TY - JOUR
AB - We study the Fröhlich polaron model in R3, and establish the subleading term in the strong coupling asymptotics of its ground state energy, corresponding to the quantum corrections to the classical energy determined by the Pekar approximation.
AU - Brooks, Morris
AU - Seiringer, Robert
ID - 14441
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy
VL - 404
ER -
TY - CONF
AB - We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in [16], [35]. As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subroutine based on in-face Frank-Wolfe directions, introduced in [4] in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html.
AU - Kolmogorov, Vladimir
ID - 14448
SN - 1063-6919
T2 - Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition
TI - Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions
VL - 2023
ER -
TY - JOUR
AB - Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.
AU - Lyons, David B.
AU - Briffa, Amy
AU - He, Shengbo
AU - Choi, Jaemyung
AU - Hollwey, Elizabeth
AU - Colicchio, Jack
AU - Anderson, Ian
AU - Feng, Xiaoqi
AU - Howard, Martin
AU - Zilberman, Daniel
ID - 12672
IS - 3
JF - Cell Reports
TI - Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons
VL - 42
ER -
TY - JOUR
AB - We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar.
AU - Mitrouskas, David Johannes
AU - Mysliwy, Krzysztof
AU - Seiringer, Robert
ID - 13178
JF - Forum of Mathematics
TI - Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron
VL - 11
ER -
TY - JOUR
AB - Intercellular signaling molecules, known as morphogens, act at a long range in developing tissues to provide spatial information and control properties such as cell fate and tissue growth. The production, transport, and removal of morphogens shape their concentration profiles in time and space. Downstream signaling cascades and gene regulatory networks within cells then convert the spatiotemporal morphogen profiles into distinct cellular responses. Current challenges are to understand the diverse molecular and cellular mechanisms underlying morphogen gradient formation, as well as the logic of downstream regulatory circuits involved in morphogen interpretation. This knowledge, combining experimental and theoretical results, is essential to understand emerging properties of morphogen-controlled systems, such as robustness and scaling.
AU - Kicheva, Anna
AU - Briscoe, James
ID - 14484
JF - Annual Review of Cell and Developmental Biology
SN - 1081-0706
TI - Control of tissue development by morphogens
VL - 39
ER -
TY - JOUR
AB - Portrait viewpoint and illumination editing is an important problem with several applications in VR/AR, movies, and photography. Comprehensive knowledge of geometry and illumination is critical for obtaining photorealistic results. Current methods are unable to explicitly model in 3D while handling both viewpoint and illumination editing from a single image. In this paper, we propose VoRF, a novel approach that can take even a single portrait image as input and relight human heads under novel illuminations that can be viewed from arbitrary viewpoints. VoRF represents a human head as a continuous volumetric field and learns a prior model of human heads using a coordinate-based MLP with individual latent spaces for identity and illumination. The prior model is learned in an auto-decoder manner over a diverse class of head shapes and appearances, allowing VoRF to generalize to novel test identities from a single input image. Additionally, VoRF has a reflectance MLP that uses the intermediate features of the prior model for rendering One-Light-at-A-Time (OLAT) images under novel views. We synthesize novel illuminations by combining these OLAT images with target environment maps. Qualitative and quantitative evaluations demonstrate the effectiveness of VoRF for relighting and novel view synthesis, even when applied to unseen subjects under uncontrolled illumination. This work is an extension of Rao et al. (VoRF: Volumetric Relightable Faces 2022). We provide extensive evaluation and ablative studies of our model and also provide an application, where any face can be relighted using textual input.
AU - Rao, Pramod
AU - Mallikarjun, B. R.
AU - Fox, Gereon
AU - Weyrich, Tim
AU - Bickel, Bernd
AU - Pfister, Hanspeter
AU - Matusik, Wojciech
AU - Zhan, Fangneng
AU - Tewari, Ayush
AU - Theobalt, Christian
AU - Elgharib, Mohamed
ID - 14488
JF - International Journal of Computer Vision
SN - 0920-5691
TI - A deeper analysis of volumetric relightiable faces
ER -
TY - JOUR
AB - High Mountain Asia (HMA) is among the most vulnerable water towers globally and yet future projections of water availability in and from its high-mountain catchments remain uncertain, as their hydrologic response to ongoing environmental changes is complex. Mechanistic modeling approaches incorporating cryospheric, hydrological, and vegetation processes in high spatial, temporal, and physical detail have never been applied for high-elevation catchments of HMA. We use a land surface model at high spatial and temporal resolution (100 m and hourly) to simulate the coupled dynamics of energy, water, and vegetation for the 350 km2 Langtang catchment (Nepal). We compare our model outputs for one hydrological year against a large set of observations to gain insight into the partitioning of the water balance at the subseasonal scale and across elevation bands. During the simulated hydrological year, we find that evapotranspiration is a key component of the total water balance, as it causes about the equivalent of 20% of all the available precipitation or 154% of the water production from glacier melt in the basin to return directly to the atmosphere. The depletion of the cryospheric water budget is dominated by snow melt, but at high elevations is primarily dictated by snow and ice sublimation. Snow sublimation is the dominant vapor flux (49%) at the catchment scale, accounting for the equivalent of 11% of snowfall, 17% of snowmelt, and 75% of ice melt, respectively. We conclude that simulations should consider sublimation and other evaporative fluxes explicitly, as otherwise water balance estimates can be ill-quantified.
AU - Buri, Pascal
AU - Fatichi, Simone
AU - Shaw, Thomas
AU - Miles, Evan S.
AU - Mccarthy, Michael
AU - Fyffe, Catriona Louise
AU - Fugger, Stefan
AU - Ren, Shaoting
AU - Kneib, Marin
AU - Jouberton, Achille
AU - Steiner, Jakob
AU - Fujita, Koji
AU - Pellicciotti, Francesca
ID - 14487
IS - 10
JF - Water Resources Research
SN - 0043-1397
TI - Land surface modeling in the Himalayas: On the importance of evaporative fluxes for the water balance of a high-elevation catchment
VL - 59
ER -
TY - CONF
AB - Batching is a technique that stores multiple keys/values in each node of a data structure. In sequential search data structures, batching reduces latency by reducing the number of cache misses and shortening the chain of pointers to dereference. Applying batching to concurrent data structures is challenging, because it is difficult to maintain the search property and keep contention low in the presence of batching.
