TY - GEN
AB - Codes and data for reproducing the results of N. B. Budanur and B. Hof "An autonomous compartmental model for accelerating epidemics"
AU - Budanur, Nazmi B
ID - 11711
TI - burakbudanur/autoacc-public
ER -
TY - JOUR
AB - Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.
AU - Abualia, Rashed
AU - Ötvös, Krisztina
AU - Novák, Ondřej
AU - Bouguyon, Eleonore
AU - Domanegg, Kevin
AU - Krapp, Anne
AU - Nacry, Philip
AU - Gojon, Alain
AU - Lacombe, Benoit
AU - Benková, Eva
ID - 11734
IS - 31
JF - Proceedings of the National Academy of Sciences of the United States of America
TI - Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses
VL - 119
ER -
TY - JOUR
AB - Interlocking puzzles are intriguing geometric games where the puzzle pieces are held together based on their geometric arrangement, preventing the puzzle from falling apart. High-level-of-difficulty, or simply high-level, interlocking puzzles are a subclass of interlocking puzzles that require multiple moves to take out the first subassembly from the puzzle. Solving a high-level interlocking puzzle is a challenging task since one has to explore many different configurations of the puzzle pieces until reaching a configuration where the first subassembly can be taken out. Designing a high-level interlocking puzzle with a user-specified level of difficulty is even harder since the puzzle pieces have to be interlocking in all the configurations before the first subassembly is taken out.
In this paper, we present a computational approach to design high-level interlocking puzzles. The core idea is to represent all possible configurations of an interlocking puzzle as well as transitions among these configurations using a rooted, undirected graph called a disassembly graph and leverage this graph to find a disassembly plan that requires a minimal number of moves to take out the first subassembly from the puzzle. At the design stage, our algorithm iteratively constructs the geometry of each puzzle piece to expand the disassembly graph incrementally, aiming to achieve a user-specified level of difficulty. We show that our approach allows efficient generation of high-level interlocking puzzles of various shape complexities, including new solutions not attainable by state-of-the-art approaches.
AU - Chen, Rulin
AU - Wang, Ziqi
AU - Song, Peng
AU - Bickel, Bernd
ID - 11735
IS - 4
JF - ACM Transactions on Graphics
SN - 0730-0301
TI - Computational design of high-level interlocking puzzles
VL - 41
ER -
TY - JOUR
AB - Spin-orbit coupling in thin HgTe quantum wells results in a relativistic-like electron band structure, making it a versatile solid state platform to observe and control nontrivial electrodynamic phenomena. Here we report an observation of universal terahertz (THz) transparency determined by fine-structure constant α≈1/137 in 6.5-nm-thick HgTe layer, close to the critical thickness separating phases with topologically different electronic band structure. Using THz spectroscopy in a magnetic field we obtain direct evidence of asymmetric spin splitting of the Dirac cone. This particle-hole asymmetry facilitates optical control of edge spin currents in the quantum wells.
AU - Dziom, Uladzislau
AU - Shuvaev, A.
AU - Gospodarič, J.
AU - Novik, E. G.
AU - Dobretsova, A. A.
AU - Mikhailov, N. N.
AU - Kvon, Z. D.
AU - Alpichshev, Zhanybek
AU - Pimenov, A.
ID - 11737
IS - 4
JF - Physical Review B
SN - 2469-9950
TI - Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells
VL - 106
ER -
TY - JOUR
AB - We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.
AU - Forkert, Dominik L
AU - Maas, Jan
AU - Portinale, Lorenzo
ID - 11739
IS - 4
JF - SIAM Journal on Mathematical Analysis
KW - Fokker--Planck equation
KW - gradient flow
KW - evolutionary $\Gamma$-convergence
SN - 0036-1410
TI - Evolutionary $\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions
VL - 54
ER -
TY - JOUR
AB - We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].
We consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition.
AU - Cooley, Oliver
AU - Del Giudice, Nicola
AU - Kang, Mihyun
AU - Sprüssel, Philipp
ID - 11740
IS - 3
JF - Electronic Journal of Combinatorics
TI - Phase transition in cohomology groups of non-uniform random simplicial complexes
VL - 29
ER -
TY - JOUR
AB - Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
ID - 11741
JF - Probability Theory and Related Fields
SN - 0178-8051
TI - Quenched universality for deformed Wigner matrices
ER -
TY - THES
AB - In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.
Our main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.
For the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\in \mathbb{N}}$ and $(H_n)_{n\in\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).
Via the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\mathrm{PGL}_{d+2}(\mathbb{F}_q)$ for any $\varepsilon>0$ and sufficiently large $q=q(\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.
By improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\mathrm{PGL}_{2}(\mathbb{F}_q)$ is not tight.
In a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.
AU - Wild, Pascal
ID - 11777
SN - 2663-337X
TI - High-dimensional expansion and crossing numbers of simplicial complexes
ER -
TY - CONF
AB - Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time.
AU - Henzinger, Thomas A
AU - Mazzocchi, Nicolas Adrien
AU - Sarac, Naci E
ID - 11775
SN - 0302-9743
T2 - 22nd International Conference on Runtime Verification
TI - Abstract monitors for quantitative specifications
VL - 13498
ER -
TY - JOUR
AB - We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix.
AU - Bossmann, Lea
ID - 11783
IS - 6
JF - Journal of Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0022-2488
TI - Low-energy spectrum and dynamics of the weakly interacting Bose gas
VL - 63
ER -
TY - CONF
AB - This paper presents a comprehensive study of algorithms for maintaining the number of all connected four-vertex subgraphs in a dynamic graph. Specifically, our algorithms maintain the number of paths of length three in deterministic amortized O(m^{1/2}) update time, and any other connected four-vertex subgraph which is not a clique in deterministic amortized update time O(m^{2/3}). Queries can be answered in constant time. We also study the query times for subgraphs containing an arbitrary edge that is supplied only with the query as well as the case where only subgraphs containing a vertex s that is fixed beforehand are considered. For length-3 paths, paws, 4-cycles, and diamonds our bounds match or are not far from (conditional) lower bounds: Based on the OMv conjecture we show that any dynamic algorithm that detects the existence of paws, diamonds, or 4-cycles or that counts length-3 paths takes update time Ω(m^{1/2-δ}).
Additionally, for 4-cliques and all connected induced subgraphs, we show a lower bound of Ω(m^{1-δ}) for any small constant δ > 0 for the amortized update time, assuming the static combinatorial 4-clique conjecture holds. This shows that the O(m) algorithm by Eppstein et al. [David Eppstein et al., 2012] for these subgraphs cannot be improved by a polynomial factor.
AU - Hanauer, Kathrin
AU - Henzinger, Monika H
AU - Hua, Qi Cheng
ID - 11812
SN - 1868-8969
T2 - 1st Symposium on Algorithmic Foundations of Dynamic Networks
TI - Fully dynamic four-vertex subgraph counting
VL - 221
ER -
TY - CONF
AB - In recent years, significant advances have been made in the design and analysis of fully dynamic algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. Here, we present a quick reference guide to recent engineering and theory results in the area of fully dynamic graph algorithms.
AU - Hanauer, Kathrin
AU - Henzinger, Monika H
AU - Schulz, Christian
ID - 11808
SN - 9783959772242
T2 - 1st Symposium on Algorithmic Foundations of Dynamic Networks
TI - Recent advances in fully dynamic graph algorithms
VL - 221
ER -
TY - JOUR
AB - We consider the flow of two viscous and incompressible fluids within a bounded domain modeled by means of a two-phase Navier–Stokes system. The two fluids are assumed to be immiscible, meaning that they are separated by an interface. With respect to the motion of the interface, we consider pure transport by the fluid flow. Along the boundary of the domain, a complete slip boundary condition for the fluid velocities and a constant ninety degree contact angle condition for the interface are assumed. In the present work, we devise for the resulting evolution problem a suitable weak solution concept based on the framework of varifolds and establish as the main result a weak-strong uniqueness principle in 2D. The proof is based on a relative entropy argument and requires a non-trivial further development of ideas from the recent work of Fischer and the first author (Arch. Ration. Mech. Anal. 236, 2020) to incorporate the contact angle condition. To focus on the effects of the necessarily singular geometry of the evolving fluid domains, we work for simplicity in the regime of same viscosities for the two fluids.
AU - Hensel, Sebastian
AU - Marveggio, Alice
ID - 11842
IS - 3
JF - Journal of Mathematical Fluid Mechanics
SN - 1422-6928
TI - Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities
VL - 24
ER -
TY - JOUR
AB - Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.
AU - Toprakcioglu, Zenon
AU - Kamada, Ayaka
AU - Michaels, Thomas C.T.
AU - Xie, Mengqi
AU - Krausser, Johannes
AU - Wei, Jiapeng
AU - Šarić, Anđela
AU - Vendruscolo, Michele
AU - Knowles, Tuomas P.J.
ID - 11841
IS - 31
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Adsorption free energy predicts amyloid protein nucleation rates
VL - 119
ER -
TY - CONF
AB - It is a highly desirable property for deep networks to be robust against
small input changes. One popular way to achieve this property is by designing
networks with a small Lipschitz constant. In this work, we propose a new
technique for constructing such Lipschitz networks that has a number of
desirable properties: it can be applied to any linear network layer
(fully-connected or convolutional), it provides formal guarantees on the
Lipschitz constant, it is easy to implement and efficient to run, and it can be
combined with any training objective and optimization method. In fact, our
technique is the first one in the literature that achieves all of these
properties simultaneously. Our main contribution is a rescaling-based weight
matrix parametrization that guarantees each network layer to have a Lipschitz
constant of at most 1 and results in the learned weight matrices to be close to
orthogonal. Hence we call such layers almost-orthogonal Lipschitz (AOL).
Experiments and ablation studies in the context of image classification with
certified robust accuracy confirm that AOL layers achieve results that are on
par with most existing methods. Yet, they are simpler to implement and more
broadly applicable, because they do not require computationally expensive
matrix orthogonalization or inversion steps as part of the network
architecture. We provide code at https://github.com/berndprach/AOL.
AU - Prach, Bernd
AU - Lampert, Christoph
ID - 11839
SN - 9783031198021
T2 - Computer Vision – ECCV 2022
TI - Almost-orthogonal layers for efficient general-purpose Lipschitz networks
VL - 13681
ER -
TY - JOUR
AB - A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.
AU - Tomasek, Kathrin
AU - Leithner, Alexander F
AU - Glatzová, Ivana
AU - Lukesch, Michael S.
AU - Guet, Calin C
AU - Sixt, Michael K
ID - 11843
JF - eLife
TI - Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14
VL - 11
ER -
TY - CONF
AB - In the stochastic population protocol model, we are given a connected graph with n nodes, and in every time step, a scheduler samples an edge of the graph uniformly at random and the nodes connected by this edge interact. A fundamental task in this model is stable leader election, in which all nodes start in an identical state and the aim is to reach a configuration in which (1) exactly one node is elected as leader and (2) this node remains as the unique leader no matter what sequence of interactions follows. On cliques, the complexity of this problem has recently been settled: time-optimal protocols stabilize in Θ(n log n) expected steps using Θ(log log n) states, whereas protocols that use O(1) states require Θ(n2) expected steps.
In this work, we investigate the complexity of stable leader election on general graphs. We provide the first non-trivial time lower bounds for leader election on general graphs, showing that, when moving beyond cliques, the complexity landscape of leader election becomes very diverse: the time required to elect a leader can range from O(1) to Θ(n3) expected steps. On the upper bound side, we first observe that there exists a protocol that is time-optimal on many graph families, but uses polynomially-many states. In contrast, we give a near-time-optimal protocol that uses only O(log2n) states that is at most a factor log n slower. Finally, we show that the constant-state protocol of Beauquier et al. [OPODIS 2013] is at most a factor n log n slower than the fast polynomial-state protocol. Moreover, among constant-state protocols, this protocol has near-optimal average case complexity on dense random graphs.
