshift evolution of XLAE for M1500 ∈ [ − 21.75; −17.75] for the first time with a equivalent width range EW(Lyα) ≥ 65 Å and found low values of XLAE ≲ 30% at z ≲ 6. The best-fit linear relation is XLAE = 0.07+0.06−0.03z − 0.22+0.12−0.24. For M1500 ∈ [ − 20.25; −18.75] and EW(Lyα) ≥ 25 Å, our XLAE values are consistent with those in the literature within 1σ at z ≲ 5, but our median values are systematically lower than reported values over the whole redshift range. In addition, we do not find a significant dependence of XLAE on M1500 for EW(Lyα) ≥ 50 Å at z ≈ 3–4, in contrast with previous work. The differences in XLAE mainly arise from selection biases for Lyman Break Galaxies (LBGs) in the literature: UV-faint LBGs are more easily selected if they have strong Lyα emission, hence XLAE is biased towards higher values when those samples are used. Conclusions. Our results suggest either a lower increase of XLAE towards z ≈ 6 than previously suggested, or even a turnover of XLAE at z ≈ 5.5, which may be the signature of a late or patchy reionization process. We compared our results with predictions from a cosmological galaxy evolution model. We find that a model with a bursty star formation (SF) can reproduce our observed LAE fractions much better than models where SF is a smooth function of time. AU - Kusakabe, Haruka AU - Blaizot, Jérémy AU - Garel, Thibault AU - Verhamme, Anne AU - Bacon, Roland AU - Richard, Johan AU - Hashimoto, Takuya AU - Inami, Hanae AU - Conseil, Simon AU - Guiderdoni, Bruno AU - Drake, Alyssa B. AU - Christian Herenz, Edmund AU - Schaye, Joop AU - Oesch, Pascal AU - Matthee, Jorryt J AU - Anna Marino, Raffaella AU - Borello Schmidt, Kasper AU - Pelló, Roser AU - Maseda, Michael AU - Leclercq, Floriane AU - Kerutt, Josephine AU - Mahler, Guillaume ID - 11503 JF - Astronomy & Astrophysics KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - dark ages / reionization / first stars / early Universe / cosmology: observations / galaxies: evolution / galaxies: high-redshift / intergalactic medium SN - 0004-6361 TI - The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6 VL - 638 ER - TY - JOUR AB - We present spatially resolved maps of six individually-detected Lyman α haloes (LAHs) as well as a first statistical analysis of the Lyman α (Lyα) spectral signature in the circum-galactic medium of high-redshift star-forming galaxies (−17.5 >  MUV >  −21.5) using the Multi-Unit Spectroscopic Explorer. Our resolved spectroscopic analysis of the LAHs reveals significant intrahalo variations of the Lyα line profile. Using a three-dimensional two-component model for the Lyα emission, we measured the full width at half maximum (FWHM), the peak velocity shift, and the asymmetry of the Lyα line in the core and in the halo of 19 galaxies. We find that the Lyα line shape is statistically different in the halo compared to the core (in terms of width, peak wavelength, and asymmetry) for ≈40% of our galaxies. Similarly to object-by-object based studies and a recent resolved study using lensing, we find a correlation between the peak velocity shift and the width of the Lyα line both at the interstellar and circum-galactic scales. This trend has been predicted by radiative transfer simulations of galactic winds as a result of resonant scattering in outflows. While there is a lack of correlation between the spectral properties and the spatial scale lengths of our LAHs, we find a correlation between the width of the line in the LAH and the halo flux fraction. Interestingly, UV bright galaxies (MUV <  −20) show broader, more redshifted, and less asymmetric Lyα lines in their haloes. The most significant correlation found is for the FWHM of the line and the UV continuum slope of the galaxy, suggesting that the redder galaxies have broader Lyα lines. The generally broad and red line shapes found in the halo component suggest that the Lyα haloes are powered either by scattering processes through an outflowing medium, fluorescent emission from outflowing cold clumps of gas, or a mix of both. Considering the large diversity of the Lyα line profiles observed in our sample and the lack of strong correlation, the interpretation of our results is still broadly open and underlines the need for realistic spatially resolved models of the LAHs. AU - Leclercq, Floriane AU - Bacon, Roland AU - Verhamme, Anne AU - Garel, Thibault AU - Blaizot, Jérémy AU - Brinchmann, Jarle AU - Cantalupo, Sebastiano AU - Claeyssens, Adélaïde AU - Conseil, Simon AU - Contini, Thierry AU - Hashimoto, Takuya AU - Herenz, Edmund Christian AU - Kusakabe, Haruka AU - Marino, Raffaella Anna AU - Maseda, Michael AU - Matthee, Jorryt J AU - Mitchell, Peter AU - Pezzulli, Gabriele AU - Richard, Johan AU - Schmidt, Kasper Borello AU - Wisotzki, Lutz ID - 11504 JF - Astronomy & Astrophysics KW - Space and Planetary Science KW - Astronomy and Astrophysics galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations SN - 0004-6361 TI - The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3 VL - 635 ER - TY - JOUR AB - We investigated the ultraviolet (UV) spectral properties of faint Lyman-α emitters (LAEs) in the redshift range 2.9 ≤ z ≤ 4.6, and we provide material to prepare future observations of the faint Universe. We used data from the MUSE Hubble Ultra Deep Survey to construct mean rest-frame spectra of continuum-faint (median MUV of −18 and down to MUV of −16), low stellar mass (median value of 108.4 M⊙ and down to 107 M⊙) LAEs at redshift z ≳ 3. We computed various averaged spectra of LAEs, subsampled on the basis of their observational (e.g., Lyα strength, UV magnitude and spectral slope) and physical (e.g., stellar mass and star-formation rate) properties. We searched for UV spectral features other than Lyα, such as higher ionization nebular emission lines and absorption features. We successfully observed the O III]λ1666 and [C III]λ1907+C III]λ1909 collisionally excited emission lines and the He IIλ1640 recombination feature, as well as the resonant C IVλλ1548,1551 doublet either in emission or P-Cygni. We compared the observed spectral properties of the different mean spectra and find the emission lines to vary with the observational and physical properties of the LAEs. In particular, the mean spectra of LAEs with larger Lyα equivalent widths, fainter UV magnitudes, bluer UV spectral slopes, and lower stellar masses show the strongest nebular emission. The line ratios of these lines are similar to those measured in the spectra of local metal-poor galaxies, while their equivalent widths are weaker compared to the handful of extreme values detected in individual spectra of z >  2 galaxies. This suggests that weak UV features are likely ubiquitous in high z, low-mass, and faint LAEs. We publicly released the stacked spectra, as they can serve as empirical templates for the design of future observations, such as those with the James Webb Space Telescope and the Extremely Large Telescope. AU - Feltre, Anna AU - Maseda, Michael V. AU - Bacon, Roland AU - Pradeep, Jayadev AU - Leclercq, Floriane AU - Kusakabe, Haruka AU - Wisotzki, Lutz AU - Hashimoto, Takuya AU - Schmidt, Kasper B. AU - Blaizot, Jeremy AU - Brinchmann, Jarle AU - Boogaard, Leindert AU - Cantalupo, Sebastiano AU - Carton, David AU - Inami, Hanae AU - Kollatschny, Wolfram AU - Marino, Raffaella A. AU - Matthee, Jorryt J AU - Nanayakkara, Themiya AU - Richard, Johan AU - Schaye, Joop AU - Tresse, Laurence AU - Urrutia, Tanya AU - Verhamme, Anne AU - Weilbacher, Peter M. ID - 11501 JF - Astronomy & Astrophysics KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: evolution / galaxies: high-redshift / ISM: lines and bands / ultraviolet: ISM / ultraviolet: galaxies SN - 0004-6361 TI - The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3 VL - 641 ER - TY - JOUR AB - We report the spectroscopic confirmation of a new protocluster in the COSMOS field at z ∼ 2.2, COSMOS Cluster 2.2 (CC2.2), originally identified as an overdensity of narrowband selected Hα emitting candidates. With only two masks of Keck/MOSFIRE near-IR spectroscopy in both H (∼1.47–1.81 μm) and K (∼1.92–2.40 μm) bands (∼1.5 hr each), we confirm 35 unique protocluster members with at least two emission lines detected with S/N > 3. Combined with 12 extra members from the zCOSMOS-deep spectroscopic survey (47 in total), we estimate a mean redshift and a line-of-sight velocity dispersion of zmean = 2.23224 ± 0.00101 and σlos = 645 ± 69 km s−1 for this protocluster, respectively. Assuming virialization and spherical symmetry for the system, we estimate a total mass of Mvir ∼ (1–2) ×1014M⊙ for the structure. We evaluate a number density enhancement of δg ∼ 7 for this system and we argue that the structure is likely not fully virialized at z ∼ 2.2. However, in a spherical collapse model, δg is expected to grow to a linear matter enhancement of ∼1.9 by z = 0, exceeding the collapse threshold of 1.69, and leading to a fully collapsed and virialized Coma-type structure with a total mass of Mdyn(z = 0) ∼ 9.2 × 1014M⊙ by now. This observationally efficient confirmation suggests that large narrowband emission-line galaxy surveys, when combined with ancillary photometric data, can be used to effectively trace the large-scale structure and protoclusters at a time when they are mostly dominated by star-forming galaxies. AU - Darvish, Behnam AU - Scoville, Nick Z. AU - Martin, Christopher AU - Sobral, David AU - Mobasher, Bahram AU - Rettura, Alessandro AU - Matthee, Jorryt J AU - Capak, Peter AU - Chartab, Nima AU - Hemmati, Shoubaneh AU - Masters, Daniel AU - Nayyeri, Hooshang AU - O’Sullivan, Donal AU - Paulino-Afonso, Ana AU - Sattari, Zahra AU - Shahidi, Abtin AU - Salvato, Mara AU - Lemaux, Brian C. AU - Fèvre, Olivier Le AU - Cucciati, Olga ID - 11513 IS - 1 JF - The Astrophysical Journal KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-637X TI - Spectroscopic confirmation of a coma cluster progenitor at z ∼ 2.2 VL - 892 ER - TY - JOUR AB - Ly α emission lines are typically found to be redshifted with respect to the systemic redshifts of galaxies, likely due to resonant scattering of Ly α photons. Here, we measure the average velocity offset for a sample of 96 z ≈ 3.3 Ly α emitters (LAEs) with a median Ly α flux (luminosity) of ≈10−17 erg cm−2 s−1 (⁠≈1042 erg s−1⁠) and a median star formation rate (SFR) of ≈1.3 M⊙ yr−1 (not corrected for possible dust extinction), detected by the Multi-Unit Spectroscopic Explorer as part of our MUSEQuBES circumgalactic medium (CGM) survey. By postulating that the stacked CGM absorption profiles of these LAEs, probed by eight background quasars, must be centred on the systemic redshift, we measure an average velocity offset, Voffset = 171\pm 8 km s−1, between the Ly α emission peak and the systemic redshift. The observed Voffset is lower by factors of ≈1.4 and ≈2.6 compared to the velocity offsets measured for narrow-band-selected LAEs and Lyman break galaxies, respectively, which probe galaxies with higher masses and SFRs. Consistent with earlier studies based on direct measurements for individual objects, we find that the Voffset is correlated with the full width at half-maximum of the red peak of the Ly α line, and anticorrelated with the rest-frame equivalent width. Moreover, we find that Voffset is correlated with SFR with a sub-linear scaling relation, Voffset∝SFR0.16±0.03⁠. Adopting the mass scaling for main-sequence galaxies, such a relation suggests that Voffset scales with the circular velocity of the dark matter haloes hosting the LAEs. AU - Muzahid, Sowgat AU - Schaye, Joop AU - Marino, Raffaella Anna AU - Cantalupo, Sebastiano AU - Brinchmann, Jarle AU - Contini, Thierry AU - Wendt, Martin AU - Wisotzki, Lutz AU - Zabl, Johannes AU - Bouché, Nicolas AU - Akhlaghi, Mohammad AU - Chen, Hsiao-Wen AU - Claeyssens, Adélaîde AU - Johnson, Sean AU - Leclercq, Floriane AU - Maseda, Michael AU - Matthee, Jorryt J AU - Richard, Johan AU - Urrutia, Tanya AU - Verhamme, Anne ID - 11528 IS - 2 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: haloes KW - galaxies: high-redshift KW - quasars: absorption lines SN - 0035-8711 TI - MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles VL - 496 ER - TY - JOUR AB - CR7 is among the most luminous Ly α emitters (LAEs) known at z = 6.6 and consists of at least three UV components that are surrounded by Ly α emission. Previous studies have suggested that it may host an extreme ionizing source. Here, we present deep integral field spectroscopy of CR7 with VLT/Multi Unit Spectroscopic Explorer (MUSE). We measure extended emission with a similar halo scale length as typical LAEs at z ≈ 5. CR7’s Ly α halo is clearly elongated along the direction connecting the multiple components, likely tracing the underlying gas distribution. The Ly α emission originates almost exclusively from the brightest UV component, but we also identify a faint kinematically distinct Ly α emitting region nearby a fainter component. Combined with new near-infrared data, the MUSE data show that the