TY - JOUR
AB - The brain efficiently performs nonlinear computations through its intricate networks of spiking neurons, but how this is done remains elusive. While nonlinear computations can be implemented successfully in spiking neural networks, this requires supervised training and the resulting connectivity can be hard to interpret. In contrast, the required connectivity for any computation in the form of a linear dynamical system can be directly derived and understood with the spike coding network (SCN) framework. These networks also have biologically realistic activity patterns and are highly robust to cell death. Here we extend the SCN framework to directly implement any polynomial dynamical system, without the need for training. This results in networks requiring a mix of synapse types (fast, slow, and multiplicative), which we term multiplicative spike coding networks (mSCNs). Using mSCNs, we demonstrate how to directly derive the required connectivity for several nonlinear dynamical systems. We also show how to carry out higher-order polynomials with coupled networks that use only pair-wise multiplicative synapses, and provide expected numbers of connections for each synapse type. Overall, our work demonstrates a novel method for implementing nonlinear computations in spiking neural networks, while keeping the attractive features of standard SCNs (robustness, realistic activity patterns, and interpretable connectivity). Finally, we discuss the biological plausibility of our approach, and how the high accuracy and robustness of the approach may be of interest for neuromorphic computing.
AU - Nardin, Michele
AU - Phillips, James W.
AU - Podlaski, William F.
AU - Keemink, Sander W.
ID - 10635
JF - Peer Community Journal
TI - Nonlinear computations in spiking neural networks through multiplicative synapses
VL - 1
ER -
TY - GEN
AB - The purpose of this application note is to demonstrate a working example of a superconducting qubit measurement in a Bluefors cryostat using the Keysight quantum control hardware. Our motivation is twofold. First, we provide pre-qualification data that the Bluefors cryostat, including filtering and wiring, can support long-lived qubits. Second, we demonstrate that the Keysight system (controlled using Labber) provides a straightforward solution to perform these characterization measurements. This document is intended as a brief guide for starting an experimental platform for testing superconducting qubits. The setup described here is an immediate jumping off point for a suite of applications including testing quantum logical gates, quantum optics with microwaves, or even using the qubit itself as a sensitive probe of local electromagnetic fields. Qubit measurements rely on high performance of both the physical sample environment and the measurement electronics. An overview of the cryogenic system is shown in Figure 1, and an overview of the integration between the electronics and cryostat (including wiring details) is shown in Figure 2.
AU - Lake, Russell
AU - Simbierowicz, Slawomir
AU - Krantz, Philip
AU - Hassani, Farid
AU - Fink, Johannes M
ID - 10644
KW - Application note
TI - The Bluefors dilution refrigerator as an integrated quantum measurement system
ER -
TY - GEN
AB - Superconducting qubits have emerged as a highly versatile and useful platform for quantum technological applications [1]. Bluefors and Zurich Instruments have supported the growth of this field from the 2010s onwards by providing well-engineered and reliable measurement infrastructure [2]– [6]. Having a long and stable qubit lifetime is a critical system property. Therefore, considerable effort has already gone into measuring qubit energy-relaxation timescales and their fluctuations, see Refs. [7]–[10] among others. Accurately extracting the statistics of a quantum device requires users to perform time consuming measurements. One measurement challenge is that the detection of the state-dependent
response of a superconducting resonator due to a dispersively-coupled qubit requires an inherently low signal level. Consequently, measurements must be performed using a microwave probe that contains only a few microwave photons. Improving the signal-to-noise ratio (SNR) by using near-quantum limited parametric amplifiers as well as the use of optimized signal processing enabled by efficient room temperature instrumentation help to reduce measurement time. An empirical observation for fixed frequency transmons from recent literature is that as the energy-relaxation time 𝑇𝑇1 increases, so do its natural temporal fluctuations [7], [10]. This necessitates many repeated measurements to understand the statistics (see for example, Ref. [10]). In addition, as state-of-the-art qubits increase in lifetime, longer
measurement times are expected to obtain accurate statistics. As described below, the scaling of the widths of the qubit energy-relaxation distributions also reveal clues about the origin of the energy-relaxation.
AU - Simbierowicz, Slawomir
AU - Shi, Chunyan
AU - Collodo, Michele
AU - Kirste, Moritz
AU - Hassani, Farid
AU - Fink, Johannes M
AU - Bylander, Jonas
AU - Perez Lozano, Daniel
AU - Lake, Russell
ID - 10645
KW - Application note
TI - Qubit energy-relaxation statistics in the Bluefors quantum measurement system
ER -
TY - JOUR
AB - Harnessing the properties of vortices in superconductors is crucial for fundamental science and technological applications; thus, it has been an ongoing goal to locally probe and control vortices. Here, we use a scanning probe technique that enables studies of vortex dynamics in superconducting systems by leveraging the resonant behavior of a raster-scanned, magnetic-tipped cantilever. This experimental setup allows us to image and control vortices, as well as extract key energy scales of the vortex interactions. Applying this technique to lattices of superconductor island arrays on a metal, we obtain a variety of striking spatial patterns that encode information about the energy landscape for vortices in the system. We interpret these patterns in terms of local vortex dynamics and extract the relative strengths of the characteristic energy scales in the system, such as the vortex-magnetic field and vortex-vortex interaction strengths, as well as the vortex chemical potential. We also demonstrate that the relative strengths of the interactions can be tuned and show how these interactions shift with an applied bias. The high degree of tunability and local nature of such vortex imaging and control not only enable new understanding of vortex interactions, but also have potential applications in more complex systems such as those relevant to quantum computing.
AU - Naibert, Tyler R.
AU - Polshyn, Hryhoriy
AU - Garrido-Menacho, Rita
AU - Durkin, Malcolm
AU - Wolin, Brian
AU - Chua, Victor
AU - Mondragon-Shem, Ian
AU - Hughes, Taylor
AU - Mason, Nadya
AU - Budakian, Raffi
ID - 10649
IS - 22
JF - Physical Review B
SN - 2469-9950
TI - Imaging and controlling vortex dynamics in mesoscopic superconductor-normal-metal-superconductor arrays
VL - 103
ER -
TY - CONF
AB - Electrons in the moiré flat bands of magic angle twisted bilayer graphene aligned to hexagonal boron nitride can break time reversal symmetry and open an interaction-driven, topological gap. The resulting magnetic order and associated quantized anomalous Hall effect have properties that diverge substantially from quantized anomalous Hall effects observed in other systems. I will present transport data and scanning probe magnetometry data acquired using a nanoSQUID-on-tip microscope. A quantitative analysis of the magnitude of the magnetization of the Chern magnet shows that the magnetic moment per moiré unit cell substantially exceeds 1 μB and grows rapidly in the topological gap, consistent with an orbital origin for the magnetic order. We find that the Barkhausen jumps observed in transport measurements can be mapped directly to microscopic motion of ferromagnetic domain walls. These domain walls are strongly pinned to disorder in the device and are reproducible across thermal cycles, suggesting coupling between the magnetic degrees of freedom and structural inhomogeneity.
AU - Tschirhart, Charles
AU - Serlin, Marec
AU - Polshyn, Hryhoriy
AU - Shragai, Avi G.
AU - Xia, Zhengchao
AU - Zhu, Jiacheng
AU - Zhang, Yuxuan
AU - Watanabe, Kenji
AU - Taniguchi, Takashi
AU - Huber, Martin E.
AU - Young, Andrea
ID - 10651
IS - 1
SN - 0003-0503
T2 - APS March Meeting 2021
TI - Probing orbital Chern ferromagnet phase in twisted bilayer graphene
VL - 66
ER -
TY - JOUR
AB - Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.
AU - Maes, Margaret E
AU - Wögenstein, Gabriele M.
AU - Colombo, Gloria
AU - Casado Polanco, Raquel
AU - Siegert, Sandra
ID - 10655
JF - Molecular Therapy - Methods and Clinical Development
TI - Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment
VL - 23
ER -
TY - CONF
AB - Robustness to variations in lighting conditions is a key objective for any deep vision system. To this end, our paper extends the receptive field of convolutional neural networks with two residual components, ubiquitous in the visual processing system of vertebrates: On-center and off-center pathways, with an excitatory center and inhibitory surround; OOCS for short. The On-center pathway is excited by the presence of a light stimulus in its center, but not in its surround, whereas the Off-center pathway is excited by the absence of a light stimulus in its center, but not in its surround. We design OOCS pathways via a difference of Gaussians, with their variance computed analytically from the size of the receptive fields. OOCS pathways complement each other in their response to light stimuli, ensuring this way a strong edge-detection capability, and as a result an accurate and robust inference under challenging lighting conditions. We provide extensive empirical evidence showing that networks supplied with OOCS pathways gain accuracy and illumination-robustness from the novel edge representation, compared to other baselines.
AU - Babaiee, Zahra
AU - Hasani, Ramin
AU - Lechner, Mathias
AU - Rus, Daniela
AU - Grosu, Radu
ID - 10668
SN - 2640-3498
T2 - Proceedings of the 38th International Conference on Machine Learning
TI - On-off center-surround receptive fields for accurate and robust image classification
VL - 139
ER -
TY - CONF
AB - Imitation learning enables high-fidelity, vision-based learning of policies within rich, photorealistic environments. However, such techniques often rely on traditional discrete-time neural models and face difficulties in generalizing to domain shifts by failing to account for the causal relationships between the agent and the environment. In this paper, we propose a theoretical and experimental framework for learning causal representations using continuous-time neural networks, specifically over their discrete-time counterparts. We evaluate our method in the context of visual-control learning of drones over a series of complex tasks, ranging from short- and long-term navigation, to chasing static and dynamic objects through photorealistic environments. Our results demonstrate that causal continuous-time
deep models can perform robust navigation tasks, where advanced recurrent models fail. These models learn complex causal control representations directly from raw visual inputs and scale to solve a variety of tasks using imitation learning.
