@inproceedings{9646,
abstract = {We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.},
author = {Wang, Jinyi and Sun, Yican and Fu, Hongfei and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar},
booktitle = {Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation},
isbn = {9781450383912},
location = {Online},
pages = {1171--1186},
publisher = {Association for Computing Machinery},
title = {{Quantitative analysis of assertion violations in probabilistic programs}},
doi = {10.1145/3453483.3454102},
year = {2021},
}
@inproceedings{9645,
abstract = {We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.
We first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods.},
author = {Asadi, Ali and Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir Kafshdar and Mahdavi, Mohammad},
booktitle = {Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation},
isbn = {9781450383912},
location = {Online},
pages = {772--787},
publisher = {Association for Computing Machinery},
title = {{Polynomial reachability witnesses via Stellensätze}},
doi = {10.1145/3453483.3454076},
year = {2021},
}
@inproceedings{9644,
abstract = {We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.},
author = {Chatterjee, Krishnendu and Goharshady, Ehsan Kafshdar and Novotný, Petr and Zikelic, Dorde},
booktitle = {Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation},
isbn = {9781450383912},
location = {Online},
pages = {1033--1048},
publisher = {Association for Computing Machinery},
title = {{Proving non-termination by program reversal}},
doi = {10.1145/3453483.3454093},
year = {2021},
}
@article{9649,
abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f : Rd → Rd−n. A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation T of the ambient space Rd. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently
fine triangulation T . This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary.},
author = {Boissonnat, Jean-Daniel and Wintraecken, Mathijs},
journal = {Foundations of Computational Mathematics },
publisher = {Springer Nature},
title = {{The topological correctness of PL approximations of isomanifolds}},
doi = {10.1007/s10208-021-09520-0},
year = {2021},
}
@unpublished{9698,
abstract = {Machine learning models are poised to make a transformative impact on chemical sciences by dramatically accelerating computational algorithms and amplifying insights available from computational chemistry methods. However, achieving this requires a confluence and coaction of expertise in computer science and physical sciences. This review is written for new and experienced researchers working at the intersection of both fields. We first provide concise tutorials of computational chemistry and machine learning methods, showing how insights involving both can be achieved. We then follow with a critical review of noteworthy applications that demonstrate how computational chemistry and machine learning can be used together to provide insightful (and useful) predictions in molecular and materials modeling, retrosyntheses, catalysis, and drug design.},
author = {Keith, John A. and Valentin Vassilev-Galindo, Valentin and Cheng, Bingqing and Chmiela, Stefan and Gastegger, Michael and Müller, Klaus-Robert and Tkatchenko, Alexandre},
booktitle = {arXiv},
title = {{Combining machine learning and computational chemistry for predictive insights into chemical systems}},
year = {2021},
}
@inproceedings{9678,
abstract = {We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.},
author = {Brandt, Sebastian and Keller, Barbara and Rybicki, Joel and Suomela, Jukka and Uitto, Jara},
booktitle = {Annual ACM Symposium on Parallelism in Algorithms and Architectures},
isbn = {9781450380706},
location = { Virtual Event, United States},
pages = {129--139},
title = {{Efficient load-balancing through distributed token dropping}},
doi = {10.1145/3409964.3461785},
year = {2021},
}
@inproceedings{9441,
abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. },
author = {Boissonnat, Jean-Daniel and Kachanovich, Siargey and Wintraecken, Mathijs},
booktitle = {37th International Symposium on Computational Geometry (SoCG 2021)},
isbn = {978-3-95977-184-9},
issn = {1868-8969},
location = {Virtual},
pages = {17:1--17:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations}},
doi = {10.4230/LIPIcs.SoCG.2021.17},
volume = {189},
year = {2021},
}
@inproceedings{9620,
abstract = {In this note, we introduce a distributed twist on the classic coupon collector problem: a set of m collectors wish to each obtain a set of n coupons; for this, they can each sample coupons uniformly at random, but can also meet in pairwise interactions, during which they can exchange coupons. By doing so, they hope to reduce the number of coupons that must be sampled by each collector in order to obtain a full set. This extension is natural when considering real-world manifestations of the coupon collector phenomenon, and has been remarked upon and studied empirically (Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019).
We provide the first theoretical analysis for such a scenario. We find that “coupon collecting with friends” can indeed significantly reduce the number of coupons each collector must sample, and raises interesting connections to the more traditional variants of the problem. While our analysis is in most cases asymptotically tight, there are several open questions raised, regarding finer-grained analysis of both “coupon collecting with friends,” and of a long-studied variant of the original problem in which a collector requires multiple full sets of coupons.},
author = {Alistarh, Dan-Adrian and Davies, Peter},
booktitle = {Structural Information and Communication Complexity},
isbn = {9783030795269},
issn = {1611-3349},
location = {Wrocław, Poland},
pages = {3--12},
publisher = {Springer Nature},
title = {{Collecting coupons is faster with friends}},
doi = {10.1007/978-3-030-79527-6_1},
volume = {12810},
year = {2021},
}
@inproceedings{9200,
abstract = {Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.},
author = {Garcia Soto, Miriam and Henzinger, Thomas A and Schilling, Christian},
booktitle = {HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control},
isbn = {9781450383394},
keywords = {hybrid automaton, membership, system identification},
location = {Nashville, TN, United States},
pages = {2102.12734},
publisher = {Association for Computing Machinery},
title = {{Synthesis of hybrid automata with affine dynamics from time-series data}},
doi = {10.1145/3447928.3456704},
year = {2021},
}
@inproceedings{9345,
abstract = {Modeling a crystal as a periodic point set, we present a fingerprint consisting of density functionsthat facilitates the efficient search for new materials and material properties. We prove invarianceunder isometries, continuity, and completeness in the generic case, which are necessary featuresfor the reliable comparison of crystals. The proof of continuity integrates methods from discretegeometry and lattice theory, while the proof of generic completeness combines techniques fromgeometry with analysis. The fingerprint has a fast algorithm based on Brillouin zones and relatedinclusion-exclusion formulae. We have implemented the algorithm and describe its application tocrystal structure prediction.},
author = {Edelsbrunner, Herbert and Heiss, Teresa and Kurlin , Vitaliy and Smith, Philip and Wintraecken, Mathijs},
booktitle = {37th International Symposium on Computational Geometry (SoCG 2021)},
issn = {1868-8969},
location = {Virtual},
pages = {32:1--32:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The density fingerprint of a periodic point set}},
doi = {10.4230/LIPIcs.SoCG.2021.32},
volume = {189},
year = {2021},
}
@inproceedings{9296,
abstract = { matching is compatible to two or more labeled point sets of size n with labels {1,…,n} if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to two or more labeled point sets in general position in the plane. We show that for any two labeled convex sets of n points there exists a compatible matching with ⌊2n−−√⌋ edges. More generally, for any ℓ labeled point sets we construct compatible matchings of size Ω(n1/ℓ) . As a corresponding upper bound, we use probabilistic arguments to show that for any ℓ given sets of n points there exists a labeling of each set such that the largest compatible matching has O(n2/(ℓ+1)) edges. Finally, we show that Θ(logn) copies of any set of n points are necessary and sufficient for the existence of a labeling such that any compatible matching consists only of a single edge.},
author = {Aichholzer, Oswin and Arroyo Guevara, Alan M and Masárová, Zuzana and Parada, Irene and Perz, Daniel and Pilz, Alexander and Tkadlec, Josef and Vogtenhuber, Birgit},
booktitle = {15th International Conference on Algorithms and Computation},
isbn = {9783030682101},
issn = {16113349},
location = {Yangon, Myanmar},
pages = {221--233},
publisher = {Springer Nature},
title = {{On compatible matchings}},
doi = {10.1007/978-3-030-68211-8_18},
volume = {12635},
year = {2021},
}
@article{9640,
abstract = {Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.},
author = {Tkadlec, Josef and Pavlogiannis, Andreas and Chatterjee, Krishnendu and Nowak, Martin A.},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Fast and strong amplifiers of natural selection}},
doi = {10.1038/s41467-021-24271-w},
volume = {12},
year = {2021},
}
@phdthesis{9418,
abstract = {Deep learning is best known for its empirical success across a wide range of applications
spanning computer vision, natural language processing and speech. Of equal significance,
though perhaps less known, are its ramifications for learning theory: deep networks have
been observed to perform surprisingly well in the high-capacity regime, aka the overfitting
or underspecified regime. Classically, this regime on the far right of the bias-variance curve
is associated with poor generalisation; however, recent experiments with deep networks
challenge this view.