rest-frame Ly α equivalent width (EW) is ≈100 Å. This is a factor 4 higher than the EW measured in low-redshift analogues with carefully matched Ly α profiles (and thus arguably H I column density), but this EW can plausibly be explained by star formation. Alternative scenarios requiring active galactic nucleus (AGN) powering are also disfavoured by the narrower and steeper Ly α spectrum and much smaller IR to UV ratio compared to obscured AGN in other Ly α blobs. CR7’s Ly α emission, while extremely luminous, resembles the emission in more common LAEs at lower redshifts very well and is likely powered by a young metal-poor starburst. AU - Matthee, Jorryt J AU - Pezzulli, Gabriele AU - Mackenzie, Ruari AU - Cantalupo, Sebastiano AU - Kusakabe, Haruka AU - Leclercq, Floriane AU - Sobral, David AU - Richard, Johan AU - Wisotzki, Lutz AU - Lilly, Simon AU - Boogaard, Leindert AU - Marino, Raffaella AU - Maseda, Michael AU - Nanayakkara, Themiya ID - 11529 IS - 2 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: evolution KW - galaxies: high-redshift KW - dark ages KW - reionization KW - first stars KW - cosmology: observations SN - 0035-8711 TI - The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6 VL - 498 ER - TY - JOUR AB - We explore deep rest-frame UV to FIR data in the COSMOS field to measure the individual spectral energy distributions (SED) of the ∼4000 SC4K (Sobral et al.) Lyman α (Ly α) emitters (LAEs) at z ∼ 2–6. We find typical stellar masses of 109.3 ± 0.6 M⊙ and star formation rates (SFR) of SFRSED=4.4+10.5−2.4 M⊙ yr−1 and SFRLyα=5.9+6.3−2.6 M⊙ yr−1, combined with very blue UV slopes of β=−2.1+0.5−0.4⁠, but with significant variations within the population. MUV and β are correlated in a similar way to UV-selected sources, but LAEs are consistently bluer. This suggests that LAEs are the youngest and/or most dust-poor subset of the UV-selected population. We also study the Ly α rest-frame equivalent width (EW0) and find 45 ‘extreme’ LAEs with EW0 > 240 Å (3σ), implying a low number density of (7 ± 1) × 10−7 Mpc−3. Overall, we measure little to no evolution of the Ly α EW0 and scale length parameter (w0), which are consistently high (EW0=140+280−70 Å, w0=129+11−11 Å) from z ∼ 6 to z ∼ 2 and below. However, w0 is anticorrelated with MUV and stellar mass. Our results imply that sources selected as LAEs have a high Ly α escape fraction (fesc,Ly α) irrespective of cosmic time, but fesc,Ly α is still higher for UV-fainter and lower mass LAEs. The least massive LAEs (<109.5 M⊙) are typically located above the star formation ‘main sequence’ (MS), but the offset from the MS decreases towards z ∼ 6 and towards 1010 M⊙. Our results imply a lack of evolution in the properties of LAEs across time and reveals the increasing overlap in properties of LAEs and UV-continuum selected galaxies as typical star-forming galaxies at high redshift effectively become LAEs. AU - Santos, S AU - Sobral, D AU - Matthee, Jorryt J AU - Calhau, J AU - da Cunha, E AU - Ribeiro, B AU - Paulino-Afonso, A AU - Arrabal Haro, P AU - Butterworth, J ID - 11533 IS - 1 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: evolution KW - galaxies: formation KW - galaxies: high-redshift KW - galaxies: star formation SN - 0035-8711 TI - The evolution of rest-frame UV properties, Ly α EWs, and the SFR–stellar mass relation at z ∼ 2–6 for SC4K LAEs VL - 493 ER - TY - JOUR AB - The observed properties of the Lyman-α (Ly α) emission line are a powerful probe of neutral gas in and around galaxies. We present spatially resolved Ly α spectroscopy with VLT/MUSE targeting VR7, a UV-luminous galaxy at z = 6.532 with moderate Ly α equivalent width (EW0 ≈ 38 Å). These data are combined with deep resolved [CII]158μm spectroscopy obtained with ALMA and UV imaging from HST and we also detect UV continuum with MUSE. Ly α emission is clearly detected with S/N ≈ 40 and FWHM of 374 km s−1. Ly α and [C II] are similarly extended beyond the UV, with effective radius reff = 2.1 ± 0.2 kpc for a single exponential model or reff,Lyα,halo=3.45+1.08−0.87 kpc when measured jointly with the UV continuum. The Ly α profile is broader and redshifted with respect to the [C II] line (by 213 km s−1), but there are spatial variations that are qualitatively similar in both lines and coincide with resolved UV components. This suggests that the emission originates from two components with plausibly different H I column densities. We place VR7 in the context of other galaxies at similar and lower redshift. The Ly α halo scale length is similar at different redshifts and velocity shifts with respect to the systemic are typically smaller. Overall, we find little indications of a more neutral vicinity at higher redshift. This means that the local (∼10 kpc) neutral gas conditions that determine the observed Ly α properties in VR7 resemble the conditions in post-reionization galaxies. AU - Matthee, Jorryt J AU - Sobral, David AU - Gronke, Max AU - Pezzulli, Gabriele AU - Cantalupo, Sebastiano AU - Röttgering, Huub AU - Darvish, Behnam AU - Santos, Sérgio ID - 11534 IS - 2 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: evolution KW - galaxies: high-redshift KW - dark ages KW - reionization KW - first stars KW - cosmology: observations SN - 0035-8711 TI - Resolved Lyman-α properties of a luminous Lyman-break galaxy in a large ionized bubble at z = 6.53 VL - 492 ER - TY - JOUR AB - While low-luminosity galaxies dominate number counts at all redshifts, their contribution to cosmic reionization is poorly understood due to a lack of knowledge of their physical properties. We isolate a sample of 35 z ≈ 4–5 continuum-faint Lyman-α emitters from deep VLT/MUSE spectroscopy and directly measure their H α emission using stacked Spitzer/IRAC Ch. 1 photometry. Based on Hubble Space Telescope imaging, we determine that the average UV continuum magnitude is fainter than −16 (≈ 0.01 L⋆), implying a median Lyman-α equivalent width of 259 Å. By combining the H α measurement with the UV magnitude, we determine the ionizing photon production efficiency, ξion, a first for such faint galaxies. The measurement of log10 (ξion [Hz erg−1]) = 26.28 (⁠+0.28−0.40⁠) is in excess of literature measurements of both continuum- and emission line-selected samples, implying a more efficient production of ionizing photons in these lower luminosity, Lyman-α-selected systems. We conclude that this elevated efficiency can be explained by stellar populations with metallicities between 4 × 10−4 and 0.008, with light-weighted ages less than 3 Myr. AU - Maseda, Michael V AU - Bacon, Roland AU - Lam, Daniel AU - Matthee, Jorryt J AU - Brinchmann, Jarle AU - Schaye, Joop AU - Labbe, Ivo AU - Schmidt, Kasper B AU - Boogaard, Leindert AU - Bouwens, Rychard AU - Cantalupo, Sebastiano AU - Franx, Marijn AU - Hashimoto, Takuya AU - Inami, Hanae AU - Kusakabe, Haruka AU - Mahler, Guillaume AU - Nanayakkara, Themiya AU - Richard, Johan AU - Wisotzki, Lutz ID - 11531 IS - 4 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - Galaxies: evolution KW - Galaxies: high-redshift KW - Galaxies: ISM SN - 0035-8711 TI - Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters VL - 493 ER - TY - JOUR AB - A prediction of the classic active galactic nucleus (AGN) unification model is the presence of ionization cones with different orientations depending on the AGN type. Confirmations of this model exist for present times, but it is less clear in the early Universe. Here, we use the morphology of giant Ly α nebulae around AGNs at redshift z ∼ 3 to probe AGN emission and therefore the validity of the AGN unification model at this redshift. We compare the spatial morphology of 19 nebulae previously found around type I AGNs with a new sample of four Ly α nebulae detected around type II AGNs. Using two independent techniques, we find that nebulae around type II AGNs are more asymmetric than around type I, at least at radial distances r > 30 physical kpc (pkpc) from the ionizing source. We conclude that the type I and type II AGNs in our sample show evidence of different surrounding ionizing geometries. This suggests that the classical AGN unification model is also valid for high-redshift sources. Finally, we discuss how the lack of asymmetry in the inner parts (r ≲ 30 pkpc) and the associated high values of the He II to Ly α ratios in these regions could indicate additional sources of (hard) ionizing radiation originating within or in proximity of the AGN host galaxies. This work demonstrates that the morphologies of giant Ly α nebulae can be used to understand and study the geometry of high-redshift AGNs on circumnuclear scales and it lays the foundation for future studies using much larger statistical samples. AU - den Brok, J S AU - Cantalupo, S AU - Mackenzie, R AU - Marino, R A AU - Pezzulli, G AU - Matthee, Jorryt J AU - Johnson, S D AU - Krumpe, M AU - Urrutia, T AU - Kollatschny, W ID - 11530 IS - 2 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: active KW - galaxies: high-redshift KW - intergalactic medium KW - quasars: emission lines KW - quasars: general SN - 0035-8711 TI - Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae VL - 495 ER - TY - JOUR AB - Despite recent progress in understanding Ly α emitters (LAEs), relatively little is known regarding their typical black hole activity across cosmic time. Here, we study the X-ray and radio properties of ∼4000 LAEs at 2.2 < z < 6 from the SC4K survey in the COSMOS field. We detect 254 (⁠6.8per cent±0.4per cent⁠) LAEs individually in the X-rays (S/N > 3) with an average luminosity of 1044.31±0.01ergs−1 and average black hole accretion rate (BHAR) of 0.72±0.01 M⊙ yr−1, consistent with moderate to high accreting active galactic neuclei (AGNs). We detect 120 sources in deep radio data (radio AGN fraction of 3.2per cent±0.3per cent⁠). The global AGN fraction (⁠8.6per cent±0.4per cent⁠) rises with Ly α luminosity and declines with increasing redshift. For X-ray-detected LAEs, Ly α luminosities correlate with the BHARs, suggesting that Ly α luminosity becomes a BHAR indicator. Most LAEs (⁠93.1per cent±0.6per cent⁠) at 2 < z < 6 have no detectable X-ray emission (BHARs < 0.017 M⊙ yr−1). The median star formation rate (SFR) of star-forming LAEs from Ly α and radio luminosities is 7.6+6.6−2.8 M⊙ yr−1. The black hole to galaxy growth ratio (BHAR/SFR) for LAEs is <0.0022, consistent with typical star-forming galaxies and the local BHAR/SFR relation. We conclude that LAEs at 2 < z < 6 include two different populations: an AGN population, where Ly α luminosity traces BHAR, and another with low SFRs which remain undetected in even the deepest X-ray stacks but is detected in the radio stacks. AU - Calhau, João AU - Sobral, David AU - Santos, Sérgio AU - Matthee, Jorryt J AU - Paulino-Afonso, Ana AU - Stroe, Andra AU - Simmons, Brooke AU - Barlow-Hall, Cassandra AU - Adams, Benjamin ID - 11539 IS - 3 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics KW - galaxies: active KW - galaxies: evolution KW - galaxies: high-redshift KW - quasars: supermassive black holes KW - galaxies: star formation KW - cosmology: observations KW - X-rays: galaxies SN - 0035-8711 TI - The X-ray and radio activity of typical and luminous Ly α emitters from z ∼ 2 to z ∼ 6: Evidence for a diverse, evolving population VL - 493 ER - TY - CONF AB - Distant luminous Lyman-α emitters are excellent targets for detailed observations of galaxies in the epoch of reionisation. Spatially resolved observations of these galaxies allow us to simultaneously probe the emission from young stars, partially ionised gas in the interstellar medium and to constrain the properties of the surrounding hydrogen in the circumgalactic medium. We review recent results from (spectroscopic) follow-up studies of the rest-frame UV, Lyman-α and [CII] emission in luminous galaxies observed ∼500 Myr after the Big Bang with ALMA, HST/WFC3 and VLT/X-SHOOTER. These galaxies likely reside in early ionised bubbles and are complex systems, consisting of multiple well separated and resolved components where traces of metals are already present. AU - Matthee, Jorryt J AU - Sobral, David ID - 11586 IS - S352 KW - Astronomy and Astrophysics KW - Space and Planetary Science KW - galaxies: formation KW - galaxies: evolution KW - galaxies: high-redshift SN - 1743-9213 T2 - Proceedings of the International Astronomical Union TI - Unveiling the most luminous Lyman-α emitters in the epoch of reionisation VL - 15 ER - TY - JOUR AB - Studies of Galactic structure and evolution have benefited enormously from Gaia kinematic information, though additional, intrinsic stellar parameters like age are required to best constrain Galactic models. Asteroseismology is the most precise method of providing such information for field star populations en masse, but existing samples for the most part have been limited to a few narrow fields of view by the CoRoT and Kepler missions. In an effort to provide well-characterized stellar parameters across a wide range in Galactic position, we present the second data