TY - JOUR
AB - Tattoos are a highly popular medium, with both artistic and medical applications. Although the mechanical process of tattoo application has evolved historically, the results are reliant on the artisanal skill of the artist. This can be especially challenging for some skin tones, or in cases where artists lack experience. We provide the first systematic overview of tattooing as a computational fabrication technique. We built an automated tattooing rig and a recipe for the creation of silicone sheets mimicking realistic skin tones, which allowed us to create an accurate model predicting tattoo appearance. This enables several exciting applications including tattoo previewing, color retargeting, novel ink spectra optimization, color-accurate prosthetics, and more.
AU - Piovarci, Michael
AU - Chapiro, Alexandre
AU - Bickel, Bernd
ID - 12984
IS - 4
JF - Transactions on Graphics
KW - appearance
KW - modeling
KW - reproduction
KW - tattoo
KW - skin color
KW - gamut mapping
KW - ink-optimization
KW - prosthetic
TI - Skin-Screen: A computational fabrication framework for color tattoos
VL - 42
ER -
TY - CONF
AB - Color and gloss are fundamental aspects of surface appearance. State-of-the-art fabrication techniques can manipulate both properties of the printed 3D objects. However, in the context of appearance reproduction, perceptual aspects of color and gloss are usually handled separately, even though previous perceptual studies suggest their interaction. Our work is motivated by previous studies demonstrating a perceived color shift due to a change in the object's gloss, i.e., two samples with the same color but different surface gloss appear as they have different colors. In this paper, we conduct new experiments which support this observation and provide insights into the magnitude and direction of the perceived color change. We use the observations as guidance to design a new method that estimates and corrects the color shift enabling the fabrication of objects with the same perceived color but different surface gloss. We formulate the problem as an optimization procedure solved using differentiable rendering. We evaluate the effectiveness of our method in perceptual experiments with 3D objects fabricated using a multi-material 3D printer and demonstrate potential applications.
AU - Condor, Jorge
AU - Piovarci, Michael
AU - Bickel, Bernd
AU - Didyk, Piotr
ID - 12979
KW - color
KW - gloss
KW - perception
KW - color compensation
KW - color management
SN - 9798400701597
T2 - SIGGRAPH ’23 Conference Proceedings
TI - Gloss-aware color correction for 3D printing
ER -
TY - CONF
AB - 3D printing based on continuous deposition of materials, such as filament-based 3D printing, has seen widespread
adoption thanks to its versatility in working with a wide range of materials. An important shortcoming of this type of technology is its limited multi-material capabilities. While there are simple hardware designs that enable multi-material printing in principle, the required software is heavily underdeveloped. A typical hardware design fuses together individual materials fed into a single chamber from multiple inlets before they are deposited. This design, however, introduces a time delay between the intended material mixture and its actual deposition. In this work, inspired by diverse path planning research in robotics, we show that this mechanical challenge can be addressed via improved printer control. We propose to formulate the search for optimal multi-material printing policies in a reinforcement
learning setup. We put forward a simple numerical deposition model that takes into account the non-linear material mixing and delayed material deposition. To validate our system we focus on color fabrication, a problem known for its strict requirements for varying material mixtures at a high spatial frequency. We demonstrate that our learned control policy outperforms state-of-the-art hand-crafted algorithms.
AU - Liao, Kang
AU - Tricard, Thibault
AU - Piovarci, Michael
AU - Seidel, Hans-Peter
AU - Babaei, Vahid
ID - 12976
KW - reinforcement learning
KW - deposition
KW - control
KW - color
KW - multi-filament
T2 - 2023 IEEE International Conference on Robotics and Automation
TI - Learning deposition policies for fused multi-material 3D printing
ER -
TY - CONF
AB - In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.
AU - Lieutier, André
AU - Wintraecken, Mathijs
ID - 13048
SN - 9781450399135
T2 - Proceedings of the 55th Annual ACM Symposium on Theory of Computing
TI - Hausdorff and Gromov-Hausdorff stable subsets of the medial axis
ER -
TY - CONF
AB - Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .
AU - Peste, Elena-Alexandra
AU - Vladu, Adrian
AU - Kurtic, Eldar
AU - Lampert, Christoph
AU - Alistarh, Dan-Adrian
ID - 13053
T2 - 11th International Conference on Learning Representations
TI - CrAM: A Compression-Aware Minimizer
ER -
TY - CONF
AB - A classical problem for Markov chains is determining their stationary (or steady-state) distribution. This problem has an equally classical solution based on eigenvectors and linear equation systems. However, this approach does not scale to large instances, and iterative solutions are desirable. It turns out that a naive approach, as used by current model checkers, may yield completely wrong results. We present a new approach, which utilizes recent advances in partial exploration and mean payoff computation to obtain a correct, converging approximation.
AU - Meggendorfer, Tobias
ID - 13139
SN - 0302-9743
T2 - TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems
TI - Correct approximation of stationary distributions
VL - 13993
ER -
TY - CONF
AB - GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.
In this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.
Our approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality.
AU - Hoffmann, Charlotte
AU - Hubáček, Pavel
AU - Kamath, Chethan
AU - Pietrzak, Krzysztof Z
ID - 13143
SN - 0302-9743
T2 - Public-Key Cryptography - PKC 2023
TI - Certifying giant nonprimes
VL - 13940
ER -
TY - CONF
AB - Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Lechner, Mathias
AU - Zikelic, Dorde
ID - 13142
SN - 0302-9743
T2 - Tools and Algorithms for the Construction and Analysis of Systems
TI - A learner-verifier framework for neural network controllers and certificates of stochastic systems
VL - 13993
ER -
TY - CONF
AB - We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ
can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).
For parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω
-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive.
AU - Anand, Ashwani
AU - Mallik, Kaushik
AU - Nayak, Satya Prakash
AU - Schmuck, Anne Kathrin
ID - 13141
SN - 0302-9743
T2 - TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems
TI - Computing adequately permissive assumptions for synthesis
VL - 13994
ER -
TY - JOUR
AB - We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes.
AU - Dello Schiavo, Lorenzo
AU - Lytvynov, Eugene
ID - 13145
JF - Electronic Communications in Probability
TI - A Mecke-type characterization of the Dirichlet–Ferguson measure
VL - 28
ER -
TY - JOUR
AB - We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of
established PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs.
Our approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved.
Our technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs.
AU - Freire, Marco
AU - Bhargava, Manas
AU - Schreck, Camille
AU - Hugron, Pierre-Alexandre
AU - Bickel, Bernd
AU - Lefebvre, Sylvain
ID - 13049
IS - 4
JF - Transactions on Graphics
KW - PCB design and layout
KW - Mesh geometry models
SN - 0730-0301
TI - PCBend: Light up your 3D shapes with foldable circuit boards
VL - 42
ER -
TY - THES
AB - During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion.
Firstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.
Secondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.
Taken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.
AU - Pokusaeva, Victoria
ID - 12826
SN - 2663 - 337X
TI - Neural control of optic flow-based navigation in Drosophila melanogaster
ER -
TY - JOUR
AB - Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways.
AU - Xu, Jiayuan
AU - Liu, Nana
AU - Polemiti, Elli
AU - Garcia-Mondragon, Liliana
AU - Tang, Jie
AU - Liu, Xiaoxuan
AU - Lett, Tristram
AU - Yu, Le
AU - Nöthen, Markus M.
AU - Feng, Jianfeng
AU - Yu, Chunshui
AU - Marquand, Andre
AU - Schumann, Gunter
AU - Walter, Henrik
AU - Heinz, Andreas
AU - Ralser, Markus
AU - Twardziok, Sven
AU - Vaidya, Nilakshi
AU - Serin, Emin
AU - Jentsch, Marcel
AU - Hitchen, Esther
AU - Eils, Roland
AU - Taron, Ulrike Helene
AU - Schütz, Tatjana
AU - Schepanski, Kerstin
AU - Banks, Jamie
AU - Banaschewski, Tobias
AU - Jansone, Karina
AU - Christmann, Nina
AU - Meyer-Lindenberg, Andreas
AU - Tost, Heike
AU - Holz, Nathalie
AU - Schwarz, Emanuel
AU - Stringaris, Argyris
AU - Neidhart, Maja
AU - Nees, Frauke
AU - Siehl, Sebastian
AU - A. Andreassen, Ole
AU - T. Westlye, Lars
AU - Van Der Meer, Dennis
AU - Fernandez, Sara
AU - Kjelkenes, Rikka
AU - Ask, Helga
AU - Rapp, Michael
AU - Tschorn, Mira
AU - Böttger, Sarah Jane
AU - Novarino, Gaia
AU - Marr, Lena
AU - Slater, Mel
AU - Viapiana, Guillem Feixas
AU - Orosa, Francisco Eiroa
AU - Gallego, Jaime
AU - Pastor, Alvaro
AU - Forstner, Andreas
AU - Hoffmann, Per
AU - M. Nöthen, Markus
AU - J. Forstner, Andreas
AU - Claus, Isabelle
AU - Miller, Abbi
AU - Heilmann-Heimbach, Stefanie
AU - Sommer, Peter
AU - Boye, Mona
AU - Wilbertz, Johannes
AU - Schmitt, Karen
AU - Jirsa, Viktor
AU - Petkoski, Spase
AU - Pitel, Séverine
AU - Otten, Lisa
AU - Athanasiadis, Anastasios Polykarpos
AU - Pearmund, Charlie
AU - Spanlang, Bernhard
AU - Alvarez, Elena
AU - Sanchez, Mavi
AU - Giner, Arantxa
AU - Hese, Sören
AU - Renner, Paul
AU - Jia, Tianye
AU - Gong, Yanting
AU - Xia, Yunman
AU - Chang, Xiao
AU - Calhoun, Vince
AU - Liu, Jingyu
AU - Thompson, Paul
AU - Clinton, Nicholas
AU - Desrivieres, Sylvane
AU - H. Young, Allan
AU - Stahl, Bernd
AU - Ogoh, George
ID - 13168
JF - Nature Medicine
SN - 1078-8956
TI - Effects of urban living environments on mental health in adults
VL - 29
ER -
TY - JOUR
AB - Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization.
AU - Gert, Krista R.B.
AU - Panser, Karin
AU - Surm, Joachim
AU - Steinmetz, Benjamin S.
AU - Schleiffer, Alexander
AU - Jovine, Luca
AU - Moran, Yehu
AU - Kondrashov, Fyodor
AU - Pauli, Andrea
ID - 13164
JF - Nature Communications
TI - Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries
VL - 14
ER -
TY - JOUR
AB - A graph G=(V, E) is called fully regular if for every independent set I c V, the number of vertices in V\I that are not connected to any element of I depends only on the size of I. A linear ordering of the vertices of G is called successive if for every i, the first i vertices induce a connected subgraph of G. We give an explicit formula for the number of successive vertex orderings of a fully regular graph.
As an application of our results, we give alternative proofs of two theorems of Stanley and Gao & Peng, determining the number of linear edge orderings of complete graphs and complete bipartite graphs, respectively, with the property that the first i edges induce a connected subgraph.
As another application, we give a simple product formula for the number of linear orderings of the hyperedges of a complete 3-partite 3-uniform hypergraph such that, for every i, the first i hyperedges induce a connected subgraph. We found similar formulas for complete (non-partite) 3-uniform hypergraphs and in another closely related case, but we managed to verify them only when the number of vertices is small.
AU - Fang, Lixing
AU - Huang, Hao
AU - Pach, János
AU - Tardos, Gábor
AU - Zuo, Junchi
ID - 13165
IS - 10
JF - Journal of Combinatorial Theory. Series A
SN - 0097-3165
TI - Successive vertex orderings of fully regular graphs
VL - 199
ER -
TY - JOUR
AB - We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.
AU - Edelsbrunner, Herbert
AU - Osang, Georg F
ID - 12086
JF - Algorithmica
SN - 0178-4617
TI - A simple algorithm for higher-order Delaunay mosaics and alpha shapes
VL - 85
ER -
TY - JOUR
AB - We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.
AU - Dello Schiavo, Lorenzo
AU - Wirth, Melchior
ID - 12104
IS - 1
JF - Journal of Evolution Equations
SN - 1424-3199
TI - Ergodic decompositions of Dirichlet forms under order isomorphisms
VL - 23
ER -
TY - JOUR
AB - The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.
AU - Goswami, Bidyut B
ID - 11434
JF - Climate Dynamics
SN - 0930-7575
TI - Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend
VL - 60
ER -
TY - JOUR
AB - We characterize critical points of 1-dimensional maps paired in persistent homology
geometrically and this way get elementary proofs of theorems about the symmetry
of persistence diagrams and the variation of such maps. In particular, we identify
branching points and endpoints of networks as the sole source of asymmetry and
relate the cycle basis in persistent homology with a version of the stable marriage
problem. Our analysis provides the foundations of fast algorithms for maintaining a
collection of sorted lists together with its persistence diagram.
AU - Biswas, Ranita
AU - Cultrera Di Montesano, Sebastiano
AU - Edelsbrunner, Herbert
AU - Saghafian, Morteza
ID - 13182
JF - Journal of Applied and Computational Topology
SN - 2367-1726
TI - Geometric characterization of the persistence of 1D maps
ER -
TY - JOUR
AB - Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.