AU - Vorbach, Charles J
AU - Hasani, Ramin
AU - Amini, Alexander
AU - Lechner, Mathias
AU - Rus, Daniela
ID - 10670
T2 - 35th Conference on Neural Information Processing Systems
TI - Causal navigation by continuous-time neural networks
ER -
TY - CONF
AB - Civl is a static verifier for concurrent programs designed around the conceptual framework of layered refinement,
which views the task of verifying a program as a sequence of program simplification steps each justified by its own invariant. Civl verifies a layered concurrent program that compactly expresses all the programs in this sequence and the supporting invariants. This paper presents the design and implementation of the Civl verifier.
AU - Kragl, Bernhard
AU - Qadeer, Shaz
ED - Ruzica, Piskac
ED - Whalen, Michael W.
ID - 10688
SN - 978-3-85448-046-4
T2 - Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design
TI - The Civl verifier
VL - 2
ER -
TY - CONF
AB - We experimentally investigate narrow and topologically nontrivial moiré minibands hosted by van der Waals heterostructures consisting of a graphene monolayer rotationally faulted with respect to a Bernal-stacked bilayer. At fillings ν= 1 and 3 electrons per moiré unit cell within these bands, we observe quantized anomalous Hall effects with Rxy≈h/2e2, indicative of spontaneous polarization of the system into a single valley-projected band with Chern number C= 2. Remarkably, we also observe the evidence of symmetry broken Chern insulator states at ν= 1.5 and 3.5. At ν= 3 we find that the sign of the quantum anomalous Hall effect can be reversed via field-effect control of the chemical potential. This curious effect arises from the magnetization contribution due to topological edge states, which drive a reversal of the total magnetization and thus a switch of the favored magnetic state. Remarkably, we find that this switch is hysteretic, which we use to demonstrate non-volatile electric-field-induced reversal of the magnetic state. Voltage control of magnetic states can be used to electrically pattern nonvolatile magnetic domain structures hosting chiral edge states, with applications ranging from reconfigurable microwave circuit elements to ultra-low-power magnetic memory.
AU - Polshyn, Hryhoriy
AU - Zhu, Jihang
AU - Kumar, Manish
AU - Zhang, Yuxuan
AU - Yang, Fangyuan
AU - Tschirhart, Charles
AU - Serlin, Marec
AU - Watanabe, Kenji
AU - Tanaguchi, Takashi
AU - MacDonald, Allan
AU - Young, Andrea
ID - 10692
IS - 1
SN - 0003-0503
T2 - APS March Meeting 2021
TI - Orbital Chern insulator states in twisted monolayer-bilayer graphene and electrical switching of topological and magnetic order
VL - 66
ER -
TY - CONF
AB - In a two-player zero-sum graph game the players move a token throughout a graph to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In bidding games, however, the players have budgets, and in each turn, we hold an “auction” (bidding) to determine which player moves the token: both players simultaneously submit bids and the higher bidder moves the token. The bidding mechanisms differ in their payment schemes. Bidding games were largely studied with variants of first-price bidding in which only the higher bidder pays his bid. We focus on all-pay bidding, where both players pay their bids. Finite-duration all-pay bidding games were studied and shown to be technically more challenging than their first-price counterparts. We study for the first time, infinite-duration all-pay bidding games. Our most interesting results are for mean-payoff objectives: we portray a complete picture for games played on strongly-connected graphs. We study both pure (deterministic) and mixed (probabilistic) strategies and completely characterize the optimal and almost-sure (with probability 1) payoffs the players can respectively guarantee. We show that mean-payoff games under all-pay bidding exhibit the intriguing mathematical properties of their first-price counterparts; namely, an equivalence with random-turn games in which in each turn, the player who moves is selected according to a (biased) coin toss. The equivalences for all-pay bidding are more intricate and unexpected than for first-price bidding.
AU - Avni, Guy
AU - Jecker, Ismael R
AU - Zikelic, Dorde
ED - Marx, Dániel
ID - 10694
SN - 978-1-61197-646-5
T2 - Proceedings of the 2021 ACM-SIAM Symposium on Discrete Algorithms
TI - Infinite-duration all-pay bidding games
ER -
TY - JOUR
AB - In this paper, we investigate the distribution of the maximum of partial sums of families of m -periodic complex-valued functions satisfying certain conditions. We obtain precise uniform estimates for the distribution function of this maximum in a near-optimal range. Our results apply to partial sums of Kloosterman sums and other families of ℓ -adic trace functions, and are as strong as those obtained by Bober, Goldmakher, Granville and Koukoulopoulos for character sums. In particular, we improve on the recent work of the third author for Birch sums. However, unlike character sums, we are able to construct families of m -periodic complex-valued functions which satisfy our conditions, but for which the Pólya–Vinogradov inequality is sharp.
AU - Autissier, Pascal
AU - Bonolis, Dante
AU - Lamzouri, Youness
ID - 10711
IS - 7
JF - Compositio Mathematica
KW - Algebra and Number Theory
SN - 0010-437X
TI - The distribution of the maximum of partial sums of Kloosterman sums and other trace functions
VL - 157
ER -
TY - JOUR
AB - We prove an adiabatic theorem for the Landau–Pekar equations. This allows us to derive new results on the accuracy of their use as effective equations for the time evolution generated by the Fröhlich Hamiltonian with large coupling constant α. In particular, we show that the time evolution of Pekar product states with coherent phonon field and the electron being trapped by the phonons is well approximated by the Landau–Pekar equations until times short compared to α2.
AU - Leopold, Nikolai K
AU - Rademacher, Simone Anna Elvira
AU - Schlein, Benjamin
AU - Seiringer, Robert
ID - 10738
IS - 7
JF - Analysis and PDE
SN - 2157-5045
TI - The Landau–Pekar equations: Adiabatic theorem and accuracy
VL - 14
ER -
TY - GEN
AB - Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a new variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of non-additive systems very well. In particular, we observe substantial improvement over the standard coherent state estimates in the most challenging intermediate coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications.
AU - Rzadkowski, Wojciech
AU - Lemeshko, Mikhail
AU - Mentink, Johan H.
ID - 10762
T2 - arXiv
TI - Artificial neural network states for non-additive systems
ER -
TY - GEN
AB - Given the abundance of applications of ranking in recent years, addressing fairness concerns around automated ranking systems becomes necessary for increasing the trust among end-users. Previous work on fair ranking has mostly focused on application-specific fairness notions, often tailored to online advertising, and it rarely considers learning as part of the process. In this
work, we show how to transfer numerous fairness notions from binary classification to a learning to rank setting. Our formalism allows us to design methods for incorporating fairness objectives with provable generalization guarantees. An extensive experimental evaluation shows that our method can improve ranking fairness substantially with no or only little loss of model quality.
AU - Konstantinov, Nikola H
AU - Lampert, Christoph
ID - 10803
T2 - arXiv
TI - Fairness through regularization for learning to rank
ER -
TY - JOUR
AB - Ligands are a fundamental part of nanocrystals. They control and direct nanocrystal syntheses and provide colloidal stability. Bound ligands also affect the nanocrystals’ chemical reactivity and electronic structure. Surface chemistry is thus crucial to understand nanocrystal properties and functionality. Here, we investigate the synthesis of metal oxide nanocrystals (CeO2-x, ZnO, and NiO) from metal nitrate precursors, in the presence of oleylamine ligands. Surprisingly, the nanocrystals are capped exclusively with a fatty acid instead of oleylamine. Analysis of the reaction mixtures with nuclear magnetic resonance spectroscopy revealed several reaction byproducts and intermediates that are common to the decomposition of Ce, Zn, Ni, and Zr nitrate precursors. Our evidence supports the oxidation of alkylamine and formation of a carboxylic acid, thus unraveling this counterintuitive surface chemistry.
AU - Calcabrini, Mariano
AU - Van den Eynden, Dietger
AU - Sanchez Ribot, Sergi
AU - Pokratath, Rohan
AU - Llorca, Jordi
AU - De Roo, Jonathan
AU - Ibáñez, Maria
ID - 10806
IS - 11
JF - JACS Au
KW - general medicine
SN - 2691-3704
TI - Ligand conversion in nanocrystal synthesis: The oxidation of alkylamines to fatty acids by nitrate
VL - 1
ER -
TY - JOUR
AB - Hematopoietic-specific protein 1 (Hem1) is an essential subunit of the WAVE regulatory complex (WRC) in immune cells. WRC is crucial for Arp2/3 complex activation and the protrusion of branched actin filament networks. Moreover, Hem1 loss of function in immune cells causes autoimmune diseases in humans. Here, we show that genetic removal of Hem1 in macrophages diminishes frequency and efficacy of phagocytosis as well as phagocytic cup formation in addition to defects in lamellipodial protrusion and migration. Moreover, Hem1-null macrophages displayed strong defects in cell adhesion despite unaltered podosome formation and concomitant extracellular matrix degradation. Specifically, dynamics of both adhesion and de-adhesion as well as concomitant phosphorylation of paxillin and focal adhesion kinase (FAK) were significantly compromised. Accordingly, disruption of WRC function in non-hematopoietic cells coincided with both defects in adhesion turnover and altered FAK and paxillin phosphorylation. Consistently, platelets exhibited reduced adhesion and diminished integrin αIIbβ3 activation upon WRC removal. Interestingly, adhesion phenotypes, but not lamellipodia formation, were partially rescued by small molecule activation of FAK. A full rescue of the phenotype, including lamellipodia formation, required not only the presence of WRCs but also their binding to and activation by Rac. Collectively, our results uncover that WRC impacts on integrin-dependent processes in a FAK-dependent manner, controlling formation and dismantling of adhesions, relevant for properly grabbing onto extracellular surfaces and particles during cell edge expansion, like in migration or phagocytosis.
AU - Stahnke, Stephanie
AU - Döring, Hermann
AU - Kusch, Charly
AU - de Gorter, David J.J.
