TY - DATA
AB - This .zip File contains the data for figures presented in the main text and supplementary material of "A singlet triplet hole spin qubit in planar Ge" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python.
AU - Jirovec, Daniel
ID - 9323
TI - Research data for "A singlet-triplet hole spin qubit planar Ge"
ER -
TY - CONF
AB - In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision.
AU - Henzinger, Thomas A
AU - Sarac, Naci E
ID - 9356
T2 - Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science
TI - Quantitative and approximate monitoring
ER -
TY - CONF
AB - The convex grabbing game is a game where two players, Alice and Bob, alternate taking extremal points from the convex hull of a point set on the plane. Rational weights are given to the points. The goal of each player is to maximize the total weight over all points that they obtain. We restrict the setting to the case of binary weights. We show a construction of an arbitrarily large odd-sized point set that allows Bob to obtain almost 3/4 of the total weight. This construction answers a question asked by Matsumoto, Nakamigawa, and Sakuma in [Graphs and Combinatorics, 36/1 (2020)]. We also present an arbitrarily large even-sized point set where Bob can obtain the entirety of the total weight. Finally, we discuss conjectures about optimum moves in the convex grabbing game for both players in general.
AU - Dvorak, Martin
AU - Nicholson, Sara
ID - 9592
KW - convex grabbing game
KW - graph grabbing game
KW - combinatorial game
KW - convex geometry
T2 - Proceedings of the 33rd Canadian Conference on Computational Geometry
TI - Massively winning configurations in the convex grabbing game on the plane
ER -
TY - JOUR
AB - We investigate how the critical driving amplitude at the Floquet many-body localized (MBL) to ergodic phase transition differs between smooth and nonsmooth drives. To this end, we numerically study a disordered spin-1/2 chain which is periodically driven by a sine or square-wave drive over a wide range of driving frequencies. In both cases the critical driving amplitude increases monotonically with the frequency, and at large frequencies it is identical for the two drives. However, at low and intermediate frequencies the critical amplitude of the square-wave drive depends strongly on the frequency, while that of the sinusoidal drive is almost constant over a wide frequency range. By analyzing the density of drive-induced resonances we conclude that this difference is due to resonances induced by the higher harmonics which are present (absent) in the Fourier spectrum of the square-wave (sine) drive. Furthermore, we suggest a numerically efficient method for estimating the frequency dependence of the critical driving amplitudes for different drives which is based on calculating the density of drive-induced resonances. We conclude that delocalization occurs once the density of drive-induced resonances reaches a critical value determined only by the static system.
AU - Diringer, Asaf A.
AU - Gulden, Tobias
ID - 8198
IS - 21
JF - Physical Review B
SN - 24699950
TI - Impact of drive harmonics on the stability of Floquet many-body localization
VL - 103
ER -
TY - JOUR
AB - When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability.
AU - Aichholzer, Oswin
AU - Akitaya, Hugo A.
AU - Cheung, Kenneth C.
AU - Demaine, Erik D.
AU - Demaine, Martin L.
AU - Fekete, Sándor P.
AU - Kleist, Linda
AU - Kostitsyna, Irina
AU - Löffler, Maarten
AU - Masárová, Zuzana
AU - Mundilova, Klara
AU - Schmidt, Christiane
ID - 8317
JF - Computational Geometry: Theory and Applications
SN - 09257721
TI - Folding polyominoes with holes into a cube
VL - 93
ER -
TY - JOUR
AB - Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.
AU - Lombardi, Fabrizio
AU - Shriki, Oren
AU - Herrmann, Hans J
AU - de Arcangelis, Lucilla
ID - 7463
JF - Neurocomputing
SN - 09252312
TI - Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches
ER -
TY - CONF
AB - Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness.
AU - Corbet, René
AU - Kerber, Michael
AU - Lesnick, Michael
AU - Osang, Georg F
ID - 9605
SN - 18688969
T2 - Leibniz International Proceedings in Informatics
TI - Computing the multicover bifiltration
VL - 189
ER -
TY - JOUR
AB - The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science.
AU - Bluvstein, D.
AU - Omran, A.
AU - Levine, H.
AU - Keesling, A.
AU - Semeghini, G.
AU - Ebadi, S.
AU - Wang, T. T.
AU - Michailidis, Alexios
AU - Maskara, N.
AU - Ho, W. W.
AU - Choi, S.
AU - Serbyn, Maksym
AU - Greiner, M.
AU - Vuletić, V.
AU - Lukin, M. D.
ID - 9618
IS - 6536
JF - Science
KW - Multidisciplinary
SN - 0036-8075
TI - Controlling quantum many-body dynamics in driven Rydberg atom arrays
VL - 371
ER -
TY - JOUR
AB - As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods.
AU - Ramezani-Kebrya, Ali
AU - Faghri, Fartash
AU - Markov, Ilya
AU - Aksenov, Vitalii
AU - Alistarh, Dan-Adrian
AU - Roy, Daniel M.