AU - Minchington, Thomas
AU - Rus, Stefanie
AU - Kicheva, Anna
ID - 13136
JF - Current Opinion in Systems Biology
TI - Control of tissue dimensions in the developing neural tube and somites
VL - 35
ER -
TY - CONF
AB - Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.
AU - Henzinger, Thomas A
AU - Mazzocchi, Nicolas Adrien
AU - Sarac, Naci E
ID - 12467
SN - 0302-9743
T2 - 26th International Conference Foundations of Software Science and Computation Structures
TI - Quantitative safety and liveness
VL - 13992
ER -
TY - JOUR
AB - Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.
This paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives.
AU - Koval, Nikita
AU - Khalanskiy, Dmitry
AU - Alistarh, Dan-Adrian
ID - 13179
JF - Proceedings of the ACM on Programming Languages
TI - CQS: A formally-verified framework for fair and abortable synchronization
VL - 7
ER -
TY - JOUR
AB - Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.
AU - Chen, Huihuang
AU - Li, Lanxin
AU - Zou, Minxia
AU - Qi, Linlin
AU - Friml, Jiří
ID - 13212
JF - Molecular Plant
SN - 1752-9867
TI - Distinct functions of TIR1 and AFB1 receptors in auxin signalling.
ER -
TY - JOUR
AB - The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture.
AU - Xia, Jing
AU - Kong, Mengjuan
AU - Yang, Zhisen
AU - Sun, Lianghanxiao
AU - Peng, Yakun
AU - Mao, Yanbo
AU - Wei, Hong
AU - Ying, Wei
AU - Gao, Yongxiao
AU - Friml, Jiří
AU - Weng, Jianping
AU - Liu, Xin
AU - Sun, Linfeng
AU - Tan, Shutang
ID - 13209
JF - Plant Communications
TI - Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen
ER -
TY - JOUR
AB - We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface
AU - Browning, Timothy D
AU - Lyczak, Julian
AU - Sarapin, Roman
ID - 13180
IS - 2
JF - Involve
SN - 1944-4176
TI - Local solubility for a family of quadrics over a split quadric surface
VL - 16
ER -
TY - JOUR
AB - The Kirchhoff rod model describes the bending and twisting of slender elastic rods in three dimensions, and has been widely studied to enable the prediction of how a rod will deform, given its geometry and boundary conditions. In this work, we study a number of inverse problems with the goal of computing the geometry of a straight rod that will automatically deform to match a curved target shape after attaching its endpoints to a support structure. Our solution lets us finely control the static equilibrium state of a rod by varying the cross-sectional profiles along its length.
We also show that the set of physically realizable equilibrium states admits a concise geometric description in terms of linear line complexes, which leads to very efficient computational design algorithms. Implemented in an interactive software tool, they allow us to convert three-dimensional hand-drawn spline curves to elastic rods, and give feedback about the feasibility and practicality of a design in real time. We demonstrate the efficacy of our method by designing and manufacturing several physical prototypes with applications to interior design and soft robotics.
AU - Hafner, Christian
AU - Bickel, Bernd
ID - 13188
JF - ACM Transactions on Graphics
KW - Computer Graphics
KW - Computational Design
KW - Computational Geometry
KW - Shape Modeling
SN - 0730-0301
TI - The design space of Kirchhoff rods
ER -
TY - CONF
AB - We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.
.
AU - Schmid, Stefan
AU - Svoboda, Jakub
AU - Yeo, Michelle X
ID - 13238
SN - 0302-9743
T2 - SIROCCO 2023: Structural Information and Communication Complexity
TI - Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation
VL - 13892
ER -
TY - CONF
AB - We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1−ε)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time O(mε−1log(ε−1)), matching the running time of the linear-time approximation algorithm of Duan and Pettie [JACM ’14]. Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1−ε)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is O(mε−1log(ε−1)), where m is the sum of the number of initially existing and inserted edges.
AU - Zheng, Da Wei
AU - Henzinger, Monika H
ID - 13236
SN - 0302-9743
T2 - International Conference on Integer Programming and Combinatorial Optimization
TI - Multiplicative auction algorithm for approximate maximum weight bipartite matching
VL - 13904
ER -
TY - CONF
AB - A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox.
AU - Henzinger, Thomas A
AU - Karimi, Mahyar
AU - Kueffner, Konstantin
AU - Mallik, Kaushik
ID - 13228
SN - 9781450372527
T2 - FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency
TI - Runtime monitoring of dynamic fairness properties
ER -
TY - JOUR
AB - Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.
AU - Benedikter, Niels P
AU - Porta, Marcello
AU - Schlein, Benjamin
AU - Seiringer, Robert
ID - 13225
IS - 4
JF - Archive for Rational Mechanics and Analysis
SN - 0003-9527
TI - Correlation energy of a weakly interacting Fermi gas with large interaction potential
VL - 247
ER -
TY - JOUR
AB - We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion.
AU - Bossmann, Lea
AU - Petrat, Sören P
ID - 13226
IS - 4
JF - Letters in Mathematical Physics
SN - 0377-9017
TI - Weak Edgeworth expansion for the mean-field Bose gas
VL - 113
ER -
TY - JOUR
AB - Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis.
AU - Hassani, Farid
AU - Peruzzo, Matilda
AU - Kapoor, Lucky
AU - Trioni, Andrea
AU - Zemlicka, Martin
AU - Fink, Johannes M
ID - 13227
JF - Nature Communications
TI - Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours
VL - 14
ER -
TY - CONF
AB - The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications.
AU - Boker, Udi
AU - Henzinger, Thomas A
AU - Mazzocchi, Nicolas Adrien
AU - Sarac, Naci E
ID - 13221
T2 - 34th International Conference on Concurrency Theory
TI - Safety and liveness of quantitative automata
ER -
TY - GEN
AU - Elefante, Stefano
AU - Stadlbauer, Stephan
AU - Alexander, Michael F
AU - Schlögl, Alois
ID - 13162
T2 - ASHPC23 - Austrian-Slovenian HPC Meeting 2023
TI - Cryo-EM software packages: A sys-admins point of view
ER -
TY - GEN
AU - Schlögl, Alois
AU - Elefante, Stefano
AU - Hodirnau, Victor-Valentin
ID - 13161
T2 - ASHPC23 - Austrian-Slovenian HPC Meeting 2023
TI - Running Windows-applications on a Linux HPC cluster using WINE
ER -
TY - JOUR
AB - A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.
AU - Wei, Yujing
AU - Volosniev, Artem
AU - Lorenc, Dusan
AU - Zhumekenov, Ayan A.