AU - Dütting, Sebastian
AU - Guledani, Aleks
AU - Pleines, Irina
AU - Schnoor, Michael
AU - Sixt, Michael K
AU - Geffers, Robert
AU - Rohde, Manfred
AU - Müsken, Mathias
AU - Kage, Frieda
AU - Steffen, Anika
AU - Faix, Jan
AU - Nieswandt, Bernhard
AU - Rottner, Klemens
AU - Stradal, Theresia E.B.
ID - 10834
IS - 10
JF - Current Biology
KW - General Agricultural and Biological Sciences
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0960-9822
TI - Loss of Hem1 disrupts macrophage function and impacts migration, phagocytosis, and integrin-mediated adhesion
VL - 31
ER -
TY - JOUR
AU - Pranger, Christina L.
AU - Fazekas-Singer, Judit
AU - Köhler, Verena K.
AU - Pali‐Schöll, Isabella
AU - Fiocchi, Alessandro
AU - Karagiannis, Sophia N.
AU - Zenarruzabeitia, Olatz
AU - Borrego, Francisco
AU - Jensen‐Jarolim, Erika
ID - 10836
IS - 5
JF - Allergy
KW - Immunology
KW - Immunology and Allergy
SN - 0105-4538
TI - PIPE‐cloned human IgE and IgG4 antibodies: New tools for investigating cow's milk allergy and tolerance
VL - 76
ER -
TY - JOUR
AB - Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.
AU - Westram, Anja M
AU - Faria, Rui
AU - Johannesson, Kerstin
AU - Butlin, Roger
ID - 10838
IS - 15
JF - Molecular Ecology
KW - Genetics
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 0962-1083
TI - Using replicate hybrid zones to understand the genomic basis of adaptive divergence
VL - 30
ER -
TY - JOUR
AB - We review old and new results on the Fröhlich polaron model. The discussion includes the validity of the (classical) Pekar approximation in the strong coupling limit, quantum corrections to this limit, as well as the divergence of the effective polaron mass.
AU - Seiringer, Robert
ID - 10852
IS - 01
JF - Reviews in Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0129-055X
TI - The polaron at strong coupling
VL - 33
ER -
TY - CONF
AB - Dynamic Connectivity is a fundamental algorithmic graph problem, motivated by a wide range of applications to social and communication networks and used as a building block in various other algorithms, such as the bi-connectivity and the dynamic minimal spanning tree problems. In brief, we wish to maintain the connected components of the graph under dynamic edge insertions and deletions. In the sequential case, the problem has been well-studied from both theoretical and practical perspectives. However, much less is known about efficient concurrent solutions to this problem. This is the gap we address in this paper. We start from one of the classic data structures used to solve this problem, the Euler Tour Tree. Our first contribution is a non-blocking single-writer implementation of it. We leverage this data structure to obtain the first truly concurrent generalization of dynamic connectivity, which preserves the time complexity of its sequential counterpart, but is also scalable in practice. To achieve this, we rely on three main techniques. The first is to ensure that connectivity queries, which usually dominate real-world workloads, are non-blocking. The second non-trivial technique expands the above idea by making all queries that do not change the connectivity structure non-blocking. The third ingredient is applying fine-grained locking for updating the connected components, which allows operations on disjoint components to occur in parallel. We evaluate the resulting algorithm on various workloads, executing on both real and synthetic graphs. The results show the efficiency of each of the proposed optimizations; the most efficient variant improves the performance of a coarse-grained based implementation on realistic scenarios up to 6x on average and up to 30x when connectivity queries dominate.
AU - Fedorov, Alexander
AU - Koval, Nikita
AU - Alistarh, Dan-Adrian
ID - 10853
SN - 9781450380706
T2 - Proceedings of the 33rd ACM Symposium on Parallelism in Algorithms and Architectures
TI - A scalable concurrent algorithm for dynamic connectivity
ER -
TY - JOUR
AB - We study the properties of the maximal volume k-dimensional sections of the n-dimensional cube [−1, 1]n. We obtain a first order necessary condition for a k-dimensional subspace to be a local maximizer of the volume of such sections, which we formulate in a geometric way. We estimate the length of the projection of a vector of the standard basis of Rn onto a k-dimensional subspace that maximizes the volume of the intersection. We nd the optimal upper bound on the volume of a planar section of the cube [−1, 1]n , n ≥ 2.
AU - Ivanov, Grigory
AU - Tsiutsiurupa, Igor
ID - 10856
IS - 1
JF - Analysis and Geometry in Metric Spaces
KW - Applied Mathematics
KW - Geometry and Topology
KW - Analysis
SN - 2299-3274
TI - On the volume of sections of the cube
VL - 9
ER -
TY - JOUR
AB - The cost-effective conversion of low-grade heat into electricity using thermoelectric devices requires developing alternative materials and material processing technologies able to reduce the currently high device manufacturing costs. In this direction, thermoelectric materials that do not rely on rare or toxic elements such as tellurium or lead need to be produced using high-throughput technologies not involving high temperatures and long processes. Bi2Se3 is an obvious possible Te-free alternative to Bi2Te3 for ambient temperature thermoelectric applications, but its performance is still low for practical applications, and additional efforts toward finding proper dopants are required. Here, we report a scalable method to produce Bi2Se3 nanosheets at low synthesis temperatures. We studied the influence of different dopants on the thermoelectric properties of this material. Among the elements tested, we demonstrated that Sn doping resulted in the best performance. Sn incorporation resulted in a significant improvement to the Bi2Se3 Seebeck coefficient and a reduction in the thermal conductivity in the direction of the hot-press axis, resulting in an overall 60% improvement in the thermoelectric figure of merit of Bi2Se3.
AU - Li, Mengyao
AU - Zhang, Yu
AU - Zhang, Ting
AU - Zuo, Yong
AU - Xiao, Ke
AU - Arbiol, Jordi
AU - Llorca, Jordi
AU - Liu, Yu
AU - Cabot, Andreu
ID - 10858
IS - 7
JF - Nanomaterials
KW - General Materials Science
KW - General Chemical Engineering
SN - 2079-4991
TI - Enhanced thermoelectric performance of n-type Bi2Se3 nanosheets through Sn doping
VL - 11
ER -
TY - JOUR
AB - A tight frame is the orthogonal projection of some orthonormal basis of Rn onto Rk. We show that a set of vectors is a tight frame if and only if the set of all cross products of these vectors is a tight frame. We reformulate a range of problems on the volume of projections (or sections) of regular polytopes in terms of tight frames and write a first-order necessary condition for local extrema of these problems. As applications, we prove new results for the problem of maximization of the volume of zonotopes.
AU - Ivanov, Grigory
ID - 10860
IS - 4
JF - Canadian Mathematical Bulletin
KW - General Mathematics
KW - Tight frame
KW - Grassmannian
KW - zonotope
SN - 0008-4395
TI - Tight frames and related geometric problems
VL - 64
ER -
TY - GEN
AB - Brain dynamics display collective phenomena as diverse as neuronal oscillations and avalanches. Oscillations are rhythmic, with fluctuations occurring at a characteristic scale, whereas avalanches are scale-free cascades of neural activity. Here we show that such antithetic features can coexist in a very generic class of adaptive neural networks. In the most simple yet fully microscopic model from this class we make direct contact with human brain resting-state activity recordings via tractable inference of the model's two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor fluctuations, collective behaviors of nearly-synchronous extreme events on multiple sensors, to neuronal avalanches unfolding over multiple sensors across multiple time-bins. Importantly, the inferred parameters correlate with model-independent signatures of "closeness to criticality", suggesting that the coexistence of scale-specific (neural oscillations) and scale-free (neuronal avalanches) dynamics in brain activity occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.
AU - Lombardi, Fabrizio
AU - Pepic, Selver
AU - Shriki, Oren
AU - Tkačik, Gašper
AU - De Martino, Daniele
ID - 10912
TI - Quantifying the coexistence of neuronal oscillations and avalanches
ER -
TY - JOUR
AB - This paper continues the discussion started in [CK19] concerning Arnold's legacy on classical KAM theory and (some of) its modern developments. We prove a detailed and explicit `global' Arnold's KAM Theorem, which yields, in particular, the Whitney conjugacy of a non{degenerate, real{analytic, nearly-integrable Hamiltonian system to an integrable system on a closed, nowhere dense, positive measure subset of the phase space. Detailed measure estimates on the Kolmogorov's set are provided in the case the phase space is: (A) a uniform neighbourhood of an arbitrary (bounded) set times the d-torus and (B) a domain with C2 boundary times the d-torus. All constants are explicitly given.
AU - Chierchia, Luigi
AU - Koudjinan, Edmond
ID - 8689
IS - 1
JF - Regular and Chaotic Dynamics
KW - Nearly{integrable Hamiltonian systems
KW - perturbation theory
KW - KAM Theory
KW - Arnold's scheme
KW - Kolmogorov's set
KW - primary invariant tori
KW - Lagrangian tori
KW - measure estimates
KW - small divisors
KW - integrability on nowhere dense sets
KW - Diophantine frequencies.
SN - 1560-3547
TI - V.I. Arnold's ''Global'' KAM theorem and geometric measure estimates
VL - 26
ER -
TY - JOUR
AB - The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.