release of red giant asteroseismic parameters for the K2 Galactic Archaeology Program (GAP). We provide ${\nu }_{\max }$ and ${\rm{\Delta }}\nu $ based on six independent pipeline analyses; first-ascent red giant branch (RGB) and red clump (RC) evolutionary state classifications from machine learning; and ready-to-use radius and mass coefficients, κR and κM, which, when appropriately multiplied by a solar-scaled effective temperature factor, yield physical stellar radii and masses. In total, we report 4395 radius and mass coefficients, with typical uncertainties of 3.3% (stat.) ± 1% (syst.) for κR and 7.7% (stat.) ± 2% (syst.) for κM among RGB stars, and 5.0% (stat.) ± 1% (syst.) for κR and 10.5% (stat.) ± 2% (syst.) for κM among RC stars. We verify that the sample is nearly complete—except for a dearth of stars with ${\nu }_{\max }\lesssim 10\mbox{--}20\,\mu \mathrm{Hz}$—by comparing to Galactic models and visual inspection. Our asteroseismic radii agree with radii derived from Gaia Data Release 2 parallaxes to within 2.2% ± 0.3% for RGB stars and 2.0% ± 0.6% for RC stars. AU - Zinn, Joel C. AU - Stello, Dennis AU - Elsworth, Yvonne AU - García, Rafael A. AU - Kallinger, Thomas AU - Mathur, Savita AU - Mosser, Benoît AU - Bugnet, Lisa Annabelle AU - Jones, Caitlin AU - Hon, Marc AU - Sharma, Sanjib AU - Schönrich, Ralph AU - Warfield, Jack T. AU - Luger, Rodrigo AU - Pinsonneault, Marc H. AU - Johnson, Jennifer A. AU - Huber, Daniel AU - Aguirre, Victor Silva AU - Chaplin, William J. AU - Davies, Guy R. AU - Miglio, Andrea ID - 11610 IS - 2 JF - The Astrophysical Journal Supplement Series KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0067-0049 TI - The K2 galactic archaeology program data release 2: Asteroseismic results from campaigns 4, 6, and 7 VL - 251 ER - TY - JOUR AB - Over the course of its history, the Milky Way has ingested multiple smaller satellite galaxies1. Although these accreted stellar populations can be forensically identified as kinematically distinct structures within the Galaxy, it is difficult in general to date precisely the age at which any one merger occurred. Recent results have revealed a population of stars that were accreted via the collision of a dwarf galaxy, called Gaia–Enceladus1, leading to substantial pollution of the chemical and dynamical properties of the Milky Way. Here we identify the very bright, naked-eye star ν Indi as an indicator of the age of the early in situ population of the Galaxy. We combine asteroseismic, spectroscopic, astrometric and kinematic observations to show that this metal-poor, alpha-element-rich star was an indigenous member of the halo, and we measure its age to be 11.0±0.7 (stat) ±0.8 (sys) billion years. The star bears hallmarks consistent with having been kinematically heated by the Gaia–Enceladus collision. Its age implies that the earliest the merger could have begun was 11.6 and 13.2 billion years ago, at 68% and 95% confidence, respectively. Computations based on hierarchical cosmological models slightly reduce the above limits. AU - Chaplin, William J. AU - Serenelli, Aldo M. AU - Miglio, Andrea AU - Morel, Thierry AU - Mackereth, J. Ted AU - Vincenzo, Fiorenzo AU - Kjeldsen, Hans AU - Basu, Sarbani AU - Ball, Warrick H. AU - Stokholm, Amalie AU - Verma, Kuldeep AU - Mosumgaard, Jakob Rørsted AU - Silva Aguirre, Victor AU - Mazumdar, Anwesh AU - Ranadive, Pritesh AU - Antia, H. M. AU - Lebreton, Yveline AU - Ong, Joel AU - Appourchaux, Thierry AU - Bedding, Timothy R. AU - Christensen-Dalsgaard, Jørgen AU - Creevey, Orlagh AU - García, Rafael A. AU - Handberg, Rasmus AU - Huber, Daniel AU - Kawaler, Steven D. AU - Lund, Mikkel N. AU - Metcalfe, Travis S. AU - Stassun, Keivan G. AU - Bazot, Michäel AU - Beck, Paul G. AU - Bell, Keaton J. AU - Bergemann, Maria AU - Buzasi, Derek L. AU - Benomar, Othman AU - Bossini, Diego AU - Bugnet, Lisa Annabelle AU - Campante, Tiago L. AU - Orhan, Zeynep Çelik AU - Corsaro, Enrico AU - González-Cuesta, Lucía AU - Davies, Guy R. AU - Di Mauro, Maria Pia AU - Egeland, Ricky AU - Elsworth, Yvonne P. AU - Gaulme, Patrick AU - Ghasemi, Hamed AU - Guo, Zhao AU - Hall, Oliver J. AU - Hasanzadeh, Amir AU - Hekker, Saskia AU - Howe, Rachel AU - Jenkins, Jon M. AU - Jiménez, Antonio AU - Kiefer, René AU - Kuszlewicz, James S. AU - Kallinger, Thomas AU - Latham, David W. AU - Lundkvist, Mia S. AU - Mathur, Savita AU - Montalbán, Josefina AU - Mosser, Benoit AU - Bedón, Andres Moya AU - Nielsen, Martin Bo AU - Örtel, Sibel AU - Rendle, Ben M. AU - Ricker, George R. AU - Rodrigues, Thaíse S. AU - Roxburgh, Ian W. AU - Safari, Hossein AU - Schofield, Mathew AU - Seager, Sara AU - Smalley, Barry AU - Stello, Dennis AU - Szabó, Róbert AU - Tayar, Jamie AU - Themeßl, Nathalie AU - Thomas, Alexandra E. L. AU - Vanderspek, Roland K. AU - van Rossem, Walter E. AU - Vrard, Mathieu AU - Weiss, Achim AU - White, Timothy R. AU - Winn, Joshua N. AU - Yıldız, Mutlu ID - 11611 IS - 4 JF - Nature Astronomy KW - Astronomy and Astrophysics TI - Age dating of an early Milky Way merger via asteroseismology of the naked-eye star ν Indi VL - 4 ER - TY - JOUR AB - Since the onset of the "space revolution" of high-precision high-cadence photometry, asteroseismology has been demonstrated as a powerful tool for informing Galactic archeology investigations. The launch of the NASA Transiting Exoplanet Survey Satellite (TESS) mission has enabled seismic-based inferences to go full sky—providing a clear advantage for large ensemble studies of the different Milky Way components. Here we demonstrate its potential for investigating the Galaxy by carrying out the first asteroseismic ensemble study of red giant stars observed by TESS. We use a sample of 25 stars for which we measure their global asteroseimic observables and estimate their fundamental stellar properties, such as radius, mass, and age. Significant improvements are seen in the uncertainties of our estimates when combining seismic observables from TESS with astrometric measurements from the Gaia mission compared to when the seismology and astrometry are applied separately. Specifically, when combined we show that stellar radii can be determined to a precision of a few percent, masses to 5%–10%, and ages to the 20% level. This is comparable to the precision typically obtained using end-of-mission Kepler data. AU - Aguirre, Víctor Silva AU - Stello, Dennis AU - Stokholm, Amalie AU - Mosumgaard, Jakob R. AU - Ball, Warrick H. AU - Basu, Sarbani AU - Bossini, Diego AU - Bugnet, Lisa Annabelle AU - Buzasi, Derek AU - Campante, Tiago L. AU - Carboneau, Lindsey AU - Chaplin, William J. AU - Corsaro, Enrico AU - Davies, Guy R. AU - Elsworth, Yvonne AU - García, Rafael A. AU - Gaulme, Patrick AU - Hall, Oliver J. AU - Handberg, Rasmus AU - Hon, Marc AU - Kallinger, Thomas AU - Kang, Liu AU - Lund, Mikkel N. AU - Mathur, Savita AU - Mints, Alexey AU - Mosser, Benoit AU - Çelik Orhan, Zeynep AU - Rodrigues, Thaíse S. AU - Vrard, Mathieu AU - Yıldız, Mutlu AU - Zinn, Joel C. AU - Örtel, Sibel AU - Beck, Paul G. AU - Bell, Keaton J. AU - Guo, Zhao AU - Jiang, Chen AU - Kuszlewicz, James S. AU - Kuehn, Charles A. AU - Li, Tanda AU - Lundkvist, Mia S. AU - Pinsonneault, Marc AU - Tayar, Jamie AU - Cunha, Margarida S. AU - Hekker, Saskia AU - Huber, Daniel AU - Miglio, Andrea AU - F. G. Monteiro, Mario J. P. AU - Slumstrup, Ditte AU - Winther, Mark L. AU - Angelou, George AU - Benomar, Othman AU - Bódi, Attila AU - De Moura, Bruno L. AU - Deheuvels, Sébastien AU - Derekas, Aliz AU - Di Mauro, Maria Pia AU - Dupret, Marc-Antoine AU - Jiménez, Antonio AU - Lebreton, Yveline AU - Matthews, Jaymie AU - Nardetto, Nicolas AU - do Nascimento, Jose D. AU - Pereira, Filipe AU - Rodríguez Díaz, Luisa F. AU - Serenelli, Aldo M. AU - Spitoni, Emanuele AU - Stonkutė, Edita AU - Suárez, Juan Carlos AU - Szabó, Robert AU - Van Eylen, Vincent AU - Ventura, Rita AU - Verma, Kuldeep AU - Weiss, Achim AU - Wu, Tao AU - Barclay, Thomas AU - Christensen-Dalsgaard, Jørgen AU - Jenkins, Jon M. AU - Kjeldsen, Hans AU - Ricker, George R. AU - Seager, Sara AU - Vanderspek, Roland ID - 11612 IS - 2 JF - The Astrophysical Journal Letters KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-637X TI - Detection and characterization of oscillating red giants: First results from the TESS satellite VL - 889 ER - TY - CHAP AB - The recent discovery of low-amplitude dipolar oscillation mixed modes in massive red giants indicates the presence of a missing physical process inside their cores. Stars more massive than ∼ 1.3 M⊙ are known to develop a convective core during the main-sequence: the dynamo process triggered by this convection could be the origin of a strong magnetic field inside the core of the star, trapped when it becomes stably stratified and for the rest of its evolution. The presence of highly magnetized white dwarfs strengthens the hypothesis of buried fossil magnetic fields inside the core of evolved low-mass stars. If such a fossil field exists, it should affect the mixed modes of red giants as they are sensitive to processes affecting the deepest layers of these stars. The impact of a magnetic field on dipolar oscillations modes was one of Pr. Michael J. Thompson’s research topics during the 90s when preparing the helioseismic SoHO space mission. As the detection of gravity modes in the Sun is still controversial, the investigation of the solar oscillation modes did not provide any hint of the existence of a magnetic field in the solar radiative core. Today we have access to the core of evolved stars thanks to the asteroseismic observation of mixed modes from CoRoT, Kepler, K2 and TESS missions. The idea of applying and generalizing the work done for the Sun came from discussions with Pr. Michael Thompson in early 2018 before we lost him. Following the path we drew together, we theoretically investigate the effect of a stable axisymmetric mixed poloidal and toroidal magnetic field, aligned with the rotation axis of the star, on the mixed modes frequencies of a typical evolved low-mass star. This enables us to estimate the magnetic perturbations to the eigenfrequencies of mixed dipolar modes, depending on the magnetic field strength and the evolutionary state of the star. We conclude that strong magnetic fields of ∼ 1MG should perturb the mixed-mode frequency pattern enough for its effects to be detectable inside current asteroseismic data. AU - Bugnet, Lisa Annabelle AU - Prat, V. AU - Mathis, S. AU - García, R. A. AU - Mathur, S. AU - Augustson, K. AU - Neiner, C. AU - Thompson, M. J. ED - Monteiro, Mario ED - Garcia, Rafael A ED - Christensen-Dalsgaard, Jorgen ED - McIntosh, Scott W ID - 11622 SN - 1570-6591 T2 - Dynamics of the Sun and Stars TI - The impact of a fossil magnetic field on dipolar mixed-mode frequencies in sub- and red-giant stars VL - 57 ER - TY - JOUR AB - We consider the problems of maintaining an approximate maximum matching and an approximate minimum vertex cover in a dynamic graph undergoing a sequence of edge insertions/deletions. Starting with the seminal work of Onak and Rubinfeld (in: Proceedings of the ACM symposium on theory of computing (STOC), 2010), this problem has received significant attention in recent years. Very recently, extending the framework of Baswana et al. (in: Proceedings of the IEEE symposium on foundations of computer science (FOCS), 2011) , Solomon (in: Proceedings of the IEEE symposium on foundations of computer science (FOCS), 2016) gave a randomized dynamic algorithm for this problem that has an approximation ratio of 2 and an amortized update time of O(1) with high probability. This algorithm requires the assumption of an oblivious adversary, meaning that the future sequence of edge insertions/deletions in the graph cannot depend in any way on the algorithm’s past output. A natural way to remove the assumption on oblivious adversary is to give a deterministic dynamic algorithm for the same problem in O(1) update time. In this paper, we resolve this question. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya et al. (in: Proceedings of the ACM-SIAM symposium on discrete algorithms (SODA), 2015); it had an approximation ratio of (2+ε) and an amortized update time of O(logn/ε2). Our result can be generalized to give a fully dynamic O(f3)-approximate algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional hypergraph matching problem, where every hyperedge has at most f vertices. AU - Bhattacharya, Sayan AU - Chakrabarty, Deeparnab AU - Henzinger, Monika H ID - 11675 IS - 4 JF - Algorithmica KW - Dynamic algorithms KW - Data structures KW - Graph algorithms KW - Matching KW - Vertex cover SN - 0178-4617 TI - Deterministic dynamic matching in O(1) update time VL - 82 ER - TY - JOUR AB - In this paper, we study the problem of opening centers to cluster a set of clients in a metric space so as to minimize the sum of the costs of the centers and of the cluster radii, in a dynamic environment where clients arrive and depart, and the solution must be updated efficiently while remaining competitive with respect to the current optimal solution. We call this dynamic sum-of-radii clustering problem. We present a data structure that maintains a solution whose cost is within a constant factor of the cost of an optimal solution in metric spaces with bounded doubling dimension and whose worst-case update time is logarithmic in the parameters of the problem. AU - Henzinger, Monika H AU - Leniowski, Dariusz AU - Mathieu, Claire ID - 11674 IS - 11 JF - Algorithmica SN - 0178-4617 TI - Dynamic clustering to minimize the sum of radii VL - 82 ER - TY - CONF AB - With input sizes becoming massive, coresets - small yet representative summary of the input - are relevant more than ever. A weighted set C_w that is a subset of the input is an ε-coreset if the cost of any feasible solution S with respect to C_w is within [1±ε] of the cost of S with respect to the original input. We give a very general technique to compute coresets in the fully-dynamic setting where input points can be added or deleted. Given a static (i.e., not dynamic) ε-coreset-construction algorithm that runs in time t(n, ε, λ) and computes a coreset of size s(n, ε, λ), where n is the number of input points and 1-λ is the success probability, we give a fully-dynamic algorithm that computes an ε-coreset with worst-case update time O((log n) ⋅ t(s(n, ε/log n, λ/n), ε/log n, λ/n)) (this bound is stated informally), where the success probability is 1-λ. Our technique is a fully-dynamic analog of the merge-and-reduce technique, which is due to Har-Peled and Mazumdar [Har-Peled and Mazumdar, 2004] and is based on a technique of Bentley and Saxe [Jon Louis Bentley and James B. Saxe, 1980], that applies to the insertion-only setting where points can only be added. Although, our space usage is O(n), our technique works in the presence of an adaptive adversary, and we show that Ω(n) space is required when adversary is adaptive. As a concrete implication of our technique, using the result of Braverman et al. [{Braverman} et al., 2016], we get fully-dynamic ε-coreset-construction algorithms for k-median and k-means with worst-case update time O(ε^{-2} k² log⁵ n log³ k) and coreset size O(ε^{-2} k log n log² k) ignoring log log n and log(1/ε) factors and assuming that ε = Ω(1/poly(n)) and λ = Ω(1/poly(n)) (which are very weak assumptions made only to make these bounds easy to parse). This results in the first fully-dynamic constant-approximation algorithms for k-median and k-means with update times O(poly(k, log n, ε^{-1})). Specifically, the dependence on k is only quadratic, and the bounds are worst-case. The best previous bound for both problems was amortized O(nlog n) by Cohen-Addad et al. [Cohen-Addad et al., 2019] via randomized O(1)-coresets in O(n) space. We also show that under the OMv conjecture [Monika Henzinger et al., 2015], a fully-dynamic (4 - δ)-approximation algorithm for k-means must either have an amortized update time of Ω(k^{1-γ}) or amortized query time of Ω(k^{2 - γ}), where γ > 0 is a constant. AU - Henzinger, Monika H AU - Kale, Sagar ID - 11818 SN - 1868-8969 T2 - 28th Annual European Symposium on Algorithms TI - Fully-dynamic coresets VL - 173 ER - TY - CONF AB - In recent years, significant advances have been made in the design and analysis of fully dynamic maximal matching algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. In this paper, we attempt to bridge the gap between theory and practice that is currently observed for the fully dynamic maximal matching problem. We engineer several algorithms and empirically study those algorithms on an extensive set of dynamic instances. AU - Henzinger, Monika H AU - Shahbaz, Khan AU - Paul, Richard AU - Schulz, Christian ID - 11816 SN - 1868-8969 T2 - 8th Annual European Symposium on Algorithms TI - Dynamic matching algorithms in practice VL - 173 ER - TY - CONF AB - Independent set is a fundamental problem in combinatorial optimization. While in general graphs the problem is essentially inapproximable, for many important graph classes there are approximation algorithms known in the offline setting. These graph classes include interval graphs and geometric intersection graphs, where vertices correspond to intervals/geometric objects and an edge indicates that the two corresponding objects intersect. We present dynamic approximation algorithms for independent set of intervals, hypercubes and hyperrectangles in d dimensions. They work in the fully dynamic model where each update inserts or deletes a geometric object. All our algorithms are deterministic and have worst-case update times that are polylogarithmic for constant d and ε>0, assuming that the coordinates of all input objects are in [0, N]^d and each of their edges has length at least 1. We obtain the following results: - For weighted intervals, we maintain a (1+ε)-approximate solution. - For d-dimensional hypercubes we maintain a (1+ε)2^d-approximate solution in the unweighted case and a O(2^d)-approximate solution in the weighted case. Also, we show that for maintaining an unweighted (1+ε)-approximate solution one needs polynomial update time for d ≥ 2 if the ETH holds. - For weighted d-dimensional hyperrectangles we present a dynamic algorithm with approximation ratio (1+ε)log^{d-1}N. AU - Henzinger, Monika H AU - Neumann, Stefan AU - Wiese, Andreas ID - 11824 SN - 1868-8969 T2 - 36th International Symposium on Computational Geometry TI - Dynamic approximate maximum independent set of intervals, hypercubes and hyperrectangles VL - 164 ER - TY - CONF AB - The fully dynamic transitive closure problem asks to maintain reachability information in a directed graph between arbitrary pairs of vertices, while the graph undergoes a sequence of edge insertions and deletions. The problem has been thoroughly investigated in theory and many specialized algorithms for solving it have been proposed in the last decades. In two large studies [Frigioni ea, 2001; Krommidas and Zaroliagis, 2008], a number of these algorithms have been evaluated experimentally against simple, static algorithms for graph traversal, showing the competitiveness and even superiority of the simple algorithms in practice, except for very dense random graphs or very high ratios of queries. A major drawback of those studies is that only small and mostly randomly generated graphs are considered. In this paper, we engineer new algorithms to maintain all-pairs reachability information which are simple and space-efficient. Moreover, we perform an extensive experimental evaluation on both generated and real-world instances that are several orders of magnitude larger than those in the previous studies. Our results indicate that our new algorithms outperform all state-of-the-art algorithms on all types of input considerably in practice. AU - Hanauer, Kathrin AU - Henzinger, Monika H AU - Schulz, Christian ID - 11822 SN - 1868-8969 T2 - 18th International Symposium on Experimental Algorithms TI - Faster fully dynamic transitive closure in practice VL - 160 ER - TY - CONF AB - We give a fully dynamic (Las-Vegas style) algorithm with constant expected amortized time per update that maintains a proper (Δ+1)-vertex coloring of a graph with maximum degree at most Δ. This improves upon the previous O(log Δ)-time algorithm by Bhattacharya et al. (SODA 2018). Our algorithm uses an approach based on assigning random ranks to vertices and does not need to maintain a hierarchical graph decomposition. We show that our result does not only have optimal running time, but is also optimal in the sense that already deciding whether a Δ-coloring exists in a dynamically changing graph with maximum degree at most Δ takes Ω(log n) time per operation. AU - Henzinger, Monika H AU - Peng, Pan ID - 11825 SN - 1868-8969 T2 - 37th International Symposium on Theoretical Aspects of Computer Science TI - Constant-time dynamic (Δ+1)-coloring VL - 154 ER - TY - CONF AB - We present a practically efficient algorithm that finds all global minimum cuts in huge undirected graphs. Our algorithm uses a multitude of kernelization rules to reduce the graph to a small equivalent instance and then finds all minimum cuts using an optimized version of the algorithm of Nagamochi, Nakao and Ibaraki. In shared memory we are able to find all minimum cuts of graphs with up to billions of edges and millions of minimum cuts in a few minutes. We also give a new linear time algorithm to find the most balanced minimum cuts given as input the representation of all minimum cuts. AU - Henzinger, Monika H AU - Noe, Alexander AU - Schulz, Christian AU - Strash, Darren ID - 11819 SN - 1868-8969 T2 - 28th Annual European Symposium on Algorithms TI - Finding all global minimum cuts in practice VL - 173 ER - TY - CONF AB - We present a general framework of designing efficient dynamic approximate algorithms for optimization problems on undirected graphs. In particular, we develop a technique that, given any problem that admits a certain notion of vertex sparsifiers, gives data structures that maintain approximate solutions in sub-linear update and query time. We illustrate the applicability of our paradigm to the following problems. (1)A fully-dynamic algorithm that approximates all-pair maximum-flows/minimum-cuts up to a nearly logarithmic factor in O~(n2/3) 11The O~(⋅) notation is used in this paper to hide poly-logarithmic factors. amortized time against an oblivious adversary, and O~(m3/4) time against an adaptive adversary. (2)An incremental data structure that maintains O(1) - approximate shortest path in no(1) time per operation, as well as fully dynamic approximate all-pair shortest path and transshipment in O~(n2/3+o(1)) amortized time per operation. (3)A fully-dynamic algorithm that approximates all-pair effective resistance up to an (1+ϵ) factor in O~(n2/3+o(1)ϵ−O(1)) amortized update time per operation. The key tool behind result (1) is the dynamic maintenance of an algorithmic construction due to Madry [FOCS' 10], which partitions a graph into a collection of simpler graph structures (known as j-trees) and approximately captures the cut-flow and metric structure of the graph. The O(1)-approximation guarantee of (2) is by adapting the distance oracles by [Thorup-Zwick JACM '05]. Result (3) is obtained by invoking the random-walk based spectral vertex sparsifier by [Durfee et al. STOC '19] in a hierarchical manner, while carefully keeping track of the recourse among levels in the hierarchy. See https://arxiv.org/pdf/2005.02368.pdf for the full version of this paper. AU - Chen, Li AU - Goranci, Gramoz AU - Henzinger, Monika H AU - Peng, Richard AU - Saranurak, Thatchaphol ID - 11852 SN - 978-1-7281-9622-0 T2 - 61st Annual Symposium on Foundations of Computer Science TI - Fast dynamic cuts, distances and effective resistances via vertex sparsifiers ER - TY - CONF AB - Given a directed graph and a source vertex, the fully dynamic single-source reachability problem is to maintain the set of vertices that are reachable from the given vertex, subject to edge deletions and insertions. It is one of the most fundamental problems on graphs and appears directly or indirectly in many and varied applications. While there has been theoretical work on this problem, showing both linear conditional lower bounds for the fully dynamic problem and insertions-only and deletions-only upper bounds beating these conditional lower bounds, there has been no experimental study that compares the performance of fully dynamic reachability algorithms in practice. Previous experimental studies in this area concentrated only on the more general all-pairs reachability or transitive closure problem and did not use real-world dynamic graphs. In this paper, we bridge this gap by empirically studying an extensive set of algorithms for the single-source reachability problem in the fully dynamic setting. In particular, we design several fully dynamic variants of well-known approaches to obtain and maintain reachability information with respect to a distinguished source. Moreover, we extend the existing insertions-only or deletions-only upper bounds into fully dynamic algorithms. Even though the worst-case time per operation of all the fully dynamic algorithms we evaluate is at least linear in the number of edges in the graph (as is to be expected given the conditional lower bounds) we show in our extensive experimental evaluation that their performance differs greatly, both on generated as well as on real-world instances. AU - Hanauer, Kathrin AU - Henzinger, Monika H AU - Schulz, Christian ID - 11880 T2 - 2020 Symposium on Algorithm Engineering and Experiments TI - Fully dynamic single-source reachability in practice: An experimental study ER - TY - CONF AB - We introduce the fastest known exact algorithm for the multiterminal cut problem with k terminals. In particular, we engineer existing as well as new data reduction rules. We use the rules within a branch-and-reduce framework and to boost the performance of an ILP formulation. Our algorithms achieve improvements in running time of up to