AU - Bakr, Osman M.
AU - Lemeshko, Mikhail
AU - Alpichshev, Zhanybek
ID - 13251
IS - 27
JF - The Journal of Physical Chemistry Letters
KW - General Materials Science
KW - Physical and Theoretical Chemistry
TI - Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites
VL - 14
ER -
TY - JOUR
AB - In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,
for parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems.
AU - Zhang, Haonan
ID - 13271
JF - Annales Henri Poincare
SN - 1424-0637
TI - Some convexity and monotonicity results of trace functionals
ER -
TY - JOUR
AB - We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations.
AU - Huybrechts, D.
AU - Mauri, Mirko
ID - 13268
IS - 1
JF - Mathematical Research Letters
SN - 1073-2780
TI - On type II degenerations of hyperkähler manifolds
VL - 30
ER -
TY - JOUR
AB - In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality.
AU - Zhong, Fanchao
AU - Xu, Yonglai
AU - Zhao, Haisen
AU - Lu, Lin
ID - 13265
IS - 3
JF - ACM Transactions on Graphics
SN - 0730-0301
TI - As-Continuous-As-Possible extrusion-based fabrication of surface models
VL - 42
ER -
TY - JOUR
AB - This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point.
AU - Polyanskii, Nikita
AU - Zhang, Yihan
ID - 13269
JF - IEEE Transactions on Information Theory
SN - 0018-9448
TI - Codes for the Z-channel
ER -
TY - JOUR
AB - How do statistical dependencies in measurement noise influence high-dimensional inference? To answer this, we study the paradigmatic spiked matrix model of principal components analysis (PCA), where a rank-one matrix is corrupted by additive noise. We go beyond the usual independence assumption on the noise entries, by drawing the noise from a low-order polynomial orthogonal matrix ensemble. The resulting noise correlations make the setting relevant for applications but analytically challenging. We provide characterization of the Bayes optimal limits of inference in this model. If the spike is rotation invariant, we show that standard spectral PCA is optimal. However, for more general priors, both PCA and the existing approximate message-passing algorithm (AMP) fall short of achieving the information-theoretic limits, which we compute using the replica method from statistical physics. We thus propose an AMP, inspired by the theory of adaptive Thouless–Anderson–Palmer equations, which is empirically observed to saturate the conjectured theoretical limit. This AMP comes with a rigorous state evolution analysis tracking its performance. Although we focus on specific noise distributions, our methodology can be generalized to a wide class of trace matrix ensembles at the cost of more involved expressions. Finally, despite the seemingly strong assumption of rotation-invariant noise, our theory empirically predicts algorithmic performance on real data, pointing at strong universality properties.
AU - Barbier, Jean
AU - Camilli, Francesco
AU - Mondelli, Marco
AU - Sáenz, Manuel
ID - 13315
IS - 30
JF - Proceedings of the National Academy of Sciences of the United States of America
TI - Fundamental limits in structured principal component analysis and how to reach them
VL - 120
ER -
TY - JOUR
AB - Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN.
AU - Toshima, Junko Y.
AU - Tsukahara, Ayana
AU - Nagano, Makoto
AU - Tojima, Takuro
AU - Siekhaus, Daria E
AU - Nakano, Akihiko
AU - Toshima, Jiro
ID - 13316
JF - eLife
TI - The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network
VL - 12
ER -
TY - JOUR
AB - We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction.
AU - Sugimoto, Shoki
AU - Henheik, Sven Joscha
AU - Riabov, Volodymyr
AU - Erdös, László
ID - 13317
IS - 7
JF - Journal of Statistical Physics
SN - 0022-4715
TI - Eigenstate thermalisation hypothesis for translation invariant spin systems
VL - 190
ER -
TY - CONF
AB - We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm.
AU - Xu, Yizhou
AU - Hou, Tian Qi
AU - Liang, Shan Suo
AU - Mondelli, Marco
ID - 13321
SN - 9798350301496
T2 - 2023 IEEE Information Theory Workshop
TI - Approximate message passing for multi-layer estimation in rotationally invariant models
ER -
TY - JOUR
AB - Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes.
AU - Volberg, Alexander
AU - Zhang, Haonan
ID - 13318
JF - Mathematische Annalen
SN - 0025-5831
TI - Noncommutative Bohnenblust–Hille inequalities
ER -
TY - CONF
AB - The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.
AU - Henzinger, Thomas A
AU - Kebis, Pavol
AU - Mazzocchi, Nicolas Adrien
AU - Sarac, Naci E
ID - 13292
SN - 9783959772785
T2 - 50th International Colloquium on Automata, Languages, and Programming
TI - Regular methods for operator precedence languages
VL - 261
ER -
TY - JOUR
AB - Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results.
AU - Tucci, Gennaro
AU - De Nicola, Stefano
AU - Wald, Sascha
AU - Gambassi, Andrea
ID - 13277
IS - 2
JF - SciPost Physics Core
KW - Statistical and Nonlinear Physics
KW - Atomic and Molecular Physics
KW - and Optics
KW - Nuclear and High Energy Physics
KW - Condensed Matter Physics
SN - 2666-9366
TI - Stochastic representation of the quantum quartic oscillator
VL - 6
ER -
TY - JOUR
AB - We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.
AU - Rammelmüller, Lukas
AU - Huber, David
AU - Volosniev, Artem
ID - 13276
JF - SciPost Physics Codebases
SN - 2949-804X
TI - A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D
ER -
TY - JOUR
AB - We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity "breaks" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms.
AU - Rammelmüller, Lukas
AU - Huber, David
AU - Čufar, Matija
AU - Brand, Joachim
AU - Hammer, Hans-Werner
AU - Volosniev, Artem
ID - 13278
IS - 1
JF - SciPost Physics
KW - General Physics and Astronomy
SN - 2542-4653
TI - Magnetic impurity in a one-dimensional few-fermion system
VL - 14
ER -
TY - JOUR
AB - Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics.
AU - Paranjape, Chaitanya S
AU - Yalniz, Gökhan
AU - Duguet, Yohann
AU - Budanur, Nazmi B
AU - Hof, Björn
ID - 13274
IS - 3
JF - Physical Review Letters
KW - General Physics and Astronomy
SN - 0031-9007
TI - Direct path from turbulence to time-periodic solutions
VL - 131
ER -
TY - GEN
AB - We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.
AU - Rammelmüller, Lukas
AU - Huber, David
AU - Volosniev, Artem
ID - 13275
TI - Codebase release 1.0 for FermiFCI
ER -
TY - CONF
AB - Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.