In this paper, we present a general methodology for leveraging batching in concurrent search data structures, called BatchBoost. BatchBoost builds a search data structure from distinct "data" and "index" layers. The data layer’s purpose is to store a batch of key/value pairs in each of its nodes. The index layer uses an unmodified concurrent search data structure to route operations to a position in the data layer that is "close" to where the corresponding key should exist. The requirements on the index and data layers are low: with minimal effort, we were able to compose three highly scalable concurrent search data structures based on three original data structures as the index layers with a batched version of the Lazy List as the data layer. The resulting BatchBoost data structures provide significant performance improvements over their original counterparts.
AU - Aksenov, Vitaly
AU - Anoprenko, Michael
AU - Fedorov, Alexander
AU - Spear, Michael
ID - 14485
SN - 1868-8969
T2 - 37th International Symposium on Distributed Computing
TI - Brief announcement: BatchBoost: Universal batching for concurrent data structures
VL - 281
ER -
TY - JOUR
AB - We present a minimal model of ferroelectric large polarons, which are suggested as one of the mechanisms responsible for the unique charge transport properties of hybrid perovskites. We demonstrate that short-ranged charge–rotor interactions lead to long-range ferroelectric ordering of rotors, which strongly affects the carrier mobility. In the nonperturbative regime, where our theory cannot be reduced to any of the earlier models, we reveal that the polaron is characterized by large coherence length and a roughly tenfold increase of the effective mass as compared to the bare mass. These results are in good agreement with other theoretical predictions for ferroelectric polarons. Our model establishes a general phenomenological framework for ferroelectric polarons providing the starting point for future studies of their role in the transport properties of hybrid organic-inorganic perovskites.
AU - Koutentakis, Georgios
AU - Ghazaryan, Areg
AU - Lemeshko, Mikhail
ID - 14486
IS - 4
JF - Physical Review Research
SN - 2643-1564
TI - Rotor lattice model of ferroelectric large polarons
VL - 5
ER -
TY - JOUR
AB - To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.
AU - Fiedler, Lukas
AU - Friml, Jiří
ID - 14313
IS - 10
JF - Current Opinion in Plant Biology
SN - 1369-5266
TI - Rapid auxin signaling: Unknowns old and new
VL - 75
ER -
TY - GEN
AB - We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023).
Buri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841
AU - Buri, Pascal
AU - Fatichi, Simone
AU - Shaw, Thomas
AU - Miles, Evan
AU - McCarthy, Michael
AU - Fyffe, Catriona Louise
AU - Fugger, Stefan
AU - Ren, Shaoting
AU - Kneib, Marin
AU - Jouberton, Achille
AU - Steiner, Jakob
AU - Fujita, Koji
AU - Pellicciotti, Francesca
ID - 14494
TI - Model output data to "Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment"
ER -
TY - JOUR
AB - An n-vertex graph is called C-Ramsey if it has no clique or independent set of size Clog2n (i.e., if it has near-optimal Ramsey behavior). In this paper, we study edge statistics in Ramsey graphs, in particular obtaining very precise control of the distribution of the number of edges in a random vertex subset of a C-Ramsey graph. This brings together two ongoing lines of research: the study of ‘random-like’ properties of Ramsey graphs and the study of small-ball probability for low-degree polynomials of independent random variables.
The proof proceeds via an ‘additive structure’ dichotomy on the degree sequence and involves a wide range of different tools from Fourier analysis, random matrix theory, the theory of Boolean functions, probabilistic combinatorics and low-rank approximation. In particular, a key ingredient is a new sharpened version of the quadratic Carbery–Wright theorem on small-ball probability for polynomials of Gaussians, which we believe is of independent interest. One of the consequences of our result is the resolution of an old conjecture of Erdős and McKay, for which Erdős reiterated in several of his open problem collections and for which he offered one of his notorious monetary prizes.
AU - Kwan, Matthew Alan
AU - Sah, Ashwin
AU - Sauermann, Lisa
AU - Sawhney, Mehtaab
ID - 14499
JF - Forum of Mathematics, Pi
KW - Discrete Mathematics and Combinatorics
KW - Geometry and Topology
KW - Mathematical Physics
KW - Statistics and Probability
KW - Algebra and Number Theory
KW - Analysis
SN - 2050-5086
TI - Anticoncentration in Ramsey graphs and a proof of the Erdős–McKay conjecture
VL - 11
ER -
TY - JOUR
AB - In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.
AU - Praetorius, Florian M
AU - Leung, Philip J. Y.
AU - Tessmer, Maxx H.
AU - Broerman, Adam
AU - Demakis, Cullen
AU - Dishman, Acacia F.
AU - Pillai, Arvind
AU - Idris, Abbas
AU - Juergens, David
AU - Dauparas, Justas
AU - Li, Xinting
AU - Levine, Paul M.
AU - Lamb, Mila
AU - Ballard, Ryanne K.
AU - Gerben, Stacey R.
AU - Nguyen, Hannah
AU - Kang, Alex
AU - Sankaran, Banumathi
AU - Bera, Asim K.
AU - Volkman, Brian F.
AU - Nivala, Jeff
AU - Stoll, Stefan
AU - Baker, David
ID - 14281
IS - 6659
JF - Science
SN - 0036-8075
TI - Design of stimulus-responsive two-state hinge proteins
VL - 381
ER -
TY - GEN
AB - Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways.
AU - Edman, Natasha I
AU - Redler, Rachel L
AU - Phal, Ashish
AU - Schlichthaerle, Thomas
AU - Srivatsan, Sanjay R
AU - Etemadi, Ali
AU - An, Seong
AU - Favor, Andrew
AU - Ehnes, Devon
AU - Li, Zhe
AU - Praetorius, Florian M
AU - Gordon, Max
AU - Yang, Wei
AU - Coventry, Brian
AU - Hicks, Derrick R
AU - Cao, Longxing
AU - Bethel, Neville
AU - Heine, Piper
AU - Murray, Analisa N
AU - Gerben, Stacey
AU - Carter, Lauren
AU - Miranda, Marcos
AU - Negahdari, Babak
AU - Lee, Sangwon
AU - Trapnell, Cole
AU - Stewart, Lance
AU - Ekiert, Damian C
AU - Schlessinger, Joseph
AU - Shendure, Jay
AU - Bhabha, Gira
AU - Ruohola-Baker, Hannele
AU - Baker, David
ID - 14294
T2 - bioRxiv
TI - Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
ER -
TY - JOUR
AB - Cold atomic gases have become a paradigmatic system for exploring fundamental physics, which at the same time allows for applications in quantum technologies. The accelerating developments in the field have led to a highly advanced set of engineering techniques that, for example, can tune interactions, shape the external geometry, select among a large set of atomic species with different properties, or control the number of atoms. In particular, it is possible to operate in lower dimensions and drive atomic systems into the strongly correlated regime. In this review, we discuss recent advances in few-body cold atom systems confined in low dimensions from a theoretical viewpoint. We mainly focus on bosonic systems in one dimension and provide an introduction to the static properties before we review the state-of-the-art research into quantum dynamical processes stimulated by the presence of correlations. Besides discussing the fundamental physical phenomena arising in these systems, we also provide an overview of the calculational and numerical tools and methods that are commonly used, thus delivering a balanced and comprehensive overview of the field. We conclude by giving an outlook on possible future directions that are interesting to explore in these correlated systems.