multiple orders of magnitudes over the ILP formulation without data reductions, which has been the de facto standard used by practitioners. This allows us to solve instances to optimality that are significantly larger than was previously possible. AU - Henzinger, Monika H AU - Noe, Alexander AU - Schulz, Christian ID - 11881 T2 - 2020 Symposium on Algorithm Engineering and Experiments TI - Shared-memory branch-and-reduce for multiterminal cuts ER - TY - JOUR AB - Graph sparsification aims at compressing large graphs into smaller ones while preserving important characteristics of the input graph. In this work we study vertex sparsifiers, i.e., sparsifiers whose goal is to reduce the number of vertices. We focus on the following notions: (1) Given a digraph 𝐺=(𝑉,𝐸) and terminal vertices 𝐾⊂𝑉 with |𝐾|=𝑘, a (vertex) reachability sparsifier of 𝐺 is a digraph 𝐻=(𝑉𝐻,𝐸𝐻), 𝐾⊂𝑉𝐻 that preserves all reachability information among terminal pairs. Let |𝑉𝐻| denote the size of 𝐻. In this work we introduce the notion of reachability-preserving minors (RPMs), i.e., we require 𝐻 to be a minor of 𝐺. We show any directed graph 𝐺 admits an RPM 𝐻 of size 𝑂(𝑘3), and if 𝐺 is planar, then the size of 𝐻 improves to 𝑂(𝑘2log𝑘). We complement our upper bound by showing that there exists an infinite family of grids such that any RPM must have Ω(𝑘2) vertices. (2) Given a weighted undirected graph 𝐺=(𝑉,𝐸) and terminal vertices 𝐾 with |𝐾|=𝑘, an exact (vertex) cut sparsifier of 𝐺 is a graph 𝐻 with 𝐾⊂𝑉𝐻 that preserves the value of minimum cuts separating any bipartition of 𝐾. We show that planar graphs with all the 𝑘 terminals lying on the same face admit exact cut sparsifiers of size 𝑂(𝑘2) that are also planar. Our result extends to flow and distance sparsifiers. It improves the previous best-known bound of 𝑂(𝑘222𝑘) for cut and flow sparsifiers by an exponential factor and matches an Ω(𝑘2) lower-bound for this class of graphs. AU - Goranci, Gramoz AU - Henzinger, Monika H AU - Peng, Pan ID - 11894 IS - 1 JF - SIAM Journal on Discrete Mathematics SN - 0895-4801 TI - Improved guarantees for vertex sparsification in planar graphs VL - 34 ER - TY - JOUR AB - The combination of nickel and photocatalysis has unlocked a variety of cross-couplings. These protocols rely on a few photocatalysts that can only convert a small portion of visible light (<500 nm) into chemical energy. The high-energy photons that excite the photocatalyst can result in unwanted side reactions. Dyes that absorb a much broader spectrum of light are not applicable because of their short-lived singlet excited states. Here, we describe a self-assembling catalyst system that overcomes this limitation. Immobilization of a nickel catalyst on dye-sensitized titanium dioxide results in a material that catalyzes carbon–heteroatom and carbon–carbon bond formations. The modular approach of dye-sensitized metallaphotocatalysts accesses the entire visible light spectrum and allows tackling selectivity issues resulting from low wavelengths strategically. The concept overcomes current limitations of metallaphotocatalysis by unlocking the potential of dyes that were previously unsuitable. AU - Reischauer, Susanne AU - Strauss, Volker AU - Pieber, Bartholomäus ID - 11954 IS - 22 JF - ACS Catalysis TI - Modular, self-assembling metallaphotocatalyst for cross-couplings using the full visible-light spectrum VL - 10 ER - TY - JOUR AB - Photochemistry enables new synthetic means to form carbon–heteroatom bonds. Photocatalysts can catalyze carbon–heteroatom cross-couplings by electron or energy transfer either alone or in combination with a second catalyst. Photocatalyst-free methods are possible using photolabile substrates or by generating photoactive electron donor-acceptor complexes. This review summarizes and discusses the strategies used in light-mediated carbon–heteroatom bond formations based on the proposed mechanisms. AU - Cavedon, Cristian AU - Seeberger, Peter H. AU - Pieber, Bartholomäus ID - 11969 IS - 10 JF - European Journal of Organic Chemistry SN - 1434-193X TI - Photochemical strategies for carbon–heteroatom bond formation VL - 2020 ER - TY - JOUR AB - Dual photocatalysis and nickel catalysis can effect cross-coupling under mild conditions, but little is known about the in situ kinetics of this class of reactions. We report a comprehensive kinetic examination of a model carboxylate O-arylation, comparing a state-of-the-art homogeneous photocatalyst (Ir(ppy)3) with a competitive heterogeneous photocatalyst (graphitic carbon nitride). Experimental conditions were adjusted such that the nickel catalytic cycle is saturated with excited photocatalyst. This approach was designed to remove the role of the photocatalyst, by which only the intrinsic behaviors of the nickel catalytic cycles are observed. The two reactions did not display identical kinetics. Ir(ppy)3 deactivates the nickel catalytic cycle and creates more dehalogenated side product. Kinetic data for the reaction using Ir(ppy)3 supports a turnover-limiting reductive elimination. Graphitic carbon nitride gave higher selectivity, even at high photocatalyst-to-nickel ratios. The heterogeneous reaction also showed a rate dependence on aryl halide, indicating that oxidative addition plays a role in rate determination. The results argue against the current mechanistic hypothesis, which states that the photocatalyst is only involved to trigger reductive elimination. AU - Malik, Jamal A. AU - Madani, Amiera AU - Pieber, Bartholomäus AU - Seeberger, Peter H. ID - 11978 IS - 25 JF - Journal of the American Chemical Society SN - 0002-7863 TI - Evidence for photocatalyst involvement in oxidative additions of nickel-catalyzed carboxylate O-arylations VL - 142 ER - TY - JOUR AB - Small organic radicals are ubiquitous intermediates in photocatalysis and are used in organic synthesis to install functional groups and to tune electronic properties and pharmacokinetic parameters of the final molecule. Development of new methods to generate small organic radicals with added functionality can further extend the utility of photocatalysis for synthetic needs. Herein, we present a method to generate dichloromethyl radicals from chloroform using a heterogeneous potassium poly(heptazine imide) (K-PHI) photocatalyst under visible light irradiation for C1-extension of the enone backbone. The method is applied on 15 enones, with γ,γ-dichloroketones yields of 18–89%. Due to negative zeta-potential (−40 mV) and small particle size (100 nm) K-PHI suspension is used in quasi-homogeneous flow-photoreactor increasing the productivity by 19 times compared to the batch approach. The resulting γ,γ-dichloroketones, are used as bifunctional building blocks to access value-added organic compounds such as substituted furans and pyrroles. AU - Mazzanti, Stefano AU - Kurpil, Bogdan AU - Pieber, Bartholomäus AU - Antonietti, Markus AU - Savateev, Aleksandr ID - 11980 JF - Nature Communications TI - Dichloromethylation of enones by carbon nitride photocatalysis VL - 11 ER - TY - JOUR AB - Dual photoredox/nickel-catalysed C–N cross-couplings suffer from low yields for electron-rich aryl halides. The formation of catalytically inactive nickel-black is responsible for this limitation and causes severe reproducibility issues. Here, we demonstrate that catalyst deactivation can be avoided by using a carbon nitride photocatalyst. The broad absorption of the heterogeneous photocatalyst enables wavelength-dependent control of the rate of reductive elimination to prevent nickel-black formation during the coupling of cyclic, secondary amines and aryl halides. A second approach, which is applicable to a broader set of electron-rich aryl halides, is to run the reactions at high concentrations to increase the rate of oxidative addition. Less nucleophilic, primary amines can be coupled with electron-rich aryl halides by stabilizing low-valent nickel intermediates with a suitable additive. The developed protocols enable reproducible, selective C–N cross-couplings of electron-rich aryl bromides and can also be applied for electron-poor aryl chlorides. AU - Gisbertz, Sebastian AU - Reischauer, Susanne AU - Pieber, Bartholomäus ID - 11979 IS - 8 JF - Nature Catalysis TI - Overcoming limitations in dual photoredox/nickel-catalysed C–N cross-couplings due to catalyst deactivation VL - 3 ER - TY - JOUR AB - Carbon nitride materials have emerged as an efficient and sustainable class of heterogeneous photocatalysts, particularly when paired with nickel in dual catalytic cross-coupling reactions. Performing these transformations on larger scales using a continuous process is difficult due to the problems associated with handling solids in flow. By combining an oscillatory pump with a microstructured plug flow photoreactor, a stable suspension of the photocatalyst can be maintained, circumventing clogging of the reactor channels. Through careful tuning of the oscillator properties, the residence time distribution (RTD) was optimized, whilst maintaining a stable catalyst suspension. Short residence times (20 min) were achieved using optimized conditions and the recyclability of the photocatalyst was demonstrated over 10 cycles with no loss of activity. During a stable 4.5 hour scale-out demonstration, the model substrate could be isolated on 12 g scale (90% yield, 2.67 g h−1). Moreover, the method was applied for the gram scale synthesis of an intermediate of the active pharmaceutical ingredient tetracaine. AU - Rosso, Cristian AU - Gisbertz, Sebastian AU - Williams, Jason D. AU - Gemoets, Hannes P. L. AU - Debrouwer, Wouter AU - Pieber, Bartholomäus AU - Kappe, C. Oliver ID - 11986 IS - 3 JF - Reaction Chemistry and Engineering TI - An oscillatory plug flow photoreactor facilitates semi-heterogeneous dual nickel/carbon nitride photocatalytic C–N couplings VL - 5 ER - TY - JOUR AB - The unusual correlated state that emerges in URu2Si2 below THO = 17.5 K is known as “hidden order” because even basic characteristics of the order parameter, such as its dimensionality (whether it has one component or two), are “hidden.” We use resonant ultrasound spectroscopy to measure the symmetry-resolved elastic anomalies across THO. We observe no anomalies in the shear elastic moduli, providing strong thermodynamic evidence for a one-component order parameter. We develop a machine learning framework that reaches this conclusion directly from the raw data, even in a crystal that is too small for traditional resonant ultrasound. Our result rules out a broad class of theories of hidden order based on two-component order parameters, and constrains the nature of the fluctuations from which unconventional superconductivity emerges at lower temperature. Our machine learning framework is a powerful new tool for classifying the ubiquitous competing orders in correlated electron systems. AU - Ghosh, Sayak AU - Matty, Michael AU - Baumbach, Ryan AU - Bauer, Eric D. AU - Modic, Kimberly A AU - Shekhter, Arkady AU - Mydosh, J. A. AU - Kim, Eun-Ah AU - Ramshaw, B. J. ID - 7084 IS - 10 JF - Science Advances TI - One-component order parameter in URu2Si2 uncovered by resonant ultrasound spectroscopy and machine learning VL - 6 ER - TY - CONF AB - Many systems rely on optimistic concurrent search trees for multi-core scalability. In principle, optimistic trees have a simple performance story: searches are read-only and so run in parallel, with writes to shared memory occurring only when modifying the data structure. However, this paper shows that in practice, obtaining the full performance benefits of optimistic search trees is not so simple. We focus on optimistic binary search trees (BSTs) and perform a detailed performance analysis of 10 state-of-the-art BSTs on large scale x86-64 hardware, using both microbenchmarks and an in-memory database system. We find and explain significant unexpected performance differences between BSTs with similar tree structure and search implementations, which we trace to subtle performance-degrading interactions of BSTs with systems software and hardware subsystems. We further derive a prescriptive approach to avoid this performance degradation, as well as algorithmic insights on optimistic BST design. Our work underlines the gap between the theory and practice of multi-core performance, and calls for further research to help bridge this gap. AU - Arbel-Raviv, Maya AU - Brown, Trevor A AU - Morrison, Adam ID - 7272 SN - 9781939133021 T2 - Proceedings of the 2018 USENIX Annual Technical Conference TI - Getting to the root of concurrent binary search tree performance ER - TY - CONF AB - The Price of Anarchy (PoA) is a well-established game-theoretic concept to shed light on coordination issues arising in open distributed systems. Leaving agents to selfishly optimize comes with the risk of ending up in sub-optimal states (in terms of performance and/or costs), compared to a centralized system design. However, the PoA relies on strong assumptions about agents' rationality (e.g., resources and information) and interactions, whereas in many