This thesis is devoted to investigating various aspects of underspecification in deep learning.
First, we argue that deep learning models are underspecified on two levels: a) any given
training dataset can be fit by many different functions, and b) any given function can be
expressed by many different parameter configurations. We refer to the second kind of
underspecification as parameterisation redundancy and we precisely characterise its extent.
Second, we characterise the implicit criteria (the inductive bias) that guide learning in the
underspecified regime. Specifically, we consider a nonlinear but tractable classification
setting, and show that given the choice, neural networks learn classifiers with a large margin.
Third, we consider learning scenarios where the inductive bias is not by itself sufficient to
deal with underspecification. We then study different ways of ‘tightening the specification’: i)
In the setting of representation learning with variational autoencoders, we propose a hand-
crafted regulariser based on mutual information. ii) In the setting of binary classification, we
consider soft-label (real-valued) supervision. We derive a generalisation bound for linear
networks supervised in this way and verify that soft labels facilitate fast learning. Finally, we
explore an application of soft-label supervision to the training of multi-exit models.},
author = {Bui Thi Mai, Phuong},
pages = {125},
publisher = {IST Austria},
title = {{Underspecification in Deep Learning}},
doi = {10.15479/AT:ISTA:9418},
year = {2021},
}
@inproceedings{9543,
abstract = {We consider the problem ofdistributed mean estimation (DME), in which n machines are each given a local d-dimensional vector xv∈Rd, and must cooperate to estimate the mean of their inputs μ=1n∑nv=1xv, while minimizing total communication cost. DME is a fundamental construct in distributed machine learning, and there has been considerable work on variants of this problem, especially in the context of distributed variance reduction for stochastic gradients in parallel SGD. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an error bound in terms of this norm. However, in many real applications, the input vectors are concentrated around the correct output μ, but μ itself has large norm. In such cases, previous output error bounds perform poorly. In this paper, we show that output error bounds need not depend on input norm. We provide a method of quantization which allows distributed mean estimation to be performed with solution quality dependent only on the distance between inputs, not on input norm, and show an analogous result for distributed variance reduction. The technique is based on a new connection with lattice theory. We also provide lower bounds showing that the communication to error trade-off of our algorithms is asymptotically optimal. As the lattices achieving optimal bounds under l2-norm can be computationally impractical, we also present an extension which leverages easy-to-use cubic lattices, and is loose only up to a logarithmic factor ind. We show experimentally that our method yields practical improvements for common applications, relative to prior approaches.},
author = {Davies, Peter and Gurunanthan, Vijaykrishna and Moshrefi, Niusha and Ashkboos, Saleh and Alistarh, Dan-Adrian},
booktitle = {9th International Conference on Learning Representations},
location = {Virtual},
title = {{New bounds for distributed mean estimation and variance reduction}},
year = {2021},
}
@inproceedings{9416,
abstract = {We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks.},
author = {Bui Thi Mai, Phuong and Lampert, Christoph},
booktitle = {9th International Conference on Learning Representations},
location = {Virtual},
title = {{The inductive bias of ReLU networks on orthogonally separable data}},
year = {2021},
}
@phdthesis{8934,
abstract = {In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.
We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.},
author = {Goharshady, Amir Kafshdar},
issn = {2663-337X},
pages = {278},
publisher = {IST Austria},
title = {{Parameterized and algebro-geometric advances in static program analysis}},
doi = {10.15479/AT:ISTA:8934},
year = {2021},
}
@article{7956,
abstract = {When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.},
author = {Pȩkalski, J. and Rzadkowski, Wojciech and Panagiotopoulos, A. Z.},
issn = {10897690},
journal = {The Journal of chemical physics},
number = {20},
publisher = {AIP},
title = {{Shear-induced ordering in systems with competing interactions: A machine learning study}},
doi = {10.1063/5.0005194},
volume = {152},
year = {2020},
}
@article{7957,
abstract = {Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of
mutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.},
author = {Parenti, Ilaria and Garcia Rabaneda, Luis E and Schön, Hanna and Novarino, Gaia},
issn = {1878108X},
journal = {Trends in Neurosciences},
number = {8},
pages = {608--621},
publisher = {Elsevier},
title = {{Neurodevelopmental disorders: From genetics to functional pathways}},
doi = {10.1016/j.tins.2020.05.004},
volume = {43},
year = {2020},
}
@article{7960,
abstract = {Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces.},
author = {Kalai, Gil and Patakova, Zuzana},
issn = {14320444},
journal = {Discrete and Computational Geometry},
pages = {304--323},
publisher = {Springer Nature},
title = {{Intersection patterns of planar sets}},
doi = {10.1007/s00454-020-00205-z},
volume = {64},
year = {2020},
}
@article{7962,
abstract = {A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.},
author = {Pach, János and Reed, Bruce and Yuditsky, Yelena},
issn = {14320444},
journal = {Discrete and Computational Geometry},
number = {4},
pages = {888--917},
publisher = {Springer Nature},
title = {{Almost all string graphs are intersection graphs of plane convex sets}},
doi = {10.1007/s00454-020-00213-z},
volume = {63},
year = {2020},
}
@inproceedings{7966,
abstract = {For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).
For Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.