AU - Mistakidis, S. I.
AU - Volosniev, Artem
AU - Barfknecht, R. E.
AU - Fogarty, T.
AU - Busch, Th
AU - Foerster, A.
AU - Schmelcher, P.
AU - Zinner, N. T.
ID - 14513
JF - Physics Reports
SN - 0370-1573
TI - Few-body Bose gases in low dimensions - A laboratory for quantum dynamics
VL - 1042
ER -
TY - DATA
AB - We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders.
AU - Klausen, Frederik Ravn
AU - Lauritsen, Asbjørn Bækgaard
ID - 12869
TI - Research data for: A stochastic cellular automaton model of culture formation
ER -
TY - JOUR
AB - We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.
AU - Klausen, Frederik Ravn
AU - Lauritsen, Asbjørn Bækgaard
ID - 12890
IS - 5
JF - Physical Review E
SN - 2470-0045
TI - Stochastic cellular automaton model of culture formation
VL - 108
ER -
TY - CONF
AB - We revisit decentralized random beacons with a focus on practical distributed applications. Decentralized random beacons (Beaver and So, Eurocrypt'93) provide the functionality for n parties to generate an unpredictable sequence of bits in a way that cannot be biased, which is useful for any decentralized protocol requiring trusted randomness. Existing beacon constructions are highly inefficient in practical settings where protocol parties need to rejoin after crashes or disconnections, and more significantly where smart contracts may rely on arbitrary index points in high-volume streams. For this, we introduce a new notion of history-generating decentralized random beacons (HGDRBs). Roughly, the history-generation property of HGDRBs allows for previous beacon outputs to be efficiently generated knowing only the current value and the public key. At application layers, history-generation supports registering a sparser set of on-chain values if desired, so that apps like lotteries can utilize on-chain values without incurring high-frequency costs, enjoying all the benefits of DRBs implemented off-chain or with decoupled, special-purpose chains. Unlike rollups, HG is tailored specifically to recovering and verifying pseudorandom bit sequences and thus enjoys unique optimizations investigated in this work. We introduce STROBE: an efficient HGDRB construction which generalizes the original squaring-based RSA approach of Beaver and So. STROBE enjoys several useful properties that make it suited for practical applications that use beacons: 1) history-generating: it can regenerate and verify high-throughput beacon streams, supporting sparse (thus cost-effective) ledger entries; 2) concisely self-verifying: NIZK-free, with state and validation employing a single ring element; 3) eco-friendly: stake-based rather than work based; 4) unbounded: refresh-free, addressing limitations of Beaver and So; 5) delay-free: results are immediately available. 6) storage-efficient: the last beacon suffices to derive all past outputs, thus O(1) storage requirements for nodes serving the whole history.
AU - Beaver, Donald
AU - Kelkar, Mahimna
AU - Lewi, Kevin
AU - Nikolaenko, Valeria
AU - Sonnino, Alberto
AU - Chalkias, Konstantinos
AU - Kokoris Kogias, Eleftherios
AU - Naurois, Ladi De
AU - Roy, Arnab
ID - 14516
SN - 1868-8969
T2 - 5th Conference on Advances in Financial Technologies
TI - STROBE: Streaming Threshold Random Beacons
VL - 282
ER -
TY - JOUR
AB - State-of-the-art transmon qubits rely on large capacitors, which systematically improve their coherence due to reduced surface-loss participation. However, this approach increases both the footprint and the parasitic cross-coupling and is ultimately limited by radiation losses—a potential roadblock for scaling up quantum processors to millions of qubits. In this work we present transmon qubits with sizes as low as 36 × 39 µm2 with 100-nm-wide vacuum-gap capacitors that are micromachined from commercial silicon-on-insulator wafers and shadow evaporated with aluminum. We achieve a vacuum participation ratio up to 99.6% in an in-plane design that is compatible with standard coplanar circuits. Qubit relaxationtime measurements for small gaps with high zero-point electric field variance of up to 22 V/m reveal a double exponential decay indicating comparably strong qubit interaction with long-lived two-level systems. The exceptionally high selectivity of up to 20 dB to the superconductor-vacuum interface allows us to precisely back out the sub-single-photon dielectric loss tangent of aluminum oxide previously exposed to ambient conditions. In terms of future scaling potential, we achieve a ratio of qubit quality factor to a footprint area equal to 20 µm−2, which is comparable with the highest T1 devices relying on larger geometries, a value that could improve substantially for lower surface-loss superconductors.
AU - Zemlicka, Martin
AU - Redchenko, Elena
AU - Peruzzo, Matilda
AU - Hassani, Farid
AU - Trioni, Andrea
AU - Barzanjeh, Shabir
AU - Fink, Johannes M
ID - 14517
IS - 4
JF - Physical Review Applied
TI - Compact vacuum-gap transmon qubits: Selective and sensitive probes for superconductor surface losses
VL - 20
ER -
TY - JOUR
AB - Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger.
AU - Reinhardt, Manuel
AU - Tkačik, Gašper
AU - Ten Wolde, Pieter Rein
ID - 14515
IS - 4
JF - Physical Review X
TI - Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories
VL - 13
ER -
TY - JOUR
AB - The elastic Leidenfrost effect occurs when a vaporizable soft solid is lowered onto a hot surface. Evaporative flow couples to elastic deformation, giving spontaneous bouncing or steady-state floating. The effect embodies an unexplored interplay between thermodynamics, elasticity, and lubrication: despite being observed, its basic theoretical description remains a challenge. Here, we provide a theory of elastic Leidenfrost floating. As weight increases, a rigid solid sits closer to the hot surface. By contrast, we discover an elasticity-dominated regime where the heavier the solid, the higher it floats. This geometry-governed behavior is reminiscent of the dynamics of large liquid Leidenfrost drops. We show that this elastic regime is characterized by Hertzian behavior of the solid’s underbelly and derive how the float height scales with materials parameters. Introducing a dimensionless elastic Leidenfrost number, we capture the crossover between rigid and Hertzian behavior. Our results provide theoretical underpinning for recent experiments, and point to the design of novel soft machines.