ID - 9571
IS - 114
JF - Journal of Machine Learning Research
SN - 15324435
TI - NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization
VL - 22
ER -
TY - JOUR
AB - The set of known stable phases of water may not be complete, and some of the phase boundaries between them are fuzzy. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the phase diagram at three hybrid density-functional-theory levels of approximation, accounting for thermal and nuclear fluctuations as well as proton disorder. Such calculations are only made tractable because we combine machine-learning methods and advanced free-energy techniques. The computed phase diagram is in qualitative agreement with experiment, particularly at pressures ≲ 8000 bar, and the discrepancy in chemical potential is comparable with the subtle uncertainties introduced by proton disorder and the spread between the three hybrid functionals. None of the hypothetical ice phases considered is thermodynamically stable in our calculations, suggesting the completeness of the experimental water phase diagram in the region considered. Our work demonstrates the feasibility of predicting the phase diagram of a polymorphic system from first principles and provides a thermodynamic way of testing the limits of quantum-mechanical calculations.
AU - Reinhardt, Aleks
AU - Cheng, Bingqing
ID - 9669
IS - 1
JF - Nature Communications
TI - Quantum-mechanical exploration of the phase diagram of water
VL - 12
ER -
TY - JOUR
AB - Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain.
AU - Venturino, Alessandro
AU - Schulz, Rouven
AU - De Jesús-Cortés, Héctor
AU - Maes, Margaret E
AU - Nagy, Balint
AU - Reilly-Andújar, Francis
AU - Colombo, Gloria
AU - Cubero, Ryan J
AU - Schoot Uiterkamp, Florianne E
AU - Bear, Mark F.
AU - Siegert, Sandra
ID - 9642
IS - 1
JF - Cell Reports
TI - Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain
VL - 36
ER -
TY - JOUR
AB - At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation.
AU - Fredes, Felipe
AU - Shigemoto, Ryuichi
ID - 9641
JF - Neurobiology of Learning and Memory
SN - 10747427
TI - The role of hippocampal mossy cells in novelty detection
VL - 183
ER -
TY - JOUR
AB - The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.
AU - Huber, David
AU - Marchukov, Oleksandr V.
AU - Hammer, Hans Werner
AU - Volosniev, Artem
ID - 9679
IS - 6
JF - New Journal of Physics
TI - Morphology of three-body quantum states from machine learning
VL - 23
ER -
TY - JOUR
AB - To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.
AU - Gao, Z
AU - Chen, Z
AU - Cui, Y
AU - Ke, M
AU - Xu, H
AU - Xu, Q
AU - Chen, J
AU - Li, Y
AU - Huang, L
AU - Zhao, H
AU - Huang, D
AU - Mai, S
AU - Xu, T
AU - Liu, X
AU - Li, S
AU - Guan, Y
AU - Yang, W
AU - Friml, Jiří
AU - Petrášek, J
AU - Zhang, J
AU - Chen, X
ID - 9657
JF - Plant Cell
SN - 1040-4651
TI - GmPIN-dependent polar auxin transport is involved in soybean nodule development
ER -
TY - GEN
AB - Real-world data typically contain a large number of features that are often heterogeneous in nature, relevance, and also units of measure. When assessing the similarity between data points, one can build various distance measures using subsets of these features. Using the fewest features but still retaining sufficient information about the system is crucial in many statistical learning approaches, particularly when data are sparse. We introduce a statistical test that can assess the relative information retained when using two different distance measures, and determine if they are equivalent, independent, or if one is more informative than the other. This in turn allows finding the most informative distance measure out of a pool of candidates. The approach is applied to find the most relevant policy variables for controlling the Covid-19 epidemic and to find compact yet informative representations of atomic structures, but its potential applications are wide ranging in many branches of science.
AU - Glielmo, Aldo
AU - Zeni, Claudio
AU - Cheng, Bingqing
AU - Csanyi, Gabor
AU - Laio, Alessandro
ID - 9695
T2 - arXiv
TI - Ranking the information content of distance measures
ER -
TY - JOUR
AB - A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity.
AU - Valentini, Marco
AU - Peñaranda, Fernando
AU - Hofmann, Andrea C
AU - Brauns, Matthias
AU - Hauschild, Robert
AU - Krogstrup, Peter
AU - San-Jose, Pablo
AU - Prada, Elsa
AU - Aguado, Ramón
AU - Katsaros, Georgios
ID - 8910
IS - 6550
JF - Science
SN - 00368075
TI - Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states
VL - 373
ER -
TY - JOUR
AB - We compute the deficiency spaces of operators of the form 𝐻𝐴⊗̂ 𝐼+𝐼⊗̂ 𝐻𝐵, for symmetric 𝐻𝐴 and self-adjoint 𝐻𝐵. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of 𝐻𝐵 having discrete, non-degenerate spectrum.
AU - Lenz, Daniel
AU - Weinmann, Timon
AU - Wirth, Melchior
ID - 9627
JF - Proceedings of the Edinburgh Mathematical Society
SN - 00130915
TI - Self-adjoint extensions of bipartite Hamiltonians
ER -
TY - GEN
AB - We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.
AU - Dymond, Michael
AU - Kaluza, Vojtech
ID - 9651
T2 - arXiv
TI - Divergence of separated nets with respect to displacement equivalence
ER -
TY - GEN
AB - Most water in the universe may be superionic, and its thermodynamic and transport properties are crucial for planetary science but difficult to probe experimentally or theoretically. We use machine learning and free energy methods to overcome the limitations of quantum mechanical simulations, and characterize hydrogen diffusion, superionic transitions, and phase behaviors of water at extreme conditions. We predict that a close-packed superionic phase with mixed stacking is stable over a wide temperature and pressure range, while a body-centered cubic phase is only thermodynamically stable in a small window but is kinetically favored. Our phase boundaries, which are consistent with the existing-albeit scarce-experimental observations, help resolve the fractions of insulating ice, different superionic phases, and liquid water inside of ice giants.