As our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem.},
author = {Auerbach, Benedikt and Giacon, Federico and Kiltz, Eike},
booktitle = {Advances in Cryptology – EUROCRYPT 2020},
isbn = {9783030457266},
issn = {0302-9743},
pages = {475--506},
publisher = {Springer Nature},
title = {{Everybody’s a target: Scalability in public-key encryption}},
doi = {10.1007/978-3-030-45727-3_16},
volume = {12107},
year = {2020},
}
@article{7968,
abstract = {Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role.},
author = {Ghazaryan, Areg and Paltiel, Yossi and Lemeshko, Mikhail},
issn = {1932-7447},
journal = {The Journal of Physical Chemistry C},
number = {21},
pages = {11716--11721},
publisher = {American Chemical Society},
title = {{Analytic model of chiral-induced spin selectivity}},
doi = {10.1021/acs.jpcc.0c02584},
volume = {124},
year = {2020},
}
@article{7971,
abstract = {Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state.},
author = {Rao, Peng and Serbyn, Maksym},
issn = {2469-9950},
journal = {Physical Review B},
number = {24},
publisher = {American Physical Society},
title = {{Gully quantum Hall ferromagnetism in biased trilayer graphene}},
doi = {10.1103/physrevb.101.245411},
volume = {101},
year = {2020},
}
@article{7985,
abstract = {The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.},
author = {Kwak, WJ and Sharon, D and Xia, C and Kim, H and Johnson, LR and Bruce, PG and Nazar, LF and Sun, YK and Frimer, AA and Noked, M and Freunberger, Stefan Alexander and Aurbach, D},
issn = {0009-2665},
journal = {Chemical Reviews},
number = {14},
pages = {6626--6683},
publisher = {American Chemical Society},
title = {{Lithium-oxygen batteries and related systems: Potential, status, and future}},
doi = {10.1021/acs.chemrev.9b00609},
volume = {120},
year = {2020},
}
@inproceedings{7989,
abstract = {We prove general topological Radon-type theorems for sets in ℝ^d, smooth real manifolds or finite dimensional simplicial complexes. Combined with a recent result of Holmsen and Lee, it gives fractional Helly theorem, and consequently the existence of weak ε-nets as well as a (p,q)-theorem. More precisely: Let X be either ℝ^d, smooth real d-manifold, or a finite d-dimensional simplicial complex. Then if F is a finite, intersection-closed family of sets in X such that the ith reduced Betti number (with ℤ₂ coefficients) of any set in F is at most b for every non-negative integer i less or equal to k, then the Radon number of F is bounded in terms of b and X. Here k is the smallest integer larger or equal to d/2 - 1 if X = ℝ^d; k=d-1 if X is a smooth real d-manifold and not a surface, k=0 if X is a surface and k=d if X is a d-dimensional simplicial complex. Using the recent result of the author and Kalai, we manage to prove the following optimal bound on fractional Helly number for families of open sets in a surface: Let F be a finite family of open sets in a surface S such that the intersection of any subfamily of F is either empty, or path-connected. Then the fractional Helly number of F is at most three. This also settles a conjecture of Holmsen, Kim, and Lee about an existence of a (p,q)-theorem for open subsets of a surface.},
author = {Patakova, Zuzana},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Bounding radon number via Betti numbers}},
doi = {10.4230/LIPIcs.SoCG.2020.61},
volume = {164},
year = {2020},
}
@inproceedings{7990,
abstract = {Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).},
author = {Wagner, Uli and Welzl, Emo},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)}},
doi = {10.4230/LIPIcs.SoCG.2020.67},
volume = {164},
year = {2020},
}
@inproceedings{7991,
abstract = {We define and study a discrete process that generalizes the convex-layer decomposition of a planar point set. Our process, which we call homotopic curve shortening (HCS), starts with a closed curve (which might self-intersect) in the presence of a set P⊂ ℝ² of point obstacles, and evolves in discrete steps, where each step consists of (1) taking shortcuts around the obstacles, and (2) reducing the curve to its shortest homotopic equivalent. We find experimentally that, if the initial curve is held fixed and P is chosen to be either a very fine regular grid or a uniformly random point set, then HCS behaves at the limit like the affine curve-shortening flow (ACSF). This connection between HCS and ACSF generalizes the link between "grid peeling" and the ACSF observed by Eppstein et al. (2017), which applied only to convex curves, and which was studied only for regular grids. We prove that HCS satisfies some properties analogous to those of ACSF: HCS is invariant under affine transformations, preserves convexity, and does not increase the total absolute curvature. Furthermore, the number of self-intersections of a curve, or intersections between two curves (appropriately defined), does not increase. Finally, if the initial curve is simple, then the number of inflection points (appropriately defined) does not increase.},
author = {Avvakumov, Sergey and Nivasch, Gabriel},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Homotopic curve shortening and the affine curve-shortening flow}},
doi = {10.4230/LIPIcs.SoCG.2020.12},
volume = {164},
year = {2020},
}
@inproceedings{7992,
abstract = {Let K be a convex body in ℝⁿ (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K ∩ h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p₀ is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n ≥ 2, there are always at least three distinct barycentric cuts through the point p₀ ∈ K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p₀ are guaranteed if n ≥ 3.},
author = {Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Barycentric cuts through a convex body}},
doi = {10.4230/LIPIcs.SoCG.2020.62},
volume = {164},
year = {2020},
}
@inproceedings{7994,
abstract = {In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of K_n was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible.},
author = {Arroyo Guevara, Alan M and Bensmail, Julien and Bruce Richter, R.},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Extending drawings of graphs to arrangements of pseudolines}},
doi = {10.4230/LIPIcs.SoCG.2020.9},
volume = {164},
year = {2020},
}
@article{7995,
abstract = {When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.},
author = {Perini, Samuel and Rafajlović, Marina and Westram, Anja M and Johannesson, Kerstin and Butlin, Roger K.},
issn = {15585646},
journal = {Evolution},
number = {7},
pages = {1482--1497},
publisher = {Wiley},
title = {{Assortative mating, sexual selection, and their consequences for gene flow in Littorina}},
doi = {10.1111/evo.14027},
volume = {74},
year = {2020},
}
@phdthesis{7996,
abstract = {Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and
calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.
Here we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element
resonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.},
author = {Kukucka, Josip},
issn = {2663-337X},
pages = {178},
publisher = {IST Austria},
title = {{Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing}},
doi = {10.15479/AT:ISTA:7996},
year = {2020},
}
@article{7999,
abstract = {Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal. },
author = {Trejo Banos, D and McCartney, DL and Patxot, M and Anchieri, L and Battram, T and Christiansen, C and Costeira, R and Walker, RM and Morris, SW and Campbell, A and Zhang, Q and Porteous, DJ and McRae, AF and Wray, NR and Visscher, PM and Haley, CS and Evans, KL and Deary, IJ and McIntosh, AM and Hemani, G and Bell, JT and Marioni, RE and Robinson, Matthew Richard},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Bayesian reassessment of the epigenetic architecture of complex traits}},
doi = {10.1038/s41467-020-16520-1},
volume = {11},
year = {2020},
}
@article{8001,
abstract = {Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network.},
author = {Vandael, David H and Borges Merjane, Carolina and Zhang, Xiaomin and Jonas, Peter M},
issn = {10974199},
journal = {Neuron},
number = {3},
pages = {509--521},
publisher = {Elsevier},
title = {{Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation}},
doi = {10.1016/j.neuron.2020.05.013},
volume = {107},
year = {2020},
}
@article{8002,
abstract = {Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.},
author = {Hörmayer, Lukas and Montesinos López, Juan C and Marhavá, Petra and Benková, Eva and Yoshida, Saiko and Friml, Jiří},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {26},
publisher = {Proceedings of the National Academy of Sciences},
title = {{Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots}},
doi = {10.1073/pnas.2003346117},
volume = {117},
year = {2020},
}
@article{8011,