AU - Binysh, Jack
AU - Chakraborty, Indrajit
AU - Chubynsky, Mykyta V.
AU - Diaz Melian, Vicente L
AU - Waitukaitis, Scott R
AU - Sprittles, James E.
AU - Souslov, Anton
ID - 14514
IS - 16
JF - Physical Review Letters
SN - 0031-9007
TI - Modeling Leidenfrost levitation of soft elastic solids
VL - 131
ER -
TY - GEN
AB - see Readme file
AU - Binysh, Jack
AU - Chakraborty, Indrajit
AU - Chubynsky, Mykyta
AU - Diaz Melian, Vicente L
AU - Waitukaitis, Scott R
AU - Sprittles, James
AU - Souslov, Anton
ID - 14523
TI - SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1
ER -
TY - CONF
AB - We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets.
AU - Avni, Guy
AU - Meggendorfer, Tobias
AU - Sadhukhan, Suman
AU - Tkadlec, Josef
AU - Zikelic, Dorde
ID - 14518
SN - 0922-6389
T2 - Frontiers in Artificial Intelligence and Applications
TI - Reachability poorman discrete-bidding games
VL - 372
ER -
TY - JOUR
AB - Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.
AU - Degen, Morris
AU - Santos, José Carlos
AU - Pluhackova, Kristyna
AU - Cebrero, Gonzalo
AU - Ramos, Saray
AU - Jankevicius, Gytis
AU - Hartenian, Ella
AU - Guillerm, Undina
AU - Mari, Stefania A.
AU - Kohl, Bastian
AU - Müller, Daniel J.
AU - Schanda, Paul
AU - Maier, Timm
AU - Perez, Camilo
AU - Sieben, Christian
AU - Broz, Petr
AU - Hiller, Sebastian
ID - 13096
JF - Nature
SN - 0028-0836
TI - Structural basis of NINJ1-mediated plasma membrane rupture in cell death
VL - 618
ER -
TY - JOUR
AB - A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance.
AU - Farag, Nadia L.
AU - Jethwa, Rajesh B
AU - Beardmore, Alice E.
AU - Insinna, Teresa
AU - O'Keefe, Christopher A.
AU - Klusener, Peter A.A.
AU - Grey, Clare P.
AU - Wright, Dominic S.
ID - 13041
IS - 13
JF - ChemSusChem
SN - 1864-5631
TI - Triarylamines as catholytes in aqueous organic redox flow batteries
VL - 16
ER -
TY - JOUR
AB - Under high pressures and temperatures, molecular systems with substantial polarization charges, such as ammonia and water, are predicted to form superionic phases and dense fluid states with dissociating molecules and high electrical conductivity. This behaviour potentially plays a role in explaining the origin of the multipolar magnetic fields of Uranus and Neptune, whose mantles are thought to result from a mixture of H2O, NH3 and CH4 ices. Determining the stability domain, melting curve and electrical conductivity of these superionic phases is therefore crucial for modelling planetary interiors and dynamos. Here we report the melting curve of superionic ammonia up to 300 GPa from laser-driven shock compression of pre-compressed samples and atomistic calculations. We show that ammonia melts at lower temperatures than water above 100 GPa and that fluid ammonia’s electrical conductivity exceeds that of water at conditions predicted by hot, super-adiabatic models for Uranus and Neptune, and enhances the conductivity in their fluid water-rich dynamo layers.
AU - Hernandez, J.-A.
AU - Bethkenhagen, Mandy
AU - Ninet, S.
AU - French, M.
AU - Benuzzi-Mounaix, A.
AU - Datchi, F.
AU - Guarguaglini, M.
AU - Lefevre, F.
AU - Occelli, F.
AU - Redmer, R.
AU - Vinci, T.
AU - Ravasio, A.
ID - 13118
JF - Nature Physics
SN - 1745-2473
TI - Melting curve of superionic ammonia at planetary interior conditions
VL - 19
ER -
TY - JOUR
AB - A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order.
AU - Helson, Victor
AU - Zwettler, Timo
AU - Mivehvar, Farokh
AU - Colella, Elvia
AU - Roux, Kevin Etienne Robert
AU - Konishi, Hideki
AU - Ritsch, Helmut
AU - Brantut, Jean Philippe
ID - 13119
JF - Nature
SN - 0028-0836
TI - Density-wave ordering in a unitary Fermi gas with photon-mediated interactions
VL - 618
ER -
TY - JOUR
AB - This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.
AU - Feliciangeli, Dario
AU - Gerolin, Augusto
AU - Portinale, Lorenzo
ID - 12911
IS - 4
JF - Journal of Functional Analysis
SN - 0022-1236
TI - A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature
VL - 285
ER -
TY - JOUR
AB - In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established.
AU - Hua, Bobo
AU - Keller, Matthias
AU - Schwarz, Michael
AU - Wirth, Melchior
ID - 13177
IS - 8
JF - Proceedings of the American Mathematical Society
SN - 0002-9939
TI - Sobolev-type inequalities and eigenvalue growth on graphs with finite measure
VL - 151
ER -
TY - JOUR
AB - n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f
in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m
and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈))
worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2
and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds.
AU - Bhattacharya, Sayan
AU - Henzinger, Monika H
AU - Nanongkai, Danupon
AU - Wu, Xiaowei
ID - 14558
IS - 5
JF - SIAM Journal on Computing
SN - 0097-5397
TI - Deterministic near-optimal approximation algorithms for dynamic set cover
VL - 52
ER -
TY - CONF
AB - We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.
AU - Ansaripour, Matin
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Lechner, Mathias
AU - Zikelic, Dorde
ID - 14559
SN - 0302-9743
T2 - 21st International Symposium on Automated Technology for Verification and Analysis
TI - Learning provably stabilizing neural controllers for discrete-time stochastic systems
VL - 14215
ER -
TY - JOUR
AB - The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format.
AU - Cornalba, Federico
AU - Shardlow, Tony
ID - 14554
IS - 5
JF - ESAIM: Mathematical Modelling and Numerical Analysis
SN - 2822-7840
TI - The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime
VL - 57
ER -
TY - JOUR
AB - Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
AU - Berdan, Emma L.