AU - Cheng, Bingqing
AU - Bethkenhagen, Mandy
AU - Pickard, Chris J.
AU - Hamel, Sebastien
ID - 9696
T2 - arXiv
TI - Predicting the phase behaviors of superionic water at planetary conditions
ER -
TY - JOUR
AB - Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.
AU - Petrov, Tatjana
AU - Igler, Claudia
AU - Sezgin, Ali
AU - Henzinger, Thomas A
AU - Guet, Calin C
ID - 9647
JF - Theoretical Computer Science
SN - 03043975
TI - Long lived transients in gene regulation
ER -
TY - CONF
AB - We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.
AU - Wang, Jinyi
AU - Sun, Yican
AU - Fu, Hongfei
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
ID - 9646
SN - 9781450383912
T2 - Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation
TI - Quantitative analysis of assertion violations in probabilistic programs
ER -
TY - CONF
AB - We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.
We first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods.
AU - Asadi, Ali
AU - Chatterjee, Krishnendu
AU - Fu, Hongfei
AU - Goharshady, Amir Kafshdar
AU - Mahdavi, Mohammad
ID - 9645
SN - 9781450383912
T2 - Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation
TI - Polynomial reachability witnesses via Stellensätze
ER -
TY - CONF
AB - We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.
AU - Chatterjee, Krishnendu
AU - Goharshady, Ehsan Kafshdar
AU - Novotný, Petr
AU - Zikelic, Dorde
ID - 9644
SN - 9781450383912
T2 - Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation
TI - Proving non-termination by program reversal
ER -
TY - JOUR
AB - Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f : Rd → Rd−n. A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation T of the ambient space Rd. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently
fine triangulation T . This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary.
AU - Boissonnat, Jean-Daniel
AU - Wintraecken, Mathijs
ID - 9649
JF - Foundations of Computational Mathematics
TI - The topological correctness of PL approximations of isomanifolds
ER -
TY - GEN
AB - Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.
AU - Keith, John A.
AU - Valentin Vassilev-Galindo, Valentin
AU - Cheng, Bingqing
AU - Chmiela, Stefan
AU - Gastegger, Michael
AU - Müller, Klaus-Robert
AU - Tkatchenko, Alexandre
ID - 9698
T2 - arXiv
TI - Combining machine learning and computational chemistry for predictive insights into chemical systems
ER -
TY - CONF
AB - We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.
AU - Brandt, Sebastian
AU - Keller, Barbara
AU - Rybicki, Joel
AU - Suomela, Jukka
AU - Uitto, Jara
ID - 9678
SN - 9781450380706
T2 - Annual ACM Symposium on Parallelism in Algorithms and Architectures
TI - Efficient load-balancing through distributed token dropping
ER -
TY - CONF
AB - Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art.
AU - Boissonnat, Jean-Daniel
AU - Kachanovich, Siargey
AU - Wintraecken, Mathijs
ID - 9441
SN - 1868-8969
T2 - 37th International Symposium on Computational Geometry (SoCG 2021)
TI - Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations
VL - 189
ER -
TY - CONF
AB - In this note, we introduce a distributed twist on the classic coupon collector problem: a set of m collectors wish to each obtain a set of n coupons; for this, they can each sample coupons uniformly at random, but can also meet in pairwise interactions, during which they can exchange coupons. By doing so, they hope to reduce the number of coupons that must be sampled by each collector in order to obtain a full set. This extension is natural when considering real-world manifestations of the coupon collector phenomenon, and has been remarked upon and studied empirically (Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019).
We provide the first theoretical analysis for such a scenario. We find that “coupon collecting with friends” can indeed significantly reduce the number of coupons each collector must sample, and raises interesting connections to the more traditional variants of the problem. While our analysis is in most cases asymptotically tight, there are several open questions raised, regarding finer-grained analysis of both “coupon collecting with friends,” and of a long-studied variant of the original problem in which a collector requires multiple full sets of coupons.
AU - Alistarh, Dan-Adrian
AU - Davies, Peter
ID - 9620
SN - 0302-9743
T2 - Structural Information and Communication Complexity
TI - Collecting coupons is faster with friends
VL - 12810
ER -
TY - CONF
AB - Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.
AU - Garcia Soto, Miriam
AU - Henzinger, Thomas A
AU - Schilling, Christian
ID - 9200
KW - hybrid automaton
KW - membership
KW - system identification
SN - 9781450383394
T2 - HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control
TI - Synthesis of hybrid automata with affine dynamics from time-series data
ER -
TY - CONF
AB - Modeling a crystal as a periodic point set, we present a fingerprint consisting of density functionsthat facilitates the efficient search for new materials and material properties. We prove invarianceunder isometries, continuity, and completeness in the generic case, which are necessary featuresfor the reliable comparison of crystals. The proof of continuity integrates methods from discretegeometry and lattice theory, while the proof of generic completeness combines techniques fromgeometry with analysis. The fingerprint has a fast algorithm based on Brillouin zones and relatedinclusion-exclusion formulae. We have implemented the algorithm and describe its application tocrystal structure prediction.
