TY - JOUR
AB - In RuCl3, inelastic neutron scattering and Raman spectroscopy reveal a continuum of non-spin-wave excitations that persists to high temperature, suggesting the presence of a spin liquid state on a honeycomb lattice. In the context of the Kitaev model, finite magnetic fields introduce interactions between the elementary excitations, and thus the effects of high magnetic fields that are comparable to the spin-exchange energy scale must be explored. Here, we report measurements of the magnetotropic coefficient—the thermodynamic coefficient associated with magnetic anisotropy—over a wide range of magnetic fields and temperatures. We find that magnetic field and temperature compete to determine the magnetic response in a way that is independent of the large intrinsic exchange-interaction energy. This emergent scale-invariant magnetic anisotropy provides evidence for a high degree of exchange frustration that favours the formation of a spin liquid state in RuCl3.
AU - Modic, Kimberly A
AU - McDonald, Ross D.
AU - Ruff, J.P.C.
AU - Bachmann, Maja D.
AU - Lai, You
AU - Palmstrom, Johanna C.
AU - Graf, David
AU - Chan, Mun K.
AU - Balakirev, F.F.
AU - Betts, J.B.
AU - Boebinger, G.S.
AU - Schmidt, Marcus
AU - Lawler, Michael J.
AU - Sokolov, D.A.
AU - Moll, Philip J.W.
AU - Ramshaw, B.J.
AU - Shekhter, Arkady
ID - 8673
JF - Nature Physics
SN - 17452473
TI - Scale-invariant magnetic anisotropy in RuCl3 at high magnetic fields
VL - 17
ER -
TY - JOUR
AB - Given a locally finite X⊆Rd and a radius r≥0, the k-fold cover of X and r consists of all points in Rd that have k or more points of X within distance r. We consider two filtrations—one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k—and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in Rd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module of Delaunay mosaics that is isomorphic to the persistence module of the multi-covers.
AU - Edelsbrunner, Herbert
AU - Osang, Georg F
ID - 9317
JF - Discrete and Computational Geometry
SN - 01795376
TI - The multi-cover persistence of Euclidean balls
ER -
TY - JOUR
AB - For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,
and overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance.
AU - Sarac, Naci E
AU - Altun, Ömer Faruk
AU - Atam, Kamil Tolga
AU - Karahoda, Sertac
AU - Kaya, Kamer
AU - Yenigün, Hüsnü
ID - 8912
IS - 4
JF - Expert Systems with Applications
SN - 09574174
TI - Boosting expensive synchronizing heuristics
VL - 167
ER -
TY - JOUR
AB - We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter.
AU - Abanin, D. A.
AU - Bardarson, J. H.
AU - De Tomasi, G.
AU - Gopalakrishnan, S.
AU - Khemani, V.
AU - Parameswaran, S. A.
AU - Pollmann, F.
AU - Potter, A. C.
AU - Serbyn, Maksym
AU - Vasseur, R.
ID - 9224
IS - 4
JF - Annals of Physics
SN - 00034916
TI - Distinguishing localization from chaos: Challenges in finite-size systems
VL - 427
ER -
TY - JOUR
AB - In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space.
AU - Virosztek, Daniel
ID - 9036
IS - 3
JF - Advances in Mathematics
KW - General Mathematics
SN - 0001-8708
TI - The metric property of the quantum Jensen-Shannon divergence
VL - 380
ER -
TY - JOUR
AB - Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.
New method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.
Results: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.
Comparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.
Conclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity.
AU - Zhang, Xiaomin
AU - Schlögl, Alois
AU - Vandael, David H
AU - Jonas, Peter M
ID - 9329
IS - 6
JF - Journal of Neuroscience Methods
SN - 01650270
TI - MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo
VL - 357
ER -
TY - JOUR
AB - In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density.
AU - Schöpf, Clemens L.
AU - Ablinger, Cornelia
AU - Geisler, Stefanie M.
AU - Stanika, Ruslan I.
AU - Campiglio, Marta
AU - Kaufmann, Walter
AU - Nimmervoll, Benedikt
AU - Schlick, Bettina
AU - Brockhaus, Johannes
AU - Missler, Markus
AU - Shigemoto, Ryuichi
AU - Obermair, Gerald J.
ID - 9330
IS - 14
JF - PNAS
TI - Presynaptic α2δ subunits are key organizers of glutamatergic synapses
VL - 118
ER -
TY - JOUR
AB - Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.