AU - Simon, Alexis
AU - Fraisse, Christelle
AU - El Ayari, Tahani
AU - Liautard‐Haag, Cathy
AU - Strelkov, Petr
AU - Welch, John J
AU - Bierne, Nicolas
ID - 8708
IS - 1
JF - Journal of Evolutionary Biology
SN - 1010061X
TI - How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels
VL - 34
ER -
TY - JOUR
AB - Deep learning at scale is dominated by communication time. Distributing samples across nodes usually yields the best performance, but poses scaling challenges due to global information dissemination and load imbalance across uneven sample lengths. State-of-the-art decentralized optimizers mitigate the problem, but require more iterations to achieve the same accuracy as their globally-communicating counterparts. We present Wait-Avoiding Group Model Averaging (WAGMA) SGD, a wait-avoiding stochastic optimizer that reduces global communication via subgroup weight exchange. The key insight is a combination of algorithmic changes to the averaging scheme and the use of a group allreduce operation. We prove the convergence of WAGMA-SGD, and empirically show that it retains convergence rates similar to Allreduce-SGD. For evaluation, we train ResNet-50 on ImageNet; Transformer for machine translation; and deep reinforcement learning for navigation at scale. Compared with state-of-the-art decentralized SGD variants, WAGMA-SGD significantly improves training throughput (e.g., 2.1× on 1,024 GPUs for reinforcement learning), and achieves the fastest time-to-solution (e.g., the highest score using the shortest training time for Transformer).
AU - Li, Shigang
AU - Tal Ben-Nun, Tal Ben-Nun
AU - Nadiradze, Giorgi
AU - Girolamo, Salvatore Di
AU - Dryden, Nikoli
AU - Alistarh, Dan-Adrian
AU - Hoefler, Torsten
ID - 8723
IS - 7
JF - IEEE Transactions on Parallel and Distributed Systems
SN - 10459219
TI - Breaking (global) barriers in parallel stochastic optimization with wait-avoiding group averaging
VL - 32
ER -
TY - JOUR
AB - P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict at the blood–brain barrier (BBB) the brain distribution of the majority of currently known molecularly targeted anticancer drugs. To improve brain delivery of dual ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques with PET. Tolerability of the erlotinib/tariquidar combination was assessed in human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3). Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar alone led to less pronounced VT,brain increases in both species. Treatment of cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly targeted anticancer drugs for a more effective treatment of brain tumors.
AU - Tournier, N
AU - Goutal, S
AU - Mairinger, S
AU - Lozano, IH
AU - Filip, T
AU - Sauberer, M
AU - Caillé, F
AU - Breuil, L
AU - Stanek, J
AU - Freeman, AF
AU - Novarino, Gaia
AU - Truillet, C
AU - Wanek, T
AU - Langer, O
ID - 8730
IS - 7
JF - Journal of Cerebral Blood Flow and Metabolism
SN - 0271-678x
TI - Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib
VL - 41
ER -
TY - JOUR
AB - We develop a version of Ekedahl’s geometric sieve for integral quadratic forms of rank at least five. As one ranges over the zeros of such quadratic forms, we use the sieve to compute the density of coprime values of polynomials, and furthermore, to address a question about local solubility in families of varieties parameterised by the zeros.
AU - Browning, Timothy D
AU - Heath-Brown, Roger
ID - 8742
IS - 1
JF - Forum Mathematicum
SN - 09337741
TI - The geometric sieve for quadrics
VL - 33
ER -
TY - JOUR
AB - Traditional scientific conferences and seminar events have been hugely disrupted by the COVID-19 pandemic, paving the way for virtual forms of scientific communication to take hold and be put to the test.
AU - Bozelos, Panagiotis
AU - Vogels, Tim P
ID - 8757
IS - 1
JF - Nature Reviews Neuroscience
SN - 1471003X
TI - Talking science, online
VL - 22
ER -
TY - JOUR
AB - Let g be a complex semisimple Lie algebra. We give a classification of contravariant forms on the nondegenerate Whittaker g-modules Y(χ,η) introduced by Kostant. We prove that the set of all contravariant forms on Y(χ,η) forms a vector space whose dimension is given by the cardinality of the Weyl group of g. We also describe a procedure for parabolically inducing contravariant forms. As a corollary, we deduce the existence of the Shapovalov form on a Verma module, and provide a formula for the dimension of the space of contravariant forms on the degenerate Whittaker modules M(χ,η) introduced by McDowell.
AU - Brown, Adam
AU - Romanov, Anna
ID - 8773
IS - 1
JF - Proceedings of the American Mathematical Society
KW - Applied Mathematics
KW - General Mathematics
SN - 0002-9939
TI - Contravariant forms on Whittaker modules
VL - 149
ER -
TY - JOUR
AB - This paper is concerned with a non-isothermal Cahn-Hilliard model based on a microforce balance. The model was derived by A. Miranville and G. Schimperna starting from the two fundamental laws of Thermodynamics, following M. Gurtin's two-scale approach. The main working assumptions are made on the behaviour of the heat flux as the absolute temperature tends to zero and to infinity. A suitable Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary value problem associated to the entropy formulation and, in a subcase, also to the weak formulation of the model is proved by deriving suitable a priori estimates and by showing weak sequential stability of families of approximating solutions. At last, some highlights are given regarding a possible approximation scheme compatible with the a-priori estimates available for the system.
AU - Marveggio, Alice
AU - Schimperna, Giulio
ID - 8792
IS - 2
JF - Journal of Differential Equations
SN - 00220396
TI - On a non-isothermal Cahn-Hilliard model based on a microforce balance
VL - 274
ER -
TY - JOUR
AB - We study optimal election sequences for repeatedly selecting a (very) small group of leaders among a set of participants (players) with publicly known unique ids. In every time slot, every player has to select exactly one player that it considers to be the current leader, oblivious to the selection of the other players, but with the overarching goal of maximizing a given parameterized global (“social”) payoff function in the limit. We consider a quite generic model, where the local payoff achieved by a given player depends, weighted by some arbitrary but fixed real parameter, on the number of different leaders chosen in a round, the number of players that choose the given player as the leader, and whether the chosen leader has changed w.r.t. the previous round or not. The social payoff can be the maximum, average or minimum local payoff of the players. Possible applications include quite diverse examples such as rotating coordinator-based distributed algorithms and long-haul formation flying of social birds. Depending on the weights and the particular social payoff, optimal sequences can be very different, from simple round-robin where all players chose the same leader alternatingly every time slot to very exotic patterns, where a small group of leaders (at most 2) is elected in every time slot. Moreover, we study the question if and when a single player would not benefit w.r.t. its local payoff when deviating from the given optimal sequence, i.e., when our optimal sequences are Nash equilibria in the restricted strategy space of oblivious strategies. As this is the case for many parameterizations of our model, our results reveal that no punishment is needed to make it rational for the players to optimize the social payoff.
AU - Zeiner, Martin
AU - Schmid, Ulrich
AU - Chatterjee, Krishnendu
ID - 8793
IS - 1
JF - Discrete Applied Mathematics
SN - 0166218X
TI - Optimal strategies for selecting coordinators
VL - 289
ER -
TY - JOUR
AB - Area-dependent quantum field theory is a modification of two-dimensional topological quantum field theory, where one equips each connected component of a bordism with a positive real number—interpreted as area—which behaves additively under glueing. As opposed to topological theories, in area-dependent theories the state spaces can be infinite-dimensional. We introduce the notion of regularised Frobenius algebras in Hilbert spaces and show that area-dependent theories are in one-to-one correspondence to commutative regularised Frobenius algebras. We also provide a state sum construction for area-dependent theories. Our main example is two-dimensional Yang–Mills theory with compact gauge group, which we treat in detail.
AU - Runkel, Ingo
AU - Szegedy, Lorant
ID - 8816
IS - 1
JF - Communications in Mathematical Physics
SN - 00103616
TI - Area-dependent quantum field theory
VL - 381
ER -
TY - JOUR
AB - The paper introduces an inertial extragradient subgradient method with self-adaptive step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence of the proposed method is obtained under the condition that the bifunction is pseudomonotone and Lipchitz continuous. Linear convergence is also given when the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations and comparisons with other related inertial methods are given using test problems including a real-world application to Nash–Cournot oligopolistic electricity market equilibrium model.
AU - Shehu, Yekini
AU - Iyiola, Olaniyi S.
AU - Thong, Duong Viet
AU - Van, Nguyen Thi Cam
ID - 8817
IS - 2
JF - Mathematical Methods of Operations Research
SN - 14322994
TI - An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems
VL - 93
ER -
TY - JOUR
AB - The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis.
AU - Ramirez Villegas, Juan F
AU - Besserve, Michel
AU - Murayama, Yusuke
AU - Evrard, Henry C.
AU - Oeltermann, Axel
AU - Logothetis, Nikos K.
ID - 8818
IS - 7840
JF - Nature
SN - 00280836
TI - Coupling of hippocampal theta and ripples with pontogeniculooccipital waves
VL - 589
ER -
TY - JOUR
AB - Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface.
AU - Marquès-Bueno, MM
AU - Armengot, L
AU - Noack, LC
AU - Bareille, J
AU - Rodriguez Solovey, Lesia
AU - Platre, MP
AU - Bayle, V
AU - Liu, M
AU - Opdenacker, D
AU - Vanneste, S
AU - Möller, BK
AU - Nimchuk, ZL
AU - Beeckman, T
AU - Caño-Delgado, AI
AU - Friml, Jiří
AU - Jaillais, Y
ID - 8824
IS - 1
JF - Current Biology
SN - 0960-9822
TI - Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism
VL - 31
ER -
TY - JOUR
AB - Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies.
AU - Jirovec, Daniel
AU - Hofmann, Andrea C
AU - Ballabio, Andrea
AU - Mutter, Philipp M.
AU - Tavani, Giulio
AU - Botifoll, Marc
AU - Crippa, Alessandro
AU - Kukucka, Josip
AU - Sagi, Oliver
AU - Martins, Frederico
AU - Saez Mollejo, Jaime
AU - Prieto Gonzalez, Ivan
AU - Borovkov, Maksim
AU - Arbiol, Jordi
AU - Chrastina, Daniel
AU - Isella, Giovanni
AU - Katsaros, Georgios
ID - 8909
IS - 8
JF - Nature Materials
SN - 1476-1122
TI - A singlet triplet hole spin qubit in planar Ge
VL - 20
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 - For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,
and overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance.