abstract = {Relaxation to a thermal state is the inevitable fate of nonequilibrium interacting quantum systems without special conservation laws. While thermalization in one-dimensional systems can often be suppressed by integrability mechanisms, in two spatial dimensions thermalization is expected to be far more effective due to the increased phase space. In this work we propose a general framework for escaping or delaying the emergence of the thermal state in two-dimensional arrays of Rydberg atoms via the mechanism of quantum scars, i.e., initial states that fail to thermalize. The suppression of thermalization is achieved in two complementary ways: by adding local perturbations or by adjusting the driving Rabi frequency according to the local connectivity of the lattice. We demonstrate that these mechanisms allow us to realize robust quantum scars in various two-dimensional lattices, including decorated lattices with nonconstant connectivity. In particular, we show that a small decrease of the Rabi frequency at the corners of the lattice is crucial for mitigating the strong boundary effects in two-dimensional systems. Our results identify synchronization as an important tool for future experiments on two-dimensional quantum scars.},
author = {Michailidis, Alexios and Turner, C. J. and Papić, Z. and Abanin, D. A. and Serbyn, Maksym},
issn = {2643-1564},
journal = {Physical Review Research},
number = {2},
publisher = {American Physical Society},
title = {{Stabilizing two-dimensional quantum scars by deformation and synchronization}},
doi = {10.1103/physrevresearch.2.022065},
volume = {2},
year = {2020},
}
@inproceedings{8012,
abstract = {Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos.},
author = {Kragl, Bernhard and Enea, Constantin and Henzinger, Thomas A and Mutluergil, Suha Orhun and Qadeer, Shaz},
booktitle = {Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation},
isbn = {9781450376136},
location = {London, United Kingdom},
pages = {227--242},
publisher = {Association for Computing Machinery},
title = {{Inductive sequentialization of asynchronous programs}},
doi = {10.1145/3385412.3385980},
year = {2020},
}
@phdthesis{8032,
abstract = {Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”
In this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.},
author = {Huszár, Kristóf},
isbn = {978-3-99078-006-0},
issn = {2663-337X},
pages = {xviii+120},
publisher = {IST Austria},
title = {{Combinatorial width parameters for 3-dimensional manifolds}},
doi = {10.15479/AT:ISTA:8032},
year = {2020},
}
@article{8036,
abstract = {When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves.},
author = {Collard, Ylona and Grosjean, Galien M and Vandewalle, Nicolas},
issn = {23993650},
journal = {Communications Physics},
publisher = {Springer Nature},
title = {{Magnetically powered metachronal waves induce locomotion in self-assemblies}},
doi = {10.1038/s42005-020-0380-9},
volume = {3},
year = {2020},
}
@article{8037,
abstract = {Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics.},
author = {Lukacisinova, Marta and Fernando, Booshini and Bollenbach, Mark Tobias},
issn = {20411723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance}},
doi = {10.1038/s41467-020-16932-z},
volume = {11},
year = {2020},
}
@article{8038,
abstract = {Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications.},
author = {Fink, Johannes M and Kalaee, M. and Norte, R. and Pitanti, A. and Painter, O.},
issn = {20589565},
journal = {Quantum Science and Technology},
number = {3},
publisher = {IOP Publishing},
title = {{Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator}},
doi = {10.1088/2058-9565/ab8dce},
volume = {5},
year = {2020},
}
@article{8042,
abstract = {We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.},
author = {Boccato, Chiara and Brennecke, Christian and Cenatiempo, Serena and Schlein, Benjamin},
issn = {14359855},
journal = {Journal of the European Mathematical Society},
number = {7},
pages = {2331--2403},
publisher = {European Mathematical Society},
title = {{The excitation spectrum of Bose gases interacting through singular potentials}},
doi = {10.4171/JEMS/966},
volume = {22},
year = {2020},
}
@article{8043,
abstract = {With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain.},
author = {Paranjape, Chaitanya S and Duguet, Yohann and Hof, Björn},
issn = {14697645},
journal = {Journal of Fluid Mechanics},
publisher = {Cambridge University Press},
title = {{Oblique stripe solutions of channel flow}},
doi = {10.1017/jfm.2020.322},
volume = {897},
year = {2020},
}
@article{8057,
abstract = {Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability.},
author = {Bouchal, Roza and Li, Zhujie and Bongu, Chandra and Le Vot, Steven and Berthelot, Romain and Rotenberg, Benjamin and Favier, Frederic and Freunberger, Stefan Alexander and Salanne, Mathieu and Fontaine, Olivier},
issn = {0044-8249},
journal = {Angewandte Chemie},
number = {37},
pages = {16047--16051},
publisher = {Wiley},
title = {{Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte}},
doi = {10.1002/ange.202005378},
volume = {132},
year = {2020},
}
@unpublished{8063,
abstract = {We present a generative model of images that explicitly reasons over the set
of objects they show. Our model learns a structured latent representation that
separates objects from each other and from the background; unlike prior works,
it explicitly represents the 2D position and depth of each object, as well as
an embedding of its segmentation mask and appearance. The model can be trained
from images alone in a purely unsupervised fashion without the need for object
masks or depth information. Moreover, it always generates complete objects,
even though a significant fraction of training images contain occlusions.
Finally, we show that our model can infer decompositions of novel images into
their constituent objects, including accurate prediction of depth ordering and
segmentation of occluded parts.},
author = {Anciukevicius, Titas and Lampert, Christoph and Henderson, Paul M},
booktitle = {arXiv},
title = {{Object-centric image generation with factored depths, locations, and appearances}},
year = {2020},
}
@misc{8067,
abstract = {With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the
mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.},
author = {Varzi, Alberto and Thanner, Katharina and Scipioni, Roberto and Di Lecce, Daniele and Hassoun, Jusef and Dörfler, Susanne and Altheus, Holger and Kaskel, Stefan and Prehal, Christian and Freunberger, Stefan Alexander},
issn = {2664-1690},
keywords = {Battery, Lithium metal, Lithium-sulphur, Lithium-air, All-solid-state},
pages = {63},
publisher = {IST Austria},
title = {{Current status and future perspectives of Lithium metal batteries}},
doi = {10.15479/AT:ISTA:8067},
year = {2020},
}
@article{8077,
abstract = {The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods.},
author = {Shehu, Yekini and Iyiola, Olaniyi S.},
issn = {0168-9274},
journal = {Applied Numerical Mathematics},
pages = {315--337},
publisher = {Elsevier},
title = {{Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence}},
doi = {10.1016/j.apnum.2020.06.009},
volume = {157},
year = {2020},
}
@unpublished{8081,
abstract = {Here, we employ micro- and nanosized cellulose particles, namely paper fines and cellulose
nanocrystals, to induce hierarchical organization over a wide length scale. After processing
them into carbonaceous materials, we demonstrate that these hierarchically organized materials
outperform the best materials for supercapacitors operating with organic electrolytes reported
in literature in terms of specific energy/power (Ragone plot) while showing hardly any capacity
fade over 4,000 cycles. The highly porous materials feature a specific surface area as high as
2500 m2ˑg-1 and exhibit pore sizes in the range of 0.5 to 200 nm as proven by scanning electron
microscopy and N2 physisorption. The carbonaceous materials have been further investigated
by X-ray photoelectron spectroscopy and RAMAN spectroscopy. Since paper fines are an
underutilized side stream in any paper production process, they are a cheap and highly available
feedstock to prepare carbonaceous materials with outstanding performance in electrochemical
applications. },
author = {Hobisch, Mathias A. and Mourad, Eléonore and Fischer, Wolfgang J. and Prehal, Christian and Eyley, Samuel and Childress, Anthony and Zankel, Armin and Mautner, Andreas and Breitenbach, Stefan and Rao, Apparao M. and Thielemans, Wim and Freunberger, Stefan Alexander and Eckhart, Rene and Bauer, Wolfgang and Spirk, Stefan },
title = {{High specific capacitance supercapacitors from hierarchically organized all-cellulose composites}},
year = {2020},
}
@article{8084,
abstract = {Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.},
author = {Lombardi, Fabrizio and Gómez-Extremera, Manuel and Bernaola-Galván, Pedro and Vetrivelan, Ramalingam and Saper, Clifford B. and Scammell, Thomas E. and Ivanov, Plamen Ch.},
issn = {0270-6474},
journal = {Journal of Neuroscience},
number = {1},
pages = {171--190},
publisher = {Society for Neuroscience},
title = {{Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake}},
doi = {10.1523/jneurosci.1278-19.2019},
volume = {40},
year = {2020},
}
@article{8091,
abstract = {In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.},