AU - Edelsbrunner, Herbert
AU - Heiss, Teresa
AU - Kurlin , Vitaliy
AU - Smith, Philip
AU - Wintraecken, Mathijs
ID - 9345
SN - 1868-8969
T2 - 37th International Symposium on Computational Geometry (SoCG 2021)
TI - The density fingerprint of a periodic point set
VL - 189
ER -
TY - CONF
AB - matching is compatible to two or more labeled point sets of size n with labels {1,…,n} if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to two or more labeled point sets in general position in the plane. We show that for any two labeled convex sets of n points there exists a compatible matching with ⌊2n−−√⌋ edges. More generally, for any ℓ labeled point sets we construct compatible matchings of size Ω(n1/ℓ) . As a corresponding upper bound, we use probabilistic arguments to show that for any ℓ given sets of n points there exists a labeling of each set such that the largest compatible matching has O(n2/(ℓ+1)) edges. Finally, we show that Θ(logn) copies of any set of n points are necessary and sufficient for the existence of a labeling such that any compatible matching consists only of a single edge.
AU - Aichholzer, Oswin
AU - Arroyo Guevara, Alan M
AU - Masárová, Zuzana
AU - Parada, Irene
AU - Perz, Daniel
AU - Pilz, Alexander
AU - Tkadlec, Josef
AU - Vogtenhuber, Birgit
ID - 9296
SN - 03029743
T2 - 15th International Conference on Algorithms and Computation
TI - On compatible matchings
VL - 12635
ER -
TY - JOUR
AB - Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.
AU - Tkadlec, Josef
AU - Pavlogiannis, Andreas
AU - Chatterjee, Krishnendu
AU - Nowak, Martin A.
ID - 9640
IS - 1
JF - Nature Communications
TI - Fast and strong amplifiers of natural selection
VL - 12
ER -
TY - THES
AB - Deep learning is best known for its empirical success across a wide range of applications
spanning computer vision, natural language processing and speech. Of equal significance,
though perhaps less known, are its ramifications for learning theory: deep networks have
been observed to perform surprisingly well in the high-capacity regime, aka the overfitting
or underspecified regime. Classically, this regime on the far right of the bias-variance curve
is associated with poor generalisation; however, recent experiments with deep networks
challenge this view.
This thesis is devoted to investigating various aspects of underspecification in deep learning.
First, we argue that deep learning models are underspecified on two levels: a) any given
training dataset can be fit by many different functions, and b) any given function can be
expressed by many different parameter configurations. We refer to the second kind of
underspecification as parameterisation redundancy and we precisely characterise its extent.
Second, we characterise the implicit criteria (the inductive bias) that guide learning in the
underspecified regime. Specifically, we consider a nonlinear but tractable classification
setting, and show that given the choice, neural networks learn classifiers with a large margin.
Third, we consider learning scenarios where the inductive bias is not by itself sufficient to
deal with underspecification. We then study different ways of ‘tightening the specification’: i)
In the setting of representation learning with variational autoencoders, we propose a hand-
crafted regulariser based on mutual information. ii) In the setting of binary classification, we
consider soft-label (real-valued) supervision. We derive a generalisation bound for linear
networks supervised in this way and verify that soft labels facilitate fast learning. Finally, we
explore an application of soft-label supervision to the training of multi-exit models.
AU - Bui Thi Mai, Phuong
ID - 9418
TI - Underspecification in Deep Learning
ER -
TY - CONF
AB - We consider the problem ofdistributed mean estimation (DME), in which n machines are each given a local d-dimensional vector xv∈Rd, and must cooperate to estimate the mean of their inputs μ=1n∑nv=1xv, while minimizing total communication cost. DME is a fundamental construct in distributed machine learning, and there has been considerable work on variants of this problem, especially in the context of distributed variance reduction for stochastic gradients in parallel SGD. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an error bound in terms of this norm. However, in many real applications, the input vectors are concentrated around the correct output μ, but μ itself has large norm. In such cases, previous output error bounds perform poorly. In this paper, we show that output error bounds need not depend on input norm. We provide a method of quantization which allows distributed mean estimation to be performed with solution quality dependent only on the distance between inputs, not on input norm, and show an analogous result for distributed variance reduction. The technique is based on a new connection with lattice theory. We also provide lower bounds showing that the communication to error trade-off of our algorithms is asymptotically optimal. As the lattices achieving optimal bounds under l2-norm can be computationally impractical, we also present an extension which leverages easy-to-use cubic lattices, and is loose only up to a logarithmic factor ind. We show experimentally that our method yields practical improvements for common applications, relative to prior approaches.
AU - Davies, Peter
AU - Gurunanthan, Vijaykrishna
AU - Moshrefi, Niusha
AU - Ashkboos, Saleh
AU - Alistarh, Dan-Adrian
ID - 9543
T2 - 9th International Conference on Learning Representations
TI - New bounds for distributed mean estimation and variance reduction
ER -
TY - CONF
AB - We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks.
AU - Bui Thi Mai, Phuong
AU - Lampert, Christoph
ID - 9416
T2 - 9th International Conference on Learning Representations
TI - The inductive bias of ReLU networks on orthogonally separable data
ER -
TY - THES
AB - In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.
We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.