AU - Fedorov, Alexander
AU - Hashemi, Diba
AU - Nadiradze, Giorgi
AU - Alistarh, Dan-Adrian
ID - 13262
SN - 9781450395458
T2 - Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures
TI - Provably-efficient and internally-deterministic parallel Union-Find
ER -
TY - JOUR
AB - Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.
Results: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models.
AU - Trinh, Van Giang
AU - Benhamou, Belaid
AU - Henzinger, Thomas A
AU - Pastva, Samuel
ID - 13263
IS - Supplement_1
JF - Bioinformatics
SN - 1367-4803
TI - Trap spaces of multi-valued networks: Definition, computation, and applications
VL - 39
ER -
TY - JOUR
AB - Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.
AU - Brückner, David
AU - Chen, Hongtao
AU - Barinov, Lev
AU - Zoller, Benjamin
AU - Gregor, Thomas
ID - 13261
IS - 6652
JF - Science
TI - Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome
VL - 380
ER -
TY - JOUR
AB - Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.
AU - Kleshnina, Maria
AU - Hilbe, Christian
AU - Simsa, Stepan
AU - Chatterjee, Krishnendu
AU - Nowak, Martin A.
ID - 13258
JF - Nature Communications
TI - The effect of environmental information on evolution of cooperation in stochastic games
VL - 14
ER -
TY - JOUR
AB - The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.
AU - Shekhter, A.
AU - Mcdonald, R. D.
AU - Ramshaw, B. J.
AU - Modic, Kimberly A
ID - 13257
IS - 3
JF - Physical Review B
SN - 2469-9950
TI - Magnetotropic susceptibility
VL - 108
ER -
TY - GEN
AU - Kleshnina, Maria
ID - 13336
TI - kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games
ER -
TY - JOUR
AB - Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency.
AU - Ogura, Nao
AU - Sasagawa, Yohei
AU - Ito, Tasuku
AU - Tameshige, Toshiaki
AU - Kawai, Satomi
AU - Sano, Masaki
AU - Doll, Yuki
AU - Iwase, Akira
AU - Kawamura, Ayako
AU - Suzuki, Takamasa
AU - Nikaido, Itoshi
AU - Sugimoto, Keiko
AU - Ikeuchi, Momoko
ID - 13259
IS - 27
JF - Science Advances
TI - WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus
VL - 9
ER -
TY - JOUR
AB - We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule.
AU - Vernooij, Matthijs
AU - Wirth, Melchior
ID - 13319
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Derivations and KMS-symmetric quantum Markov semigroups
ER -
TY - JOUR
AB - Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.
AU - Fäßler, Florian
AU - Javoor, Manjunath
AU - Datler, Julia
AU - Döring, Hermann
AU - Hofer, Florian
AU - Dimchev, Georgi A
AU - Hodirnau, Victor-Valentin
AU - Faix, Jan
AU - Rottner, Klemens
AU - Schur, Florian KM
ID - 12334
IS - 3
JF - Science Advances
KW - Multidisciplinary
SN - 2375-2548
TI - ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning
VL - 9
ER -
TY - JOUR
AB - Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.
AU - De Jode, Aurélien
AU - Le Moan, Alan
AU - Johannesson, Kerstin
AU - Faria, Rui
AU - Stankowski, Sean
AU - Westram, Anja M
AU - Butlin, Roger K.
AU - Rafajlović, Marina
AU - Fraisse, Christelle
ID - 11479
IS - 2
JF - Evolutionary Applications
TI - Ten years of demographic modelling of divergence and speciation in the sea
VL - 16
ER -
TY - JOUR
AB - In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection.
AU - Gómez, Arturo
AU - Oliveira, Goncalo
ID - 12329
JF - Scientific Reports
TI - New approaches to epidemic modeling on networks
VL - 13
ER -
TY - JOUR
AB - It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.
AU - Browning, Timothy D
AU - Boudec, Pierre Le
AU - Sawin, Will
ID - 8682
IS - 3
JF - Annals of Mathematics
SN - 0003-486X
TI - The Hasse principle for random Fano hypersurfaces
VL - 197
ER -
TY - JOUR
AB - We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors.
AU - Wilsch, Florian Alexander
ID - 9034
IS - 8
JF - International Mathematics Research Notices
SN - 1073-7928
TI - Integral points of bounded height on a log Fano threefold
VL - 2023
ER -
TY - JOUR
AB - Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.
AU - Viljakainen, Lumi
AU - Fürst, Matthias
AU - Grasse, Anna V
AU - Jurvansuu, Jaana
AU - Oh, Jinook
AU - Tolonen, Lassi
AU - Eder, Thomas
AU - Rattei, Thomas
AU - Cremer, Sylvia
ID - 12469
JF - Frontiers in Microbiology
TI - Antiviral immune response reveals host-specific virus infections in natural ant populations
VL - 14
ER -
TY - JOUR
AB - We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use.
AU - Boissonnat, Jean-Daniel
AU - Dyer, Ramsay
AU - Ghosh, Arijit
AU - Wintraecken, Mathijs
ID - 12287
JF - Discrete & Computational Geometry
KW - Computational Theory and Mathematics
KW - Discrete Mathematics and Combinatorics
KW - Geometry and Topology
KW - Theoretical Computer Science
SN - 0179-5376
TI - Local criteria for triangulating general manifolds
VL - 69
ER -
TY - JOUR
AB - Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.
AU - Gupta, Divyansh
AU - Mlynarski, Wiktor F
AU - Sumser, Anton L
AU - Symonova, Olga
AU - Svaton, Jan
AU - Jösch, Maximilian A
ID - 12349
JF - Nature Neuroscience
SN - 1097-6256
TI - Panoramic visual statistics shape retina-wide organization of receptive fields
ER -
TY - JOUR
AB - It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective.
AU - Hof, Björn
ID - 12165
JF - Nature Reviews Physics
KW - General Physics and Astronomy
TI - Directed percolation and the transition to turbulence
VL - 5
ER -
TY - JOUR
AB - The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.
AU - Fäßler, Florian
AU - Javoor, Manjunath
AU - Schur, Florian KM
ID - 12421
IS - 1
JF - Biochemical Society Transactions
KW - Biochemistry
SN - 0300-5127
TI - Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM
VL - 51
ER -
TY - JOUR
AB - Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion.
AU - Marensi, Elena
AU - Yalniz, Gökhan
AU - Hof, Björn
AU - Budanur, Nazmi B
ID - 12105
JF - Journal of Fluid Mechanics
SN - 0022-1120
TI - Symmetry-reduced dynamic mode decomposition of near-wall turbulence
VL - 954
ER -
TY - JOUR
AB - The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.
AU - Bolnick, Daniel I.
AU - Hund, Amanda K.