AU - Barton, Nicholas H
AU - Butlin, Roger
AU - Charlesworth, Brian
AU - Faria, Rui
AU - Fragata, Inês
AU - Gilbert, Kimberly J.
AU - Jay, Paul
AU - Kapun, Martin
AU - Lotterhos, Katie E.
AU - Mérot, Claire
AU - Durmaz Mitchell, Esra
AU - Pascual, Marta
AU - Peichel, Catherine L.
AU - Rafajlović, Marina
AU - Westram, Anja M
AU - Schaeffer, Stephen W.
AU - Johannesson, Kerstin
AU - Flatt, Thomas
ID - 14556
JF - Journal of Evolutionary Biology
SN - 1010-061X
TI - How chromosomal inversions reorient the evolutionary process
ER -
TY - JOUR
AB - The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems.
AU - Riedl, Michael
AU - Sixt, Michael K
ID - 14555
JF - Frontiers in Cell and Developmental Biology
TI - The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction
VL - 11
ER -
TY - JOUR
AB - The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.
AU - Kaiyrzhanov, Rauan
AU - Rad, Aboulfazl
AU - Lin, Sheng-Jia
AU - Bertoli-Avella, Aida
AU - Kallemeijn, Wouter W
AU - Godwin, Annie
AU - Zaki, Maha S
AU - Huang, Kevin
AU - Lau, Tracy
AU - Petree, Cassidy
AU - Efthymiou, Stephanie
AU - Ghayoor Karimiani, Ehsan
AU - Hempel, Maja
AU - Normand, Elizabeth A
AU - Rudnik-Schöneborn, Sabine
AU - Schatz, Ulrich A
AU - Baggelaar, Marc P
AU - Ilyas, Muhammad
AU - Sultan, Tipu
AU - Alvi, Javeria Raza
AU - Ganieva, Manizha
AU - Fowler, Ben
AU - Aanicai, Ruxandra
AU - Akay Tayfun, Gulsen
AU - Al Saman, Abdulaziz
AU - Alswaid, Abdulrahman
AU - Amiri, Nafise
AU - Asilova, Nilufar
AU - Shotelersuk, Vorasuk
AU - Yeetong, Patra
AU - Azam, Matloob
AU - Babaei, Meisam
AU - Bahrami Monajemi, Gholamreza
AU - Mohammadi, Pouria
AU - Samie, Saeed
AU - Banu, Selina Husna
AU - Basto, Jorge Pinto
AU - Kortüm, Fanny
AU - Bauer, Mislen
AU - Bauer, Peter
AU - Beetz, Christian
AU - Garshasbi, Masoud
AU - Hameed Issa, Awatif
AU - Eyaid, Wafaa
AU - Ahmed, Hind
AU - Hashemi, Narges
AU - Hassanpour, Kazem
AU - Herman, Isabella
AU - Ibrohimov, Sherozjon
AU - Abdul-Majeed, Ban A
AU - Imdad, Maria
AU - Isrofilov, Maksudjon
AU - Kaiyal, Qassem
AU - Khan, Suliman
AU - Kirmse, Brian
AU - Koster, Janet
AU - Lourenço, Charles Marques
AU - Mitani, Tadahiro
AU - Moldovan, Oana
AU - Murphy, David
AU - Najafi, Maryam
AU - Pehlivan, Davut
AU - Rocha, Maria Eugenia
AU - Salpietro, Vincenzo
AU - Schmidts, Miriam
AU - Shalata, Adel
AU - Mahroum, Mohammad
AU - Talbeya, Jawabreh Kassem
AU - Taylor, Robert W
AU - Vazquez, Dayana
AU - Vetro, Annalisa
AU - Waterham, Hans R
AU - Zaman, Mashaya
AU - Schrader, Tina A
AU - Chung, Wendy K
AU - Guerrini, Renzo
AU - Lupski, James R
AU - Gleeson, Joseph
AU - Suri, Mohnish
AU - Jamshidi, Yalda
AU - Bhatia, Kailash P
AU - Vona, Barbara
AU - Schrader, Michael
AU - Severino, Mariasavina
AU - Guille, Matthew
AU - Tate, Edward W
AU - Varshney, Gaurav K
AU - Houlden, Henry
AU - Maroofian, Reza
ID - 14543
JF - Brain
KW - Neurology (clinical)
SN - 0006-8950
TI - Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders
ER -
TY - JOUR
AB - It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ
and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit.
AU - Henheik, Sven Joscha
AU - Lauritsen, Asbjørn Bækgaard
AU - Roos, Barbara
ID - 14542
JF - Reviews in Mathematical Physics
SN - 0129-055X
TI - Universality in low-dimensional BCS theory
ER -
TY - JOUR
AB - Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.
AU - Fedotova, Ekaterina
AU - Kuznetsov, Nikolai
AU - Tiunov, Egor
AU - Ulanov, A. E.
AU - Lvovsky, A. I.
ID - 14553
IS - 4
JF - Physical Review A
SN - 2469-9926
TI - Continuous-variable quantum tomography of high-amplitude states
VL - 108
ER -
TY - JOUR
AB - Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem.
AU - Dikranjan, D.
AU - Giordano Bruno, A.
AU - Zava, Nicolò
ID - 14557
IS - S1
JF - Quaestiones Mathematicae
SN - 1607-3606
TI - Epimorphisms and closure operators of categories of semilattices
VL - 46
ER -
TY - JOUR
AB - Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.
AU - Robinson, M. L.
AU - Hahn, P. G.
AU - Inouye, B. D.
AU - Underwood, N.
AU - Whitehead, S. R.
AU - Abbott, K. C.
AU - Bruna, E. M.
AU - Cacho, N. I.
AU - Dyer, L. A.
AU - Abdala-Roberts, L.
AU - Allen, W. J.
AU - Andrade, J. F.
AU - Angulo, D. F.
AU - Anjos, D.
AU - Anstett, D. N.
AU - Bagchi, R.
AU - Bagchi, S.
AU - Barbosa, M.
AU - Barrett, S.
AU - Baskett, Carina
AU - Ben-Simchon, E.
AU - Bloodworth, K. J.
AU - Bronstein, J. L.
AU - Buckley, Y. M.
AU - Burghardt, K. T.
AU - Bustos-Segura, C.
AU - Calixto, E. S.
AU - Carvalho, R. L.
AU - Castagneyrol, B.
AU - Chiuffo, M. C.
AU - Cinoğlu, D.
AU - Cinto Mejía, E.
AU - Cock, M. C.