AU - Alistarh, Dan-Adrian
AU - Rybicki, Joel
AU - Voitovych, Sasha
ID - 11844
SN - 9781450392624
T2 - Proceedings of the Annual ACM Symposium on Principles of Distributed Computing
TI - Near-optimal leader election in population protocols on graphs
ER -
TY - JOUR
AB - This paper is a continuation of Part I of this project, where we developed a new local well-posedness theory for nonlinear stochastic PDEs with Gaussian noise. In the current Part II we consider blow-up criteria and regularization phenomena. As in Part I we can allow nonlinearities with polynomial growth and rough initial values from critical spaces. In the first main result we obtain several new blow-up criteria for quasi- and semilinear stochastic evolution equations. In particular, for semilinear equations we obtain a Serrin type blow-up criterium, which extends a recent result of Prüss–Simonett–Wilke (J Differ Equ 264(3):2028–2074, 2018) to the stochastic setting. Blow-up criteria can be used to prove global well-posedness for SPDEs. As in Part I, maximal regularity techniques and weights in time play a central role in the proofs. Our second contribution is a new method to bootstrap Sobolev and Hölder regularity in time and space, which does not require smoothness of the initial data. The blow-up criteria are at the basis of these new methods. Moreover, in applications the bootstrap results can be combined with our blow-up criteria, to obtain efficient ways to prove global existence. This gives new results even in classical 𝐿2-settings, which we illustrate for a concrete SPDE. In future works in preparation we apply the results of the current paper to obtain global well-posedness results and regularity for several concrete SPDEs. These include stochastic Navier–Stokes equations, reaction– diffusion equations and the Allen–Cahn equation. Our setting allows to put these SPDEs into a more flexible framework, where less restrictions on the nonlinearities are needed, and we are able to treat rough initial values from critical spaces. Moreover, we will obtain higher-order regularity results.
AU - Agresti, Antonio
AU - Veraar, Mark
ID - 11858
IS - 2
JF - Journal of Evolution Equations
KW - Mathematics (miscellaneous)
SN - 1424-3199
TI - Nonlinear parabolic stochastic evolution equations in critical spaces part II
VL - 22
ER -
TY - THES
AB - As the overall global mean surface temperature is increasing due to climate change, plant
adaptation to those stressful conditions is of utmost importance for their survival. Plants are
sessile organisms, thus to compensate for their lack of mobility, they evolved a variety of
mechanisms enabling them to flexibly adjust their physiological, growth and developmental
processes to fluctuating temperatures and to survive in harsh environments. While these unique
adaptation abilities provide an important evolutionary advantage, overall modulation of plant
growth and developmental program due to non-optimal temperature negatively affects biomass
production, crop productivity or sensitivity to pathogens. Thus, understanding molecular
processes underlying plant adaptation to increased temperature can provide important
resources for breeding strategies to ensure sufficient agricultural food production.
An increase in ambient temperature by a few degrees leads to profound changes in organ growth
including enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and
cotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,
one of the best-studied growth hormones, plays an essential role in this process by direct
activation of transcriptional and non-transcriptional processes resulting in elongation growth
(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature
(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key
components of the polar auxin transport (PAT) machinery, which controls the amount and
direction of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,
PIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT
through either chemical or genetic means dramatically affecting the adaptive responses to hAT.
Intriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether
and how PINs at the level of expression adapt to fluctuation in temperature is scarcely
understood.
With genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN
auxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via
adjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we
identified three Zinc-Finger (ZF) transcription factors as novel molecular components of the
thermo-regulatory network, which through negative regulation of PIN transcription adjust the
transport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the
negative feedback loop attenuating the activity of the thermo-sensing pathway to restrain
exaggerated growth and developmental responses to hAT.
AU - Artner, Christina
ID - 11879
KW - high ambient temperature
KW - auxin
KW - PINs
KW - Zinc-Finger proteins
KW - thermomorphogenesis
KW - stress
SN - 2663-337X
TI - Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature
ER -
TY - JOUR
AB - We study the many-body dynamics of an initially factorized bosonic wave function in the mean-field regime. We prove large deviation estimates for the fluctuations around the condensate. We derive an upper bound extending a recent result to more general interactions. Furthermore, we derive a new lower bound which agrees with the upper bound in leading order.
AU - Rademacher, Simone Anna Elvira
AU - Seiringer, Robert
ID - 11917
JF - Journal of Statistical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0022-4715
TI - Large deviation estimates for weakly interacting bosons
VL - 188
ER -
TY - JOUR
AB - A domain is called Kac regular for a quadratic form on L2 if every functions vanishing almost everywhere outside the domain can be approximated in form norm by functions with compact support in the domain. It is shown that this notion is stable under domination of quadratic forms. As applications measure perturbations of quasi-regular Dirichlet forms, Cheeger energies on metric measure spaces and Schrödinger operators on manifolds are studied. Along the way a characterization of the Sobolev space with Dirichlet boundary conditions on domains in infinitesimally Riemannian metric measure spaces is obtained.
AU - Wirth, Melchior
ID - 11916
IS - 3
JF - Advances in Operator Theory
KW - Algebra and Number Theory
KW - Analysis
TI - Kac regularity and domination of quadratic forms
VL - 7
ER -
TY - CONF
AB - Statistics of small subgraph counts such as triangles, four-cycles, and s-t paths of short lengths reveal important structural properties of the underlying graph. These problems have been widely studied in social network analysis. In most relevant applications, the graphs are not only massive but also change dynamically over time. Most of these problems become hard in the dynamic setting when considering the worst case. In this paper, we ask whether the question of small subgraph counting over dynamic graphs is hard also in the average case.
We consider the simplest possible average case model where the updates follow an Erdős-Rényi graph: each update selects a pair of vertices (u, v) uniformly at random and flips the existence of the edge (u, v). We develop new lower bounds and matching algorithms in this model for counting four-cycles, counting triangles through a specified point s, or a random queried point, and st paths of length 3, 4 and 5. Our results indicate while computing st paths of length 3, and 4 are easy in the average case with O(1) update time (note that they are hard in the worst case), it becomes hard when considering st paths of length 5.
We introduce new techniques which allow us to get average-case hardness for these graph problems from the worst-case hardness of the Online Matrix vector problem (OMv). Our techniques rely on recent advances in fine-grained average-case complexity. Our techniques advance this literature, giving the ability to prove new lower bounds on average-case dynamic algorithms.
AU - Henzinger, Monika H
AU - Lincoln, Andrea
AU - Saha, Barna
ID - 11918
T2 - 33rd Annual ACM-SIAM Symposium on Discrete Algorithms
TI - The complexity of average-case dynamic subgraph counting
ER -
TY - JOUR
AB - Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII′ and X are the same thermodynamic phase under different conditions, whereas superionic ice VII″ has a first-order phase boundary with ice VII′. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems.
AU - Reinhardt, Aleks
AU - Bethkenhagen, Mandy
AU - Coppari, Federica
AU - Millot, Marius
AU - Hamel, Sebastien
AU - Cheng, Bingqing
ID - 11937
JF - Nature Communications
TI - Thermodynamics of high-pressure ice phases explored with atomistic simulations
VL - 13
ER -
TY - CONF
AB - We present a practically efficient algorithm for maintaining a global minimum cut in large dynamic graphs under both edge insertions and deletions. While there has been theoretical work on this problem, our algorithm is the first implementation of a fully-dynamic algorithm. The algorithm uses the theoretical foundation and combines it with efficient and finely-tuned implementations to give an algorithm that can maintain the global minimum cut of a graph with rapid update times. We show that our algorithm gives up to multiple orders of magnitude speedup compared to static approaches both on edge insertions and deletions.
AU - Henzinger, Monika H
AU - Noe, Alexander
AU - Schulz, Christian
ID - 11930
T2 - 2022 Proceedings of the Symposium on Algorithm Engineering and Experiments
TI - Practical fully dynamic minimum cut algorithms
ER -
TY - JOUR
AB - The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.
AU - Ben Simon, Yoav
AU - Käfer, Karola
AU - Velicky, Philipp
AU - Csicsvari, Jozsef L
AU - Danzl, Johann G
AU - Jonas, Peter M
ID - 11951
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
SN - 2041-1723
TI - A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory
VL - 13
ER -
TY - JOUR
AB - Covalent organic frameworks (COFs) are structurally tuneable, porous and crystalline polymers constructed through the covalent attachment of small organic building blocks as elementary units. Using the myriad of such building blocks, a broad spectrum of functionalities has been applied for COF syntheses for broad applications, including heterogeneous catalysis. Herein, we report the synthesis of a new family of porous and crystalline COFs using a novel acridine linker and benzene-1,3,5-tricarbaldehyde derivatives bearing a variable number of hydroxy groups. With the broad absorption in the visible light region, the COFs were applied as photocatalysts in metallaphotocatalytic C−N cross-coupling. The fully β-ketoenamine linked COF showed the highest activity, due to the increased charge separation upon irradiation. The COF showed good to excellent yields for several aryl bromides, good recyclability and even catalyzed the organic transformation in presence of green light as energy source.
AU - Traxler, Michael
AU - Gisbertz, Sebastian
AU - Pachfule, Pradip
AU - Schmidt, Johannes
AU - Roeser, Jérôme
AU - Reischauer, Susanne
AU - Rabeah, Jabor
AU - Pieber, Bartholomäus
AU - Thomas, Arne
ID - 11955
IS - 21
JF - Angewandte Chemie International Edition
SN - 1433-7851
TI - Acridine‐functionalized covalent organic frameworks (COFs) as photocatalysts for metallaphotocatalytic C−N cross‐coupling
VL - 61
ER -
TY - JOUR
AB - Moulding refers to a set of manufacturing techniques in which a mould, usually a cavity or a solid frame, is used to shape a liquid or pliable material into an object of the desired shape. The popularity of moulding comes from its effectiveness, scalability and versatility in terms of employed materials. Its relevance as a fabrication process is demonstrated by the extensive literature covering different aspects related to mould design, from material flow simulation to the automation of mould geometry design. In this state-of-the-art report, we provide an extensive review of the automatic methods for the design of moulds, focusing on contributions from a geometric perspective. We classify existing mould design methods based on their computational approach and the nature of their target moulding process. We summarize the relationships between computational approaches and moulding techniques, highlighting their strengths and limitations. Finally, we discuss potential future research directions.
AU - Alderighi, Thomas
AU - Malomo, Luigi
AU - Auzinger, Thomas
AU - Bickel, Bernd
AU - Cignoni, Paulo
AU - Pietroni, Nico
ID - 11993
IS - 6
JF - Computer Graphics Forum
KW - Computer Graphics and Computer-Aided Design
SN - 0167-7055
TI - State of the art in computational mould design
VL - 41
ER -
TY - JOUR
AB - The study of the complexity of the constraint satisfaction problem (CSP), centred around the Feder-Vardi Dichotomy Conjecture, has been very prominent in the last two decades. After a long concerted effort and many partial results, the Dichotomy Conjecture has been proved in 2017 independently by Bulatov and Zhuk. At about the same time, a vast generalisation of CSP, called promise CSP, has started to gain prominence. In this survey, we explain the importance of promise CSP and highlight many new very interesting features that the study of promise CSP has brought to light. The complexity classification quest for the promise CSP is wide open, and we argue that, despite the promise CSP being more general, this quest is rather more accessible to a wide range of researchers than the dichotomy-led study of the CSP has been.