AU - Ötvös, Krisztina
AU - Miskolczi, Pál
AU - Marhavý, Peter
AU - Cruz-Ramírez, Alfredo
AU - Benková, Eva
AU - Robert, Stéphanie
AU - Bakó, László
ID - 9332
IS - 8
JF - International Journal of Molecular Sciences
SN - 16616596
TI - Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis
VL - 22
ER -
TY - JOUR
AB - We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation.
AU - Mitrouskas, David Johannes
ID - 9333
JF - Letters in Mathematical Physics
SN - 03779017
TI - A note on the Fröhlich dynamics in the strong coupling limit
VL - 111
ER -
TY - JOUR
AB - Quantum entanglement has been generated and verified in cold-atom experiments and used to make atom-interferometric measurements below the shot-noise limit. However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled) atomic states. This perspective piece asks the question: can entanglement usefully improve cold-atom sensors, in the sense that it gives new sensing capabilities unachievable with current state-of-the-art devices? We briefly review the state-of-the-art in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying the potential benefits entanglement could bring to these devices, and the challenges that need to be overcome to realize these benefits. We survey demonstrated methods of generating metrologically useful entanglement in cold-atom systems, note their relative strengths and weaknesses, and assess their prospects for near-to-medium term quantum-enhanced cold-atom sensing.
AU - Szigeti, Stuart S.
AU - Hosten, Onur
AU - Haine, Simon A.
ID - 9331
IS - 14
JF - Applied Physics Letters
SN - 00036951
TI - Improving cold-atom sensors with quantum entanglement: Prospects and challenges
VL - 118
ER -
TY - JOUR
AB - Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale.
AU - Duan, J.
AU - Álvarez-Pérez, G.
AU - Voronin, K. V.
AU - Prieto Gonzalez, Ivan
AU - Taboada-Gutiérrez, J.
AU - Volkov, V. S.
AU - Martín-Sánchez, J.
AU - Nikitin, A. Y.
AU - Alonso-González, P.
ID - 9334
IS - 14
JF - Science Advances
TI - Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition
VL - 7
ER -
TY - JOUR
AB - Various degenerate diffusion equations exhibit a waiting time phenomenon: depending on the “flatness” of the compactly supported initial datum at the boundary of the support, the support of the solution may not expand for a certain amount of time. We show that this phenomenon is captured by particular Lagrangian discretizations of the porous medium and the thin film equations, and we obtain sufficient criteria for the occurrence of waiting times that are consistent with the known ones for the original PDEs. For the spatially discrete solution, the waiting time phenomenon refers to a deviation of the edge of support from its original position by a quantity comparable to the mesh width, over a mesh-independent time interval. Our proof is based on estimates on the fluid velocity in Lagrangian coordinates. Combining weighted entropy estimates with an iteration technique à la Stampacchia leads to upper bounds on free boundary propagation. Numerical simulations show that the phenomenon is already clearly visible for relatively coarse discretizations.
AU - Fischer, Julian L
AU - Matthes, Daniel
ID - 9335
IS - 1
JF - SIAM Journal on Numerical Analysis
SN - 0036-1429
TI - The waiting time phenomenon in spatially discretized porous medium and thin film equations
VL - 59
ER -
TY - JOUR
AB - This paper provides an a priori error analysis of a localized orthogonal decomposition method for the numerical stochastic homogenization of a model random diffusion problem. If the uniformly elliptic and bounded random coefficient field of the model problem is stationary and satisfies a quantitative decorrelation assumption in the form of the spectral gap inequality, then the expected $L^2$ error of the method can be estimated, up to logarithmic factors, by $H+(\varepsilon/H)^{d/2}$, $\varepsilon$ being the small correlation length of the random coefficient and $H$ the width of the coarse finite element mesh that determines the spatial resolution. The proof bridges recent results of numerical homogenization and quantitative stochastic homogenization.
AU - Fischer, Julian L
AU - Gallistl, Dietmar
AU - Peterseim, Dietmar
ID - 9352
IS - 2
JF - SIAM Journal on Numerical Analysis
SN - 0036-1429
TI - A priori error analysis of a numerical stochastic homogenization method
VL - 59
ER -
TY - JOUR
AB - We consider the many-body quantum evolution of a factorized initial data, in the mean-field regime. We show that fluctuations around the limiting Hartree dynamics satisfy large deviation estimates that are consistent with central limit theorems that have been established in the last years.