author = {Seiringer, Robert and Yngvason, Jakob},
issn = {15729613},
journal = {Journal of Statistical Physics},
pages = {448--464},
publisher = {Springer},
title = {{Emergence of Haldane pseudo-potentials in systems with short-range interactions}},
doi = {10.1007/s10955-020-02586-0},
volume = {181},
year = {2020},
}
@inbook{8092,
abstract = {Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html.},
author = {Royer, Amélie and Bousmalis, Konstantinos and Gouws, Stephan and Bertsch, Fred and Mosseri, Inbar and Cole, Forrester and Murphy, Kevin},
booktitle = {Domain Adaptation for Visual Understanding},
editor = {Singh, Richa and Vatsa, Mayank and Patel, Vishal M. and Ratha, Nalini},
isbn = {9783030306717},
pages = {33--49},
publisher = {Springer Nature},
title = {{XGAN: Unsupervised image-to-image translation for many-to-many mappings}},
doi = {10.1007/978-3-030-30671-7_3},
year = {2020},
}
@misc{8097,
abstract = {Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology.},
author = {Kavcic, Bor},
keywords = {Escherichia coli, antibiotic combinations, translation, growth laws, drug interactions, bacterial physiology, translation inhibitors},
publisher = {IST Austria},
title = {{Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics"}},
doi = {10.15479/AT:ISTA:8097},
year = {2020},
}
@article{8099,
abstract = {Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.},
author = {Gammerdinger, William J and Toups, Melissa A and Vicoso, Beatriz},
issn = {1755-098X},
journal = {Molecular Ecology Resources},
number = {6},
pages = {1517--1525},
publisher = {Wiley},
title = {{Disagreement in FST estimators: A case study from sex chromosomes}},
doi = {10.1111/1755-0998.13210},
volume = {20},
year = {2020},
}
@article{8101,
abstract = {By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.},
author = {Grosjean, Galien M and Wald, Sebastian and Sobarzo Ponce, Juan Carlos A and Waitukaitis, Scott R},
journal = {Physical Review Materials},
keywords = {electric charge, tribocharging, soft matter, granular materials, polymers},
number = {8},
publisher = {American Physical Society},
title = {{Quantitatively consistent scale-spanning model for same-material tribocharging}},
doi = {10.1103/PhysRevMaterials.4.082602},
volume = {4},
year = {2020},
}
@article{8105,
abstract = {Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.},
author = {Lombardi, Fabrizio and Wang, Jilin W.J.L. and Zhang, Xiyun and Ivanov, Plamen Ch},
issn = {2100-014X},
journal = {EPJ Web of Conferences},
publisher = {EDP Sciences},
title = {{Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality}},
doi = {10.1051/epjconf/202023000005},
volume = {230},
year = {2020},
}
@unpublished{8125,
abstract = {Context, such as behavioral state, is known to modulate memory formation and retrieval, but is usually ignored in associative memory models. Here, we propose several types of contextual modulation for associative memory networks that greatly increase their performance. In these networks, context inactivates specific neurons and connections, which modulates the effective connectivity of the network. Memories are stored only by the active components, thereby reducing interference from memories acquired in other contexts. Such networks exhibit several beneficial characteristics, including enhanced memory capacity, high robustness to noise, increased robustness to memory overloading, and better memory retention during continual learning. Furthermore, memories can be biased to have different relative strengths, or even gated on or off, according to contextual cues, providing a candidate model for cognitive control of memory and efficient memory search. An external context-encoding network can dynamically switch the memory network to a desired state, which we liken to experimentally observed contextual signals in prefrontal cortex and hippocampus. Overall, our work illustrates the benefits of organizing memory around context, and provides an important link between behavioral studies of memory and mechanistic details of neural circuits.SIGNIFICANCEMemory is context dependent — both encoding and recall vary in effectiveness and speed depending on factors like location and brain state during a task. We apply this idea to a simple computational model of associative memory through contextual gating of neurons and synaptic connections. Intriguingly, this results in several advantages, including vastly enhanced memory capacity, better robustness, and flexible memory gating. Our model helps to explain (i) how gating and inhibition contribute to memory processes, (ii) how memory access dynamically changes over time, and (iii) how context representations, such as those observed in hippocampus and prefrontal cortex, may interact with and control memory processes.},
author = {Podlaski, William F. and Agnes, Everton J. and Vogels, Tim P},
booktitle = {bioRxiv},
pages = {30},
publisher = {Cold Spring Harbor Laboratory},
title = {{Context-modular memory networks support high-capacity, flexible, and robust associative memories}},
year = {2020},
}
@article{8126,
abstract = {Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.},
author = {Agnes, Everton J. and Luppi, Andrea I. and Vogels, Tim P},
issn = {1529-2401},
journal = {The Journal of Neuroscience},
number = {50},
pages = {9634--9649},
publisher = {Society for Neuroscience},
title = {{Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields}},
doi = {10.1523/JNEUROSCI.0276-20.2020},
volume = {40},
year = {2020},
}
@article{8127,
abstract = {Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.},
author = {Gonçalves, Pedro J. and Lueckmann, Jan-Matthis and Deistler, Michael and Nonnenmacher, Marcel and Öcal, Kaan and Bassetto, Giacomo and Chintaluri, Chaitanya and Podlaski, William F. and Haddad, Sara A. and Vogels, Tim P and Greenberg, David S. and Macke, Jakob H.},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Training deep neural density estimators to identify mechanistic models of neural dynamics}},
doi = {10.7554/eLife.56261},
volume = {9},
year = {2020},
}
@article{8130,
abstract = {We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.},
author = {Bossmann, Lea},
issn = {0003-9527},
journal = {Archive for Rational Mechanics and Analysis},
number = {11},
pages = {541--606},
publisher = {Springer Nature},
title = {{Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons}},
doi = {10.1007/s00205-020-01548-w},
volume = {238},
year = {2020},
}
@article{8131,
abstract = {The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes.},
author = {Basilico, Bernadette and Morandell, Jasmin and Novarino, Gaia},
issn = {18790380},
journal = {Current Opinion in Genetics and Development},
number = {12},
pages = {126--137},
publisher = {Elsevier},
title = {{Molecular mechanisms for targeted ASD treatments}},
doi = {10.1016/j.gde.2020.06.004},
volume = {65},
year = {2020},
}
@article{8134,
abstract = {We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.},
author = {Mayer, Simon and Seiringer, Robert},
issn = {00222488},
journal = {Journal of Mathematical Physics},
number = {6},
publisher = {AIP},
title = {{The free energy of the two-dimensional dilute Bose gas. II. Upper bound}},
doi = {10.1063/5.0005950},
volume = {61},
year = {2020},
}
@inproceedings{8135,
abstract = {Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.},
author = {Edelsbrunner, Herbert and Nikitenko, Anton and Ölsböck, Katharina and Synak, Peter},
booktitle = {Topological Data Analysis},
isbn = {9783030434076},
issn = {21978549},
pages = {181--218},
publisher = {Springer Nature},
title = {{Radius functions on Poisson–Delaunay mosaics and related complexes experimentally}},
doi = {10.1007/978-3-030-43408-3_8},
volume = {15},
year = {2020},
}
@article{8138,
abstract = {Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.},
author = {Zhang, J and Mazur, E and Balla, J and Gallei, Michelle C and Kalousek, P and Medveďová, Z and Li, Y and Wang, Y and Prat, Tomas and Vasileva, Mina K and Reinöhl, V and Procházka, S and Halouzka, R and Tarkowski, P and Luschnig, C and Brewer, PB and Friml, Jiří},
issn = {2041-1723},
journal = {Nature Communications},
number = {1},
pages = {3508},
publisher = {Springer Nature},
title = {{Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization}},
doi = {10.1038/s41467-020-17252-y},
volume = {11},
year = {2020},
}
@article{8142,
abstract = {Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.},
author = {Montesinos López, Juan C and Abuzeineh, A and Kopf, Aglaja and Juanes Garcia, Alba and Ötvös, Krisztina and Petrášek, J and Sixt, Michael K and Benková, Eva},
issn = {0261-4189},
journal = {The Embo Journal},
number = {17},
publisher = {Embo Press},
title = {{Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage}},
doi = {10.15252/embj.2019104238},
volume = {39},
year = {2020},
}
@phdthesis{8155,
abstract = {In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as
transcriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal
non-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.