AU - Krokhin, Andrei
AU - Opršal, Jakub
ID - 11991
IS - 3
JF - ACM SIGLOG News
SN - 2372-3491
TI - An invitation to the promise constraint satisfaction problem
VL - 9
ER -
TY - JOUR
AB - G protein-coupled receptors (GPCRs) regulate processes ranging from immune responses to neuronal signaling. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additionally, dissecting cell type-specific responses is challenging when the same GPCR is expressed on different cells within a tissue. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that bind clozapine-N-oxide and mimic a GPCR-of-interest. We show that chimeric DREADD-β2AR triggers responses comparable to β2AR on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation in microglia, an immune cell capable of driving central nervous system inflammation. When dissecting microglial inflammation, we included two additional DREADD-based chimeras mimicking microglia-enriched GPR65 and GPR109A. DREADD-β2AR and DREADD-GPR65 modulate the inflammatory response with high similarity to endogenous β2AR, while DREADD-GPR109A shows no impact. Our DREADD-based approach allows investigation of cell type-dependent pathways without known endogenous ligands.
AU - Schulz, Rouven
AU - Korkut, Medina
AU - Venturino, Alessandro
AU - Colombo, Gloria
AU - Siegert, Sandra
ID - 11995
JF - Nature Communications
TI - Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses
VL - 13
ER -
TY - THES
AB - G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.
We validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.
Our DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level.
AU - Schulz, Rouven
ID - 11945
SN - 2663-337X
TI - Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function
ER -
TY - JOUR
AB - Recently it became possible to study highly excited rotational states of molecules in superfluid helium through nonadiabatic alignment experiments (Cherepanov et al 2021 Phys. Rev. A 104 L061303). This calls for theoretical approaches that go beyond explaining renormalized values of molecular spectroscopic constants, which suffices when only the lowest few rotational states are involved. As the first step in this direction, here we present a basic quantum mechanical model describing highly excited rotational states of molecules in superfluid helium nanodroplets. We show that a linear molecule immersed in a superfluid can be seen as an effective symmetric top, similar to the rotational structure of radicals, such as OH or NO, but with the angular momentum of the superfluid playing the role of the electronic angular momentum in free molecules. The simple theory sheds light onto what happens when the rotational angular momentum of the molecule increases beyond the lowest excited states accessible by infrared spectroscopy. In addition, the model allows to estimate the effective rotational and centrifugal distortion constants for a broad range of species and to explain the crossover between light and heavy molecules in superfluid 4He in terms of the many-body wavefunction structure. Some of the above mentioned insights can be acquired by analyzing a simple 2 × 2 matrix.
AU - Cherepanov, Igor
AU - Bighin, Giacomo
AU - Schouder, Constant A.
AU - Chatterley, Adam S.
AU - Stapelfeldt, Henrik
AU - Lemeshko, Mikhail
ID - 11998
IS - 7
JF - New Journal of Physics
SN - 1367-2630
TI - A simple model for high rotational excitations of molecules in a superfluid
VL - 24
ER -
TY - JOUR
AB - We study the fate of an impurity in an ultracold heteronuclear Bose mixture, focusing on the experimentally relevant case of a ⁴¹K - ⁸⁷Rb mixture, with the impurity in a ⁴¹K hyperfine state. Our paper provides a comprehensive description of an impurity in a BEC mixture with contact interactions across its phase diagram. We present results for the miscible and immiscible regimes, as well as for the impurity in a self-bound quantum droplet. Here, varying the interactions, we find exotic states where the impurity localizes either at the center or
at the surface of the droplet.
AU - Bighin, Giacomo
AU - Burchianti, A.
AU - Minardi, F.
AU - Macrì, T.
ID - 11997
IS - 2
JF - Physical Review A
SN - 2469-9926
TI - Impurity in a heteronuclear two-component Bose mixture
VL - 106
ER -
TY - JOUR
AB - If you mix fruit syrups with alcohol to make a schnapps, the two liquids will remain perfectly blended forever. But if you mix oil with vinegar to make a vinaigrette, the oil and vinegar will soon separate back into their previous selves. Such liquid-liquid phase separation is a thermodynamically driven phenomenon and plays an important role in many biological processes (1). Although energy injection at the macroscale can reverse the phase separation—a strong shake is the normal response to a separated vinaigrette—little is known about the effect of energy added at the microscopic level on phase separation. This fundamental question has deep ramifications, notably in biology, because active processes also make the interior of a living cell different from a dead one. On page 768 of this issue, Adkins et al. (2) examine how mechanical activity at the microscopic scale affects liquid-liquid phase separation and allows liquids to climb surfaces.
AU - Palacci, Jérémie A
ID - 11996
IS - 6607
JF - Science
SN - 0036-8075
TI - A soft active matter that can climb walls
VL - 377
ER -
TY - DATA
AU - Schulz, Rouven
ID - 11542
TI - Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)
ER -
TY - CONF
AB - We consider the quantitative problem of obtaining lower-bounds on the probability of termination of a given non-deterministic probabilistic program. Specifically, given a non-termination threshold p∈[0,1], we aim for certificates proving that the program terminates with probability at least 1−p. The basic idea of our approach is to find a terminating stochastic invariant, i.e. a subset SI of program states such that (i) the probability of the program ever leaving SI is no more than p, and (ii) almost-surely, the program either leaves SI or terminates.
While stochastic invariants are already well-known, we provide the first proof that the idea above is not only sound, but also complete for quantitative termination analysis. We then introduce a novel sound and complete characterization of stochastic invariants that enables template-based approaches for easy synthesis of quantitative termination certificates, especially in affine or polynomial forms. Finally, by combining this idea with the existing martingale-based methods that are relatively complete for qualitative termination analysis, we obtain the first automated, sound, and relatively complete algorithm for quantitative termination analysis. Notably, our completeness guarantees for quantitative termination analysis are as strong as the best-known methods for the qualitative variant.
Our prototype implementation demonstrates the effectiveness of our approach on various probabilistic programs. We also demonstrate that our algorithm certifies lower bounds on termination probability for probabilistic programs that are beyond the reach of previous methods.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Meggendorfer, Tobias
AU - Zikelic, Dorde
ID - 12000
SN - 0302-9743
T2 - Proceedings of the 34th International Conference on Computer Aided Verification
TI - Sound and complete certificates for auantitative termination analysis of probabilistic programs
VL - 13371
ER -
TY - JOUR
AB - Changes in the short-term dynamics of excitatory synapses over development have been observed throughout cortex, but their purpose and consequences remain unclear. Here, we propose that developmental changes in synaptic dynamics buffer the effect of slow inhibitory long-term plasticity, allowing for continuously stable neural activity. Using computational modeling we demonstrate that early in development excitatory short-term depression quickly stabilises neural activity, even in the face of strong, unbalanced excitation. We introduce a model of the commonly observed developmental shift from depression to facilitation and show that neural activity remains stable throughout development, while inhibitory synaptic plasticity slowly balances excitation, consistent with experimental observations. Our model predicts changes in the input responses from phasic to phasic-and-tonic and more precise spike timings. We also observe a gradual emergence of short-lasting memory traces governed by short-term plasticity development. We conclude that the developmental depression-to-facilitation shift may control excitation-inhibition balance throughout development with important functional consequences.
AU - Jia, David W.
AU - Vogels, Tim P
AU - Costa, Rui Ponte
ID - 12009
JF - Communications biology
TI - Developmental depression-to-facilitation shift controls excitation-inhibition balance
VL - 5
ER -
TY - CONF
AB - World models learn behaviors in a latent imagination space to enhance the sample-efficiency of deep reinforcement learning (RL) algorithms. While learning world models for high-dimensional observations (e.g., pixel inputs) has become practicable on standard RL benchmarks and some games, their effectiveness in real-world robotics applications has not been explored. In this paper, we investigate how such agents generalize to real-world autonomous vehicle control tasks, where advanced model-free deep RL algorithms fail. In particular, we set up a series of time-lap tasks for an F1TENTH racing robot, equipped with a high-dimensional LiDAR sensor, on a set of test tracks with a gradual increase in their complexity. In this continuous-control setting, we show that model-based agents capable of learning in imagination substantially outperform model-free agents with respect to performance, sample efficiency, successful task completion, and generalization. Moreover, we show that the generalization ability of model-based agents strongly depends on the choice of their observation model. We provide extensive empirical evidence for the effectiveness of world models provided with long enough memory horizons in sim2real tasks.
AU - Brunnbauer, Axel
AU - Berducci, Luigi
AU - Brandstatter, Andreas
AU - Lechner, Mathias
AU - Hasani, Ramin
AU - Rus, Daniela
AU - Grosu, Radu
ID - 12010
SN - 1050-4729
T2 - 2022 International Conference on Robotics and Automation
TI - Latent imagination facilitates zero-shot transfer in autonomous racing
ER -
TY - JOUR
AB - The Tibetan plateau (TP) plays an important role in the Asian summer monsoon (ASM) dynamics as a heat source during the pre-monsoon and monsoon seasons. A significant contribution to the pre-monsoon TP heating comes from the sensible heat flux (SHF), which depend on the surface properties. A glaciated surface would have a different SHF compared to a non-glaciated surface. Therefore, the TP glaciers potentially can also impact the hydrological cycle in the Asian continent by impacting the ASM rainfall via its contribution to the total plateau heating. However, there is no assessment of this putative link available. Here, we attempt to qualitatively study the role of TP glaciers on ASM by analyzing the sensitivity of an atmospheric model to the absence of TP glaciers. We find that the absence of the glaciers is most felt in climatologically less snowy regions (which are mostly located at the south-central boundary of the TP during the pre-monsoon season), which leads to positive SHF anomalies. The resulting positive diabatic heating leads to rising air in the eastern TP and sinking air in the western TP. This altered circulation in turn leads to a positive SHF memory in the western TP, which persists until the end of the monsoon season. The impact of SHF anomalies on diabatic heating results in a large-scale subsidence over the ASM domain. The net result is a reduced seasonal ASM rainfall. Given the relentless warming and the vulnerability of glaciers to warming, this is another flag in the ASM variability and change that needs further attention.
AU - GOSWAMI, BIDYUT B
AU - An, Soon-Il
AU - Murtugudde, Raghu
ID - 12007
IS - 3-4
JF - Climatic Change
KW - Atmospheric Science
KW - Global and Planetary Change
SN - 0165-0009
TI - Role of the Tibetan plateau glaciers in the Asian summer monsoon
VL - 173
ER -
TY - CONF
AB - We characterize the capacity for the discrete-time arbitrarily varying channel with discrete inputs, outputs, and states when (a) the encoder and decoder do not share common randomness, (b) the input and state are subject to cost constraints, (c) the transition matrix of the channel is deterministic given the state, and (d) at each time step the adversary can only observe the current and past channel inputs when choosing the state at that time. The achievable strategy involves stochastic encoding together with list decoding and a disambiguation step. The converse uses a two-phase "babble-and-push" strategy where the adversary chooses the state randomly in the first phase, list decodes the output, and then chooses state inputs to symmetrize the channel in the second phase. These results generalize prior work on specific channels models (additive, erasure) to general discrete alphabets and models.
AU - Zhang, Yihan
AU - Jaggi, Sidharth
AU - Langberg, Michael
AU - Sarwate, Anand D.