AU - Cogni, R.
AU - Cope, O. L.
AU - Cornelissen, T.
AU - Cortez, D. R.
AU - Crowder, D. W.
AU - Dallstream, C.
AU - Dáttilo, W.
AU - Davis, J. K.
AU - Dimarco, R. D.
AU - Dole, H. E.
AU - Egbon, I. N.
AU - Eisenring, M.
AU - Ejomah, A.
AU - Elderd, B. D.
AU - Endara, M. J.
AU - Eubanks, M. D.
AU - Everingham, S. E.
AU - Farah, K. N.
AU - Farias, R. P.
AU - Fernandes, A. P.
AU - Fernandes, G. W.
AU - Ferrante, M.
AU - Finn, A.
AU - Florjancic, G. A.
AU - Forister, M. L.
AU - Fox, Q. N.
AU - Frago, E.
AU - França, F. M.
AU - Getman-Pickering, A. S.
AU - Getman-Pickering, Z.
AU - Gianoli, E.
AU - Gooden, B.
AU - Gossner, M. M.
AU - Greig, K. A.
AU - Gripenberg, S.
AU - Groenteman, R.
AU - Grof-Tisza, P.
AU - Haack, N.
AU - Hahn, L.
AU - Haq, S. M.
AU - Helms, A. M.
AU - Hennecke, J.
AU - Hermann, S. L.
AU - Holeski, L. M.
AU - Holm, S.
AU - Hutchinson, M. C.
AU - Jackson, E. E.
AU - Kagiya, S.
AU - Kalske, A.
AU - Kalwajtys, M.
AU - Karban, R.
AU - Kariyat, R.
AU - Keasar, T.
AU - Kersch-Becker, M. F.
AU - Kharouba, H. M.
AU - Kim, T. N.
AU - Kimuyu, D. M.
AU - Kluse, J.
AU - Koerner, S. E.
AU - Komatsu, K. J.
AU - Krishnan, S.
AU - Laihonen, M.
AU - Lamelas-López, L.
AU - Lascaleia, M. C.
AU - Lecomte, N.
AU - Lehn, C. R.
AU - Li, X.
AU - Lindroth, R. L.
AU - Lopresti, E. F.
AU - Losada, M.
AU - Louthan, A. M.
AU - Luizzi, V. J.
AU - Lynch, S. C.
AU - Lynn, J. S.
AU - Lyon, N. J.
AU - Maia, L. F.
AU - Maia, R. A.
AU - Mannall, T. L.
AU - Martin, B. S.
AU - Massad, T. J.
AU - Mccall, A. C.
AU - Mcgurrin, K.
AU - Merwin, A. C.
AU - Mijango-Ramos, Z.
AU - Mills, C. H.
AU - Moles, A. T.
AU - Moore, C. M.
AU - Moreira, X.
AU - Morrison, C. R.
AU - Moshobane, M. C.
AU - Muola, A.
AU - Nakadai, R.
AU - Nakajima, K.
AU - Novais, S.
AU - Ogbebor, C. O.
AU - Ohsaki, H.
AU - Pan, V. S.
AU - Pardikes, N. A.
AU - Pareja, M.
AU - Parthasarathy, N.
AU - Pawar, R. R.
AU - Paynter, Q.
AU - Pearse, I. S.
AU - Penczykowski, R. M.
AU - Pepi, A. A.
AU - Pereira, C. C.
AU - Phartyal, S. S.
AU - Piper, F. I.
AU - Poveda, K.
AU - Pringle, E. G.
AU - Puy, J.
AU - Quijano, T.
AU - Quintero, C.
AU - Rasmann, S.
AU - Rosche, C.
AU - Rosenheim, L. Y.
AU - Rosenheim, J. A.
AU - Runyon, J. B.
AU - Sadeh, A.
AU - Sakata, Y.
AU - Salcido, D. M.
AU - Salgado-Luarte, C.
AU - Santos, B. A.
AU - Sapir, Y.
AU - Sasal, Y.
AU - Sato, Y.
AU - Sawant, M.
AU - Schroeder, H.
AU - Schumann, I.
AU - Segoli, M.
AU - Segre, H.
AU - Shelef, O.
AU - Shinohara, N.
AU - Singh, R. P.
AU - Smith, D. S.
AU - Sobral, M.
AU - Stotz, G. C.
AU - Tack, A. J.M.
AU - Tayal, M.
AU - Tooker, J. F.
AU - Torrico-Bazoberry, D.
AU - Tougeron, K.
AU - Trowbridge, A. M.
AU - Utsumi, S.
AU - Uyi, O.
AU - Vaca-Uribe, J. L.
AU - Valtonen, A.
AU - Van Dijk, L. J.A.
AU - Vandvik, V.
AU - Villellas, J.
AU - Waller, L. P.
AU - Weber, M. G.
AU - Yamawo, A.
AU - Yim, S.
AU - Zarnetske, P. L.
AU - Zehr, L. N.
AU - Zhong, Z.
AU - Wetzel, W. C.
ID - 14552
IS - 6671
JF - Science
TI - Plant size, latitude, and phylogeny explain within-population variability in herbivory
VL - 382
ER -
TY - JOUR
AB - Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.
AU - Briffa, Amy
AU - Hollwey, Elizabeth
AU - Shahzad, Zaigham
AU - Moore, Jonathan D.
AU - Lyons, David B.
AU - Howard, Martin
AU - Zilberman, Daniel
ID - 14551
IS - 11
JF - Cell Systems
SN - 2405-4712
TI - Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations
VL - 14
ER -
TY - GEN
AB - This is associated with our paper "Plant size, latitude, and phylogeny explain within-population variability in herbivory" published in Science.
AU - Wetzel, William
ID - 14579
TI - HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0
ER -
TY - JOUR
AB - Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.
AU - Fäßler, Florian
AU - Javoor, Manjunath
AU - Datler, Julia
AU - Döring, Hermann
AU - Hofer, Florian
AU - Dimchev, Georgi A
AU - Hodirnau, Victor-Valentin
AU - Faix, Jan
AU - Rottner, Klemens
AU - Schur, Florian KM
ID - 12334
IS - 3
JF - Science Advances
KW - Multidisciplinary
SN - 2375-2548
TI - ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning
VL - 9
ER -
TY - DATA
AB - Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.
AU - Schur, Florian KM
ID - 14562
TI - Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning"
ER -
TY - COMP
AB - A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.