In the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are
hard to evolve or maintain. },
author = {Grah, Rok},
issn = {2663-337X},
pages = {310},
publisher = {IST Austria},
title = {{Gene regulation across scales – how biophysical constraints shape evolution}},
doi = {10.15479/AT:ISTA:8155},
year = {2020},
}
@phdthesis{8156,
abstract = {We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.},
author = {Avvakumov, Sergey},
pages = {119},
publisher = {IST Austria},
title = {{Topological methods in geometry and discrete mathematics}},
doi = {10.15479/AT:ISTA:8156},
year = {2020},
}
@article{8162,
abstract = {In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.},
author = {Laukoter, Susanne and Pauler, Florian and Beattie, Robert J and Amberg, Nicole and Hansen, Andi H and Streicher, Carmen and Penz, Thomas and Bock, Christoph and Hippenmeyer, Simon},
issn = {0896-6273},
journal = {Neuron},
number = {6},
pages = {1160--1179.e9},
publisher = {Elsevier},
title = {{Cell-type specificity of genomic imprinting in cerebral cortex}},
doi = {10.1016/j.neuron.2020.06.031},
volume = {107},
year = {2020},
}
@article{8163,
abstract = {Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.},
author = {Vegter, Gert and Wintraecken, Mathijs},
issn = {1588-2896},
journal = {Studia Scientiarum Mathematicarum Hungarica},
number = {2},
pages = {193--199},
publisher = {AKJournals},
title = {{Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes}},
doi = {10.1556/012.2020.57.2.1454},
volume = {57},
year = {2020},
}
@article{8167,
abstract = {The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.},
author = {Stankowski, Sean and Westram, Anja M and Zagrodzka, Zuzanna B. and Eyres, Isobel and Broquet, Thomas and Johannesson, Kerstin and Butlin, Roger K.},
issn = {1471-2970},
journal = {Philosophical Transactions of the Royal Society. Series B: Biological Sciences},
number = {1806},
publisher = {The Royal Society},
title = {{The evolution of strong reproductive isolation between sympatric intertidal snails}},
doi = {10.1098/rstb.2019.0545},
volume = {375},
year = {2020},
}
@article{8168,
abstract = {Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.},
author = {Kulmuni, Jonna and Butlin, Roger K. and Lucek, Kay and Savolainen, Vincent and Westram, Anja M},
issn = {1471-2970},
journal = {Philosophical Transactions of the Royal Society. Series B: Biological sciences},
number = {1806},
publisher = {The Royal Society},
title = {{Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers}},
doi = {10.1098/rstb.2019.0528},
volume = {375},
year = {2020},
}
@article{8170,
abstract = {Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function
of time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct
peaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and
centrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For
CS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the
gas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in
detail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in
helium droplets introduced here should apply to a range of molecules and complexes.},
author = {Chatterley, Adam S. and Christiansen, Lars and Schouder, Constant A. and Jørgensen, Anders V. and Shepperson, Benjamin and Cherepanov, Igor and Bighin, Giacomo and Zillich, Robert E. and Lemeshko, Mikhail and Stapelfeldt, Henrik},
issn = {10797114},
journal = {Physical Review Letters},
number = {1},
publisher = {American Physical Society},
title = {{Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains}},
doi = {10.1103/PhysRevLett.125.013001},
volume = {125},
year = {2020},
}
@misc{8181,
author = {Hauschild, Robert},
publisher = {IST Austria},
title = {{Amplified centrosomes in dendritic cells promote immune cell effector functions}},
doi = {10.15479/AT:ISTA:8181},
year = {2020},
}
@inproceedings{8186,
abstract = {Numerous methods have been proposed for probabilistic generative modelling of
3D objects. However, none of these is able to produce textured objects, which
renders them of limited use for practical tasks. In this work, we present the
first generative model of textured 3D meshes. Training such a model would
traditionally require a large dataset of textured meshes, but unfortunately,
existing datasets of meshes lack detailed textures. We instead propose a new
training methodology that allows learning from collections of 2D images without
any 3D information. To do so, we train our model to explain a distribution of
images by modelling each image as a 3D foreground object placed in front of a
2D background. Thus, it learns to generate meshes that when rendered, produce
images similar to those in its training set.
A well-known problem when generating meshes with deep networks is the
emergence of self-intersections, which are problematic for many use-cases. As a
second contribution we therefore introduce a new generation process for 3D
meshes that guarantees no self-intersections arise, based on the physical
intuition that faces should push one another out of the way as they move.
We conduct extensive experiments on our approach, reporting quantitative and
qualitative results on both synthetic data and natural images. These show our
method successfully learns to generate plausible and diverse textured 3D
samples for five challenging object classes.},
author = {Henderson, Paul M and Tsiminaki, Vagia and Lampert, Christoph},
booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
location = {Virtual},
pages = {7498--7507},
publisher = {CVF},
title = {{Leveraging 2D data to learn textured 3D mesh generation}},
year = {2020},
}
@inproceedings{8194,
abstract = {Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.},
author = {Baranowski, Marek and He, Shaobo and Lechner, Mathias and Nguyen, Thanh Son and Rakamarić, Zvonimir},
booktitle = {Automated Reasoning},
isbn = {9783030510732},
issn = {16113349},
location = {Paris, France},
pages = {13--31},
publisher = {Springer Nature},
title = {{An SMT theory of fixed-point arithmetic}},
doi = {10.1007/978-3-030-51074-9_2},
volume = {12166},
year = {2020},
}
@inproceedings{8195,
abstract = {This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.},
author = {Kragl, Bernhard and Qadeer, Shaz and Henzinger, Thomas A},
booktitle = {Computer Aided Verification},
isbn = {9783030532871},
issn = {0302-9743},
pages = {275--298},
publisher = {Springer Nature},
title = {{Refinement for structured concurrent programs}},
doi = {10.1007/978-3-030-53288-8_14},
volume = {12224},
year = {2020},
}
@article{8196,
abstract = {This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.},
author = {Shehu, Yekini and Dong, Qiao-Li and Liu, Lu-Lu and Yao, Jen-Chih},
issn = {1389-4420},
journal = {Optimization and Engineering},
publisher = {Springer Nature},
title = {{New strong convergence method for the sum of two maximal monotone operators}},
doi = {10.1007/s11081-020-09544-5},
year = {2020},
}
@article{8199,
abstract = {We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.},
author = {Gulden, Tobias and Berg, Erez and Rudner, Mark Spencer and Lindner, Netanel},
issn = {2542-4653},
journal = {SciPost Physics},
publisher = {SciPost Foundation},
title = {{Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps}},
doi = {10.21468/scipostphys.9.1.015},
volume = {9},
year = {2020},
}
@article{8203,
abstract = {Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits.},
author = {Katsaros, Georgios and Kukucka, Josip and Vukušić, Lada and Watzinger, Hannes and Gao, Fei and Wang, Ting and Zhang, Jian-Jun and Held, Karsten},
issn = {1530-6984},
journal = {Nano Letters},
number = {7},
pages = {5201--5206},
publisher = {ACS Publications},
title = {{Zero field splitting of heavy-hole states in quantum dots}},
doi = {10.1021/acs.nanolett.0c01466},
volume = {20},
year = {2020},
}
@article{8225,