ID - 12011
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - The capacity of causal adversarial channels
VL - 2022
ER -
TY - CONF
AB - In the classic adversarial communication problem, two parties communicate over a noisy channel in the presence of a malicious jamming adversary. The arbitrarily varying channels (AVCs) offer an elegant framework to study a wide range of interesting adversary models. The optimal throughput or capacity over such AVCs is intimately tied to the underlying adversary model; in some cases, capacity is unknown and the problem is known to be notoriously hard. The omniscient adversary, one which knows the sender’s entire channel transmission a priori, is one of such classic models of interest; the capacity under such an adversary remains an exciting open problem. The myopic adversary is a generalization of that model where the adversary’s observation may be corrupted over a noisy discrete memoryless channel. Through the adversary’s myopicity, one can unify the slew of different adversary models, ranging from the omniscient adversary to one that is completely blind to the transmission (the latter is the well known oblivious model where the capacity is fully characterized).In this work, we present new results on the capacity under both the omniscient and myopic adversary models. We completely characterize the positive capacity threshold over general AVCs with omniscient adversaries. The characterization is in terms of two key combinatorial objects: the set of completely positive distributions and the CP-confusability set. For omniscient AVCs with positive capacity, we present non-trivial lower and upper bounds on the capacity; unlike some of the previous bounds, our bounds hold under fairly general input and jamming constraints. Our lower bound improves upon the generalized Gilbert-Varshamov bound for general AVCs while the upper bound generalizes the well known Elias-Bassalygo bound (known for binary and q-ary alphabets). For the myopic AVCs, we build on prior results known for the so-called sufficiently myopic model, and present new results on the positive rate communication threshold over the so-called insufficiently myopic regime (a completely insufficient myopic adversary specializes to an omniscient adversary). We present interesting examples for the widely studied models of adversarial bit-flip and bit-erasure channels. In fact, for the bit-flip AVC with additive adversarial noise as well as random noise, we completely characterize the omniscient model capacity when the random noise is sufficiently large vis-a-vis the adversary’s budget.
AU - Yadav, Anuj Kumar
AU - Alimohammadi, Mohammadreza
AU - Zhang, Yihan
AU - Budkuley, Amitalok J.
AU - Jaggi, Sidharth
ID - 12017
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - New results on AVCs with omniscient and myopic adversaries
VL - 2022
ER -
TY - CONF
AB - We consider the problem of communication over adversarial channels with feedback. Two parties comprising sender Alice and receiver Bob seek to communicate reliably. An adversary James observes Alice's channel transmission entirely and chooses, maliciously, its additive channel input or jamming state thereby corrupting Bob's observation. Bob can communicate over a one-way reverse link with Alice; we assume that transmissions over this feedback link cannot be corrupted by James. Our goal in this work is to study the optimum throughput or capacity over such channels with feedback. We first present results for the quadratically-constrained additive channel where communication is known to be impossible when the noise-to-signal (power) ratio (NSR) is at least 1. We present a novel achievability scheme to establish that positive rate communication is possible even when the NSR is as high as 8/9. We also present new converse upper bounds on the capacity of this channel under potentially stochastic encoders and decoders. We also study feedback communication over the more widely studied q-ary alphabet channel under additive noise. For the q -ary channel, where q > 2, it is well known that capacity is positive under full feedback if and only if the adversary can corrupt strictly less than half the transmitted symbols. We generalize this result and show that the same threshold holds for positive rate communication when the noiseless feedback may only be partial; our scheme employs a stochastic decoder. We extend this characterization, albeit partially, to fully deterministic schemes under partial noiseless feedback. We also present new converse upper bounds for q-ary channels under full feedback, where the encoder and/or decoder may privately randomize. Our converse results bring to the fore an interesting alternate expression for the well known converse bound for the q—ary channel under full feedback which, when specialized to the binary channel, also equals its known capacity.
AU - Joshi, Pranav
AU - Purkayastha, Amritakshya
AU - Zhang, Yihan
AU - Budkuley, Amitalok J.
AU - Jaggi, Sidharth
ID - 12013
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - On the capacity of additive AVCs with feedback
VL - 2022
ER -
TY - CONF
AB - We consider the problem of coded distributed computing using polar codes. The average execution time of a coded computing system is related to the error probability for transmission over the binary erasure channel in recent work by Soleymani, Jamali and Mahdavifar, where the performance of binary linear codes is investigated. In this paper, we focus on polar codes and unveil a connection between the average execution time and the scaling exponent μ of the family of codes. In the finite-length characterization of polar codes, the scaling exponent is a key object capturing the speed of convergence to capacity. In particular, we show that (i) the gap between the normalized average execution time of polar codes and that of optimal MDS codes is O(n –1/μ ), and (ii) this upper bound can be improved to roughly O(n –1/2 ) by considering polar codes with large kernels. We conjecture that these bounds could be improved to O(n –2/μ ) and O(n –1 ), respectively, and provide a heuristic argument as well as numerical evidence supporting this view.
AU - Fathollahi, Dorsa
AU - Mondelli, Marco
ID - 12016
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - Polar coded computing: The role of the scaling exponent
VL - 2022
ER -
TY - CONF
AB - This paper is eligible for the Jack Keil Wolf ISIT Student Paper Award. We generalize a previous framework for designing utility-optimal differentially private (DP) mechanisms via graphs, where datasets are vertices in the graph and edges represent dataset neighborhood. The boundary set contains datasets where an individual’s response changes the binary-valued query compared to its neighbors. Previous work was limited to the homogeneous case where the privacy parameter ε across all datasets was the same and the mechanism at boundary datasets was identical. In our work, the mechanism can take different distributions at the boundary and the privacy parameter ε is a function of neighboring datasets, which recovers an earlier definition of personalized DP as special case. The problem is how to extend the mechanism, which is only defined at the boundary set, to other datasets in the graph in a computationally efficient and utility optimal manner. Using the concept of strongest induced DP condition we solve this problem efficiently in polynomial time (in the size of the graph).
AU - Torkamani, Sahel
AU - Ebrahimi, Javad B.
AU - Sadeghi, Parastoo
AU - D'Oliveira, Rafael G.L.
AU - Médard, Muriel
ID - 12012
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - Heterogeneous differential privacy via graphs
VL - 2022
ER -
TY - CONF
AB - We study the problem of characterizing the maximal rates of list decoding in Euclidean spaces for finite list sizes. For any positive integer L ≥ 2 and real N > 0, we say that a subset C⊂Rn is an (N,L – 1)-multiple packing or an (N,L– 1)-list decodable code if every Euclidean ball of radius nN−−−√ in ℝ n contains no more than L − 1 points of C. We study this problem with and without ℓ 2 norm constraints on C, and derive the best-known lower bounds on the maximal rate for (N,L−1) multiple packing. Our bounds are obtained via error exponents for list decoding over Additive White Gaussian Noise (AWGN) channels. We establish a curious inequality which relates the error exponent, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We derive various bounds on the error exponent for list decoding in both bounded and unbounded settings which could be of independent interest beyond multiple packing.
AU - Zhang, Yihan
AU - Vatedka, Shashank
ID - 12018
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - Lower bounds on list decoding capacity using error exponents
VL - 2022
ER -
TY - CONF
AB - We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let P, N > 0 and L∈Z≥2. A multiple packing is a set C of points in Bn(0–,nP−−−√) such that any point in ℝ n lies in the intersection of at most L – 1 balls of radius nN−−−√ around points in C. 1 In this paper, we derive two lower bounds on the largest possible density of a multiple packing. These bounds are obtained through a stronger notion called average-radius multiple packing. Specifically, we exactly pin down the asymptotics of (expurgated) Gaussian codes and (expurgated) spherical codes under average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. The bound for spherical codes matches the previous best known bound which was obtained for the standard (weaker) notion of multiple packing through a curious connection with error exponents [Bli99], [ZV21]. The bound for Gaussian codes suggests that they are strictly inferior to spherical codes.
AU - Zhang, Yihan
AU - Vatedka, Shashank
ID - 12015
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - Lower bounds for multiple packing
VL - 2022
ER -
TY - CONF
AB - We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L∈Z≥2. A multiple packing is a set C of points in Rn such that any point in Rn lies in the intersection of at most L – 1 balls of radius nN−−−√ around points in C. Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we exactly pin down the asymptotic density of (expurgated) Poisson Point Processes under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. This gives rise to the best known lower bound on the largest multiple packing density. Our result corrects a mistake in a previous paper by Blinovsky [Bli05].
AU - Zhang, Yihan
AU - Vatedka, Shashank
ID - 12014
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - List-decodability of Poisson Point Processes
VL - 2022
ER -
TY - CONF
AB - This paper studies combinatorial properties of codes for the Z-channel. A Z-channel with error fraction τ takes as input a length-n binary codeword and injects in an adversarial manner up to nτ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest (L − 1)-list-decodable code for the Z-channel with error fraction τ has exponential (in n) size if τ is less than a critical value that we call the Plotkin point and has constant size if τ is larger than the threshold. The (L−1)-list-decoding Plotkin point is known to be L−1L−1−L−LL−1. In this paper, we show that the largest (L−1)-list-decodable code ε-above the Plotkin point has size Θ L (ε −3/2 ) for any L − 1 ≥ 1.
AU - Polyanskii, Nikita
AU - Zhang, Yihan
ID - 12019
SN - 2157-8095
T2 - 2022 IEEE International Symposium on Information Theory
TI - List-decodable zero-rate codes for the Z-channel
VL - 2022
ER -
TY - JOUR
AB - Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.
AU - Daiß, Julia L
AU - Pilsl, Michael
AU - Straub, Kristina
AU - Bleckmann, Andrea
AU - Höcherl, Mona
AU - Heiss, Florian B
AU - Abascal-Palacios, Guillermo
AU - Ramsay, Ewan P
AU - Tluckova, Katarina
AU - Mars, Jean-Clement
AU - Fürtges, Torben
AU - Bruckmann, Astrid
AU - Rudack, Till
AU - Bernecky, Carrie A
AU - Lamour, Valérie
AU - Panov, Konstantin
AU - Vannini, Alessandro
AU - Moss, Tom
AU - Engel, Christoph
ID - 12051
IS - 11
JF - Life Science Alliance
KW - Health
KW - Toxicology and Mutagenesis
KW - Plant Science
KW - Biochemistry
KW - Genetics and Molecular Biology (miscellaneous)
KW - Ecology
SN - 2575-1077
TI - The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans
VL - 5
ER -
TY - JOUR
AB - Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very-long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of very long chain fatty acids and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level.
AU - Tian, Z
AU - Zhang, Yuzhou
AU - Zhu, L
AU - Jiang, B
AU - Wang, H
AU - Gao, R
AU - Friml, Jiří
AU - Xiao, G
ID - 12053
IS - 12
JF - The Plant Cell
SN - 1040-4651
TI - Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)
VL - 34
ER -
TY - JOUR
AB - Directionality in the intercellular transport of the plant hormone auxin is determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport proteins. However, apart from PIN phosphorylation at conserved motifs, no further determinants explicitly controlling polar PIN sorting decisions have been identified. Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized PIN proteins already immediately following completion of cell division, presumably via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings reveal an involvement of E3 ligases in the selective targeting of apically localized PINs in higher plants.
AU - Konstantinova, N
AU - Hörmayer, Lukas
AU - Glanc, Matous
AU - Keshkeih, R
AU - Tan, Shutang
AU - Di Donato, M
AU - Retzer, K
AU - Moulinier-Anzola, J
AU - Schwihla, M
AU - Korbei, B
AU - Geisler, M
AU - Friml, Jiří
AU - Luschnig, C
ID - 12052
JF - Nature Communications
SN - 2041-1723
TI - WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions
VL - 13
ER -
TY - JOUR
AB - Polar auxin transport is unique to plants and coordinates their growth and development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport3,4; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development.
AU - Yang, Z
AU - Xia, J
AU - Hong, J
AU - Zhang, C
AU - Wei, H
AU - Ying, W
AU - Sun, C
AU - Sun, L
AU - Mao, Y
AU - Gao, Y
AU - Tan, S
AU - Friml, Jiří
AU - Li, D
AU - Liu, X
AU - Sun, L
ID - 12054
IS - 7927
JF - Nature
SN - 0028-0836
TI - Structural insights into auxin recognition and efflux by Arabidopsis PIN1
VL - 609
ER -
TY - JOUR
AB - Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution-mediated LiO2 disproportionation, bringing into question the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Determining particle morphology and achievable capacities are species mobilities, true areal rate, and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface growth are high, high capacities are also achieved with weakly solvating electrolytes, which were previously considered prototypical for low capacity via surface growth.