distributed systems agents interact locally with bounded resources. They do so repeatedly over time (in contrast to "one-shot games"), and their strategies may evolve. Using a more realistic evolutionary game model, this paper introduces a realized evolutionary Price of Anarchy (ePoA). The ePoA allows an exploration of equilibrium selection in dynamic distributed systems with multiple equilibria, based on local interactions of simple memoryless agents. Considering a fundamental game related to virus propagation on networks, we present analytical bounds on the ePoA in basic network topologies and for different strategy update dynamics. In particular, deriving stationary distributions of the stochastic evolutionary process, we find that the Nash equilibria are not always the most abundant states, and that different processes can feature significant off-equilibrium behavior, leading to a significantly higher ePoA compared to the PoA studied traditionally in the literature. AU - Schmid, Laura AU - Chatterjee, Krishnendu AU - Schmid, Stefan ID - 7346 T2 - Proceedings of the 23rd International Conference on Principles of Distributed Systems TI - The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game VL - 153 ER - TY - CONF AB - The monitoring of event frequencies can be used to recognize behavioral anomalies, to identify trends, and to deduce or discard hypotheses about the underlying system. For example, the performance of a web server may be monitored based on the ratio of the total count of requests from the least and most active clients. Exact frequency monitoring, however, can be prohibitively expensive; in the above example it would require as many counters as there are clients. In this paper, we propose the efficient probabilistic monitoring of common frequency properties, including the mode (i.e., the most common event) and the median of an event sequence. We define a logic to express composite frequency properties as a combination of atomic frequency properties. Our main contribution is an algorithm that, under suitable probabilistic assumptions, can be used to monitor these important frequency properties with four counters, independent of the number of different events. Our algorithm samples longer and longer subwords of an infinite event sequence. We prove the almost-sure convergence of our algorithm by generalizing ergodic theory from increasing-length prefixes to increasing-length subwords of an infinite sequence. A similar algorithm could be used to learn a connected Markov chain of a given structure from observing its outputs, to arbitrary precision, for a given confidence. AU - Ferrere, Thomas AU - Henzinger, Thomas A AU - Kragl, Bernhard ID - 7348 SN - 1868-8969 T2 - 28th EACSL Annual Conference on Computer Science Logic TI - Monitoring event frequencies VL - 152 ER - TY - JOUR AB - We present conductance-matrix measurements of a three-terminal superconductor-semiconductor hybrid device consisting of two normal leads and one superconducting lead. Using a symmetry decomposition of the conductance, we find that antisymmetric components of pairs of local and nonlocal conductances qualitatively match at energies below the superconducting gap, and we compare this finding with symmetry relations based on a noninteracting scattering matrix approach. Further, the local charge character of Andreev bound states is extracted from the symmetry-decomposed conductance data and is found to be similar at both ends of the device and tunable with gate voltage. Finally, we measure the conductance matrix as a function of magnetic field and identify correlated splittings in low-energy features, demonstrating how conductance-matrix measurements can complement traditional single-probe measurements in the search for Majorana zero modes. AU - Ménard, G. C. AU - Anselmetti, G. L. R. AU - Martinez, E. A. AU - Puglia, D. AU - Malinowski, F. K. AU - Lee, J. S. AU - Choi, S. AU - Pendharkar, M. AU - Palmstrøm, C. J. AU - Flensberg, K. AU - Marcus, C. M. AU - Casparis, L. AU - Higginbotham, Andrew P ID - 7477 IS - 3 JF - Physical Review Letters SN - 0031-9007 TI - Conductance-matrix symmetries of a three-terminal hybrid device VL - 124 ER - TY - JOUR AB - Two-terminal conductance spectroscopy of superconducting devices is a common tool for probing Andreev and Majorana bound states. Here, we study theoretically a three-terminal setup, with two normal leads coupled to a grounded superconducting terminal. Using a single-electron scattering matrix, we derive the subgap conductance matrix for the normal leads and discuss its symmetries. In particular, we show that the local and the nonlocal elements of the conductance matrix have pairwise identical antisymmetric components. Moreover, we find that the nonlocal elements are directly related to the local BCS charges of the bound states close to the normal probes and we show how the BCS charge of overlapping Majorana bound states can be extracted from experiments. AU - Danon, Jeroen AU - Hellenes, Anna Birk AU - Hansen, Esben Bork AU - Casparis, Lucas AU - Higginbotham, Andrew P AU - Flensberg, Karsten ID - 7478 IS - 3 JF - Physical Review Letters SN - 0031-9007 TI - Nonlocal conductance spectroscopy of Andreev bound states: Symmetry relations and BCS charges VL - 124 ER - TY - JOUR AB - In developing technologies based on superconducting quantum circuits, the need to control and route heating is a significant challenge in the experimental realisation and operation of these devices. One of the more ubiquitous devices in the current quantum computing toolbox is the transmon-type superconducting quantum bit, embedded in a resonator-based architecture. In the study of heat transport in superconducting circuits, a versatile and sensitive thermometer is based on studying the tunnelling characteristics of superconducting probes weakly coupled to a normal-metal island. Here we show that by integrating superconducting quantum bit coupled to two superconducting resonators at different frequencies, each resonator terminated (and thermally populated) by such a mesoscopic thin film metal island, one can experimentally observe magnetic flux-tunable photonic heat rectification between 0 and 10%. AU - Senior, Jorden L AU - Gubaydullin, Azat AU - Karimi, Bayan AU - Peltonen, Joonas T. AU - Ankerhold, Joachim AU - Pekola, Jukka P. ID - 7530 IS - 1 JF - Communications Physics SN - 2399-3650 TI - Heat rectification via a superconducting artificial atom VL - 3 ER - TY - JOUR AB - Neuronal activity often leads to alterations in gene expression and cellular architecture. The nematode Caenorhabditis elegans, owing to its compact translucent nervous system, is a powerful system in which to study conserved aspects of the development and plasticity of neuronal morphology. Here we focus on one pair of sensory neurons, termed URX, which the worm uses to sense and avoid high levels of environmental oxygen. Previous studies have reported that the URX neuron pair has variable branched endings at its dendritic sensory tip. By controlling oxygen levels and analyzing mutants, we found that these microtubule-rich branched endings grow over time as a consequence of neuronal activity in adulthood. We also find that the growth of these branches correlates with an increase in cellular sensitivity to particular ranges of oxygen that is observable in the behavior of older worms. Given the strengths of C. elegans as a model organism, URX may serve as a potent system for uncovering genes and mechanisms involved in activity-dependent morphological changes in neurons and possible adaptive changes in the aging nervous system. AU - Cohn, Jesse A. AU - Cebul, Elizabeth R. AU - Valperga, Giulio AU - Brose, Lotti AU - de Bono, Mario AU - Heiman, Maxwell G. AU - Pierce, Jonathan T. ID - 7545 IS - 1 JF - Developmental Biology SN - 0012-1606 TI - Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron VL - 461 ER - TY - JOUR AB - Coxeter triangulations are triangulations of Euclidean space based on a single simplex. By this we mean that given an individual simplex we can recover the entire triangulation of Euclidean space by inductively reflecting in the faces of the simplex. In this paper we establish that the quality of the simplices in all Coxeter triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate the Delaunay property for these triangulations. Moreover, we consider an extension of the Delaunay property, namely protection, which is a measure of non-degeneracy of a Delaunay triangulation. In particular, one family of Coxeter triangulations achieves the protection O(1/d2). We conjecture that both bounds are optimal for triangulations in Euclidean space. AU - Choudhary, Aruni AU - Kachanovich, Siargey AU - Wintraecken, Mathijs ID - 7567 JF - Mathematics in Computer Science SN - 1661-8270 TI - Coxeter triangulations have good quality VL - 14 ER - TY - JOUR AB - The concept of the entanglement between spin and orbital degrees of freedom plays a crucial role in our understanding of various phases and exotic ground states in a broad class of materials, including orbitally ordered materials and spin liquids. We investigate how the spin-orbital entanglement in a Mott insulator depends on the value of the spin-orbit coupling of the relativistic origin. To this end, we numerically diagonalize a one-dimensional spin-orbital model with Kugel-Khomskii exchange interactions between spins and orbitals on different sites supplemented by the on-site spin-orbit coupling. In the regime of small spin-orbit coupling with regard to the spin-orbital exchange, the ground state to a large extent resembles the one obtained in the limit of vanishing spin-orbit coupling. On the other hand, for large spin-orbit coupling the ground state can, depending on the model parameters, either still show negligible spin-orbital entanglement or evolve to a highly spin-orbitally-entangled phase with completely distinct properties that are described by an effective XXZ model. The presented results suggest that (i) the spin-orbital entanglement may be induced by large on-site spin-orbit coupling, as found in the 5d transition metal oxides, such as the iridates; (ii) for Mott insulators with weak spin-orbit coupling of Ising type, such as, e.g., the alkali hyperoxides, the effects of the spin-orbit coupling on the ground state can, in the first order of perturbation theory, be neglected. AU - Gotfryd, Dorota AU - Paerschke, Ekaterina AU - Chaloupka, Jiri AU - Oles, Andrzej M. AU - Wohlfeld, Krzysztof ID - 7594 IS - 1 JF - Physical Review Research TI - How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator VL - 2 ER - TY - CONF AB - Union-Find (or Disjoint-Set Union) is one of the fundamental problems in computer science; it has been well-studied from both theoretical and practical perspectives in the sequential case. Recently, there has been mounting interest in analyzing this problem in the concurrent scenario, and several asymptotically-efficient algorithms have been proposed. Yet, to date, there is very little known about the practical performance of concurrent Union-Find. This work addresses this gap. We evaluate and analyze the performance of several concurrent Union-Find algorithms and optimization strategies across a wide range of platforms (Intel, AMD, and ARM) and workloads (social, random, and road networks, as well as integrations into more complex algorithms). We first observe that, due to the limited computational cost, the number of induced cache misses is the critical determining factor for the performance of existing algorithms. We introduce new techniques to reduce this cost by storing node priorities implicitly and by using plain reads and writes in a way that does not affect the correctness of the algorithms. Finally, we show that Union-Find implementations are an interesting application for Transactional Memory (TM): one of the fastest algorithm variants we discovered is a sequential one that uses coarse-grained locking with the lock elision optimization to reduce synchronization cost and increase scalability. AU - Alistarh, Dan-Adrian AU - Fedorov, Alexander AU - Koval, Nikita ID - 7605 SN - 18688969 T2 - 23rd International Conference on Principles of Distributed Systems TI - In search of the fastest concurrent union-find algorithm VL - 153 ER - TY - GEN AB - Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals. AU - Wei, Zhuang AU - Tan, Shutang AU - Liu, Tao AU - Wu, Yuan AU - Lei, Ji-Gang AU - Chen, ZhengJun AU - Friml, Jiří AU - Xue, Hong-Wei AU - Liao, Kan ID - 7601 T2 - bioRxiv TI - Plasmodesmata-like intercellular connections by plant remorin in animal cells ER - TY - JOUR AB - The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods. AU - Larsson, J. AU - Westram, Anja M AU - Bengmark, S. AU - Lundh, T. AU - Butlin, R. K. ID - 7651 IS - 163 JF - Journal of The Royal Society Interface SN - 1742-5689 TI - A developmentally descriptive method for quantifying shape in gastropod shells VL - 17 ER - TY - JOUR AB - We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor. AU - Nabais, Marta F. AU - Lin, Tian AU - Benyamin, Beben AU - Williams, Kelly L. AU - Garton, Fleur C. AU - Vinkhuyzen, Anna A. E. AU - Zhang, Futao AU - Vallerga, Costanza L. AU - Restuadi, Restuadi AU - Freydenzon, Anna AU - Zwamborn, Ramona A. J. AU - Hop, Paul J. AU - Robinson, Matthew Richard AU - Gratten, Jacob AU - Visscher, Peter M. AU - Hannon, Eilis AU - Mill, Jonathan AU - Brown, Matthew A. AU - Laing, Nigel G. AU - Mather, Karen A. AU - Sachdev, Perminder S. AU - Ngo, Shyuan T. AU - Steyn, Frederik J. AU - Wallace, Leanne AU - Henders, Anjali K. AU - Needham, Merrilee AU - Veldink, Jan H. AU - Mathers, Susan AU - Nicholson, Garth AU - Rowe, Dominic B. AU - Henderson, Robert D. AU - McCombe, Pamela A. AU - Pamphlett, Roger AU - Yang, Jian AU - Blair, Ian P. AU - McRae, Allan F. AU - Wray, Naomi R. ID - 7708 JF - npj Genomic Medicine SN - 2056-7944 TI - Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis VL - 5 ER - TY - JOUR AB - The growing sample size of genome-wide association studies has facilitated the discovery of gene-environment interactions (GxE). Here we propose a maximum likelihood method to estimate the contribution of GxE to continuous traits taking into account all interacting environmental variables, without the need to measure any. Extensive simulations demonstrate that our method provides unbiased interaction estimates and excellent coverage. We also offer strategies to distinguish specific GxE from general scale effects. Applying our method to 32 traits in the UK Biobank reveals that while the genetic risk score (GRS) of 376 variants explains 5.2% of body mass index (BMI) variance, GRSxE explains an additional 1.9%. Nevertheless, this interaction holds for any variable with identical correlation to BMI as the GRS, hence may not be GRS-specific. Still, we observe that the global contribution of specific GRSxE to complex traits is substantial for nine obesity-related measures (including leg impedance and trunk fat-free mass). AU - Sulc, Jonathan AU - Mounier, Ninon AU - Günther, Felix AU - Winkler, Thomas AU - Wood, Andrew R. AU - Frayling, Timothy M. AU - Heid, Iris M. AU - Robinson, Matthew Richard AU - Kutalik, Zoltán ID - 7707 JF - Nature Communications SN - 2041-1723 TI - Quantification of the overall contribution of gene-environment interaction for obesity-related traits VL - 11 ER - TY - JOUR AB - Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as oscillations in protein-level circuits remains an outstanding challenge. Few examples of biological posttranslational oscillators are known, necessitating theoretical progress to determine realizable oscillators. We construct mathematical models for two posttranslational oscillators, using few components that interact only through reversible binding and phosphorylation/dephosphorylation reactions. Our designed oscillators rely on the self-assembly of two protein species into multimeric functional enzymes that respectively inhibit and enhance this self-assembly. We limit our analysis to within experimental constraints, finding (i) significant portions of the restricted parameter space yielding oscillations and (ii) that oscillation periods can be tuned by several orders of magnitude using recent advances in computational protein design. Our work paves the way for the rational design and realization of protein-based dynamic systems. AU - Kimchi, Ofer AU - Goodrich, Carl Peter AU - Courbet, Alexis AU - Curatolo, Agnese I. AU - Woodall, Nicholas B. AU - Baker, David AU - Brenner, Michael P. ID - 7778 IS - 51 JF - Science Advances TI - Self-assembly-based posttranslational protein oscillators VL - 6 ER - TY - CONF AB - We settle the complexity of the (Δ+1)-coloring and (Δ+1)-list coloring problems in the CONGESTED CLIQUE model by presenting a simple deterministic algorithm for both problems running in a constant number of rounds. This matches the complexity of the recent breakthrough randomized constant-round (Δ+1)-list coloring algorithm due to Chang et al. (PODC'19), and significantly improves upon the state-of-the-art O(logΔ)-round deterministic (Δ+1)-coloring bound of Parter (ICALP'18). A remarkable property of our algorithm is its simplicity. Whereas the state-of-the-art randomized algorithms for this problem are based on the quite involved local coloring algorithm of Chang et al. (STOC'18), our algorithm can be described in just a few lines. At a high level, it applies a careful derandomization of a recursive procedure which partitions the nodes and their respective palettes into separate bins. We show that after O(1) recursion steps, the remaining uncolored subgraph within each bin has linear size, and thus can be solved locally by collecting it to a single node. This algorithm can also be implemented in the Massively Parallel Computation (MPC) model provided that each machine has linear (in n, the number of nodes in the input graph) space. We also show an extension of our algorithm to the MPC regime in which machines have sublinear space: we present the first deterministic (Δ+1)-list coloring algorithm designed for sublinear-space MPC, which runs in O(logΔ+loglogn) rounds. AU - Czumaj, Artur AU - Davies, Peter AU - Parter, Merav ID - 7803 T2 - Proceedings of the 2020 ACM Symposium on Principles of Distributed Computing TI - Simple, deterministic, constant-round coloring in the congested clique ER - TY - CONF AB - We consider the following decision problem EMBEDk→d in computational topology (where k ≤ d are fixed positive integers): Given a finite simplicial complex K of dimension k, does there exist a (piecewise-linear) embedding of K into ℝd? The special case EMBED1→2 is graph planarity, which is decidable in linear time, as shown by Hopcroft and Tarjan. In higher dimensions, EMBED2→3 and EMBED3→3 are known to be decidable (as well as NP-hard), and recent results of Čadek et al. in computational homotopy theory, in combination with the classical Haefliger–Weber theorem in geometric topology, imply that EMBEDk→d can be solved in polynomial time for any fixed pair (k, d) of dimensions in the so-called metastable range . Here, by contrast, we prove that EMBEDk→d is algorithmically undecidable for almost all pairs of dimensions outside the metastable range, namely for . This almost completely resolves the decidability vs. undecidability of EMBEDk→d in higher dimensions and establishes a sharp dichotomy between polynomial-time solvability and undecidability. Our result complements (and in a wide range of dimensions strengthens) earlier results of Matoušek, Tancer, and the second author, who showed that EMBEDk→d is undecidable for 4 ≤ k ϵ {d – 1, d}, and NP-hard for all remaining pairs (k, d) outside the metastable range and satisfying d ≥ 4. AU - Filakovský, Marek AU - Wagner, Uli AU - Zhechev, Stephan Y ID - 7806 SN - 9781611975994 T2 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms TI - Embeddability of simplicial complexes is undecidable VL - 2020-January ER - TY - JOUR AB - Scientific research is to date largely restricted to wealthy laboratories in developed nations due to the necessity of complex and expensive equipment. This inequality limits the capacity of science to be used as a diplomatic channel. Maker movements use open-source technologies including additive manufacturing (3D printing) and laser cutting, together with low-cost computers for developing novel products. This movement is setting the groundwork for a revolution, allowing scientific equipment to be sourced at a fraction of the cost and has the potential to increase the availability of equipment for scientists around the world. Science education is increasingly recognized as another channel for science diplomacy. In this perspective, we introduce the idea that the Maker movement and open-source technologies have the potential to revolutionize science, technology, engineering and mathematics (STEM) education worldwide. We present an open-source STEM didactic tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science). SCOPES is self-contained, independent of local resources, and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. We envision such platforms will enhance science diplomacy by providing a means for scientists to share their findings with classrooms and for educators to incorporate didactic concepts into STEM lessons. By providing students the opportunity to design, perform, and share scientific experiments, students also experience firsthand the benefits of a multinational scientific community. We provide instructions on how to build and use SCOPES on our webpage: http://scopeseducation.org. AU - Beattie, Robert J AU - Hippenmeyer, Simon AU - Pauler, Florian ID - 7814 JF - Frontiers in Education SN - 2504-284X TI - SCOPES: Sparking curiosity through Open-Source platforms in education and science VL - 5 ER - TY - JOUR AB - In this paper, we establish convergence to equilibrium for a drift–diffusion–recombination system modelling the charge transport within certain semiconductor devices. More precisely, we consider a two-level system for electrons and holes which is augmented by an intermediate energy level for electrons in so-called trapped states. The recombination dynamics use the mass action principle by taking into account this additional trap level. The main part of the paper is concerned with the derivation of an entropy–entropy production inequality, which entails exponential convergence to the equilibrium via the so-called entropy method. The novelty of our approach lies in the fact that the entropy method is applied uniformly in a fast-reaction parameter which governs the lifetime of electrons on the trap level. Thus, the resulting decay estimate for the densities of electrons and holes extends to the corresponding quasi-steady-state approximation. AU - Fellner, Klemens AU - Kniely, Michael ID - 7866 JF - Journal of Elliptic and Parabolic Equations SN - 22969020 TI - Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model VL - 6 ER - TY - JOUR AB - We explore the time evolution of two impurities in a trapped one-dimensional Bose gas that follows a change of the boson-impurity interaction. We study the induced impurity-impurity interactions and their effect on the quench dynamics. In particular, we report on the size of the impurity cloud, the impurity-impurity entanglement, and the impurity-impurity correlation function. The presented numerical simulations are based upon the variational multilayer multiconfiguration time-dependent Hartree method for bosons. To analyze and quantify induced impurity-impurity correlations, we employ an effective two-body Hamiltonian with a contact interaction. We show that the effective model consistent with the mean-field attraction of two heavy impurities explains qualitatively our results for weak interactions. Our findings suggest that the quench dynamics in cold-atom systems can be a tool for studying impurity-impurity correlations. AU - Mistakidis, S. I. AU - Volosniev, Artem AU - Schmelcher, P. ID - 7919 JF - Physical Review Research SN - 2643-1564 TI - Induced correlations between impurities in a one-dimensional quenched Bose gas VL - 2 ER - TY - CONF AB - We define and study a discrete process that generalizes the convex-layer decomposition of a planar point set. Our process, which we call homotopic curve shortening (HCS), starts with a closed curve (which might self-intersect) in the presence of a set P⊂ ℝ² of point obstacles, and evolves in discrete steps, where each step consists of (1) taking shortcuts around the obstacles, and (2) reducing the curve to its shortest homotopic equivalent. We find experimentally that, if the initial curve is held fixed and P is chosen to be either a very fine regular grid or a uniformly random point set, then HCS behaves at the limit like the affine curve-shortening flow (ACSF). This connection between HCS and ACSF generalizes the link between "grid peeling" and the ACSF observed by Eppstein et al. (2017), which applied only to convex curves, and which was studied only for regular grids. We prove that HCS satisfies some properties analogous to those of ACSF: HCS is invariant under affine transformations, preserves convexity, and does not increase the total absolute curvature. Furthermore, the number of self-intersections of a curve, or intersections between two curves (appropriately defined), does not increase. Finally, if the initial curve is simple, then the number of inflection points (appropriately defined) does not increase. AU - Avvakumov, Sergey AU - Nivasch, Gabriel ID - 7991 SN - 18688969 T2 - 36th International Symposium on Computational Geometry TI - Homotopic curve shortening and the affine curve-shortening flow VL - 164 ER - TY - CONF AB - We prove general topological Radon-type theorems for sets in ℝ^d, smooth real manifolds or finite dimensional simplicial complexes. Combined with a recent result of Holmsen and Lee, it gives fractional Helly theorem, and consequently the existence of weak ε-nets as well as a (p,q)-theorem. More precisely: Let X be either