AU - Dimchev, Georgi A
AU - Amiri, Behnam
AU - Fäßler, Florian
AU - Falcke, Martin
AU - Schur, Florian KM
ID - 14502
KW - cryo-electron tomography
KW - actin cytoskeleton
KW - toolbox
TI - Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data
ER -
TY - JOUR
AB - Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease.
AU - Kroll, Janina
AU - Hauschild, Robert
AU - Kuznetcov, Arthur
AU - Stefanowski, Kasia
AU - Hermann, Monika D.
AU - Merrin, Jack
AU - Shafeek, Lubuna B
AU - Müller-Taubenberger, Annette
AU - Renkawitz, Jörg
ID - 13342
JF - EMBO Journal
SN - 0261-4189
TI - Adaptive pathfinding by nucleokinesis during amoeboid migration
ER -
TY - JOUR
AB - AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host.
AU - Bussi, Claudio
AU - Mangiarotti, Agustín
AU - Vanhille-Campos, Christian Eduardo
AU - Aylan, Beren
AU - Pellegrino, Enrica
AU - Athanasiadi, Natalia
AU - Fearns, Antony
AU - Rodgers, Angela
AU - Franzmann, Titus M.
AU - Šarić, Anđela
AU - Dimova, Rumiana
AU - Gutierrez, Maximiliano G.
ID - 14610
JF - Nature
KW - Multidisciplinary
SN - 0028-0836
TI - Stress granules plug and stabilize damaged endolysosomal membranes
ER -
TY - DATA
AB - Data related to the following paper:
"Stress granules plug and stabilize damaged endolysosomal membranes" (https://doi.org/10.1038/s41586-023-06726-w)
Abstract:
Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in "Stress granules plug and stabilize damaged endolysosomal membranes", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.
AU - Vanhille-Campos, Christian Eduardo
AU - Šarić, Anđela
ID - 14472
TI - Stress granules plug and stabilize damaged endolysosomal membranes
ER -
TY - JOUR
AB - Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.
AU - Cikes, Domagoj
AU - Elsayad, Kareem
AU - Sezgin, Erdinc
AU - Koitai, Erika
AU - Ferenc, Torma
AU - Orthofer, Michael
AU - Yarwood, Rebecca
AU - Heinz, Leonhard X.
AU - Sedlyarov, Vitaly
AU - Darwish-Miranda, Nasser
AU - Taylor, Adrian
AU - Grapentine, Sophie
AU - al-Murshedi, Fathiya
AU - Abot, Anne
AU - Weidinger, Adelheid
AU - Kutchukian, Candice
AU - Sanchez, Colline
AU - Cronin, Shane J. F.
AU - Novatchkova, Maria
AU - Kavirayani, Anoop
AU - Schuetz, Thomas
AU - Haubner, Bernhard
AU - Haas, Lisa
AU - Hagelkruys, Astrid
AU - Jackowski, Suzanne
AU - Kozlov, Andrey
AU - Jacquemond, Vincent
AU - Knauf, Claude
AU - Superti-Furga, Giulio
AU - Rullman, Eric
AU - Gustafsson, Thomas
AU - McDermot, John
AU - Lowe, Martin
AU - Radak, Zsolt
AU - Chamberlain, Jeffrey S.
AU - Bakovic, Marica
AU - Banka, Siddharth
AU - Penninger, Josef M.
ID - 12747
JF - Nature Metabolism
KW - Cell Biology
KW - Physiology (medical)
KW - Endocrinology
KW - Diabetes and Metabolism
KW - Internal Medicine
SN - 2522-5812
TI - PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing
VL - 5
ER -
TY - JOUR
AB - The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments.
AU - Ouyang, Niuchang
AU - Zeng, Zezhu
AU - Wang, Chen
AU - Wang, Qi
AU - Chen, Yue
ID - 14605
IS - 17
JF - Physical Review B
SN - 2469-9950
TI - Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)
VL - 108
ER -
TY - CONF
AB - Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The
core ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art.
AU - Das, Sourav
AU - Xiang, Zhuolun
AU - Kokoris Kogias, Eleftherios
AU - Ren, Ling
ID - 14609
SN - 9781713879497
T2 - 32nd USENIX Security Symposium
TI - Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling
VL - 8
ER -
TY - JOUR
AB - Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.
AU - Reinhardt, Aleks
AU - Chew, Pin Yu
AU - Cheng, Bingqing
ID - 14603
IS - 18
JF - Journal of Chemical Physics
SN - 0021-9606
TI - A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals
VL - 159
ER -
TY - JOUR
AB - Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.
AU - Toups, Melissa A
AU - Vicoso, Beatriz
ID - 14604
IS - 11
JF - Evolution
TI - The X chromosome of insects likely predates the origin of class Insecta
VL - 77
ER -
TY - GEN
AB - Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.
AU - Toups, Melissa A
AU - Vicoso, Beatriz
ID - 14616
TI - The X chromosome of insects likely predates the origin of Class Insecta
ER -
TY - GEN
AB - Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.
AU - Toups, Melissa A
AU - Vicoso, Beatriz
ID - 14617
TI - The X chromosome of insects likely predates the origin of Class Insecta
ER -
TY - GEN
AB - Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).
AU - Cheng, Bingqing
ID - 14619
TI - BingqingCheng/solubility: V1.0
ER -
TY - JOUR
AB - Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized.
AU - Khouider, B.
AU - GOSWAMI, BIDYUT B
AU - Phani, R.
AU - Majda, A. J.
ID - 14564
IS - 11
JF - Journal of Advances in Modeling Earth Systems
KW - General Earth and Planetary Sciences
KW - Environmental Chemistry
KW - Global and Planetary Change
TI - A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model
VL - 15
ER -
TY - JOUR
AB - Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.
AU - Mujica, Nicolás
AU - Waitukaitis, Scott R
ID - 12789
IS - 3
JF - Physical Review E
SN - 2470-0045
TI - Accurate determination of the shapes of granular charge distributions
VL - 107
ER -
TY - CONF
AB - We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.
.
AU - Schmid, Stefan
AU - Svoboda, Jakub
AU - Yeo, Michelle X
ID - 13238
SN - 0302-9743
T2 - SIROCCO 2023: Structural Information and Communication Complexity
TI - Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation
VL - 13892
ER -
TY - THES
AB - Payment channel networks are a promising approach to improve the scalability bottleneck
of cryptocurrencies. Two design principles behind payment channel networks are
efficiency and privacy. Payment channel networks improve efficiency by allowing users
to transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding
the lengthy process of consensus on the blockchain. Transacting over payment channel
networks also improves privacy as these transactions are not broadcast to the blockchain.