AU - Prehal, Christian
AU - Mondal, Soumyadip
AU - Lovicar, Ludek
AU - Freunberger, Stefan Alexander
ID - 12065
IS - 9
JF - ACS Energy Letters
TI - Exclusive solution discharge in Li-O₂ batteries?
VL - 7
ER -
TY - GEN
AB - We present a divergent radical strategy for the fluorination of phenylacetic acid derivatives through N–F bond activation of Selectfluor® with 4-(dimethylamino)pyridine. Comprehensive reaction investigation revealed the critical role of reaction media on selectivity. In presence of water, decarboxylative fluorination through a single electron oxidation is dominant. Non-aqueous conditions result in the clean formation of α-fluoro-α-arylcarboxylic acids through hydrogen atom transfer.
AU - Madani, Amiera
AU - Anghileri, Lucia
AU - Heydenreich, Matthias
AU - Möller, Heiko M.
AU - Pieber, Bartholomäus
ID - 12067
TI - Benzylic fluorination induced by N–F bond activation of Selectfluor® with a solvent-dependent selectivity switch
ER -
TY - JOUR
AB - Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.
AU - Artan, Murat
AU - Hartl, Markus
AU - Chen, Weiqiang
AU - De Bono, Mario
ID - 12082
IS - 9
JF - Journal of Biological Chemistry
SN - 0021-9258
TI - Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans
VL - 298
ER -
TY - THES
AB - In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm
form associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations.
In the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or
integral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points.
More precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in
the power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture.
AU - Shute, Alec L
ID - 12072
SN - 2663-337X
TI - Existence and density problems in Diophantine geometry: From norm forms to Campana points
ER -
TY - JOUR
AB - We extend the recent rigorous convergence result of Abels and Moser (SIAM J Math Anal 54(1):114–172, 2022. https://doi.org/10.1137/21M1424925) concerning convergence rates for solutions of the Allen–Cahn equation with a nonlinear Robin boundary condition towards evolution by mean curvature flow with constant contact angle. More precisely, in the present work we manage to remove the perturbative assumption on the contact angle being close to 90∘. We establish under usual double-well type assumptions on the potential and for a certain class of boundary energy densities the sub-optimal convergence rate of order ε12 for general contact angles α∈(0,π). For a very specific form of the boundary energy density, we even obtain from our methods a sharp convergence rate of order ε; again for general contact angles α∈(0,π). Our proof deviates from the popular strategy based on rigorous asymptotic expansions and stability estimates for the linearized Allen–Cahn operator. Instead, we follow the recent approach by Fischer et al. (SIAM J Math Anal 52(6):6222–6233, 2020. https://doi.org/10.1137/20M1322182), thus relying on a relative entropy technique. We develop a careful adaptation of their approach in order to encode the constant contact angle condition. In fact, we perform this task at the level of the notion of gradient flow calibrations. This concept was recently introduced in the context of weak-strong uniqueness for multiphase mean curvature flow by Fischer et al. (arXiv:2003.05478v2).
AU - Hensel, Sebastian
AU - Moser, Maximilian
ID - 12079
IS - 6
JF - Calculus of Variations and Partial Differential Equations
SN - 0944-2669
TI - Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime
VL - 61
ER -
TY - JOUR
AB - Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.
AU - Hledik, Michal
AU - Barton, Nicholas H
AU - Tkačik, Gašper
ID - 12081
IS - 36
JF - Proceedings of the National Academy of Sciences
SN - 0027-8424
TI - Accumulation and maintenance of information in evolution
VL - 119
ER -
TY - JOUR
AB - We consider the many-body time evolution of weakly interacting bosons in the mean field regime for initial coherent states. We show that bounded k-particle operators, corresponding to dependent random variables, satisfy both a law of large numbers and a central limit theorem.
AU - Rademacher, Simone Anna Elvira
ID - 12083
IS - 8
JF - Journal of Mathematical Physics
SN - 0022-2488
TI - Dependent random variables in quantum dynamics
VL - 63
ER -
TY - JOUR
AB - Neuronal networks encode information through patterns of activity that define the networks’ function. The neurons’ activity relies on specific connectivity structures, yet the link between structure and function is not fully understood. Here, we tackle this structure-function problem with a new conceptual approach. Instead of manipulating the connectivity directly, we focus on upper triangular matrices, which represent the network dynamics in a given orthonormal basis obtained by the Schur decomposition. This abstraction allows us to independently manipulate the eigenspectrum and feedforward structures of a connectivity matrix. Using this method, we describe a diverse repertoire of non-normal transient amplification, and to complement the analysis of the dynamical regimes, we quantify the geometry of output trajectories through the effective rank of both the eigenvector and the dynamics matrices. Counter-intuitively, we find that shrinking the eigenspectrum’s imaginary distribution leads to highly amplifying regimes in linear and long-lasting dynamics in nonlinear networks. We also find a trade-off between amplification and dimensionality of neuronal dynamics, i.e., trajectories in neuronal state-space. Networks that can amplify a large number of orthogonal initial conditions produce neuronal trajectories that lie in the same subspace of the neuronal state-space. Finally, we examine networks of excitatory and inhibitory neurons. We find that the strength of global inhibition is directly linked with the amplitude of amplification, such that weakening inhibitory weights also decreases amplification, and that the eigenspectrum’s imaginary distribution grows with an increase in the ratio between excitatory-to-inhibitory and excitatory-to-excitatory connectivity strengths. Consequently, the strength of global inhibition reveals itself as a strong signature for amplification and a potential control mechanism to switch dynamical regimes. Our results shed a light on how biological networks, i.e., networks constrained by Dale’s law, may be optimised for specific dynamical regimes.
AU - Christodoulou, Georgia
AU - Vogels, Tim P
AU - Agnes, Everton J.
ID - 12084
IS - 8
JF - PLoS Computational Biology
TI - Regimes and mechanisms of transient amplification in abstract and biological neural networks
VL - 18
ER -
TY - JOUR
AB - Molecular catch bonds are ubiquitous in biology and essential for processes like leucocyte extravasion1 and cellular mechanosensing2. Unlike normal (slip) bonds, catch bonds strengthen under tension. The current paradigm is that this feature provides ‘strength on demand3’, thus enabling cells to increase rigidity under stress1,4,5,6. However, catch bonds are often weaker than slip bonds because they have cryptic binding sites that are usually buried7,8. Here we show that catch bonds render reconstituted cytoskeletal actin networks stronger than slip bonds, even though the individual bonds are weaker. Simulations show that slip bonds remain trapped in stress-free areas, whereas weak binding allows catch bonds to mitigate crack initiation by moving to high-tension areas. This ‘dissociation on demand’ explains how cells combine mechanical strength with the adaptability required for shape change, and is relevant to diseases where catch bonding is compromised7,9, including focal segmental glomerulosclerosis10 caused by the α-actinin-4 mutant studied here. We surmise that catch bonds are the key to create life-like materials.
AU - Mulla, Yuval
AU - Avellaneda Sarrió, Mario
AU - Roland, Antoine
AU - Baldauf, Lucia
AU - Jung, Wonyeong
AU - Kim, Taeyoon
AU - Tans, Sander J.
AU - Koenderink, Gijsje H.
ID - 12085
IS - 9
JF - Nature Materials
SN - 1476-1122
TI - Weak catch bonds make strong networks
VL - 21
ER -
TY - JOUR
AB - Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups.
AU - Wirth, Melchior
AU - Zhang, Haonan
ID - 12087
JF - Annales Henri Poincare
SN - 1424-0637
TI - Curvature-dimension conditions for symmetric quantum Markov semigroups
ER -
TY - CONF
AB - We present a quantum-enabled microwave-telecom interface with bidirectional conversion efficiencies up to 15% and added input noise quanta as low as 0.16. Moreover, we observe evidence for electro-optic laser cooling and vacuum amplification.
AU - Sahu, Rishabh
AU - Hease, William J
AU - Rueda Sanchez, Alfredo R
AU - Arnold, Georg M
AU - Qiu, Liu
AU - Fink, Johannes M
ID - 12088
SN - 9781557528209
T2 - Conference on Lasers and Electro-Optics
TI - Realizing a quantum-enabled interconnect between microwave and telecom light
ER -
TY - CONF
AB - Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset.
AU - Ahmadi, Ali
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Meggendorfer, Tobias
AU - Safavi Hemami, Roodabeh
AU - Zikelic, Dorde
ID - 12102
SN - 1868-8969
T2 - 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science
TI - Algorithms and hardness results for computing cores of Markov chains
VL - 250
ER -
TY - CONF
AB - Spatial games form a widely-studied class of games from biology and physics modeling the evolution of social behavior. Formally, such a game is defined by a square (d by d) payoff matrix M and an undirected graph G. Each vertex of G represents an individual, that initially follows some strategy i ∈ {1,2,…,d}. In each round of the game, every individual plays the matrix game with each of its neighbors: An individual following strategy i meeting a neighbor following strategy j receives a payoff equal to the entry (i,j) of M. Then, each individual updates its strategy to its neighbors' strategy with the highest sum of payoffs, and the next round starts. The basic computational problems consist of reachability between configurations and the average frequency of a strategy. For general spatial games and graphs, these problems are in PSPACE. In this paper, we examine restricted setting: the game is a prisoner’s dilemma; and G is a subgraph of grid. We prove that basic computational problems for spatial games with prisoner’s dilemma on a subgraph of a grid are PSPACE-hard.
AU - Chatterjee, Krishnendu
AU - Ibsen-Jensen, Rasmus
AU - Jecker, Ismael R
AU - Svoboda, Jakub
ID - 12101
SN - 1868-8969
T2 - 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science
TI - Complexity of spatial games
VL - 250
ER -
TY - JOUR
AB - The sensitivity of coarse-grained daily extreme precipitation to sea surface temperature is analyzed using satellite precipitation estimates over the 300–302.5 K range. A theoretical scaling is proposed, linking changes in coarse-grained precipitation to changes in fine-scale hourly precipitation area fraction and changes in conditional fine-scale precipitation rates. The analysis reveals that the extreme coarse-grained precipitation scaling with temperature (∼7%/K) is dominated by the fine-scale precipitating fraction scaling (∼6.5%/K) when using a 3 mm/h fine-scale threshold to delineate the precipitating fraction. These results are shown to be robust to the selection of the precipitation product and to the percentile used to characterize the extreme. This new coarse-grained scaling is further related to the well-known scaling for fine-scale precipitation extremes, and suggests a compensation between thermodynamic and dynamic contributions or that both contributions are small with respect to that of fractional coverage. These results suggest that processes responsible for the changes in fractional coverage are to be accounted for to assess the sensitivity of coarse-grained extreme daily precipitation to surface temperature.
AU - Roca, Rémy
AU - De Meyer, Victorien
AU - Muller, Caroline J
ID - 12107
IS - 24
JF - Geophysical Research Letters
SN - 0094-8276
TI - Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans
VL - 49
ER -
TY - JOUR
AB - A recently proposed approach for avoiding the ultraviolet divergence of Hamiltonians with particle creation is based on interior-boundary conditions (IBCs). The approach works well in the non-relativistic case, i.e., for the Laplacian operator. Here, we study how the approach can be applied to Dirac operators. While this has successfully been done already in one space dimension, and more generally for codimension-1 boundaries, the situation of point sources in three dimensions corresponds to a codimension-3 boundary. One would expect that, for such a boundary, Dirac operators do not allow for boundary conditions because they are known not to allow for point interactions in 3D, which also correspond to a boundary condition. Indeed, we confirm this expectation here by proving that there is no self-adjoint operator on a (truncated) Fock space that would correspond to a Dirac operator with an IBC at configurations with a particle at the origin. However, we also present a positive result showing that there are self-adjoint operators with an IBC (on the boundary consisting of configurations with a particle at the origin) that are away from those configurations, given by a Dirac operator plus a sufficiently strong Coulomb potential.