AU - Goharshady, Amir Kafshdar
ID - 8934
SN - 2663-337X
TI - Parameterized and algebro-geometric advances in static program analysis
ER -
TY - JOUR
AB - When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.
AU - Pȩkalski, J.
AU - Rzadkowski, Wojciech
AU - Panagiotopoulos, A. Z.
ID - 7956
IS - 20
JF - The Journal of chemical physics
TI - Shear-induced ordering in systems with competing interactions: A machine learning study
VL - 152
ER -
TY - JOUR
AB - Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of
mutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.
AU - Parenti, Ilaria
AU - Garcia Rabaneda, Luis E
AU - Schön, Hanna
AU - Novarino, Gaia
ID - 7957
IS - 8
JF - Trends in Neurosciences
SN - 01662236
TI - Neurodevelopmental disorders: From genetics to functional pathways
VL - 43
ER -
TY - JOUR
AB - Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces.
AU - Kalai, Gil
AU - Patakova, Zuzana
ID - 7960
JF - Discrete and Computational Geometry
SN - 01795376
TI - Intersection patterns of planar sets
VL - 64
ER -
TY - JOUR
AB - A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.
AU - Pach, János
AU - Reed, Bruce
AU - Yuditsky, Yelena
ID - 7962
IS - 4
JF - Discrete and Computational Geometry
SN - 01795376
TI - Almost all string graphs are intersection graphs of plane convex sets
VL - 63
ER -
TY - CONF
AB - For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).
For Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.
As our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem.
AU - Auerbach, Benedikt
AU - Giacon, Federico
AU - Kiltz, Eike
ID - 7966
SN - 0302-9743
T2 - Advances in Cryptology – EUROCRYPT 2020
TI - Everybody’s a target: Scalability in public-key encryption
VL - 12107
ER -
TY - JOUR
AB - Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role.
AU - Ghazaryan, Areg
AU - Paltiel, Yossi
AU - Lemeshko, Mikhail
ID - 7968
IS - 21
JF - The Journal of Physical Chemistry C
SN - 1932-7447
TI - Analytic model of chiral-induced spin selectivity
VL - 124
ER -
TY - JOUR
AB - Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state.
AU - Rao, Peng
AU - Serbyn, Maksym
ID - 7971
IS - 24
JF - Physical Review B
SN - 2469-9950
TI - Gully quantum Hall ferromagnetism in biased trilayer graphene
VL - 101
ER -
TY - JOUR
AB - The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.
AU - Kwak, WJ
AU - Sharon, D
AU - Xia, C
AU - Kim, H
AU - Johnson, LR
AU - Bruce, PG
AU - Nazar, LF
AU - Sun, YK
AU - Frimer, AA
AU - Noked, M
AU - Freunberger, Stefan Alexander
AU - Aurbach, D
ID - 7985
IS - 14
JF - Chemical Reviews
SN - 0009-2665
TI - Lithium-oxygen batteries and related systems: Potential, status, and future
VL - 120
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 - Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7990
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)
VL - 164
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 - 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 - When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.
AU - Perini, Samuel
AU - Rafajlović, Marina
AU - Westram, Anja M
AU - Johannesson, Kerstin
AU - Butlin, Roger K.
ID - 7995
IS - 7
JF - Evolution
SN - 00143820
TI - Assortative mating, sexual selection, and their consequences for gene flow in Littorina
VL - 74
ER -
TY - THES
AB - Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and
calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.
Here we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element
resonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.
AU - Kukucka, Josip
ID - 7996
TI - Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing
ER -
TY - JOUR
AB - Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal.
AU - Trejo Banos, D
AU - McCartney, DL
AU - Patxot, M
AU - Anchieri, L
AU - Battram, T
AU - Christiansen, C
AU - Costeira, R
AU - Walker, RM
AU - Morris, SW
AU - Campbell, A
AU - Zhang, Q
AU - Porteous, DJ
AU - McRae, AF
AU - Wray, NR
AU - Visscher, PM
AU - Haley, CS
AU - Evans, KL
AU - Deary, IJ
AU - McIntosh, AM
AU - Hemani, G
AU - Bell, JT
AU - Marioni, RE
AU - Robinson, Matthew Richard
ID - 7999
JF - Nature Communications
SN - 2041-1723
TI - Bayesian reassessment of the epigenetic architecture of complex traits
VL - 11
ER -
TY - JOUR
AB - Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network.
AU - Vandael, David H
AU - Borges Merjane, Carolina
AU - Zhang, Xiaomin
AU - Jonas, Peter M
ID - 8001
IS - 3
JF - Neuron
SN - 0896-6273
TI - Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation
VL - 107
ER -
TY - JOUR
AB - Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.
AU - Hörmayer, Lukas
AU - Montesinos López, Juan C
AU - Marhavá, Petra
AU - Benková, Eva
AU - Yoshida, Saiko
AU - Friml, Jiří
ID - 8002
IS - 26
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots
VL - 117
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 - CONF
AB - Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos.
AU - Kragl, Bernhard
AU - Enea, Constantin
AU - Henzinger, Thomas A
AU - Mutluergil, Suha Orhun
AU - Qadeer, Shaz
ID - 8012
SN - 9781450376136
T2 - Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation
TI - Inductive sequentialization of asynchronous programs
ER -
TY - THES
AB - Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”
In this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.