AU - Kirkpatrick, Kay
AU - Rademacher, Simone Anna Elvira
AU - Schlein, Benjamin
ID - 9351
JF - Annales Henri Poincare
SN - 1424-0637
TI - A large deviation principle in many-body quantum dynamics
ER -
TY - JOUR
AB - We consider the stochastic quantization of a quartic double-well energy functional in the semiclassical regime and derive optimal asymptotics for the exponentially small splitting of the ground state energy. Our result provides an infinite-dimensional version of some sharp tunneling estimates known in finite dimensions for semiclassical Witten Laplacians in degree zero. From a stochastic point of view it proves that the L2 spectral gap of the stochastic one-dimensional Allen-Cahn equation in finite volume satisfies a Kramers-type formula in the limit of vanishing noise. We work with finite-dimensional lattice approximations and establish semiclassical estimates which are uniform in the dimension. Our key estimate shows that the constant separating the two exponentially small eigenvalues from the rest of the spectrum can be taken independently of the dimension.
AU - Brooks, Morris
AU - Di Gesù, Giacomo
ID - 9348
IS - 3
JF - Journal of Functional Analysis
SN - 00221236
TI - Sharp tunneling estimates for a double-well model in infinite dimension
VL - 281
ER -
TY - COMP
AB - This archive contains the missing sweater mesh animations and displacement models for the code of "Mechanics-Aware Deformation of Yarn Pattern Geometry"
Code Repository: https://git.ist.ac.at/gsperl/MADYPG
AU - Sperl, Georg
AU - Narain, Rahul
AU - Wojtan, Christopher J
ID - 9327
TI - Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)
ER -
TY - JOUR
AB - The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development.
AU - Lenne, Pierre François
AU - Munro, Edwin
AU - Heemskerk, Idse
AU - Warmflash, Aryeh
AU - Bocanegra, Laura
AU - Kishi, Kasumi
AU - Kicheva, Anna
AU - Long, Yuchen
AU - Fruleux, Antoine
AU - Boudaoud, Arezki
AU - Saunders, Timothy E.
AU - Caldarelli, Paolo
AU - Michaut, Arthur
AU - Gros, Jerome
AU - Maroudas-Sacks, Yonit
AU - Keren, Kinneret
AU - Hannezo, Edouard B
AU - Gartner, Zev J.
AU - Stormo, Benjamin
AU - Gladfelter, Amy
AU - Rodrigues, Alan
AU - Shyer, Amy
AU - Minc, Nicolas
AU - Maître, Jean Léon
AU - Di Talia, Stefano
AU - Khamaisi, Bassma
AU - Sprinzak, David
AU - Tlili, Sham
ID - 9349
IS - 4
JF - Physical biology
TI - Roadmap for the multiscale coupling of biochemical and mechanical signals during development
VL - 18
ER -
TY - JOUR
AB - Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair.
AU - Inglés Prieto, Álvaro
AU - Furthmann, Nikolas
AU - Crossman, Samuel H.
AU - Tichy, Alexandra Madelaine
AU - Hoyer, Nina
AU - Petersen, Meike
AU - Zheden, Vanessa
AU - Bicher, Julia
AU - Gschaider-Reichhart, Eva
AU - György, Attila
AU - Siekhaus, Daria E
AU - Soba, Peter
AU - Winklhofer, Konstanze F.
AU - Janovjak, Harald L
ID - 9363
IS - 4
JF - PLoS genetics
TI - Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease
VL - 17
ER -
TY - JOUR
AB - While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches.
AU - Ojavee, Sven E
AU - Kousathanas, Athanasios
AU - Trejo Banos, Daniel
AU - Orliac, Etienne J
AU - Patxot, Marion
AU - Lall, Kristi
AU - Magi, Reedik
AU - Fischer, Krista
AU - Kutalik, Zoltan
AU - Robinson, Matthew Richard
ID - 8430
IS - 1
JF - Nature Communications
TI - Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis
VL - 12
ER -
TY - JOUR
AB - The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM.
AU - Gast, Matthieu
AU - Kadzioch, Nicole P.
AU - Milius, Doreen
AU - Origgi, Francesco
AU - Plattet, Philippe
ID - 9361
IS - 2
JF - mSphere
TI - Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein
VL - 6
ER -