AU - Henheik, Sven Joscha
AU - Tumulka, Roderich
ID - 12110
IS - 12
JF - Journal of Mathematical Physics
SN - 0022-2488
TI - Interior-boundary conditions for the Dirac equation at point sources in three dimensions
VL - 63
ER -
TY - JOUR
AB - Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.
AU - Pertl, Felix
AU - Sobarzo Ponce, Juan Carlos A
AU - Shafeek, Lubuna B
AU - Cramer, Tobias
AU - Waitukaitis, Scott R
ID - 12109
IS - 12
JF - Physical Review Materials
TI - Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach
VL - 6
ER -
TY - JOUR
AB - Quantum impurities exhibit fascinating many-body phenomena when the small interacting impurity changes the physics of a large noninteracting environment. The characterisation of such strongly correlated nonperturbative effects is particularly challenging due to the infinite size of the environment, and the inability of local correlators to capture the buildup of long-ranged entanglement in the system. Here, we harness an entanglement-based observable—the purity of the impurity—as a witness for the formation of strong correlations. We showcase the utility of our scheme by exactly solving the open Kondo box model in the small box limit, and thus describe all-electronic dot-cavity devices. Specifically, we conclusively characterize the metal-to-insulator phase transition in the system and identify how the (conducting) dot-lead Kondo singlet is quenched by an (insulating) intraimpurity singlet formation. Furthermore, we propose an experimentally feasible tomography protocol for the measurement of the purity, which motivates the observation of impurity physics through their entanglement build up.
AU - Stocker, Lidia
AU - Sack, Stefan
AU - Ferguson, Michael S.
AU - Zilberberg, Oded
ID - 12111
IS - 4
JF - Physical Review Research
SN - 2643-1564
TI - Entanglement-based observables for quantum impurities
VL - 4
ER -
TY - JOUR
AB - The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation.
AU - Meadowcroft, Billie
AU - Palaia, Ivan
AU - Pfitzner, Anna Katharina
AU - Roux, Aurélien
AU - Baum, Buzz
AU - Šarić, Anđela
ID - 12108
IS - 26
JF - Physical Review Letters
SN - 0031-9007
TI - Mechanochemical rules for shape-shifting filaments that remodel membranes
VL - 129
ER -
TY - JOUR
AB - Cerebral organoids differentiated from human-induced pluripotent stem cells (hiPSC) provide a unique opportunity to investigate brain development. However, organoids usually lack microglia, brain-resident immune cells, which are present in the early embryonic brain and participate in neuronal circuit development. Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol. Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented, 3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When we guide the retinal organoid differentiation with low-dosed BMP4, we prevent cup development and enhance microglia and 3D-cysts formation. Mass spectrometry identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed this microglia-preferred environment also within the unguided protocol, providing insight into microglial behavior and migration and offer a model to study how they enter and distribute within the human brain.
AU - Bartalska, Katarina
AU - Hübschmann, Verena
AU - Korkut, Medina
AU - Cubero, Ryan J
AU - Venturino, Alessandro
AU - Rössler, Karl
AU - Czech, Thomas
AU - Siegert, Sandra
ID - 11478
IS - 7
JF - iScience
TI - A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation
VL - 25
ER -
TY - JOUR
AB - To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.
For complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1
AU - Hübschmann, Verena
AU - Korkut, Medina
AU - Siegert, Sandra
ID - 12117
IS - 4
JF - STAR Protocols
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Neuroscience
SN - 2666-1667
TI - Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay
VL - 3
ER -
TY - JOUR
AB - The power factor of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) film can be significantly improved by optimizing the oxidation level of the film in oxidation and reduction processes. However, precise control over the oxidation and reduction effects in PEDOT:PSS remains a challenge, which greatly sacrifices both S and σ. Here, we propose a two-step post-treatment using a mixture of ethylene glycol (EG) and Arginine (Arg) and sulfuric acid (H2SO4) in sequence to engineer high-performance PEDOT:PSS thermoelectric films. The high-polarity EG dopant removes the excess non-ionized PSS and induces benzenoid-to-quinoid conformational change in the PEDOT:PSS films. In particular, basic amino acid Arg tunes the oxidation level of PEDOT:PSS and prevents the films from over-oxidation during H2SO4 post-treatment, leading to increased S. The following H2SO4 post-treatment further induces highly orientated lamellar stacking microstructures to increase σ, yielding a maximum power factor of 170.6 μW m−1 K−2 at 460 K. Moreover, a novel trigonal-shape thermoelectric device is designed and assembled by the as-prepared PEDOT:PSS films in order to harvest heat via a vertical temperature gradient. An output power density of 33 μW cm−2 is generated at a temperature difference of 40 K, showing the potential application for low-grade wearable electronic devices.
AU - Zhang, Li
AU - Liu, Xingyu
AU - Wu, Ting
AU - Xu, Shengduo
AU - Suo, Guoquan
AU - Ye, Xiaohui
AU - Hou, Xiaojiang
AU - Yang, Yanling
AU - Liu, Qingfeng
AU - Wang, Hongqiang
ID - 12113
JF - Applied Surface Science
KW - Surfaces
KW - Coatings and Films
KW - Condensed Matter Physics
KW - Surfaces and Interfaces
KW - General Physics and Astronomy
KW - General Chemistry
SN - 0169-4332
TI - Two-step post-treatment to deliver high performance thermoelectric device with vertical temperature gradient
VL - 613
ER -
TY - JOUR
AB - Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them.
AU - Chhugani, Karishma
AU - Frolova, Alina
AU - Salyha, Yuriy
AU - Fiscutean, Andrada
AU - Zlenko, Oksana
AU - Reinsone, Sanita
AU - Wolfsberger, Walter W.
AU - Ivashchenko, Oleksandra V.
AU - Maci, Megi
AU - Dziuba, Dmytro
AU - Parkhomenko, Andrii
AU - Bortz, Eric
AU - Kondrashov, Fyodor
AU - Łabaj, Paweł P.
AU - Romero, Veronika
AU - Hlávka, Jakub
AU - Oleksyk, Taras K.
AU - Mangul, Serghei
ID - 12116
IS - 6626
JF - Science
SN - 0036-8075
TI - Remote opportunities for scholars in Ukraine
VL - 378
ER -
TY - JOUR
AB - Intravascular neutrophils and platelets collaborate in maintaining host integrity, but their interaction can also trigger thrombotic complications. We report here that cooperation between neutrophil and platelet lineages extends to the earliest stages of platelet formation by megakaryocytes in the bone marrow. Using intravital microscopy, we show that neutrophils “plucked” intravascular megakaryocyte extensions, termed proplatelets, to control platelet production. Following CXCR4-CXCL12-dependent migration towards perisinusoidal megakaryocytes, plucking neutrophils actively pulled on proplatelets and triggered myosin light chain and extracellular-signal-regulated kinase activation through reactive oxygen species. By these mechanisms, neutrophils accelerate proplatelet growth and facilitate continuous release of platelets in steady state. Following myocardial infarction, plucking neutrophils drove excessive release of young, reticulated platelets and boosted the risk of recurrent ischemia. Ablation of neutrophil plucking normalized thrombopoiesis and reduced recurrent thrombosis after myocardial infarction and thrombus burden in venous thrombosis. We establish neutrophil plucking as a target to reduce thromboischemic events.
AU - Petzold, Tobias
AU - Zhang, Zhe
AU - Ballesteros, Iván
AU - Saleh, Inas
AU - Polzin, Amin
AU - Thienel, Manuela
AU - Liu, Lulu
AU - Ul Ain, Qurrat
AU - Ehreiser, Vincent
AU - Weber, Christian
AU - Kilani, Badr
AU - Mertsch, Pontus
AU - Götschke, Jeremias
AU - Cremer, Sophie
AU - Fu, Wenwen
AU - Lorenz, Michael
AU - Ishikawa-Ankerhold, Hellen
AU - Raatz, Elisabeth
AU - El-Nemr, Shaza
AU - Görlach, Agnes
AU - Marhuenda, Esther
AU - Stark, Konstantin
AU - Pircher, Joachim
AU - Stegner, David
AU - Gieger, Christian
AU - Schmidt-Supprian, Marc
AU - Gärtner, Florian R
AU - Almendros, Isaac
AU - Kelm, Malte
AU - Schulz, Christian
AU - Hidalgo, Andrés
AU - Massberg, Steffen
ID - 12119
IS - 12
JF - Immunity
KW - Infectious Diseases
KW - Immunology
KW - Immunology and Allergy
SN - 1074-7613
TI - Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease
VL - 55
ER -
TY - JOUR
AB - Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.
AU - Zhao, Jierui
AU - Bui, Mai Thu
AU - Ma, Juncai
AU - Künzl, Fabian
AU - Picchianti, Lorenzo
AU - De La Concepcion, Juan Carlos
AU - Chen, Yixuan
AU - Petsangouraki, Sofia
AU - Mohseni, Azadeh
AU - García-Leon, Marta
AU - Gomez, Marta Salas
AU - Giannini, Caterina
AU - Gwennogan, Dubois
AU - Kobylinska, Roksolana
AU - Clavel, Marion
AU - Schellmann, Swen
AU - Jaillais, Yvon
AU - Friml, Jiří
AU - Kang, Byung-Ho
AU - Dagdas, Yasin
ID - 12121
IS - 12
JF - Journal of Cell Biology
KW - Cell Biology
SN - 0021-9525
TI - Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole
VL - 221
ER -
TY - JOUR
AB - Centrosomes play a crucial role during immune cell interactions and initiation of the immune response. In proliferating cells, centrosome numbers are tightly controlled and generally limited to one in G1 and two prior to mitosis. Defects in regulating centrosome numbers have been associated with cell transformation and tumorigenesis. Here, we report the emergence of extra centrosomes in leukocytes during immune activation. Upon antigen encounter, dendritic cells pass through incomplete mitosis and arrest in the subsequent G1 phase leading to tetraploid cells with accumulated centrosomes. In addition, cell stimulation increases expression of polo-like kinase 2, resulting in diploid cells with two centrosomes in G1-arrested cells. During cell migration, centrosomes tightly cluster and act as functional microtubule-organizing centers allowing for increased persistent locomotion along gradients of chemotactic cues. Moreover, dendritic cells with extra centrosomes display enhanced secretion of inflammatory cytokines and optimized T cell responses. Together, these results demonstrate a previously unappreciated role of extra centrosomes for regular cell and tissue homeostasis.
AU - Weier, Ann-Kathrin
AU - Homrich, Mirka
AU - Ebbinghaus, Stephanie
AU - Juda, Pavel
AU - Miková, Eliška
AU - Hauschild, Robert
AU - Zhang, Lili
AU - Quast, Thomas
AU - Mass, Elvira
AU - Schlitzer, Andreas
AU - Kolanus, Waldemar
AU - Burgdorf, Sven
AU - Gruß, Oliver J.
AU - Hons, Miroslav
AU - Wieser, Stefan
AU - Kiermaier, Eva
ID - 12122
IS - 12
JF - Journal of Cell Biology
KW - Cell Biology
SN - 0021-9525
TI - Multiple centrosomes enhance migration and immune cell effector functions of mature dendritic cells
VL - 221
ER -
TY - JOUR
AB - Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.