AU - Huszár, Kristóf
ID - 8032
SN - 2663-337X
TI - Combinatorial width parameters for 3-dimensional manifolds
ER -
TY - JOUR
AB - When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves.
AU - Collard, Ylona
AU - Grosjean, Galien M
AU - Vandewalle, Nicolas
ID - 8036
JF - Communications Physics
TI - Magnetically powered metachronal waves induce locomotion in self-assemblies
VL - 3
ER -
TY - JOUR
AB - Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics.
AU - Lukacisinova, Marta
AU - Fernando, Booshini
AU - Bollenbach, Mark Tobias
ID - 8037
JF - Nature Communications
TI - Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance
VL - 11
ER -
TY - JOUR
AB - Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications.
AU - Fink, Johannes M
AU - Kalaee, M.
AU - Norte, R.
AU - Pitanti, A.
AU - Painter, O.
ID - 8038
IS - 3
JF - Quantum Science and Technology
TI - Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator
VL - 5
ER -
TY - JOUR
AB - We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.
AU - Boccato, Chiara
AU - Brennecke, Christian
AU - Cenatiempo, Serena
AU - Schlein, Benjamin
ID - 8042
IS - 7
JF - Journal of the European Mathematical Society
SN - 14359855
TI - The excitation spectrum of Bose gases interacting through singular potentials
VL - 22
ER -
TY - JOUR
AB - With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain.
AU - Paranjape, Chaitanya S
AU - Duguet, Yohann
AU - Hof, Björn
ID - 8043
JF - Journal of Fluid Mechanics
SN - 00221120
TI - Oblique stripe solutions of channel flow
VL - 897
ER -
TY - JOUR
AB - Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability.
AU - Bouchal, Roza
AU - Li, Zhujie
AU - Bongu, Chandra
AU - Le Vot, Steven
AU - Berthelot, Romain
AU - Rotenberg, Benjamin
AU - Favier, Frederic
AU - Freunberger, Stefan Alexander
AU - Salanne, Mathieu
AU - Fontaine, Olivier
ID - 8057
IS - 37
JF - Angewandte Chemie
SN - 0044-8249
TI - Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte
VL - 132
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 - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the
mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.
AU - Varzi, Alberto
AU - Thanner, Katharina
AU - Scipioni, Roberto
AU - Di Lecce, Daniele
AU - Hassoun, Jusef
AU - Dörfler, Susanne
AU - Altheus, Holger
AU - Kaskel, Stefan
AU - Prehal, Christian
AU - Freunberger, Stefan Alexander
ID - 8067
KW - Battery
KW - Lithium metal
KW - Lithium-sulphur
KW - Lithium-air
KW - All-solid-state
SN - 2664-1690
TI - Current status and future perspectives of Lithium metal batteries
ER -
TY - JOUR
AB - The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods.
AU - Shehu, Yekini
AU - Iyiola, Olaniyi S.
ID - 8077
JF - Applied Numerical Mathematics
SN - 0168-9274
TI - Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence
VL - 157
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 - Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.
AU - Lombardi, Fabrizio
AU - Gómez-Extremera, Manuel
AU - Bernaola-Galván, Pedro
AU - Vetrivelan, Ramalingam
AU - Saper, Clifford B.
AU - Scammell, Thomas E.
AU - Ivanov, Plamen Ch.
ID - 8084
IS - 1
JF - Journal of Neuroscience
SN - 0270-6474
TI - Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake
VL - 40
ER -
TY - JOUR
AB - In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.
AU - Seiringer, Robert
AU - Yngvason, Jakob
ID - 8091
JF - Journal of Statistical Physics
SN - 00224715
TI - Emergence of Haldane pseudo-potentials in systems with short-range interactions
VL - 181
ER -
TY - CHAP
AB - Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html.
AU - Royer, Amélie
AU - Bousmalis, Konstantinos
AU - Gouws, Stephan
AU - Bertsch, Fred
AU - Mosseri, Inbar
AU - Cole, Forrester
AU - Murphy, Kevin
ED - Singh, Richa
ED - Vatsa, Mayank
ED - Patel, Vishal M.
ED - Ratha, Nalini
ID - 8092
SN - 9783030306717
T2 - Domain Adaptation for Visual Understanding
TI - XGAN: Unsupervised image-to-image translation for many-to-many mappings
ER -
TY - DATA
AB - Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology.
AU - Kavcic, Bor
ID - 8097
KW - Escherichia coli
KW - antibiotic combinations
KW - translation
KW - growth laws
KW - drug interactions
KW - bacterial physiology
KW - translation inhibitors
TI - Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics"
ER -
TY - JOUR
AB - Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.
AU - Gammerdinger, William J
AU - Toups, Melissa A
AU - Vicoso, Beatriz
ID - 8099
IS - 6
JF - Molecular Ecology Resources
SN - 1755-098X
TI - Disagreement in FST estimators: A case study from sex chromosomes
VL - 20
ER -
TY - JOUR
AB - By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.