AU - Sarac, Naci E
AU - Altun, Ömer Faruk
AU - Atam, Kamil Tolga
AU - Karahoda, Sertac
AU - Kaya, Kamer
AU - Yenigün, Hüsnü
ID - 8912
IS - 4
JF - Expert Systems with Applications
SN - 09574174
TI - Boosting expensive synchronizing heuristics
VL - 167
ER -
TY - JOUR
AB - The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19.
AU - Nardo, Alexander D.
AU - Schneeweiss-Gleixner, Mathias
AU - Bakail, May M
AU - Dixon, Emmanuel D.
AU - Lax, Sigurd F.
AU - Trauner, Michael
ID - 8927
IS - 1
JF - Liver International
SN - 14783223
TI - Pathophysiological mechanisms of liver injury in COVID-19
VL - 41
ER -
TY - JOUR
AB - We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric.
AU - Boissonnat, Jean-Daniel
AU - Kachanovich, Siargey
AU - Wintraecken, Mathijs
ID - 8940
IS - 1
JF - Discrete & Computational Geometry
KW - Theoretical Computer Science
KW - Computational Theory and Mathematics
KW - Geometry and Topology
KW - Discrete Mathematics and Combinatorics
SN - 0179-5376
TI - Triangulating submanifolds: An elementary and quantified version of Whitney’s method
VL - 66
ER -
TY - JOUR
AB - During development, a single cell is transformed into a highly complex organism through progressive cell division, specification and rearrangement. An important prerequisite for the emergence of patterns within the developing organism is to establish asymmetries at various scales, ranging from individual cells to the entire embryo, eventually giving rise to the different body structures. This becomes especially apparent during gastrulation, when the earliest major lineage restriction events lead to the formation of the different germ layers. Traditionally, the unfolding of the developmental program from symmetry breaking to germ layer formation has been studied by dissecting the contributions of different signaling pathways and cellular rearrangements in the in vivo context of intact embryos. Recent efforts, using the intrinsic capacity of embryonic stem cells to self-assemble and generate embryo-like structures de novo, have opened new avenues for understanding the many ways by which an embryo can be built and the influence of extrinsic factors therein. Here, we discuss and compare divergent and conserved strategies leading to germ layer formation in embryos as compared to in vitro systems, their upstream molecular cascades and the role of extrinsic factors in this process.
AU - Schauer, Alexandra
AU - Heisenberg, Carl-Philipp J
ID - 8966
JF - Developmental Biology
KW - Developmental Biology
KW - Cell Biology
KW - Molecular Biology
SN - 0012-1606
TI - Reassembling gastrulation
VL - 474
ER -
TY - JOUR
AB - The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.
AU - Tan, Shutang
AU - Luschnig, Christian
AU - Friml, Jiří
ID - 8992
IS - 1
JF - Molecular Plant
SN - 16742052
TI - Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling
VL - 14
ER -
TY - JOUR
AB - Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.
AU - Kavcic, Bor
AU - Tkačik, Gašper
AU - Bollenbach, Tobias
ID - 8997
JF - PLOS Computational Biology
KW - Modelling and Simulation
KW - Genetics
KW - Molecular Biology
KW - Antibiotics
KW - Drug interactions
SN - 1553-7358
TI - Minimal biophysical model of combined antibiotic action
VL - 17
ER -
TY - JOUR
AB - In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not
arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available.
AU - Avila, Kerstin
AU - Hof, Björn
ID - 8999
IS - 1
JF - Entropy
TI - Second-order phase transition in counter-rotating taylor-couette flow experiment
VL - 23
ER -
TY - JOUR
AB - Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field.
AU - Brooks, Morris
AU - Lemeshko, Mikhail
AU - Lundholm, D.
AU - Yakaboylu, Enderalp
ID - 9005
IS - 1
JF - Physical Review Letters
SN - 00319007
TI - Molecular impurities as a realization of anyons on the two-sphere
VL - 126
ER -
TY - JOUR
AB - Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.
AU - Ötvös, Krisztina
AU - Marconi, Marco
AU - Vega, Andrea
AU - O’Brien, Jose
AU - Johnson, Alexander J
AU - Abualia, Rashed
AU - Antonielli, Livio
AU - Montesinos López, Juan C
AU - Zhang, Yuzhou
AU - Tan, Shutang
AU - Cuesta, Candela
AU - Artner, Christina
AU - Bouguyon, Eleonore
AU - Gojon, Alain
AU - Friml, Jiří
AU - Gutiérrez, Rodrigo A.
AU - Wabnik, Krzysztof T
AU - Benková, Eva
ID - 9010
IS - 3
JF - EMBO Journal
SN - 02614189
TI - Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport
VL - 40
ER -
TY - JOUR
AB - We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels.
AU - Gulden, Tobias
AU - Kamenev, Alex
ID - 9020
IS - 1
JF - Entropy
TI - Dynamics of ion channels via non-hermitian quantum mechanics
VL - 23
ER -
TY - THES
AB - In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.
In the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time
(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.
In the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result
improves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.
AU - Cipolloni, Giorgio
ID - 9022
TI - Fluctuations in the spectrum of random matrices
ER -
TY - GEN
AB - We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of $\mathbb{P}^3$ outside certain planes using universal torsors.
AU - Wilsch, Florian Alexander
ID - 9034
T2 - arXiv
TI - Integral points of bounded height on a log Fano threefold
ER -
TY - JOUR
AB - In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space.
AU - Virosztek, Daniel
ID - 9036
IS - 3
JF - Advances in Mathematics
KW - General Mathematics
SN - 0001-8708
TI - The metric property of the quantum Jensen-Shannon divergence
VL - 380
ER -
TY - JOUR
AB - We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak 𝜀 ‐net theorem in Banach spaces of type 𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma.
AU - Ivanov, Grigory
ID - 9037
IS - 2
JF - Bulletin of the London Mathematical Society
SN - 00246093
TI - No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p
VL - 53
ER -
TY - JOUR
AB - Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices.
AU - Aguilar-Merino, Patricia
AU - Álvarez-Pérez, Gonzalo
AU - Taboada-Gutiérrez, Javier
AU - Duan, Jiahua
AU - Prieto Gonzalez, Ivan
AU - Álvarez-Prado, Luis Manuel
AU - Nikitin, Alexey Y.
AU - Martín-Sánchez, Javier
AU - Alonso-González, Pablo
ID - 9038
IS - 1
JF - Nanomaterials
TI - Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal
VL - 11
ER -
TY - JOUR
AU - Römhild, Roderich
AU - Andersson, Dan I.
ID - 9046
IS - 1
JF - PLoS Pathogens
SN - 15537366
TI - Mechanisms and therapeutic potential of collateral sensitivity to antibiotics
VL - 17
ER -
TY - JOUR
AB - This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.
AU - Mondelli, Marco
AU - Hashemi, Seyyed Ali
AU - Cioffi, John M.
AU - Goldsmith, Andrea
ID - 9047
IS - 1
JF - IEEE Transactions on Wireless Communications
SN - 15361276
TI - Sublinear latency for simplified successive cancellation decoding of polar codes
VL - 20
ER -
TY - JOUR
AB - The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.
AU - De Nicola, Stefano
AU - Michailidis, Alexios
AU - Serbyn, Maksym
ID - 9048
IS - 4
JF - Physical Review Letters
KW - General Physics and Astronomy
SN - 0031-9007
TI - Entanglement view of dynamical quantum phase transitions
VL - 126
ER -
TY - THES
AB - In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations. The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,
and thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics. We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration
function on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss the implications on persistence for periodic data sets.
AU - Osang, Georg F
ID - 9056
SN - 2663-337X
TI - Multi-cover persistence and Delaunay mosaics
ER -
TY - GEN
AB - Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans.
AU - Anderson, Donovan J.
AU - Pauler, Florian
AU - McKenna, Aaron
AU - Shendure, Jay
AU - Hippenmeyer, Simon
AU - Horwitz, Marshall S.
ID - 9082
T2 - bioRxiv
TI - Simultaneous identification of brain cell type and lineage via single cell RNA sequencing
ER -
TY - JOUR
AB - We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation.
AU - Marchukov, Oleksandr
AU - Volosniev, Artem
ID - 9093
IS - 2
JF - SciPost Physics
SN - 2542-4653
TI - Shape of a sound wave in a weakly-perturbed Bose gas
VL - 10
ER -
TY - JOUR
AB - Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of TNFα would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis.
AU - Pandey, Rakesh
AU - Al-Nuaimi, Yusur
AU - Mishra, Rajiv Kumar
AU - Spurgeon, Sarah K.
AU - Goodfellow, Marc
ID - 9097
JF - Scientific Reports
TI - Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis
VL - 11
ER -
TY - JOUR
AB - We study properties of the volume of projections of the n-dimensional
cross-polytope $\crosp^n = \{ x \in \R^n \mid |x_1| + \dots + |x_n| \leqslant 1\}.$ We prove that the projection of $\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3.
We obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\crosp^n$ onto a k-dimensional subspace for any n>k⩾2.
AU - Ivanov, Grigory
ID - 9098
IS - 5
JF - Discrete Mathematics
SN - 0012365X
TI - On the volume of projections of the cross-polytope
VL - 344
ER -
TY - JOUR
AB - We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations.
AU - Srivastava, Tanya K
ID - 9099
IS - 5
JF - Archiv der Mathematik
SN - 0003889X
TI - Lifting automorphisms on Abelian varieties as derived autoequivalences
VL - 116
ER -
TY - JOUR
AB - Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.