ℝ^d, smooth real d-manifold, or a finite d-dimensional simplicial complex. Then if F is a finite, intersection-closed family of sets in X such that the ith reduced Betti number (with ℤ₂ coefficients) of any set in F is at most b for every non-negative integer i less or equal to k, then the Radon number of F is bounded in terms of b and X. Here k is the smallest integer larger or equal to d/2 - 1 if X = ℝ^d; k=d-1 if X is a smooth real d-manifold and not a surface, k=0 if X is a surface and k=d if X is a d-dimensional simplicial complex. Using the recent result of the author and Kalai, we manage to prove the following optimal bound on fractional Helly number for families of open sets in a surface: Let F be a finite family of open sets in a surface S such that the intersection of any subfamily of F is either empty, or path-connected. Then the fractional Helly number of F is at most three. This also settles a conjecture of Holmsen, Kim, and Lee about an existence of a (p,q)-theorem for open subsets of a surface. AU - Patakova, Zuzana ID - 7989 SN - 18688969 T2 - 36th International Symposium on Computational Geometry TI - Bounding radon number via Betti numbers VL - 164 ER - TY - CONF AB - Let K be a convex body in ℝⁿ (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K ∩ h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p₀ is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n ≥ 2, there are always at least three distinct barycentric cuts through the point p₀ ∈ K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p₀ are guaranteed if n ≥ 3. AU - Patakova, Zuzana AU - Tancer, Martin AU - Wagner, Uli ID - 7992 SN - 18688969 T2 - 36th International Symposium on Computational Geometry TI - Barycentric cuts through a convex body VL - 164 ER - TY - CONF AB - In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of K_n was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible. AU - Arroyo Guevara, Alan M AU - Bensmail, Julien AU - Bruce Richter, R. ID - 7994 SN - 18688969 T2 - 36th International Symposium on Computational Geometry TI - Extending drawings of graphs to arrangements of pseudolines VL - 164 ER - TY - JOUR AB - Relaxation to a thermal state is the inevitable fate of nonequilibrium interacting quantum systems without special conservation laws. While thermalization in one-dimensional systems can often be suppressed by integrability mechanisms, in two spatial dimensions thermalization is expected to be far more effective due to the increased phase space. In this work we propose a general framework for escaping or delaying the emergence of the thermal state in two-dimensional arrays of Rydberg atoms via the mechanism of quantum scars, i.e., initial states that fail to thermalize. The suppression of thermalization is achieved in two complementary ways: by adding local perturbations or by adjusting the driving Rabi frequency according to the local connectivity of the lattice. We demonstrate that these mechanisms allow us to realize robust quantum scars in various two-dimensional lattices, including decorated lattices with nonconstant connectivity. In particular, we show that a small decrease of the Rabi frequency at the corners of the lattice is crucial for mitigating the strong boundary effects in two-dimensional systems. Our results identify synchronization as an important tool for future experiments on two-dimensional quantum scars. AU - Michailidis, Alexios AU - Turner, C. J. AU - Papić, Z. AU - Abanin, D. A. AU - Serbyn, Maksym ID - 8011 IS - 2 JF - Physical Review Research SN - 2643-1564 TI - Stabilizing two-dimensional quantum scars by deformation and synchronization VL - 2 ER - TY - GEN AB - We present a generative model of images that explicitly reasons over the set of objects they show. Our model learns a structured latent representation that separates objects from each other and from the background; unlike prior works, it explicitly represents the 2D position and depth of each object, as well as an embedding of its segmentation mask and appearance. The model can be trained from images alone in a purely unsupervised fashion without the need for object masks or depth information. Moreover, it always generates complete objects, even though a significant fraction of training images contain occlusions. Finally, we show that our model can infer decompositions of novel images into their constituent objects, including accurate prediction of depth ordering and segmentation of occluded parts. AU - Anciukevicius, Titas AU - Lampert, Christoph AU - Henderson, Paul M ID - 8063 T2 - arXiv TI - Object-centric image generation with factored depths, locations, and appearances ER - TY - GEN AB - Here, we employ micro- and nanosized cellulose particles, namely paper fines and cellulose nanocrystals, to induce hierarchical organization over a wide length scale. After processing them into carbonaceous materials, we demonstrate that these hierarchically organized materials outperform the best materials for supercapacitors operating with organic electrolytes reported in literature in terms of specific energy/power (Ragone plot) while showing hardly any capacity fade over 4,000 cycles. The highly porous materials feature a specific surface area as high as 2500 m2ˑg-1 and exhibit pore sizes in the range of 0.5 to 200 nm as proven by scanning electron microscopy and N2 physisorption. The carbonaceous materials have been further investigated by X-ray photoelectron spectroscopy and RAMAN spectroscopy. Since paper fines are an underutilized side stream in any paper production process, they are a cheap and highly available feedstock to prepare carbonaceous materials with outstanding performance in electrochemical applications. AU - Hobisch, Mathias A. AU - Mourad, Eléonore AU - Fischer, Wolfgang J. AU - Prehal, Christian AU - Eyley, Samuel AU - Childress, Anthony AU - Zankel, Armin AU - Mautner, Andreas AU - Breitenbach, Stefan AU - Rao, Apparao M. AU - Thielemans, Wim AU - Freunberger, Stefan Alexander AU - Eckhart, Rene AU - Bauer, Wolfgang AU - Spirk, Stefan ID - 8081 TI - High specific capacitance supercapacitors from hierarchically organized all-cellulose composites ER - TY - JOUR AB - Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality. AU - Lombardi, Fabrizio AU - Wang, Jilin W.J.L. AU - Zhang, Xiyun AU - Ivanov, Plamen Ch ID - 8105 JF - EPJ Web of Conferences SN - 2100-014X TI - Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality VL - 230 ER - TY - CONF AB - Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics. AU - Edelsbrunner, Herbert AU - Nikitenko, Anton AU - Ölsböck, Katharina AU - Synak, Peter ID - 8135 SN - 21932808 T2 - Topological Data Analysis TI - Radius functions on Poisson–Delaunay mosaics and related complexes experimentally VL - 15 ER - TY - COMP AU - Hauschild, Robert ID - 8181 TI - Amplified centrosomes in dendritic cells promote immune cell effector functions ER - TY - JOUR AB - Birch pollen allergy is among the most prevalent pollen allergies in Northern and Central Europe. This IgE-mediated disease can be treated with allergen immunotherapy (AIT), which typically gives rise to IgG antibodies inducing tolerance. Although the main mechanisms of allergen immunotherapy (AIT) are known, questions regarding possible Fc-mediated effects of IgG antibodies remain unanswered. This can mainly be attributed to the unavailability of appropriate tools, i.e., well-characterised recombinant antibodies (rAbs). We hereby aimed at providing human rAbs of several classes for mechanistic studies and as possible candidates for passive immunotherapy. We engineered IgE, IgG1, and IgG4 sharing the same variable region against the major birch pollen allergen Bet v 1 using Polymerase Incomplete Primer Extension (PIPE) cloning. We tested IgE functionality and IgG blocking capabilities using appropriate model cell lines. In vitro studies showed IgE engagement with FcεRI and CD23 and Bet v 1-dependent degranulation. Overall, we hereby present fully functional, human IgE, IgG1, and IgG4 sharing the same variable region against Bet v 1 and showcase possible applications in first mechanistic studies. Furthermore, our IgG antibodies might be useful candidates for passive immunotherapy of birch pollen allergy. AU - Köhler, Verena K. AU - Crescioli, Silvia AU - Fazekas-Singer, Judit AU - Bax, Heather J. AU - Hofer, Gerhard AU - Pranger, Christina L. AU - Hufnagl, Karin AU - Bianchini, Rodolfo AU - Flicker, Sabine AU - Keller, Walter AU - Karagiannis, Sophia N. AU - Jensen-Jarolim, Erika ID - 8225 IS - 16 JF - International Journal of Molecular Sciences SN - 1422-0067 TI - Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1 VL - 21 ER - TY - JOUR AU - Gotovina, Jelena AU - Bianchini, Rodolfo AU - Fazekas-Singer, Judit AU - Herrmann, Ina AU - Pellizzari, Giulia AU - Haidl, Ian D. AU - Hufnagl, Karin AU - Karagiannis, Sophia N. AU - Marshall, Jean S. AU - Jensen‐Jarolim, Erika ID - 8226 JF - Allergy SN - 0105-4538 TI - Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro ER - TY - COMP AB - Automated root growth analysis and tracking of root tips. AU - Hauschild, Robert ID - 8294 TI - RGtracker ER - TY - GEN AB - Classic Byzantine fault-tolerant consensus protocols forfeit liveness in the face of asynchrony in order to preserve safety, whereas most deployed blockchain protocols forfeit safety in order to remain live. In this work, we achieve the best of both worlds by proposing a novel abstractions called the finality gadget. A finality gadget allows for transactions to always optimistically commit but informs the clients that these transactions might be unsafe. As a result, a blockchain can execute transactions optimistically and only commit them after they have been sufficiently and provably audited. In this work, we formally model the finality gadget abstraction, prove that it is impossible to solve it deterministically in full asynchrony (even though it is stronger than consensus) and provide a partially synchronous protocol which is currently securing a major blockchain. This way we show that the protocol designer can decouple safety and liveness in order to speed up recovery from failures. We believe that there can be other types of finality gadgets that provide weaker safety (e.g., probabilistic) in order to gain more efficiency and this can depend on the probability that the network is not in synchrony. AU - Stewart, Alistair AU - Kokoris Kogias, Eleftherios ID - 8307 T2 - arXiv TI - GRANDPA: A Byzantine finality gadget ER - TY - CONF AB - Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question. In this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way. Our core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001). AU - Chakraborty, Suvradip AU - Dziembowski, Stefan AU - Nielsen, Jesper Buus ID - 8322 SN - 03029743 T2 - Advances in Cryptology – CRYPTO 2020 TI - Reverse firewalls for actively secure MPCs VL - 12171 ER - TY - CONF AB - Discrete Gaussian distributions over lattices are central to lattice-based cryptography, and to the computational and mathematical aspects of lattices more broadly. The literature contains a wealth of useful theorems about the behavior of discrete Gaussians under convolutions and related operations. Yet despite their structural similarities, most of these theorems are formally incomparable, and their proofs tend to be monolithic and written nearly “from scratch,” making them unnecessarily hard to verify, understand, and extend. In this work we present a modular framework for analyzing linear operations on discrete Gaussian distributions. The framework abstracts away the particulars of Gaussians, and usually reduces proofs to the choice of appropriate linear transformations and elementary linear algebra. To showcase the approach, we establish several general properties of discrete Gaussians, and show how to obtain all prior convolution theorems (along with some new ones) as straightforward corollaries. As another application, we describe a self-reduction for Learning With Errors (LWE) that uses a fixed number of samples to generate an unlimited number of additional ones (having somewhat larger error). The distinguishing features of our reduction are its simple analysis in our framework, and its exclusive use of discrete Gaussians without any loss in parameters relative to a prior mixed discrete-and-continuous approach. As a contribution of independent interest, for subgaussian random matrices we prove a singular value concentration bound with explicitly stated constants, and we give tighter heuristics for specific distributions that are commonly used for generating lattice trapdoors. These bounds yield improvements in the concrete bit-security estimates for trapdoor lattice cryptosystems. AU - Genise, Nicholas AU - Micciancio, Daniele AU - Peikert, Chris AU - Walter, Michael ID - 8339 SN - 03029743 T2 - 23rd IACR International Conference on the Practice and Theory of Public-Key Cryptography TI - Improved discrete Gaussian and subgaussian analysis for lattice cryptography VL - 12110 ER -