AU - Grosjean, Galien M
AU - Wald, Sebastian
AU - Sobarzo Ponce, Juan Carlos A
AU - Waitukaitis, Scott R
ID - 8101
IS - 8
JF - Physical Review Materials
KW - electric charge
KW - tribocharging
KW - soft matter
KW - granular materials
KW - polymers
TI - Quantitatively consistent scale-spanning model for same-material tribocharging
VL - 4
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 - GEN
AB - Context, such as behavioral state, is known to modulate memory formation and retrieval, but is usually ignored in associative memory models. Here, we propose several types of contextual modulation for associative memory networks that greatly increase their performance. In these networks, context inactivates specific neurons and connections, which modulates the effective connectivity of the network. Memories are stored only by the active components, thereby reducing interference from memories acquired in other contexts. Such networks exhibit several beneficial characteristics, including enhanced memory capacity, high robustness to noise, increased robustness to memory overloading, and better memory retention during continual learning. Furthermore, memories can be biased to have different relative strengths, or even gated on or off, according to contextual cues, providing a candidate model for cognitive control of memory and efficient memory search. An external context-encoding network can dynamically switch the memory network to a desired state, which we liken to experimentally observed contextual signals in prefrontal cortex and hippocampus. Overall, our work illustrates the benefits of organizing memory around context, and provides an important link between behavioral studies of memory and mechanistic details of neural circuits.SIGNIFICANCEMemory is context dependent — both encoding and recall vary in effectiveness and speed depending on factors like location and brain state during a task. We apply this idea to a simple computational model of associative memory through contextual gating of neurons and synaptic connections. Intriguingly, this results in several advantages, including vastly enhanced memory capacity, better robustness, and flexible memory gating. Our model helps to explain (i) how gating and inhibition contribute to memory processes, (ii) how memory access dynamically changes over time, and (iii) how context representations, such as those observed in hippocampus and prefrontal cortex, may interact with and control memory processes.
AU - Podlaski, William F.
AU - Agnes, Everton J.
AU - Vogels, Tim P
ID - 8125
T2 - bioRxiv
TI - Context-modular memory networks support high-capacity, flexible, and robust associative memories
ER -
TY - JOUR
AB - Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.
AU - Agnes, Everton J.
AU - Luppi, Andrea I.
AU - Vogels, Tim P
ID - 8126
IS - 50
JF - The Journal of Neuroscience
TI - Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields
VL - 40
ER -
TY - JOUR
AB - Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.
AU - Gonçalves, Pedro J.
AU - Lueckmann, Jan-Matthis
AU - Deistler, Michael
AU - Nonnenmacher, Marcel
AU - Öcal, Kaan
AU - Bassetto, Giacomo
AU - Chintaluri, Chaitanya
AU - Podlaski, William F.
AU - Haddad, Sara A.
AU - Vogels, Tim P
AU - Greenberg, David S.
AU - Macke, Jakob H.
ID - 8127
JF - eLife
TI - Training deep neural density estimators to identify mechanistic models of neural dynamics
VL - 9
ER -
TY - JOUR
AB - We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.
AU - Bossmann, Lea
ID - 8130
IS - 11
JF - Archive for Rational Mechanics and Analysis
SN - 0003-9527
TI - Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons
VL - 238
ER -
TY - JOUR
AB - The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes.
AU - Basilico, Bernadette
AU - Morandell, Jasmin
AU - Novarino, Gaia
ID - 8131
IS - 12
JF - Current Opinion in Genetics and Development
SN - 0959437X
TI - Molecular mechanisms for targeted ASD treatments
VL - 65
ER -
TY - JOUR
AB - We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.
AU - Mayer, Simon
AU - Seiringer, Robert
ID - 8134
IS - 6
JF - Journal of Mathematical Physics
SN - 00222488
TI - The free energy of the two-dimensional dilute Bose gas. II. Upper bound
VL - 61
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 - JOUR
AB - Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.
AU - Zhang, J
AU - Mazur, E
AU - Balla, J
AU - Gallei, Michelle C
AU - Kalousek, P
AU - Medveďová, Z
AU - Li, Y
AU - Wang, Y
AU - Prat, Tomas
AU - Vasileva, Mina K
AU - Reinöhl, V
AU - Procházka, S
AU - Halouzka, R
AU - Tarkowski, P
AU - Luschnig, C
AU - Brewer, PB
AU - Friml, Jiří
ID - 8138
IS - 1
JF - Nature Communications
SN - 2041-1723
TI - Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
VL - 11
ER -
TY - JOUR
AB - Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.
AU - Montesinos López, Juan C
AU - Abuzeineh, A
AU - Kopf, Aglaja
AU - Juanes Garcia, Alba
AU - Ötvös, Krisztina
AU - Petrášek, J
AU - Sixt, Michael K
AU - Benková, Eva
ID - 8142
IS - 17
JF - The Embo Journal
SN - 0261-4189
TI - Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage
VL - 39
ER -
TY - THES
AB - In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as
transcriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal
non-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.
In the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are
hard to evolve or maintain.
AU - Grah, Rok
ID - 8155
SN - 2663-337X
TI - Gene regulation across scales – how biophysical constraints shape evolution
ER -
TY - THES
AB - We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.
AU - Avvakumov, Sergey
ID - 8156
TI - Topological methods in geometry and discrete mathematics
ER -
TY - JOUR
AB - In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.
AU - Laukoter, Susanne
AU - Pauler, Florian
AU - Beattie, Robert J
AU - Amberg, Nicole
AU - Hansen, Andi H
AU - Streicher, Carmen
AU - Penz, Thomas
AU - Bock, Christoph
AU - Hippenmeyer, Simon
ID - 8162
IS - 6
JF - Neuron
SN - 0896-6273
TI - Cell-type specificity of genomic imprinting in cerebral cortex
VL - 107
ER -
TY - JOUR
AB - Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.