AU - Faria, Rui
AU - Johannesson, Kerstin
AU - Stankowski, Sean
ID - 9100
IS - 1
JF - Journal of Evolutionary Biology
SN - 1010061X
TI - Speciation in marine environments: Diving under the surface
VL - 34
ER -
TY - JOUR
AB - Behavioral predispositions are innate tendencies of animals to behave in a given way without the input of learning. They increase survival chances and, due to environmental and ecological challenges, may vary substantially even between closely related taxa. These differences are likely to be especially pronounced in long-lived species like crocodilians. This order is particularly relevant for comparative cognition due to its phylogenetic proximity to birds. Here we compared early life behavioral predispositions in two Alligatoridae species. We exposed American alligator and spectacled caiman hatchlings to three different novel situations: a novel object, a novel environment that was open and a novel environment with a shelter. This was then repeated a week later. During exposure to the novel environments, alligators moved around more and explored a larger range of the arena than the caimans. When exposed to the novel object, the alligators reduced the mean distance to the novel object in the second phase, while the caimans further increased it, indicating diametrically opposite ontogenetic development in behavioral predispositions. Although all crocodilian hatchlings face comparable challenges, e.g., high predation pressure, the effectiveness of parental protection might explain the observed pattern. American alligators are apex predators capable of protecting their offspring against most dangers, whereas adult spectacled caimans are frequently predated themselves. Their distancing behavior might be related to increased predator avoidance and also explain the success of invasive spectacled caimans in the natural habitats of other crocodilians.
AU - Reber, Stephan A.
AU - Oh, Jinook
AU - Janisch, Judith
AU - Stevenson, Colin
AU - Foggett, Shaun
AU - Wilkinson, Anna
ID - 9101
IS - 4
JF - Animal Cognition
SN - 14359448
TI - Early life differences in behavioral predispositions in two Alligatoridae species
VL - 24
ER -
TY - JOUR
AB - We study the probabilistic convergence between the mapper graph and the Reeb graph of a topological space X equipped with a continuous function f:X→R. We first give a categorification of the mapper graph and the Reeb graph by interpreting them in terms of cosheaves and stratified covers of the real line R. We then introduce a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium on point-based graphics, 2007), referred to as the enhanced mapper graph, and demonstrate that such a construction approximates the Reeb graph of (X,f) when it is applied to points randomly sampled from a probability density function concentrated on (X,f). Our techniques are based on the interleaving distance of constructible cosheaves and topological estimation via kernel density estimates. Following Munch and Wang (In: 32nd international symposium on computational geometry, volume 51 of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany, pp 53:1–53:16, 2016), we first show that the mapper graph of (X,f), a constructible R-space (with a fixed open cover), approximates the Reeb graph of the same space. We then construct an isomorphism between the mapper of (X,f) to the mapper of a super-level set of a probability density function concentrated on (X,f). Finally, building on the approach of Bobrowski et al. (Bernoulli 23(1):288–328, 2017b), we show that, with high probability, we can recover the mapper of the super-level set given a sufficiently large sample. Our work is the first to consider the mapper construction using the theory of cosheaves in a probabilistic setting. It is part of an ongoing effort to combine sheaf theory, probability, and statistics, to support topological data analysis with random data.
AU - Brown, Adam
AU - Bobrowski, Omer
AU - Munch, Elizabeth
AU - Wang, Bei
ID - 9111
IS - 1
JF - Journal of Applied and Computational Topology
SN - 2367-1726
TI - Probabilistic convergence and stability of random mapper graphs
VL - 5
ER -
TY - JOUR
AB - “Hydrogen economy” could enable a carbon-neutral sustainable energy chain. However, issues with safety, storage, and transport of molecular hydrogen impede its realization. Alcohols as liquid H2 carriers could be enablers, but state-of-the-art reforming is difficult, requiring high temperatures >200 °C and pressures >25 bar, and the resulting H2 is carbonized beyond tolerance levels for direct use in fuel cells. Here, we demonstrate ambient temperature and pressure alcohol reforming in a fuel cell (ARFC) with a simultaneous electrical power output. The alcohol is oxidized at the alkaline anode, where the resulting CO2 is sequestrated as carbonate. Carbon-free H2 is liberated at the acidic cathode. The neutralization energy between the alkaline anode and the acidic cathode drives the process, particularly the unusually high entropy gain (1.27-fold ΔH). The significantly positive temperature coefficient of the resulting electromotive force allows us to harvest a large fraction of the output energy from the surrounding, achieving a thermodynamic efficiency as high as 2.27. MoS2 as the cathode catalyst allows alcohol reforming even under open-air conditions, a challenge that state-of-the-art alcohol reforming failed to overcome. We further show reforming of a wide range of alcohols. The ARFC offers an unprecedented route toward hydrogen economy as CO2 is simultaneously captured and pure H2 produced at mild conditions.
AU - Manzoor Bhat, Zahid Manzoor
AU - Thimmappa, Ravikumar
AU - Dargily, Neethu Christudas
AU - Raafik, Abdul
AU - Kottaichamy, Alagar Raja
AU - Devendrachari, Mruthyunjayachari Chattanahalli
AU - Itagi, Mahesh
AU - Makri Nimbegondi Kotresh, Harish
AU - Freunberger, Stefan Alexander
AU - Ottakam Thotiyl, Musthafa
ID - 9113
IS - 8
JF - ACS Sustainable Chemistry and Engineering
TI - Ambient condition alcohol reforming to hydrogen with electricity output
VL - 9
ER -
TY - JOUR
AB - Cesium lead halides have intrinsically unstable crystal lattices and easily transform within perovskite and nonperovskite structures. In this work, we explore the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6 nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into the PbS lattice with a consequent increase in the concentration of free charge carriers. This new doping strategy enables the adjustment of the density of charge carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for doping other nanocrystal-based semiconductors.
AU - Calcabrini, Mariano
AU - Genc, Aziz
AU - Liu, Yu
AU - Kleinhanns, Tobias
AU - Lee, Seungho
AU - Dirin, Dmitry N.
AU - Akkerman, Quinten A.
AU - Kovalenko, Maksym V.
AU - Arbiol, Jordi
AU - Ibáñez, Maria
ID - 9118
IS - 2
JF - ACS Energy Letters
TI - Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites
VL - 6
ER -
TY - JOUR
AB - We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.
AU - Fraisse, Christelle
AU - Popovic, Iva
AU - Mazoyer, Clément
AU - Spataro, Bruno
AU - Delmotte, Stéphane
AU - Romiguier, Jonathan
AU - Loire, Étienne
AU - Simon, Alexis
AU - Galtier, Nicolas
AU - Duret, Laurent
AU - Bierne, Nicolas
AU - Vekemans, Xavier
AU - Roux, Camille
ID - 9119
JF - Molecular Ecology Resources
SN - 1755098X
TI - DILS: Demographic inferences with linked selection by using ABC
VL - 21
ER -
TY - JOUR
AB - We show that the energy gap for the BCS gap equation is
Ξ=μ(8e−2+o(1))exp(π2μ−−√a)
in the low density limit μ→0. Together with the similar result for the critical temperature by Hainzl and Seiringer (Lett Math Phys 84: 99–107, 2008), this shows that, in the low density limit, the ratio of the energy gap and critical temperature is a universal constant independent of the interaction potential V. The results hold for a class of potentials with negative scattering length a and no bound states.
AU - Lauritsen, Asbjørn Bækgaard
ID - 9121
JF - Letters in Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0377-9017
TI - The BCS energy gap at low density
VL - 111
ER -
TY - JOUR
AB - We investigate how mesoscale circulations associated with convective aggregation can modulate the sensitivity of the hydrologic cycle to warming. We quantify changes in the full distribution of rain across radiative‐convective equilibrium states in a cloud‐resolving model. For a given SST, the shift in mean rainfall between disorganized and organized states is associated with a shift in atmospheric radiative cooling, and is roughly analogous to the effect of a 4K SST increase. With rising temperatures, the increase in mean rain rate is insensitive to the presence of organization, while extremes can intensify faster in the aggregated state, leading to a faster amplification in the sporadic nature of rain. When convection aggregates, heavy rain is enhanced by 20‐30% and nonlinear behaviors are observed as a function of SST and strength of aggregation feedbacks. First, radiative‐ and surface‐flux aggregation feedbacks have multiplicative effects on extremes, illustrating a non‐trivial sensitivity to the degree of organization. Second, alternating Clausius‐Clapeyron and super‐Clausius‐Clapeyron regimes in extreme rainfall are found as a function of SST, corresponding to varying thermodynamic and dynamic contributions, and a large sensitivity to precipitation efficiency variations in some SST ranges.
The potential for mesoscale circulations in amplifying the hydrologic cycle is established. However these nonlinear distortions question the quantitative relevance of idealized self‐aggregation. This calls for a deeper investigation of relationships which capture the coupling between global energetics, aggregation feedbacks and local convection, and for systematic tests of their sensitivity to domain configurations, surface boundary conditions, microphysics and turbulence schemes.
AU - Fildier, Benjamin
AU - Collins, William D.
AU - Muller, Caroline J
ID - 9151
IS - 2
JF - Journal of Advances in Modeling Earth Systems
KW - Global and Planetary Change
KW - General Earth and Planetary Sciences
KW - Environmental Chemistry
SN - 1942-2466
TI - Distortions of the rain distribution with warming, with and without self‐aggregation
VL - 13
ER -
TY - JOUR
AB - While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes.
AU - De Nicola, Stefano
ID - 9158
IS - 1
JF - Journal of Statistical Mechanics: Theory and Experiment
KW - Statistics
KW - Probability and Uncertainty
KW - Statistics and Probability
KW - Statistical and Nonlinear Physics
SN - 1742-5468
TI - Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation
VL - 2021
ER -
TY - JOUR
AB - Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.
AU - Fraisse, Christelle
AU - Sachdeva, Himani
ID - 9168
IS - 2
JF - Genetics
SN - 1943-2631
TI - The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes
VL - 217
ER -
TY - JOUR
AB - We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem.
AU - Srivastava, Tanya K
ID - 9173
IS - 03
JF - Bulletin des Sciences Mathematiques
SN - 0007-4497
TI - Pathologies of the Hilbert scheme of points of a supersingular Enriques surface
VL - 167
ER -
TY - JOUR
AB - Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues.