AU - Nosil, Patrik
AU - Peng, Foen
AU - Ravinet, Mark
AU - Stankowski, Sean
AU - Subramanian, Swapna
AU - Wolf, Jochen B.W.
AU - Yukilevich, Roman
ID - 12514
IS - 1
JF - Evolution: International journal of organic evolution
TI - A multivariate view of the speciation continuum
VL - 77
ER -
TY - JOUR
AB - Let X be a sufficiently large positive integer. We prove that one may choose a subset S of primes with cardinality O(logX) such that a positive proportion of integers less than X can be represented by x2+py2 for at least one p∈S.
AU - Diao, Yijie
ID - 12406
JF - Acta Arithmetica
KW - Algebra
KW - Number Theory
SN - 0065-1036
TI - Density of the union of positive diagonal binary quadratic forms
VL - 207
ER -
TY - CONF
AB - The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts.
AU - Forghani, Mohammad
AU - Claramunt, Christophe
AU - Karimipour, Farid
AU - Heiler, Georg
ID - 12548
T2 - 2022 IEEE International Conference on Data Mining Workshops
TI - Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic
ER -
TY - JOUR
AB - he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems.
AU - Krokhin, Andrei
AU - Opršal, Jakub
AU - Wrochna, Marcin
AU - Živný, Stanislav
ID - 12563
IS - 1
JF - SIAM Journal on Computing
KW - General Mathematics
KW - General Computer Science
SN - 0097-5397
TI - Topology and adjunction in promise constraint satisfaction
VL - 52
ER -
TY - JOUR
AB - We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front.
AU - Rojas Vega, Mauricio Nicolas
AU - De Castro, Pablo
AU - Soto, Rodrigo
ID - 12545
IS - 1
JF - Physical Review E
SN - 2470-0045
TI - Wetting dynamics by mixtures of fast and slow self-propelled particles
VL - 107
ER -
TY - JOUR
AB - Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent.
AU - Balestrieri, Francesca
ID - 12427
IS - 3
JF - Proceedings of the American Mathematical Society
SN - 0002-9939
TI - Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups
VL - 151
ER -
TY - JOUR
AB - In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.
AU - Villalba Requena, Ana
AU - Hippenmeyer, Simon
ID - 12542
IS - 3
JF - Neuron
TI - Going back in time with TEMPO
VL - 111
ER -
TY - JOUR
AB - Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.
AU - Lyons, David B.
AU - Briffa, Amy
AU - He, Shengbo
AU - Choi, Jaemyung
AU - Hollwey, Elizabeth
AU - Colicchio, Jack
AU - Anderson, Ian
AU - Feng, Xiaoqi
AU - Howard, Martin
AU - Zilberman, Daniel
ID - 12672
IS - 3
JF - Cell Reports
TI - Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons
VL - 42
ER -
TY - JOUR
AB - Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations.
AU - Mrestani, Achmed
AU - Lichter, Katharina
AU - Sirén, Anna Leena
AU - Heckmann, Manfred
AU - Paul, Mila M.
AU - Pauli, Martin
ID - 12567
IS - 3
JF - International Journal of Molecular Sciences
TI - Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation
VL - 24
ER -
TY - JOUR
AB - Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that
– all the outputs are within distance 1 of one another, and
– each output value lies on a shortest path between two input values.
From prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).
In this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs.
AU - Alistarh, Dan-Adrian
AU - Ellen, Faith
AU - Rybicki, Joel
ID - 12566
IS - 2
JF - Theoretical Computer Science
SN - 0304-3975
TI - Wait-free approximate agreement on graphs
VL - 948
ER -
TY - JOUR
AB - The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT.
AU - Dubief, Yves
AU - Terrapon, Vincent E.
AU - Hof, Björn
ID - 12681
IS - 1
JF - Annual Review of Fluid Mechanics
SN - 0066-4189
TI - Elasto-inertial turbulence
VL - 55
ER -
TY - JOUR
AB - We study the eigenvalue trajectories of a time dependent matrix Gt=H+itvv∗ for t≥0, where H is an N×N Hermitian random matrix and v is a unit vector. In particular, we establish that with high probability, an outlier can be distinguished at all times t>1+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices.
AU - Dubach, Guillaume
AU - Erdös, László
ID - 12683
JF - Electronic Communications in Probability
TI - Dynamics of a rank-one perturbation of a Hermitian matrix
VL - 28
ER -
TY - JOUR
AB - Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.
AU - Avila, Marc
AU - Barkley, Dwight
AU - Hof, Björn
ID - 12682
JF - Annual Review of Fluid Mechanics
SN - 0066-4189
TI - Transition to turbulence in pipe flow
VL - 55
ER -
TY - JOUR
AB - Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.
AU - Araújo, Nuno A.M.
AU - Janssen, Liesbeth M.C.
AU - Barois, Thomas
AU - Boffetta, Guido
AU - Cohen, Itai
AU - Corbetta, Alessandro
AU - Dauchot, Olivier
AU - Dijkstra, Marjolein
AU - Durham, William M.
AU - Dussutour, Audrey
AU - Garnier, Simon
AU - Gelderblom, Hanneke
AU - Golestanian, Ramin
AU - Isa, Lucio
AU - Koenderink, Gijsje H.
AU - Löwen, Hartmut
AU - Metzler, Ralf
AU - Polin, Marco
AU - Royall, C. Patrick
AU - Šarić, Anđela
AU - Sengupta, Anupam
AU - Sykes, Cécile
AU - Trianni, Vito
AU - Tuval, Idan
AU - Vogel, Nicolas
AU - Yeomans, Julia M.
AU - Zuriguel, Iker
AU - Marin, Alvaro
AU - Volpe, Giorgio
ID - 12708
JF - Soft Matter
SN - 1744-683X
TI - Steering self-organisation through confinement
VL - 19
ER -
TY - JOUR
AB - Hydrocarbon mixtures are extremely abundant in the Universe, and diamond formation from them can play a crucial role in shaping the interior structure and evolution of planets. With first-principles accuracy, we first estimate the melting line of diamond, and then reveal the nature of chemical bonding in hydrocarbons at extreme conditions. We finally establish the pressure-temperature phase boundary where it is thermodynamically possible for diamond to form from hydrocarbon mixtures with different atomic fractions of carbon. Notably, here we show a depletion zone at pressures above 200 GPa and temperatures below 3000 K-3500 K where diamond formation is thermodynamically favorable regardless of the carbon atomic fraction, due to a phase separation mechanism. The cooler condition of the interior of Neptune compared to Uranus means that the former is much more likely to contain the depletion zone. Our findings can help explain the dichotomy of the two ice giants manifested by the low luminosity of Uranus, and lead to a better understanding of (exo-)planetary formation and evolution.