AU - Xiao, Huixin
AU - Hu, Yumei
AU - Wang, Yaping
AU - Cheng, Jinkui
AU - Wang, Jinyi
AU - Chen, Guojingwei
AU - Li, Qian
AU - Wang, Shuwei
AU - Wang, Yalu
AU - Wang, Shao-Shuai
AU - Wang, Yi
AU - Xuan, Wei
AU - Li, Zhen
AU - Guo, Yan
AU - Gong, Zhizhong
AU - Friml, Jiří
AU - Zhang, Jing
ID - 12120
IS - 23
JF - Developmental Cell
KW - Developmental Biology
KW - Cell Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Molecular Biology
SN - 1534-5807
TI - Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth
VL - 57
ER -
TY - JOUR
AB - Replication-incompetent adenoviral vectors have been extensively used as a platform for vaccine design, with at least four anti-COVID-19 vaccines authorized to date. These vaccines elicit neutralizing antibody responses directed against SARS-CoV-2 Spike protein and confer significant level of protection against SARS-CoV-2 infection. Immunization with adenovirus-vectored vaccines is known to be accompanied by the production of anti-vector antibodies, which may translate into reduced efficacy of booster or repeated rounds of revaccination. Here, we used blood samples from patients who received an adenovirus-based Gam-COVID-Vac vaccine to address the question of whether anti-vector antibodies may influence the magnitude of SARS-CoV-2-specific humoral response after booster vaccination. We observed that rAd26-based prime vaccination with Gam-COVID-Vac induced the development of Ad26-neutralizing antibodies, which persisted in circulation for at least 9 months. Our analysis further indicates that high pre-boost Ad26 neutralizing antibody titers do not appear to affect the humoral immunogenicity of the Gam-COVID-Vac boost. The titers of anti-SARS-CoV-2 RBD IgGs and antibodies, which neutralized both the wild type and the circulating variants of concern of SARS-CoV-2 such as Delta and Omicron, were independent of the pre-boost levels of Ad26-neutralizing antibodies. Thus, our results support the development of repeated immunization schedule with adenovirus-based COVID-19 vaccines.
AU - Byazrova, Maria G.
AU - Astakhova, Ekaterina A.
AU - Minnegalieva, Aygul
AU - Sukhova, Maria M.
AU - Mikhailov, Artem A.
AU - Prilipov, Alexey G.
AU - Gorchakov, Andrey A.
AU - Filatov, Alexander V.
ID - 12131
JF - npj Vaccines
KW - Pharmacology (medical)
KW - Infectious Diseases
KW - Pharmacology
KW - Immunology
KW - SARS-COV-2
KW - COVID
SN - 2059-0105
TI - Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination
VL - 7
ER -
TY - JOUR
AB - Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants.
AU - Huang, Jian
AU - Zhao, Lei
AU - Malik, Shikha
AU - Gentile, Benjamin R.
AU - Xiong, Va
AU - Arazi, Tzahi
AU - Owen, Heather A.
AU - Friml, Jiří
AU - Zhao, Dazhong
ID - 12130
JF - Nature Communications
KW - General Physics and Astronomy
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Chemistry
KW - Multidisciplinary
SN - 2041-1723
TI - Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis
VL - 13
ER -
TY - JOUR
AB - We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, in addition to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness.
AU - Poelking, Carl
AU - Faber, Felix A
AU - Cheng, Bingqing
ID - 12128
IS - 4
JF - Machine Learning: Science and Technology
KW - Artificial Intelligence
KW - Human-Computer Interaction
KW - Software
SN - 2632-2153
TI - BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale
VL - 3
ER -
TY - JOUR
AB - Social distancing is an effective way to prevent the spread of disease in societies, whereas infection elimination is a key element of organismal immunity. Here, we discuss how the study of social insects such as ants — which form a superorganism of unconditionally cooperative individuals and thus represent a level of organization that is intermediate between a classical society of individuals and an organism of cells — can help to determine common principles of disease defence across levels of organization.
AU - Cremer, Sylvia
AU - Sixt, Michael K
ID - 12133
IS - 12
JF - Nature Reviews Immunology
KW - Energy Engineering and Power Technology
KW - Fuel Technology
SN - 1474-1733
TI - Principles of disease defence in organisms, superorganisms and societies
VL - 22
ER -
TY - CONF
AB - A good match of material appearance between real-world objects and their digital on-screen representations is critical for many applications such as fabrication, design, and e-commerce. However, faithful appearance reproduction is challenging, especially for complex phenomena, such as gloss. In most cases, the view-dependent nature of gloss and the range of luminance values required for reproducing glossy materials exceeds the current capabilities of display devices. As a result, appearance reproduction poses significant problems even with accurately rendered images. This paper studies the gap between the gloss perceived from real-world objects and their digital counterparts. Based on our psychophysical experiments on a wide range of 3D printed samples and their corresponding photographs, we derive insights on the influence of geometry, illumination, and the display’s brightness and measure the change in gloss appearance due to the display limitations. Our evaluation experiments demonstrate that using the prediction to correct material parameters in a rendering system improves the match of gloss appearance between real objects and their visualization on a display device.
AU - Chen, Bin
AU - Piovarci, Michael
AU - Wang, Chao
AU - Seidel, Hans-Peter
AU - Didyk, Piotr
AU - Myszkowski, Karol
AU - Serrano, Ana
ID - 12135
SN - 9781450394703
T2 - SIGGRAPH Asia 2022 Conference Papers
TI - Gloss management for consistent reproduction of real and virtual objects
VL - 2022
ER -
TY - JOUR
AB - Microglia are dynamic cells, constantly surveying their surroundings and interacting with neurons and synapses. Indeed, a wealth of knowledge has revealed a critical role of microglia in modulating synaptic transmission and plasticity in the developing brain. In the past decade, novel pharmacological and genetic strategies have allowed the acute removal of microglia, opening the possibility to explore and understand the role of microglia also in the adult brain. In this review, we summarized and discussed the contribution of microglia depletion strategies to the current understanding of the role of microglia on synaptic function, learning and memory, and behavior both in physiological and pathological conditions. We first described the available microglia depletion methods highlighting their main strengths and weaknesses. We then reviewed the impact of microglia depletion on structural and functional synaptic plasticity. Next, we focused our analysis on the effects of microglia depletion on behavior, including general locomotor activity, sensory perception, motor function, sociability, learning and memory both in healthy animals and animal models of disease. Finally, we integrated the findings from the reviewed studies and discussed the emerging roles of microglia on the maintenance of synaptic function, learning, memory strength and forgetfulness, and the implications of microglia depletion in models of brain disease.
AU - Basilico, Bernadette
AU - Ferrucci, Laura
AU - Khan, Azka
AU - Di Angelantonio, Silvia
AU - Ragozzino, Davide
AU - Reverte, Ingrid
ID - 12140
JF - Frontiers in Cellular Neuroscience
KW - Cellular and Molecular Neuroscience
SN - 1662-5102
TI - What microglia depletion approaches tell us about the role of microglia on synaptic function and behavior
VL - 16
ER -
TY - JOUR
AB - Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.
AU - Kravchuk, Vladyslav
AU - Petrova, Olga
AU - Kampjut, Domen
AU - Wojciechowska-Bason, Anna
AU - Breese, Zara
AU - Sazanov, Leonid A
ID - 12138
IS - 7928
JF - Nature
KW - Multidisciplinary
SN - 0028-0836
TI - A universal coupling mechanism of respiratory complex I
VL - 609
ER -
TY - JOUR
AB - Standard epidemic models exhibit one continuous, second order phase transition to macroscopic outbreaks. However, interventions to control outbreaks may fundamentally alter epidemic dynamics. Here we reveal how such interventions modify the type of phase transition. In particular, we uncover three distinct types of explosive phase transitions for epidemic dynamics with capacity-limited interventions. Depending on the capacity limit, interventions may (i) leave the standard second order phase transition unchanged but exponentially suppress the probability of large outbreaks, (ii) induce a first-order discontinuous transition to macroscopic outbreaks, or (iii) cause a secondary explosive yet continuous third-order transition. These insights highlight inherent limitations in predicting and containing epidemic outbreaks. More generally our study offers a cornerstone example of a third-order explosive phase transition in complex systems.
AU - Börner, Georg
AU - Schröder, Malte
AU - Scarselli, Davide
AU - Budanur, Nazmi B
AU - Hof, Björn
AU - Timme, Marc
ID - 12134
IS - 4
JF - Journal of Physics: Complexity
KW - Artificial Intelligence
KW - Computer Networks and Communications
KW - Computer Science Applications
KW - Information Systems
SN - 2632-072X
TI - Explosive transitions in epidemic dynamics
VL - 3
ER -
TY - JOUR
AB - We investigate the local self-sustained process underlying spiral turbulence in counter-rotating Taylor–Couette flow using a periodic annular domain, shaped as a parallelogram, two of whose sides are aligned with the cylindrical helix described by the spiral pattern. The primary focus of the study is placed on the emergence of drifting–rotating waves (DRW) that capture, in a relatively small domain, the main features of coherent structures typically observed in developed turbulence. The transitional dynamics of the subcritical region, far below the first instability of the laminar circular Couette flow, is determined by the upper and lower branches of DRW solutions originated at saddle-node bifurcations. The mechanism whereby these solutions self-sustain, and the chaotic dynamics they induce, are conspicuously reminiscent of other subcritical shear flows. Remarkably, the flow properties of DRW persist even as the Reynolds number is increased beyond the linear stability threshold of the base flow. Simulations in a narrow parallelogram domain stretched in the azimuthal direction to revolve around the apparatus a full turn confirm that self-sustained vortices eventually concentrate into a localised pattern. The resulting statistical steady state satisfactorily reproduces qualitatively, and to a certain degree also quantitatively, the topology and properties of spiral turbulence as calculated in a large periodic domain of sufficient aspect ratio that is representative of the real system.
AU - Wang, B.
AU - Ayats López, Roger
AU - Deguchi, K.
AU - Mellibovsky, F.
AU - Meseguer, A.
ID - 12137
JF - Journal of Fluid Mechanics
KW - Mechanical Engineering
KW - Mechanics of Materials
KW - Condensed Matter Physics
KW - Applied Mathematics
SN - 0022-1120
TI - Self-sustainment of coherent structures in counter-rotating Taylor–Couette flow
VL - 951
ER -
TY - JOUR
AB - We demonstrate the formation of robust zero-energy modes close to magnetic impurities in the iron-based superconductor FeSe1-z Tez. We find that the Zeeman field generated by the impurity favors a spin-triplet interorbital pairing as opposed to the spin-singlet intraorbital pairing prevalent in the bulk. The preferred spin-triplet pairing preserves time-reversal symmetry and is topological, as robust, topologically protected zero modes emerge at the boundary between regions with different pairing states. Moreover, the zero modes form Kramers doublets that are insensitive to the direction of the spin polarization or to the separation between impurities. We argue that our theoretical results are consistent with recent experimental measurements on FeSe1-z Tez.
AU - Ghazaryan, Areg
AU - Kirmani, Ammar
AU - Fernandes, Rafael M.
AU - Ghaemi, Pouyan
ID - 12139
IS - 20
JF - Physical Review B
SN - 2469-9950
TI - Anomalous Shiba states in topological iron-based superconductors
VL - 106
ER -
TY - JOUR
AB - Continuous-time neural networks are a class of machine learning systems that can tackle representation learning on spatiotemporal decision-making tasks. These models are typically represented by continuous differential equations. However, their expressive power when they are deployed on computers is bottlenecked by numerical differential equation solvers. This limitation has notably slowed down the scaling and understanding of numerous natural physical phenomena such as the dynamics of nervous systems. Ideally, we would circumvent this bottleneck by solving the given dynamical system in closed form. This is known to be intractable in general. Here, we show that it is possible to closely approximate the interaction between neurons and synapses—the building blocks of natural and artificial neural networks—constructed by liquid time-constant networks efficiently in closed form. To this end, we compute a tightly bounded approximation of the solution of an integral appearing in liquid time-constant dynamics that has had no known closed-form solution so far. This closed-form solution impacts the design of continuous-time and continuous-depth neural models. For instance, since time appears explicitly in closed form, the formulation relaxes the need for complex numerical solvers. Consequently, we obtain models that are between one and five orders of magnitude faster in training and inference compared with differential equation-based counterparts. More importantly, in contrast to ordinary differential equation-based continuous networks, closed-form networks can scale remarkably well compared with other deep learning instances. Lastly, as these models are derived from liquid networks, they show good performance in time-series modelling compared with advanced recurrent neural network models.