AU - Pauler, Florian
AU - Hudson, Quanah
AU - Laukoter, Susanne
AU - Hippenmeyer, Simon
ID - 9188
IS - 5
JF - Neurochemistry International
KW - Cell Biology
KW - Cellular and Molecular Neuroscience
SN - 0197-0186
TI - Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond
VL - 145
ER -
TY - JOUR
AB - Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.
AU - Zhao, Y
AU - Wu, L
AU - Fu, Q
AU - Wang, D
AU - Li, J
AU - Yao, B
AU - Yu, S
AU - Jiang, L
AU - Qian, J
AU - Zhou, X
AU - Han, L
AU - Zhao, S
AU - Ma, C
AU - Zhang, Y
AU - Luo, C
AU - Dong, Q
AU - Li, S
AU - Zhang, L
AU - Jiang, X
AU - Li, Y
AU - Luo, H
AU - Li, K
AU - Yang, J
AU - Luo, Q
AU - Li, L
AU - Peng, S
AU - Huang, H
AU - Zuo, Z
AU - Liu, C
AU - Wang, L
AU - Li, C
AU - He, X
AU - Friml, Jiří
AU - Du, Y
ID - 9189
IS - 6
JF - Plant, Cell & Environment
SN - 0140-7791
TI - INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance
VL - 44
ER -
TY - GEN
AB - We associate a certain tensor product lattice to any primitive integer lattice and ask about its typical shape. These lattices are related to the tangent bundle of Grassmannians and their study is motivated by Peyre's programme on "freeness" for rational points of bounded height on Fano
varieties.
AU - Browning, Timothy D
AU - Horesh, Tal
AU - Wilsch, Florian Alexander
ID - 9199
T2 - arXiv
TI - Equidistribution and freeness on Grassmannians
ER -
TY - CONF
AB - We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function.
AU - Garcia Soto, Miriam
AU - Prabhakar, Pavithra
ID - 9202
T2 - 2020 IEEE Real-Time Systems Symposium
TI - Hybridization for stability verification of nonlinear switched systems
ER -
TY - JOUR
AB - Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.
AU - Kampjut, Domen
AU - Steiner, Julia
AU - Sazanov, Leonid A
ID - 9205
IS - 3
JF - iScience
TI - Cryo-EM grid optimization for membrane proteins
VL - 24
ER -
TY - JOUR
AB - The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS.
AU - Cadavid, Doris
AU - Wei, Kaya
AU - Liu, Yu
AU - Zhang, Yu
AU - Li, Mengyao
AU - Genç, Aziz
AU - Berestok, Taisiia
AU - Ibáñez, Maria
AU - Shavel, Alexey
AU - Nolas, George S.
AU - Cabot, Andreu
ID - 9206
IS - 4
JF - Materials
TI - Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks
VL - 14
ER -
TY - JOUR
AB - In this paper we experimentally study the transitional range of Reynolds numbers in
plane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures
triggered by a strong impulsive jet and the large-scale flow generated around these
structures. We present a detailed investigation of the large-scale flow and show how
its amplitude depends on Reynolds number and amplitude perturbation. In addition,
we characterize the initial dynamics of the localized turbulent spot, which includes the
coupling between the small and large scales, as well as the dependence of the advection
speed on the large-scale flow generated around the spot. Finally, we provide the first
experimental measurements of the large-scale flow around an oblique turbulent band.
AU - Klotz, Lukasz
AU - Pavlenko, A. M.
AU - Wesfreid, J. E.
ID - 9207
JF - Journal of Fluid Mechanics
SN - 0022-1120
TI - Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow
VL - 912
ER -
TY - JOUR
AB - We re-examine attempts to study the many-body localization transition using measures that are physically natural on the ergodic/quantum chaotic regime of the phase diagram. Using simple scaling arguments and an analysis of various models for which rigorous results are available, we find that these measures can be particularly adversely affected by the strong finite-size effects observed in nearly all numerical studies of many-body localization. This severely impacts their utility in probing the transition and the localized phase. In light of this analysis, we discuss a recent study (Šuntajs et al., 2020) of the behaviour of the Thouless energy and level repulsion in disordered spin chains, and its implications for the question of whether MBL is a true phase of matter.
AU - Abanin, D. A.
AU - Bardarson, J. H.
AU - De Tomasi, G.
AU - Gopalakrishnan, S.
AU - Khemani, V.
AU - Parameswaran, S. A.
AU - Pollmann, F.
AU - Potter, A. C.
AU - Serbyn, Maksym
AU - Vasseur, R.
ID - 9224
IS - 4
JF - Annals of Physics
SN - 00034916
TI - Distinguishing localization from chaos: Challenges in finite-size systems
VL - 427
ER -
TY - CONF
AB - In the multiway cut problem we are given a weighted undirected graph G=(V,E) and a set T⊆V of k terminals. The goal is to find a minimum weight set of edges E′⊆E with the property that by removing E′ from G all the terminals become disconnected. In this paper we present a simple local search approximation algorithm for the multiway cut problem with approximation ratio 2−2k . We present an experimental evaluation of the performance of our local search algorithm and show that it greatly outperforms the isolation heuristic of Dalhaus et al. and it has similar performance as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and Buchbinder et al. which have the currently best known approximation ratios for this problem.
AU - Bloch-Hansen, Andrew
AU - Samei, Nasim
AU - Solis-Oba, Roberto
ID - 9227
SN - 0302-9743
T2 - Conference on Algorithms and Discrete Applied Mathematics
TI - Experimental evaluation of a local search approximation algorithm for the multiway cut problem
VL - 12601
ER -
TY - GEN
AB - We consider a model of the Riemann zeta function on the critical axis and study its maximum over intervals of length (log T)θ, where θ is either fixed or tends to zero at a suitable rate.
It is shown that the deterministic level of the maximum interpolates smoothly between the ones
of log-correlated variables and of i.i.d. random variables, exhibiting a smooth transition ‘from
3/4 to 1/4’ in the second order. This provides a natural context where extreme value statistics of
log-correlated variables with time-dependent variance and rate occur. A key ingredient of the
proof is a precise upper tail tightness estimate for the maximum of the model on intervals of
size one, that includes a Gaussian correction. This correction is expected to be present for the
Riemann zeta function and pertains to the question of the correct order of the maximum of
the zeta function in large intervals.
AU - Arguin, Louis-Pierre
AU - Dubach, Guillaume
AU - Hartung, Lisa
ID - 9230
T2 - arXiv
TI - Maxima of a random model of the Riemann zeta function over intervals of varying length
ER -
TY - JOUR
AB - In this paper, we present two new inertial projection-type methods for solving multivalued variational inequality problems in finite-dimensional spaces. We establish the convergence of the sequence generated by these methods when the multivalued mapping associated with the problem is only required to be locally bounded without any monotonicity assumption. Furthermore, the inertial techniques that we employ in this paper are quite different from the ones used in most papers. Moreover, based on the weaker assumptions on the inertial factor in our methods, we derive several special cases of our methods. Finally, we present some experimental results to illustrate the profits that we gain by introducing the inertial extrapolation steps.
AU - Izuchukwu, Chinedu
AU - Shehu, Yekini
ID - 9234
IS - 2
JF - Networks and Spatial Economics
KW - Computer Networks and Communications
KW - Software
KW - Artificial Intelligence
SN - 1566-113X
TI - New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity
VL - 21
ER -
TY - JOUR
AB - Cu2–xS has become one of the most promising thermoelectric materials for application in the middle-high temperature range. Its advantages include the abundance, low cost, and safety of its elements and a high performance at relatively elevated temperatures. However, stability issues limit its operation current and temperature, thus calling for the optimization of the material performance in the middle temperature range. Here, we present a synthetic protocol for large scale production of covellite CuS nanoparticles at ambient temperature and atmosphere, and using water as a solvent. The crystal phase and stoichiometry of the particles are afterward tuned through an annealing process at a moderate temperature under inert or reducing atmosphere. While annealing under argon results in Cu1.8S nanopowder with a rhombohedral crystal phase, annealing in an atmosphere containing hydrogen leads to tetragonal Cu1.96S. High temperature X-ray diffraction analysis shows the material annealed in argon to transform to the cubic phase at ca. 400 K, while the material annealed in the presence of hydrogen undergoes two phase transitions, first to hexagonal and then to the cubic structure. The annealing atmosphere, temperature, and time allow adjustment of the density of copper vacancies and thus tuning of the charge carrier concentration and material transport properties. In this direction, the material annealed under Ar is characterized by higher electrical conductivities but lower Seebeck coefficients than the material annealed in the presence of hydrogen. By optimizing the charge carrier concentration through the annealing time, Cu2–xS with record figures of merit in the middle temperature range, up to 1.41 at 710 K, is obtained. We finally demonstrate that this strategy, based on a low-cost and scalable solution synthesis process, is also suitable for the production of high performance Cu2–xS layers using high throughput and cost-effective printing technologies.
AU - Li, Mengyao
AU - Liu, Yu
AU - Zhang, Yu
AU - Han, Xu
AU - Zhang, Ting
AU - Zuo, Yong
AU - Xie, Chenyang
AU - Xiao, Ke
AU - Arbiol, Jordi
AU - Llorca, Jordi
AU - Ibáñez, Maria
AU - Liu, Junfeng
AU - Cabot, Andreu
ID - 9235
IS - 3
JF - ACS Nano
KW - General Engineering
KW - General Physics and Astronomy
KW - General Materials Science
SN - 1936-0851
TI - Effect of the annealing atmosphere on crystal phase and thermoelectric properties of copper sulfide
VL - 15
ER -
TY - GEN
AB - Metabolic adaptation to changing demands underlies homeostasis. During inflammation or metastasis, cells leading migration into challenging environments require an energy boost, however what controls this capacity is unknown. We identify a previously unstudied nuclear protein, Atossa, as changing metabolism in Drosophila melanogaster immune cells to promote tissue invasion. Atossa’s vertebrate orthologs, FAM214A-B, can fully substitute for Atossa, indicating functional conservation from flies to mammals. Atossa increases mRNA levels of Porthos, an unstudied RNA helicase and two metabolic enzymes, LKR/SDH and GR/HPR. Porthos increases translation of a gene subset, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Respiration measurements and metabolomics indicate that Atossa and Porthos powers up mitochondrial oxidative phosphorylation to produce sufficient energy for leading macrophages to forge a path into tissues. As increasing oxidative phosphorylation enables many crucial physiological responses, this unique genetic program may modulate a wide range of cellular behaviors beyond migration.