abstract = {Birch pollen allergy is among the most prevalent pollen allergies in Northern and Central Europe. This IgE-mediated disease can be treated with allergen immunotherapy (AIT), which typically gives rise to IgG antibodies inducing tolerance. Although the main mechanisms of allergen immunotherapy (AIT) are known, questions regarding possible Fc-mediated effects of IgG antibodies remain unanswered. This can mainly be attributed to the unavailability of appropriate tools, i.e., well-characterised recombinant antibodies (rAbs). We hereby aimed at providing human rAbs of several classes for mechanistic studies and as possible candidates for passive immunotherapy. We engineered IgE, IgG1, and IgG4 sharing the same variable region against the major birch pollen allergen Bet v 1 using Polymerase Incomplete Primer Extension (PIPE) cloning. We tested IgE functionality and IgG blocking capabilities using appropriate model cell lines. In vitro studies showed IgE engagement with FcεRI and CD23 and Bet v 1-dependent degranulation. Overall, we hereby present fully functional, human IgE, IgG1, and IgG4 sharing the same variable region against Bet v 1 and showcase possible applications in first mechanistic studies. Furthermore, our IgG antibodies might be useful candidates for passive immunotherapy of birch pollen allergy.},
author = {Köhler, Verena K. and Crescioli, Silvia and Fazekas-Singer, Judit and Bax, Heather J. and Hofer, Gerhard and Pranger, Christina L. and Hufnagl, Karin and Bianchini, Rodolfo and Flicker, Sabine and Keller, Walter and Karagiannis, Sophia N. and Jensen-Jarolim, Erika},
issn = {1422-0067},
journal = {International Journal of Molecular Sciences},
number = {16},
publisher = {MDPI},
title = {{Filling the antibody pipeline in allergy: PIPE cloning of IgE, IgG1 and IgG4 against the major birch pollen allergen Bet v 1}},
doi = {10.3390/ijms21165693},
volume = {21},
year = {2020},
}
@article{8226,
author = {Gotovina, Jelena and Bianchini, Rodolfo and Fazekas-Singer, Judit and Herrmann, Ina and Pellizzari, Giulia and Haidl, Ian D. and Hufnagl, Karin and Karagiannis, Sophia N. and Marshall, Jean S. and Jensen‐Jarolim, Erika},
issn = {0105-4538},
journal = {Allergy},
publisher = {Wiley},
title = {{Epinephrine drives human M2a allergic macrophages to a regulatory phenotype reducing mast cell degranulation in vitro}},
doi = {10.1111/all.14299},
year = {2020},
}
@article{8248,
abstract = {We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic.},
author = {Boissonnat, Jean-Daniel and Dyer, Ramsay and Ghosh, Arijit and Lieutier, Andre and Wintraecken, Mathijs},
issn = {0179-5376},
journal = {Discrete and Computational Geometry},
publisher = {Springer Nature},
title = {{Local conditions for triangulating submanifolds of Euclidean space}},
doi = {10.1007/s00454-020-00233-9},
year = {2020},
}
@article{8250,
abstract = {Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.},
author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Mechanisms of drug interactions between translation-inhibiting antibiotics}},
doi = {10.1038/s41467-020-17734-z},
volume = {11},
year = {2020},
}
@unpublished{8253,
abstract = {Brains process information in spiking neural networks. Their intricate connections shape the diverse functions these networks perform. In comparison, the functional capabilities of models of spiking networks are still rudimentary. This shortcoming is mainly due to the lack of insight and practical algorithms to construct the necessary connectivity. Any such algorithm typically attempts to build networks by iteratively reducing the error compared to a desired output. But assigning credit to hidden units in multi-layered spiking networks has remained challenging due to the non-differentiable nonlinearity of spikes. To avoid this issue, one can employ surrogate gradients to discover the required connectivity in spiking network models. However, the choice of a surrogate is not unique, raising the question of how its implementation influences the effectiveness of the method. Here, we use numerical simulations to systematically study how essential design parameters of surrogate gradients impact learning performance on a range of classification problems. We show that surrogate gradient learning is robust to different shapes of underlying surrogate derivatives, but the choice of the derivative’s scale can substantially affect learning performance. When we combine surrogate gradients with a suitable activity regularization technique, robust information processing can be achieved in spiking networks even at the sparse activity limit. Our study provides a systematic account of the remarkable robustness of surrogate gradient learning and serves as a practical guide to model functional spiking neural networks.},
author = {Zenke, Friedemann and Vogels, Tim P},
booktitle = {bioRxiv},
title = {{The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks}},
year = {2020},
}
@article{8261,
abstract = {Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.},
author = {Zhang, Xiaomin and Schlögl, Alois and Jonas, Peter M},
issn = {0896-6273},
journal = {Neuron},
number = {6},
pages = {1212--1225},
publisher = {Elsevier},
title = {{Selective routing of spatial information flow from input to output in hippocampal granule cells}},
doi = {10.1016/j.neuron.2020.07.006},
volume = {107},
year = {2020},
}
@article{8268,
abstract = {Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.},
author = {Gurel, Nezihe Merve and Kara, Kaan and Stojanov, Alen and Smith, Tyler and Lemmin, Thomas and Alistarh, Dan-Adrian and Puschel, Markus and Zhang, Ce},
issn = {19410476},
journal = {IEEE Transactions on Signal Processing},
pages = {4268--4282},
publisher = {IEEE},
title = {{Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications}},
doi = {10.1109/TSP.2020.3010355},
volume = {68},
year = {2020},
}
@inproceedings{8272,
abstract = {We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies.},
author = {Chatterjee, Krishnendu and Katoen, Joost P and Weininger, Maximilian and Winkler, Tobias},
booktitle = {International Conference on Computer Aided Verification},
isbn = {9783030532901},
issn = {16113349},
pages = {398--420},
publisher = {Springer Nature},
title = {{Stochastic games with lexicographic reachability-safety objectives}},
doi = {10.1007/978-3-030-53291-8_21},
volume = {12225},
year = {2020},
}
@article{8283,
abstract = {Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. },
author = {Chen, Huihuang and Lai, Linyi and Li, Lanxin and Liu, Liping and Jakada, Bello Hassan and Huang, Youmei and He, Qing and Chai, Mengnan and Niu, Xiaoping and Qin, Yuan},
issn = {14220067},
journal = {International Journal of Molecular Sciences},
number = {16},
publisher = {MDPI},
title = {{AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling}},
doi = {10.3390/ijms21165727},
volume = {21},
year = {2020},
}
@article{8284,
abstract = {Multiple resistance and pH adaptation (Mrp) antiporters are multi-subunit Na+ (or K+)/H+ exchangers representing an ancestor of many essential redox-driven proton pumps, such as respiratory complex I. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3.0 Å resolution. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each. Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.},
author = {Steiner, Julia and Sazanov, Leonid A},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter}},
doi = {10.7554/eLife.59407},
volume = {9},
year = {2020},
}
@article{8285,
abstract = {We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively.},
author = {Malia, Benjamin K. and Martínez-Rincón, Julián and Wu, Yunfan and Hosten, Onur and Kasevich, Mark A.},
issn = {10797114},
journal = {Physical Review Letters},
number = {4},
title = {{Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit}},
doi = {10.1103/PhysRevLett.125.043202},
volume = {125},
year = {2020},
}
@inproceedings{8286,
abstract = {We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a "gap covering" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor. },
author = {Alistarh, Dan-Adrian and Nadiradze, Giorgi and Sabour, Amirmojtaba},
booktitle = {47th International Colloquium on Automata, Languages, and Programming},
isbn = {9783959771382},
issn = {18688969},
location = {Virtual, Online; Germany},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Dynamic averaging load balancing on cycles}},
doi = {10.4230/LIPIcs.ICALP.2020.7},
volume = {168},
year = {2020},
}
@inproceedings{8287,
abstract = {Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.},
author = {Bogomolov, Sergiy and Forets, Marcelo and Frehse, Goran and Potomkin, Kostiantyn and Schilling, Christian},
booktitle = {Proceedings of the International Conference on Embedded Software},
keywords = {Reachability, Hybrid systems, Decomposition},
location = {Virtual },
title = {{Reachability analysis of linear hybrid systems via block decomposition}},
year = {2020},
}
@misc{8294,
abstract = {Automated root growth analysis and tracking of root tips. },
author = {Hauschild, Robert},