AU - Cheng, Bingqing
AU - Hamel, Sebastien
AU - Bethkenhagen, Mandy
ID - 12702
JF - Nature Communications
TI - Thermodynamics of diamond formation from hydrocarbon mixtures in planets
VL - 14
ER -
TY - JOUR
AB - Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.
AU - Mckerral, Jody C.
AU - Kleshnina, Maria
AU - Ejov, Vladimir
AU - Bartle, Louise
AU - Mitchell, James G.
AU - Filar, Jerzy A.
ID - 12706
IS - 2
JF - PLoS One
TI - Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations
VL - 18
ER -
TY - JOUR
AB - The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.
AU - Sorichetti, Valerio
AU - Ninarello, Andrea
AU - Ruiz-Franco, José
AU - Hugouvieux, Virginie
AU - Zaccarelli, Emanuela
AU - Micheletti, Cristian
AU - Kob, Walter
AU - Rovigatti, Lorenzo
ID - 12705
IS - 7
JF - Journal of Chemical Physics
SN - 0021-9606
TI - Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks
VL - 158
ER -
TY - JOUR
AB - We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail.
AU - Erdös, László
AU - Xu, Yuanyuan
ID - 12707
IS - 2
JF - Bernoulli
SN - 1350-7265
TI - Small deviation estimates for the largest eigenvalue of Wigner matrices
VL - 29
ER -
TY - JOUR
AB - Background
Epigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture.
Methods
First, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women’s Health Initiative study).
Results
Through the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10−52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10−60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations.
Conclusions
The integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.
AU - Bernabeu, Elena
AU - Mccartney, Daniel L.
AU - Gadd, Danni A.
AU - Hillary, Robert F.
AU - Lu, Ake T.
AU - Murphy, Lee
AU - Wrobel, Nicola
AU - Campbell, Archie
AU - Harris, Sarah E.
AU - Liewald, David
AU - Hayward, Caroline
AU - Sudlow, Cathie
AU - Cox, Simon R.
AU - Evans, Kathryn L.
AU - Horvath, Steve
AU - Mcintosh, Andrew M.
AU - Robinson, Matthew Richard
AU - Vallejos, Catalina A.
AU - Marioni, Riccardo E.
ID - 12719
JF - Genome Medicine
TI - Refining epigenetic prediction of chronological and biological age
VL - 15
ER -
TY - JOUR
AB - Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not come for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off but inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in conjunction with adversarial robot learning, are capable of making adversarial training suitable for real-world robot applications. We evaluate three different robot learning tasks ranging from autonomous driving in a high-fidelity environment amenable to sim-to-real deployment to mobile robot navigation and gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative impact on the nominal accuracy caused by adversarial training still outweighs the improved robustness by an order of magnitude. We conclude that although progress is happening, further advances in robust learning methods are necessary before they can benefit robot learning tasks in practice.
AU - Lechner, Mathias
AU - Amini, Alexander
AU - Rus, Daniela
AU - Henzinger, Thomas A
ID - 12704
IS - 3
JF - IEEE Robotics and Automation Letters
TI - Revisiting the adversarial robustness-accuracy tradeoff in robot learning
VL - 8
ER -
TY - JOUR
AB - The substitution of heavier, more metallic atoms into classical organic ligand frameworks provides an important strategy for tuning ligand properties, such as ligand bite and donor character, and is the basis for the emerging area of main-group supramolecular chemistry. In this paper, we explore two new ligands [E(2-Me-8-qy)3] [E = Sb (1), Bi (2); qy = quinolyl], allowing a fundamental comparison of their coordination behavior with classical tris(2-pyridyl) ligands of the type [E′(2-py)3] (E = a range of bridgehead atoms and groups, py = pyridyl). A range of new coordination modes to Cu+, Ag+, and Au+ is seen for 1 and 2, in the absence of steric constraints at the bridgehead and with their more remote N-donor atoms. A particular feature is the adaptive nature of these new ligands, with the ability to adjust coordination mode in response to the hard–soft character of coordinated metal ions, influenced also by the character of the bridgehead atom (Sb or Bi). These features can be seen in a comparison between [Cu2{Sb(2-Me-8-qy)3}2](PF6)2 (1·CuPF6) and [Cu{Bi(2-Me-8-qy)3}](PF6) (2·CuPF6), the first containing a dimeric cation in which 1 adopts an unprecedented intramolecular N,N,Sb-coordination mode while in the second, 2 adopts an unusual N,N,(π-)C coordination mode. In contrast, the previously reported analogous ligands [E(6-Me-2-py)3] (E = Sb, Bi; 2-py = 2-pyridyl) show a tris-chelating mode in their complexes with CuPF6, which is typical for the extensive tris(2-pyridyl) family with a range of metals. The greater polarity of the Bi–C bond in 2 results in ligand transfer reactions with Au(I). Although this reactivity is not in itself unusual, the characterization of several products by single-crystal X-ray diffraction provides snapshots of the ligand transfer reaction involved, with one of the products (the bimetallic complex [(BiCl){ClAu2(2-Me-8-qy)3}] (8)) containing a Au2Bi core in which the shortest Au → Bi donor–acceptor bond to date is observed.
AU - García-Romero, Álvaro
AU - Waters, Jessica E.
AU - Jethwa, Rajesh B
AU - Bond, Andrew D.
AU - Colebatch, Annie L.
AU - García-Rodríguez, Raúl
AU - Wright, Dominic S.
ID - 12737
IS - 11
JF - Inorganic Chemistry
SN - 0020-1669
TI - Highly adaptive nature of group 15 tris(quinolyl) ligands─studies with coinage metals
VL - 62
ER -
TY - JOUR
AB - Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness.
AU - Corbet, René
AU - Kerber, Michael
AU - Lesnick, Michael
AU - Osang, Georg F
ID - 12709
JF - Discrete and Computational Geometry
SN - 0179-5376
TI - Computing the multicover bifiltration
ER -
TY - JOUR
AB - Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order.
AU - Volosniev, Artem
AU - Shiva Kumar, Abhishek
AU - Lorenc, Dusan
AU - Ashourishokri, Younes
AU - Zhumekenov, Ayan A.
AU - Bakr, Osman M.
AU - Lemeshko, Mikhail
AU - Alpichshev, Zhanybek
ID - 12723
IS - 10
JF - Physical Review Letters
KW - General Physics and Astronomy
SN - 0031-9007
TI - Spin-electric coupling in lead halide perovskites
VL - 130
ER -
TY - JOUR
AB - We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation.