AU - Emtenani, Shamsi
AU - Martin, Elliott T.
AU - György, Attila
AU - Bicher, Julia
AU - Genger, Jakob-Wendelin
AU - Hurd, Thomas R.
AU - Köcher, Thomas
AU - Bergthaler, Andreas
AU - Rangan, Prashanth
AU - Siekhaus, Daria E
ID - 9238
T2 - bioRxiv
TI - A genetic program boosts mitochondrial function to power macrophage tissue invasion
ER -
TY - JOUR
AB - A stochastic PDE, describing mesoscopic fluctuations in systems of weakly interacting inertial particles of finite volume, is proposed and analysed in any finite dimension . It is a regularised and inertial version of the Dean–Kawasaki model. A high-probability well-posedness theory for this model is developed. This theory improves significantly on the spatial scaling restrictions imposed in an earlier work of the same authors, which applied only to significantly larger particles in one dimension. The well-posedness theory now applies in d-dimensions when the particle-width ϵ is proportional to for and N is the number of particles. This scaling is optimal in a certain Sobolev norm. Key tools of the analysis are fractional Sobolev spaces, sharp bounds on Bessel functions, separability of the regularisation in the d-spatial dimensions, and use of the Faà di Bruno's formula.
AU - Cornalba, Federico
AU - Shardlow, Tony
AU - Zimmer, Johannes
ID - 9240
IS - 5
JF - Journal of Differential Equations
SN - 0022-0396
TI - Well-posedness for a regularised inertial Dean–Kawasaki model for slender particles in several space dimensions
VL - 284
ER -
TY - JOUR
AB - Volumetric light transport is a pervasive physical phenomenon, and therefore its accurate simulation is important for a broad array of disciplines. While suitable mathematical models for computing the transport are now available, obtaining the necessary material parameters needed to drive such simulations is a challenging task: direct measurements of these parameters from material samples are seldom possible. Building on the inverse scattering paradigm, we present a novel measurement approach which indirectly infers the transport parameters from extrinsic observations of multiple-scattered radiance. The novelty of the proposed approach lies in replacing structured illumination with a structured reflector bonded to the sample, and a robust fitting procedure that largely compensates for potential systematic errors in the calibration of the setup. We show the feasibility of our approach by validating simulations of complex 3D compositions of the measured materials against physical prints, using photo-polymer resins. As presented in this paper, our technique yields colorspace data suitable for accurate appearance reproduction in the area of 3D printing. Beyond that, and without fundamental changes to the basic measurement methodology, it could equally well be used to obtain spectral measurements that are useful for other application areas.
AU - Elek, Oskar
AU - Zhang, Ran
AU - Sumin, Denis
AU - Myszkowski, Karol
AU - Bickel, Bernd
AU - Wilkie, Alexander
AU - Křivánek, Jaroslav
AU - Weyrich, Tim
ID - 9241
IS - 5
JF - Optics Express
TI - Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing
VL - 29
ER -
TY - JOUR
AB - In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing.
AU - Rueda Sanchez, Alfredo R
ID - 9242
IS - 2
JF - Physical Review A
SN - 2469-9926
TI - Frequency-multiplexed hybrid optical entangled source based on the Pockels effect
VL - 103
ER -
TY - JOUR
AB - Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.
AU - Hernández-Rocamora, Víctor M.
AU - Baranova, Natalia S.
AU - Peters, Katharina
AU - Breukink, Eefjan
AU - Loose, Martin
AU - Vollmer, Waldemar
ID - 9243
JF - eLife
TI - Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins
VL - 10
ER -
TY - JOUR
AB - Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.
AU - Hankeova, Simona
AU - Salplachta, Jakub
AU - Zikmund, Tomas
AU - Kavkova, Michaela
AU - Van Hul, Noémi
AU - Brinek, Adam
AU - Smekalova, Veronika
AU - Laznovsky, Jakub
AU - Dawit, Feven
AU - Jaros, Josef
AU - Bryja, Vítězslav
AU - Lendahl, Urban
AU - Ellis, Ewa
AU - Nemeth, Antal
AU - Fischler, Björn
AU - Hannezo, Edouard B
AU - Kaiser, Jozef
AU - Andersson, Emma Rachel
ID - 9244
JF - eLife
TI - DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome
VL - 10
ER -
TY - JOUR
AB - We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic particles weakly couple to the quantized phonon field. For large particle numbers and a suitably small coupling, we show that the dynamics of the system is approximately described by the Landau–Pekar equations. These describe a Bose–Einstein condensate interacting with a classical polarization field, whose dynamics is effected by the condensate, i.e., the back-reaction of the phonons that are created by the particles during the time evolution is of leading order.
AU - Leopold, Nikolai K
AU - Mitrouskas, David Johannes
AU - Seiringer, Robert
ID - 9246
JF - Archive for Rational Mechanics and Analysis
SN - 00039527
TI - Derivation of the Landau–Pekar equations in a many-body mean-field limit
VL - 240
ER -
TY - JOUR
AB - This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.
AU - Szep, Eniko
AU - Sachdeva, Himani
AU - Barton, Nicholas H
ID - 9252
IS - 5
JF - Evolution
KW - Genetics
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
KW - General Agricultural and Biological Sciences
SN - 0014-3820
TI - Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model
VL - 75
ER -
TY - CONF
AB - In March 2020, the Austrian government introduced a widespread lock-down in response to the COVID-19 pandemic. Based on subjective impressions and anecdotal evidence, Austrian public and private life came to a sudden halt. Here we assess the effect of the lock-down quantitatively for all regions in Austria and present an analysis of daily changes of human mobility throughout Austria using near-real-time anonymized mobile phone data. We describe an efficient data aggregation pipeline and analyze the mobility by quantifying mobile-phone traffic at specific point of interests (POIs), analyzing individual trajectories and investigating the cluster structure of the origin-destination graph. We found a reduction of commuters at Viennese metro stations of over 80% and the number of devices with a radius of gyration of less than 500 m almost doubled. The results of studying crowd-movement behavior highlight considerable changes in the structure of mobility networks, revealed by a higher modularity and an increase from 12 to 20 detected communities. We demonstrate the relevance of mobility data for epidemiological studies by showing a significant correlation of the outflow from the town of Ischgl (an early COVID-19 hotspot) and the reported COVID-19 cases with an 8-day time lag. This research indicates that mobile phone usage data permits the moment-by-moment quantification of mobility behavior for a whole country. We emphasize the need to improve the availability of such data in anonymized form to empower rapid response to combat COVID-19 and future pandemics.
AU - Heiler, Georg
AU - Reisch, Tobias
AU - Hurt, Jan
AU - Forghani, Mohammad
AU - Omani, Aida
AU - Hanbury, Allan
AU - Karimipour, Farid
ID - 9253
SN - 9781728162515
T2 - 2020 IEEE International Conference on Big Data
TI - Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic
ER -
TY - JOUR
AB - Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.
AU - Hu, Yangjie
AU - Omary, Moutasem
AU - Hu, Yun
AU - Doron, Ohad
AU - Hörmayer, Lukas
AU - Chen, Qingguo
AU - Megides, Or
AU - Chekli, Ori
AU - Ding, Zhaojun
AU - Friml, Jiří
AU - Zhao, Yunde
AU - Tsarfaty, Ilan
AU - Shani, Eilon
ID - 9254
JF - Nature Communications
TI - Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing
VL - 12
ER -
TY - JOUR
AB - Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates.
AU - Pivoluska, Matej
AU - Plesch, Martin
AU - Farkas, Máté
AU - Ruzickova, Natalia
AU - Flegel, Clara
AU - Valencia, Natalia Herrera
AU - Mccutcheon, Will
AU - Malik, Mehul
AU - Aguilar, Edgar A.
ID - 9255
JF - npj Quantum Information
TI - Semi-device-independent random number generation with flexible assumptions
VL - 7
ER -
TY - JOUR
AB - The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.
AU - Goodrich, Carl Peter
AU - King, Ella M.
AU - Schoenholz, Samuel S.
AU - Cubuk, Ekin D.
AU - Brenner, Michael P.
ID - 9257
IS - 10
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - Designing self-assembling kinetics with differentiable statistical physics models
VL - 118
ER -
TY - JOUR
AU - Pinkard, Henry
AU - Stuurman, Nico
AU - Ivanov, Ivan E.
AU - Anthony, Nicholas M.
AU - Ouyang, Wei
AU - Li, Bin
AU - Yang, Bin
AU - Tsuchida, Mark A.
AU - Chhun, Bryant
AU - Zhang, Grace
AU - Mei, Ryan
AU - Anderson, Michael
AU - Shepherd, Douglas P.
AU - Hunt-Isaak, Ian
AU - Dunn, Raymond L.
AU - Jahr, Wiebke
AU - Kato, Saul
AU - Royer, Loïc A.
AU - Thiagarajah, Jay R.
AU - Eliceiri, Kevin W.
AU - Lundberg, Emma
AU - Mehta, Shalin B.
AU - Waller, Laura
ID - 9258
IS - 3
JF - Nature Methods
SN - 1548-7091
TI - Pycro-Manager: Open-source software for customized and reproducible microscope control
VL - 18
ER -