AU - Vegter, Gert
AU - Wintraecken, Mathijs
ID - 8163
IS - 2
JF - Studia Scientiarum Mathematicarum Hungarica
SN - 0081-6906
TI - Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes
VL - 57
ER -
TY - JOUR
AB - The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.
AU - Stankowski, Sean
AU - Westram, Anja M
AU - Zagrodzka, Zuzanna B.
AU - Eyres, Isobel
AU - Broquet, Thomas
AU - Johannesson, Kerstin
AU - Butlin, Roger K.
ID - 8167
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
TI - The evolution of strong reproductive isolation between sympatric intertidal snails
VL - 375
ER -
TY - JOUR
AB - Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.
AU - Kulmuni, Jonna
AU - Butlin, Roger K.
AU - Lucek, Kay
AU - Savolainen, Vincent
AU - Westram, Anja M
ID - 8168
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological sciences
SN - 0962-8436
TI - Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers
VL - 375
ER -
TY - JOUR
AB - Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function
of time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct
peaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and
centrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For
CS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the
gas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in
detail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in
helium droplets introduced here should apply to a range of molecules and complexes.
AU - Chatterley, Adam S.
AU - Christiansen, Lars
AU - Schouder, Constant A.
AU - Jørgensen, Anders V.
AU - Shepperson, Benjamin
AU - Cherepanov, Igor
AU - Bighin, Giacomo
AU - Zillich, Robert E.
AU - Lemeshko, Mikhail
AU - Stapelfeldt, Henrik
ID - 8170
IS - 1
JF - Physical Review Letters
SN - 00319007
TI - Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains
VL - 125
ER -
TY - COMP
AU - Hauschild, Robert
ID - 8181
TI - Amplified centrosomes in dendritic cells promote immune cell effector functions
ER -
TY - CONF
AB - Numerous methods have been proposed for probabilistic generative modelling of
3D objects. However, none of these is able to produce textured objects, which
renders them of limited use for practical tasks. In this work, we present the
first generative model of textured 3D meshes. Training such a model would
traditionally require a large dataset of textured meshes, but unfortunately,
existing datasets of meshes lack detailed textures. We instead propose a new
training methodology that allows learning from collections of 2D images without
any 3D information. To do so, we train our model to explain a distribution of
images by modelling each image as a 3D foreground object placed in front of a
2D background. Thus, it learns to generate meshes that when rendered, produce
images similar to those in its training set.
A well-known problem when generating meshes with deep networks is the
emergence of self-intersections, which are problematic for many use-cases. As a
second contribution we therefore introduce a new generation process for 3D
meshes that guarantees no self-intersections arise, based on the physical
intuition that faces should push one another out of the way as they move.
We conduct extensive experiments on our approach, reporting quantitative and
qualitative results on both synthetic data and natural images. These show our
method successfully learns to generate plausible and diverse textured 3D
samples for five challenging object classes.
AU - Henderson, Paul M
AU - Tsiminaki, Vagia
AU - Lampert, Christoph
ID - 8186
T2 - Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition
TI - Leveraging 2D data to learn textured 3D mesh generation
ER -
TY - CONF
AB - Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.
AU - Baranowski, Marek
AU - He, Shaobo
AU - Lechner, Mathias
AU - Nguyen, Thanh Son
AU - Rakamarić, Zvonimir
ID - 8194
SN - 03029743
T2 - Automated Reasoning
TI - An SMT theory of fixed-point arithmetic
VL - 12166
ER -
TY - CONF
AB - This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.
AU - Kragl, Bernhard
AU - Qadeer, Shaz
AU - Henzinger, Thomas A
ID - 8195
SN - 0302-9743
T2 - Computer Aided Verification
TI - Refinement for structured concurrent programs
VL - 12224
ER -
TY - JOUR
AB - This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.
AU - Shehu, Yekini
AU - Dong, Qiao-Li
AU - Liu, Lu-Lu
AU - Yao, Jen-Chih
ID - 8196
JF - Optimization and Engineering
SN - 1389-4420
TI - New strong convergence method for the sum of two maximal monotone operators
ER -
TY - JOUR
AB - We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.
AU - Gulden, Tobias
AU - Berg, Erez
AU - Rudner, Mark Spencer
AU - Lindner, Netanel
ID - 8199
JF - SciPost Physics
SN - 2542-4653
TI - Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps
VL - 9
ER -
TY - JOUR
AB - Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits.
AU - Katsaros, Georgios
AU - Kukucka, Josip
AU - Vukušić, Lada
AU - Watzinger, Hannes
AU - Gao, Fei
AU - Wang, Ting
AU - Zhang, Jian-Jun
AU - Held, Karsten
ID - 8203
IS - 7
JF - Nano Letters
SN - 1530-6984
TI - Zero field splitting of heavy-hole states in quantum dots
VL - 20
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 - JOUR
AB - We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic.
AU - Boissonnat, Jean-Daniel
AU - Dyer, Ramsay
AU - Ghosh, Arijit
AU - Lieutier, Andre
AU - Wintraecken, Mathijs
ID - 8248
JF - Discrete and Computational Geometry
SN - 0179-5376
TI - Local conditions for triangulating submanifolds of Euclidean space
ER -