AU - Hasani, Ramin
AU - Lechner, Mathias
AU - Amini, Alexander
AU - Liebenwein, Lucas
AU - Ray, Aaron
AU - Tschaikowski, Max
AU - Teschl, Gerald
AU - Rus, Daniela
ID - 12147
IS - 11
JF - Nature Machine Intelligence
KW - Artificial Intelligence
KW - Computer Networks and Communications
KW - Computer Vision and Pattern Recognition
KW - Human-Computer Interaction
KW - Software
SN - 2522-5839
TI - Closed-form continuous-time neural networks
VL - 4
ER -
TY - JOUR
AB - MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer⋅miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.
AU - Zapletal, David
AU - Taborska, Eliska
AU - Pasulka, Josef
AU - Malik, Radek
AU - Kubicek, Karel
AU - Zanova, Martina
AU - Much, Christian
AU - Sebesta, Marek
AU - Buccheri, Valeria
AU - Horvat, Filip
AU - Jenickova, Irena
AU - Prochazkova, Michaela
AU - Prochazka, Jan
AU - Pinkas, Matyas
AU - Novacek, Jiri
AU - Joseph, Diego F.
AU - Sedlacek, Radislav
AU - Bernecky, Carrie A
AU - O’Carroll, Dónal
AU - Stefl, Richard
AU - Svoboda, Petr
ID - 12143
IS - 21
JF - Molecular Cell
KW - Cell Biology
KW - Molecular Biology
SN - 1097-2765
TI - Structural and functional basis of mammalian microRNA biogenesis by Dicer
VL - 82
ER -
TY - JOUR
AB - Theory for liability-scale models of the underlying genetic basis of complex disease provides an important way to interpret, compare, and understand results generated from biological studies. In particular, through estimation of the liability-scale heritability (LSH), liability models facilitate an understanding and comparison of the relative importance of genetic and environmental risk factors that shape different clinically important disease outcomes. Increasingly, large-scale biobank studies that link genetic information to electronic health records, containing hundreds of disease diagnosis indicators that mostly occur infrequently within the sample, are becoming available. Here, we propose an extension of the existing liability-scale model theory suitable for estimating LSH in biobank studies of low-prevalence disease. In a simulation study, we find that our derived expression yields lower mean square error (MSE) and is less sensitive to prevalence misspecification as compared to previous transformations for diseases with =< 2% population prevalence and LSH of =< 0.45, especially if the biobank sample prevalence is less than that of the wider population. Applying our expression to 13 diagnostic outcomes of =< 3% prevalence in the UK Biobank study revealed important differences in LSH obtained from the different theoretical expressions that impact the conclusions made when comparing LSH across disease outcomes. This demonstrates the importance of careful consideration for estimation and prediction of low-prevalence disease outcomes and facilitates improved inference of the underlying genetic basis of =< 2% population prevalence diseases, especially where biobank sample ascertainment results in a healthier sample population.
AU - Ojavee, Sven E.
AU - Kutalik, Zoltan
AU - Robinson, Matthew Richard
ID - 12142
IS - 11
JF - The American Journal of Human Genetics
KW - Genetics (clinical)
KW - Genetics
SN - 0002-9297
TI - Liability-scale heritability estimation for biobank studies of low-prevalence disease
VL - 109
ER -
TY - JOUR
AB - We prove a general local law for Wigner matrices that optimally handles observables of arbitrary rank and thus unifies the well-known averaged and isotropic local laws. As an application, we prove a central limit theorem in quantum unique ergodicity (QUE): that is, we show that the quadratic forms of a general deterministic matrix A on the bulk eigenvectors of a Wigner matrix have approximately Gaussian fluctuation. For the bulk spectrum, we thus generalise our previous result [17] as valid for test matrices A of large rank as well as the result of Benigni and Lopatto [7] as valid for specific small-rank observables.
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
ID - 12148
JF - Forum of Mathematics, Sigma
KW - Computational Mathematics
KW - Discrete Mathematics and Combinatorics
KW - Geometry and Topology
KW - Mathematical Physics
KW - Statistics and Probability
KW - Algebra and Number Theory
KW - Theoretical Computer Science
KW - Analysis
SN - 2050-5094
TI - Rank-uniform local law for Wigner matrices
VL - 10
ER -
TY - JOUR
AB - The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants.
AU - Qi, Linlin
AU - Kwiatkowski, Mateusz
AU - Chen, Huihuang
AU - Hörmayer, Lukas
AU - Sinclair, Scott A
AU - Zou, Minxia
AU - del Genio, Charo I.
AU - Kubeš, Martin F.
AU - Napier, Richard
AU - Jaworski, Krzysztof
AU - Friml, Jiří
ID - 12144
IS - 7934
JF - Nature
SN - 0028-0836
TI - Adenylate cyclase activity of TIR1/AFB auxin receptors in plants
VL - 611
ER -
TY - JOUR
AB - Editorial on the Research Topic
AU - Gambino, Giuditta
AU - Bhik-Ghanie, Rebecca
AU - Giglia, Giuseppe
AU - Puig, M. Victoria
AU - Ramirez Villegas, Juan F
AU - Zaldivar, Daniel
ID - 12149
JF - Frontiers in Neural Circuits
KW - Cellular and Molecular Neuroscience
KW - Cognitive Neuroscience
KW - Sensory Systems
KW - Neuroscience (miscellaneous)
SN - 1662-5110
TI - Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels
VL - 16
ER -
TY - JOUR
AB - In this paper, we explore the stability and dynamical relevance of a wide variety of steady, time-periodic, quasiperiodic, and chaotic flows arising between orthogonally stretching parallel plates. We first explore the stability of all the steady flow solution families formerly identified by Ayats et al. [“Flows between orthogonally stretching parallel plates,” Phys. Fluids 33, 024103 (2021)], concluding that only the one that originates from the Stokesian approximation is actually stable. When both plates are shrinking at identical or nearly the same deceleration rates, this Stokesian flow exhibits a Hopf bifurcation that leads to stable time-periodic regimes. The resulting time-periodic orbits or flows are tracked for different Reynolds numbers and stretching rates while monitoring their Floquet exponents to identify secondary instabilities. It is found that these time-periodic flows also exhibit Neimark–Sacker bifurcations, generating stable quasiperiodic flows (tori) that may sometimes give rise to chaotic dynamics through a Ruelle–Takens–Newhouse scenario. However, chaotic dynamics is unusually observed, as the quasiperiodic flows generally become phase-locked through a resonance mechanism before a strange attractor may arise, thus restoring the time-periodicity of the flow. In this work, we have identified and tracked four different resonance regions, also known as Arnold tongues or horns. In particular, the 1 : 4 strong resonance region is explored in great detail, where the identified scenarios are in very good agreement with normal form theory.
AU - Wang, B.
AU - Ayats López, Roger
AU - Meseguer, A.
AU - Marques, F.
ID - 12146
IS - 11
JF - Physics of Fluids
KW - Condensed Matter Physics
KW - Fluid Flow and Transfer Processes
KW - Mechanics of Materials
KW - Computational Mechanics
KW - Mechanical Engineering
SN - 1070-6631
TI - Phase-locking flows between orthogonally stretching parallel plates
VL - 34
ER -
TY - JOUR
AB - In the class of strictly convex smooth boundaries each of which has no strip around its boundary foliated by invariant curves, we prove that the Taylor coefficients of the “normalized” Mather’s β-function are invariant under C∞-conjugacies. In contrast, we prove that any two elliptic billiard maps are C0-conjugate near their respective boundaries, and C∞-conjugate, near the boundary and away from a line passing through the center of the underlying ellipse. We also prove that, if the billiard maps corresponding to two ellipses are topologically conjugate, then the two ellipses are similar.
AU - Koudjinan, Edmond
AU - Kaloshin, Vadim
ID - 12145
IS - 6
JF - Regular and Chaotic Dynamics
KW - Mechanical Engineering
KW - Applied Mathematics
KW - Mathematical Physics
KW - Modeling and Simulation
KW - Statistical and Nonlinear Physics
KW - Mathematics (miscellaneous)
SN - 1560-3547
TI - On some invariants of Birkhoff billiards under conjugacy
VL - 27
ER -
TY - JOUR
AB - ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.
AU - Jiang, Xiuyun
AU - Harker-Kirschneck, Lena
AU - Vanhille-Campos, Christian Eduardo
AU - Pfitzner, Anna-Katharina
AU - Lominadze, Elene
AU - Roux, Aurélien
AU - Baum, Buzz
AU - Šarić, Anđela
ID - 12152
IS - 10
JF - PLOS Computational Biology
KW - Computational Theory and Mathematics
KW - Cellular and Molecular Neuroscience
KW - Genetics
KW - Molecular Biology
KW - Ecology
KW - Modeling and Simulation
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 1553-7358
TI - Modelling membrane reshaping by staged polymerization of ESCRT-III filaments
VL - 18
ER -
TY - JOUR
AB - Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.
AU - Zoller, Benjamin
AU - Gregor, Thomas
AU - Tkačik, Gašper
ID - 12156
IS - 9
JF - Current Opinion in Systems Biology
KW - Applied Mathematics
KW - Computer Science Applications
KW - Drug Discovery
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Modeling and Simulation
SN - 2452-3100
TI - Eukaryotic gene regulation at equilibrium, or non?
VL - 31
ER -
TY - JOUR
AB - We review our theoretical results of the sound propagation in two-dimensional (2D) systems of ultracold fermionic and bosonic atoms. In the superfluid phase, characterized by the spontaneous symmetry breaking of the U(1) symmetry, there is the coexistence of first and second sound. In the case of weakly-interacting repulsive bosons, we model the recent measurements of the sound velocities of 39K atoms in 2D obtained in the weakly-interacting regime and around the Berezinskii–Kosterlitz–Thouless (BKT) superfluid-to-normal transition temperature. In particular, we perform a quite accurate computation of the superfluid density and show that it is reasonably consistent with the experimental results. For superfluid attractive fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover. In the low-temperature regime, we reproduce the recent measurements of first-sound speed with 6Li atoms. We also predict that there is mixing between sound modes only in the finite-temperature BEC regime.
AU - Salasnich, Luca
AU - Cappellaro, Alberto
AU - Furutani, Koichiro
AU - Tononi, Andrea
AU - Bighin, Giacomo
ID - 12154
IS - 10
JF - Symmetry
KW - Physics and Astronomy (miscellaneous)
KW - General Mathematics
KW - Chemistry (miscellaneous)
KW - Computer Science (miscellaneous)
SN - 2073-8994
TI - First and second sound in two-dimensional bosonic and fermionic superfluids
VL - 14
ER -
TY - JOUR
AB - Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.
AU - Hayward, Laura
AU - Sella, Guy
ID - 12157
JF - eLife
KW - General Immunology and Microbiology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Medicine
KW - General Neuroscience
TI - Polygenic adaptation after a sudden change in environment
VL - 11
ER -
TY - JOUR
AB - Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of nonadditive systems very well. In particular, we recover exact diagonalization in all regimes tested and observe substantial improvement over the standard coherent state estimates in the most challenging intermediate-coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications.
AU - Rzadkowski, Wojciech
AU - Lemeshko, Mikhail
AU - Mentink, Johan H.
ID - 12150
IS - 15
JF - Physical Review B
SN - 2469-9950
TI - Artificial neural network states for nonadditive systems
VL - 106
ER -