publisher = {IST Austria},
title = {{RGtracker}},
doi = {10.15479/AT:ISTA:8294},
year = {2020},
}
@unpublished{8307,
abstract = {Classic Byzantine fault-tolerant consensus protocols forfeit liveness in the face of asynchrony in order to preserve safety, whereas most deployed blockchain protocols forfeit safety in order to remain live. In this work, we achieve the best of both worlds by proposing a novel abstractions called the finality gadget. A finality gadget allows for transactions to always optimistically commit but informs the clients that these transactions might be unsafe. As a result, a blockchain can execute transactions optimistically and only commit them after they have been sufficiently and provably audited. In
this work, we formally model the finality gadget abstraction, prove that it is impossible to solve it deterministically in full asynchrony (even though it is stronger than consensus) and provide a partially synchronous protocol which is currently securing a major blockchain. This way we show that the protocol designer can decouple safety and liveness in order to speed up recovery from failures. We believe that there can be other types of finality gadgets that provide weaker safety (e.g., probabilistic) in order to gain more efficiency and this can depend on the probability that the network is not in synchrony.},
author = {Stewart, Alistair and Kokoris Kogias, Eleftherios},
booktitle = {arXiv},
title = {{GRANDPA: A Byzantine finality gadget}},
year = {2020},
}
@article{8308,
abstract = {Many-body localization provides a mechanism to avoid thermalization in isolated interacting quantum systems. The breakdown of thermalization may be complete, when all eigenstates in the many-body spectrum become localized, or partial, when the so-called many-body mobility edge separates localized and delocalized parts of the spectrum. Previously, De Roeck et al. [Phys. Rev. B 93, 014203 (2016)] suggested a possible instability of the many-body mobility edge in energy density. The local ergodic regions—so-called “bubbles”—resonantly spread throughout the system, leading to delocalization. In order to study such instability mechanism, in this work we design a model featuring many-body mobility edge in particle density: the states at small particle density are localized, while increasing the density of particles leads to delocalization. Using numerical simulations with matrix product states, we demonstrate the stability of many-body localization with respect to small bubbles in large dilute systems for experimentally relevant timescales. In addition, we demonstrate that processes where the bubble spreads are favored over processes that lead to resonant tunneling, suggesting a possible mechanism behind the observed stability of many-body mobility edge. We conclude by proposing experiments to probe particle density mobility edge in the Bose-Hubbard model.},
author = {Brighi, Pietro and Abanin, Dmitry A. and Serbyn, Maksym},
issn = {2469-9969},
journal = {Physical Review B},
number = {6},
publisher = {American Physical Society},
title = {{Stability of mobility edges in disordered interacting systems}},
doi = {10.1103/physrevb.102.060202},
volume = {102},
year = {2020},
}
@article{8318,
abstract = {Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.},
author = {Gutierrez-Fernandez, Javier and Kaszuba, Karol and Minhas, Gurdeep S. and Baradaran, Rozbeh and Tambalo, Margherita and Gallagher, David T. and Sazanov, Leonid A},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Key role of quinone in the mechanism of respiratory complex I}},
doi = {10.1038/s41467-020-17957-0},
volume = {11},
year = {2020},
}
@article{8319,
abstract = {We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.},
author = {Wu, Yunfan and Krishnakumar, Rajiv and Martínez-Rincón, Julián and Malia, Benjamin K. and Hosten, Onur and Kasevich, Mark A.},
issn = {24699934},
journal = {Physical Review A},
number = {1},
publisher = {APS},
title = {{Retrieval of cavity-generated atomic spin squeezing after free-space release}},
doi = {10.1103/PhysRevA.102.012224},
volume = {102},
year = {2020},
}
@inproceedings{8322,
abstract = {Reverse firewalls were introduced at Eurocrypt 2015 by Miro-nov and Stephens-Davidowitz, as a method for protecting cryptographic protocols against attacks on the devices of the honest parties. In a nutshell: a reverse firewall is placed outside of a device and its goal is to “sanitize” the messages sent by it, in such a way that a malicious device cannot leak its secrets to the outside world. It is typically assumed that the cryptographic devices are attacked in a “functionality-preserving way” (i.e. informally speaking, the functionality of the protocol remains unchanged under this attacks). In their paper, Mironov and Stephens-Davidowitz construct a protocol for passively-secure two-party computations with firewalls, leaving extension of this result to stronger models as an open question.
In this paper, we address this problem by constructing a protocol for secure computation with firewalls that has two main advantages over the original protocol from Eurocrypt 2015. Firstly, it is a multiparty computation protocol (i.e. it works for an arbitrary number n of the parties, and not just for 2). Secondly, it is secure in much stronger corruption settings, namely in the active corruption model. More precisely: we consider an adversary that can fully corrupt up to 𝑛−1 parties, while the remaining parties are corrupt in a functionality-preserving way.
Our core techniques are: malleable commitments and malleable non-interactive zero-knowledge, which in particular allow us to create a novel protocol for multiparty augmented coin-tossing into the well with reverse firewalls (that is based on a protocol of Lindell from Crypto 2001).},
author = {Chakraborty, Suvradip and Dziembowski, Stefan and Nielsen, Jesper Buus},
booktitle = {Advances in Cryptology – CRYPTO 2020},
isbn = {9783030568795},
issn = {16113349},
location = {Santa Barbara, CA, United States},
pages = {732--762},
publisher = {Springer Nature},
title = {{Reverse firewalls for actively secure MPCs}},
doi = {10.1007/978-3-030-56880-1_26},
volume = {12171},
year = {2020},
}
@article{8323,
author = {Pach, János},
issn = {14320444},
journal = {Discrete and Computational Geometry},
pages = {571--574},
publisher = {Springer Nature},
title = {{A farewell to Ricky Pollack}},
doi = {10.1007/s00454-020-00237-5},
volume = {64},
year = {2020},
}
@article{8325,
abstract = {Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. },
author = {Kalinin, Nikita and Shkolnikov, Mikhail},
issn = {14320916},
journal = {Communications in Mathematical Physics},
number = {9},
pages = {1649--1675},
publisher = {Springer Nature},
title = {{Sandpile solitons via smoothing of superharmonic functions}},
doi = {10.1007/s00220-020-03828-8},
volume = {378},
year = {2020},
}
@article{8329,
abstract = {We show the synthesis of a redox‐active quinone, 2‐methoxy‐1,4‐hydroquinone (MHQ), from a bio‐based feedstock and its suitability as electrolyte in aqueous redox flow batteries. We identified semiquinone intermediates at insufficiently low pH and quinoid radicals as responsible for decomposition of MHQ under electrochemical conditions. Both can be avoided and/or stabilized, respectively, using H 3 PO 4 electrolyte, allowing for reversible cycling in a redox flow battery for hundreds of cycles.},
author = {Schlemmer, Werner and Nothdurft, Philipp and Petzold, Alina and Frühwirt, Philipp and Schmallegger, Max and Gescheidt-Demner, Georg and Fischer, Roland and Freunberger, Stefan Alexander and Kern, Wolfgang and Spirk, Stefan},
issn = {1433-7851},
journal = {Angewandte Chemie International Edition},
number = {51},
pages = {22943--22946},
publisher = {Wiley},
title = {{2‐methoxyhydroquinone from vanillin for aqueous redox‐flow batteries}},
doi = {10.1002/anie.202008253},
volume = {59},
year = {2020},
}
@phdthesis{8332,
abstract = {Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.
In a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.
In a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.
Our approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step.},
author = {Kragl, Bernhard},
issn = {2663-337X},
pages = {120},
publisher = {IST Austria},
title = {{Verifying concurrent programs: Refinement, synchronization, sequentialization}},
doi = {10.15479/AT:ISTA:8332},
year = {2020},
}