AU - Volosniev, Artem
AU - Shiva Kumar, Abhishek
AU - Lorenc, Dusan
AU - Ashourishokri, Younes
AU - Zhumekenov, Ayan
AU - Bakr, Osman M.
AU - Lemeshko, Mikhail
AU - Alpichshev, Zhanybek
ID - 12724
IS - 12
JF - Physical Review B
SN - 2469-9950
TI - Effective model for studying optical properties of lead halide perovskites
VL - 107
ER -
TY - JOUR
AB - Stereological methods for estimating the 3D particle size and density from 2D projections are essential to many research fields. These methods are, however, prone to errors arising from undetected particle profiles due to sectioning and limited resolution, known as ‘lost caps’. A potential solution developed by Keiding, Jensen, and Ranek in 1972, which we refer to as the Keiding model, accounts for lost caps by quantifying the smallest detectable profile in terms of its limiting ‘cap angle’ (ϕ), a size-independent measure of a particle’s distance from the section surface. However, this simple solution has not been widely adopted nor tested. Rather, model-independent design-based stereological methods, which do not explicitly account for lost caps, have come to the fore. Here, we provide the first experimental validation of the Keiding model by comparing the size and density of particles estimated from 2D projections with direct measurement from 3D EM reconstructions of the same tissue. We applied the Keiding model to estimate the size and density of somata, nuclei and vesicles in the cerebellum of mice and rats, where high packing density can be problematic for design-based methods. Our analysis reveals a Gaussian distribution for ϕ rather than a single value. Nevertheless, curve fits of the Keiding model to the 2D diameter distribution accurately estimate the mean ϕ and 3D diameter distribution. While systematic testing using simulations revealed an upper limit to determining ϕ, our analysis shows that estimated ϕ can be used to determine the 3D particle density from the 2D density under a wide range of conditions, and this method is potentially more accurate than minimum-size-based lost-cap corrections and disector methods. Our results show the Keiding model provides an efficient means of accurately estimating the size and density of particles from 2D projections even under conditions of a high density.
AU - Rothman, Jason Seth
AU - Borges Merjane, Carolina
AU - Holderith, Noemi
AU - Jonas, Peter M
AU - Angus Silver, R.
ID - 12759
IS - 3 March
JF - PLoS ONE
TI - Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy
VL - 18
ER -
TY - JOUR
AB - ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III–dependent membrane remodeling.
AU - Hurtig, Fredrik
AU - Burgers, Thomas C.Q.
AU - Cezanne, Alice
AU - Jiang, Xiuyun
AU - Mol, Frank N.
AU - Traparić, Jovan
AU - Pulschen, Andre Arashiro
AU - Nierhaus, Tim
AU - Tarrason-Risa, Gabriel
AU - Harker-Kirschneck, Lena
AU - Löwe, Jan
AU - Šarić, Anđela
AU - Vlijm, Rifka
AU - Baum, Buzz
ID - 12756
IS - 11
JF - Science Advances
TI - The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division
VL - 9
ER -
TY - JOUR
AB - Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
AU - Cikes, Domagoj
AU - Elsayad, Kareem
AU - Sezgin, Erdinc
AU - Koitai, Erika
AU - Ferenc, Torma
AU - Orthofer, Michael
AU - Yarwood, Rebecca
AU - Heinz, Leonhard X.
AU - Sedlyarov, Vitaly
AU - Darwish-Miranda, Nasser
AU - Taylor, Adrian
AU - Grapentine, Sophie
AU - al-Murshedi, Fathiya
AU - Abot, Anne
AU - Weidinger, Adelheid
AU - Kutchukian, Candice
AU - Sanchez, Colline
AU - Cronin, Shane J. F.
AU - Novatchkova, Maria
AU - Kavirayani, Anoop
AU - Schuetz, Thomas
AU - Haubner, Bernhard
AU - Haas, Lisa
AU - Hagelkruys, Astrid
AU - Jackowski, Suzanne
AU - Kozlov, Andrey
AU - Jacquemond, Vincent
AU - Knauf, Claude
AU - Superti-Furga, Giulio
AU - Rullman, Eric
AU - Gustafsson, Thomas
AU - McDermot, John
AU - Lowe, Martin
AU - Radak, Zsolt
AU - Chamberlain, Jeffrey S.
AU - Bakovic, Marica
AU - Banka, Siddharth
AU - Penninger, Josef M.
ID - 12747
JF - Nature Metabolism
KW - Cell Biology
KW - Physiology (medical)
KW - Endocrinology
KW - Diabetes and Metabolism
KW - Internal Medicine
SN - 2522-5812
TI - PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
ER -
TY - JOUR
AB - AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding.
AU - Pak, Marina A.
AU - Markhieva, Karina A.
AU - Novikova, Mariia S.
AU - Petrov, Dmitry S.
AU - Vorobyev, Ilya S.
AU - Maksimova, Ekaterina
AU - Kondrashov, Fyodor
AU - Ivankov, Dmitry N.
ID - 12758
IS - 3
JF - PLoS ONE
TI - Using AlphaFold to predict the impact of single mutations on protein stability and function
VL - 18
ER -
TY - JOUR
AB - My group and myself have studied respiratory complex I for almost 30 years, starting in 1994 when it was known as a L-shaped giant ‘black box' of bioenergetics. First breakthrough was the X-ray structure of the peripheral arm, followed by structures of the membrane arm and finally the entire complex from Thermus thermophilus. The developments in cryo-EM technology allowed us to solve the first complete structure of the twice larger, ∼1 MDa mammalian enzyme in 2016. However, the mechanism coupling, over large distances, the transfer of two electrons to pumping of four protons across the membrane remained an enigma. Recently we have solved high-resolution structures of mammalian and bacterial complex I under a range of redox conditions, including catalytic turnover. This allowed us to propose a robust and universal mechanism for complex I and related protein families. Redox reactions initially drive conformational changes around the quinone cavity and a long-distance transfer of substrate protons. These set up a stage for a series of electrostatically driven proton transfers along the membrane arm (‘domino effect'), eventually resulting in proton expulsion from the distal antiporter-like subunit. The mechanism radically differs from previous suggestions, however, it naturally explains all the unusual structural features of complex I. In this review I discuss the state of knowledge on complex I, including the current most controversial issues.
AU - Sazanov, Leonid A
ID - 12757
IS - 5
JF - The Biochemical Journal
SN - 0264-6021
TI - From the 'black box' to 'domino effect' mechanism: What have we learned from the structures of respiratory complex I
VL - 480
ER -
TY - JOUR
AB - We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine
the fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent
multiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048).
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
ID - 12761
IS - 1
JF - Annals of Applied Probability
SN - 1050-5164
TI - Functional central limit theorems for Wigner matrices
VL - 33
ER -