Despite the influx of recent protocols built on top of payment channel networks and
their analysis, a common shortcoming of many of these protocols is that they typically
focus only on either improving efficiency or privacy, but not both. Another limitation
on the efficiency front is that the models used to model actions, costs and utilities of
users are limited or come with unrealistic assumptions.
This thesis aims to address some of the shortcomings of recent protocols and algorithms
on payment channel networks, particularly in their privacy and efficiency aspects. We
first present a payment route discovery protocol based on hub labelling and private
information retrieval that hides the route query and is also efficient. We then present
a rebalancing protocol that formulates the rebalancing problem as a linear program
and solves the linear program using multiparty computation so as to hide the channel
balances. The rebalancing solution as output by our protocol is also globally optimal.
We go on to develop more realistic models of the action space, costs, and utilities of
both existing and new users that want to join the network. In each of these settings,
we also develop algorithms to optimise the utility of these users with good guarantees
on the approximation and competitive ratios.
AU - Yeo, Michelle X
ID - 14506
SN - 2663 - 337X
TI - Advances in efficiency and privacy in payment channel network analysis
ER -
TY - CONF
AB - Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium.
AU - Avarikioti, Zeta
AU - Lizurej, Tomasz
AU - Michalak, Tomasz
AU - Yeo, Michelle X
ID - 14490
SN - 9798350339864
T2 - 43rd International Conference on Distributed Computing Systems
TI - Lightning creation games
VL - 2023
ER -
TY - THES
AB - Most motions of many-body systems at any scale in nature with sufficient degrees
of freedom tend to be chaotic; reaching from the orbital motion of planets, the air
currents in our atmosphere, down to the water flowing through our pipelines or
the movement of a population of bacteria. To the observer it is therefore intriguing
when a moving collective exhibits order. Collective motion of flocks of birds, schools
of fish or swarms of self-propelled particles or robots have been studied extensively
over the past decades but the mechanisms involved in the transition from chaos to
order remain unclear. Here, the interactions, that in most systems give rise to chaos,
sustain order. In this thesis we investigate mechanisms that preserve, destabilize
or lead to the ordered state. We show that endothelial cells migrating in circular
confinements transition to a collective rotating state and concomitantly synchronize
the frequencies of nucleating actin waves within individual cells. Consequently,
the frequency dependent cell migration speed uniformizes across the population.
Complementary to the WAVE dependent nucleation of traveling actin waves, we
show that in leukocytes the actin polymerization depending on WASp generates
pushing forces locally at stationary patches. Next, in pipe flows, we study methods
to disrupt the self–sustaining cycle of turbulence and therefore relaminarize the
flow. While we find in pulsating flow conditions that turbulence emerges through a
helical instability during the decelerating phase. Finally, we show quantitatively in
brain slices of mice that wild-type control neurons can compensate the migratory
deficits of a genetically modified neuronal sub–population in the developing cortex.
AU - Riedl, Michael
ID - 12726
SN - 2663-337X
TI - Synchronization in collectively moving active matter
ER -
TY - THES
AB - Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex.
AU - Riedl, Michael
ID - 14530
KW - Synchronization
KW - Collective Movement
KW - Active Matter
KW - Cell Migration
KW - Active Colloids
SN - 2663 - 337X
TI - Synchronization in collectively moving active matter
ER -
TY - THES
AB - Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.
Despite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.
In this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface.
The second focuses on a technological application, a gate-tunable Josephson parametric amplifier.
In the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.
We embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.
The behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \pm ip$ pairing in InAs.
Measuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.
We observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.
In contrast, the data can be captured quantitatively by fitting to a two-component model.
We find the evidence of the intraband $p \pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\mathrm{T}$.
From the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.
By systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.
Strong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.
In the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.
The device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.
By applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.
Modelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.
We observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.
The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.
In general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.
The noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.
As a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.
We found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier.
AU - Phan, Duc T
ID - 14547
KW - superconductor-semiconductor
KW - superconductivity
KW - Al
KW - InAs
KW - p-wave
KW - superconductivity
KW - JPA
KW - microwave
SN - 2663 - 337X
TI - Resonant microwave spectroscopy of Al-InAs
ER -
TY - JOUR
AB - We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.
AU - Phan, Duc T
AU - Falthansl-Scheinecker, Paul
AU - Mishra, Umang
AU - Strickland, W. M.
AU - Langone, D.
AU - Shabani, J.
AU - Higginbotham, Andrew P
ID - 13264
IS - 6
JF - Physical Review Applied
TI - Gate-tunable superconductor-semiconductor parametric amplifier
VL - 19
ER -
TY - GEN
AB - Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.
AU - Gnyliukh, Nataliia
AU - Johnson, Alexander J
AU - Nagel, Marie-Kristin
AU - Monzer, Aline
AU - Hlavata, Annamaria
AU - Isono, Erika
AU - Loose, Martin
AU - Friml, Jiří
ID - 14591
T2 - bioRxiv
TI - Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants
ER -
TY - JOUR
AB - Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.
Methods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.
Results: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.
Conclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”.
AU - Lin, Sheng-Jia
AU - Vona, Barbara
AU - Lau, Tracy
AU - Huang, Kevin
AU - Zaki, Maha S.
AU - Aldeen, Huda Shujaa
AU - Karimiani, Ehsan Ghayoor
AU - Rocca, Clarissa
AU - Noureldeen, Mahmoud M.
AU - Saad, Ahmed K.
AU - Petree, Cassidy
AU - Bartolomaeus, Tobias
AU - Abou Jamra, Rami
AU - Zifarelli, Giovanni
AU - Gotkhindikar, Aditi
AU - Wentzensen, Ingrid M.
AU - Liao, Mingjuan
AU - Cork, Emalyn Elise
AU - Varshney, Pratishtha
AU - Hashemi, Narges
AU - Mohammadi, Mohammad Hasan
AU - Rad, Aboulfazl
AU - Neira, Juanita
AU - Toosi, Mehran Beiraghi
AU - Knopp, Cordula
AU - Kurth, Ingo
AU - Challman, Thomas D.
AU - Smith, Rebecca
AU - Abdalla, Asmahan
AU - Haaf, Thomas
AU - Suri, Mohnish
AU - Joshi, Manali
AU - Chung, Wendy K.
AU - Moreno-De-Luca, Andres
AU - Houlden, Henry
AU - Maroofian, Reza
AU - Varshney, Gaurav K.
ID - 14639
JF - Genome Medicine
KW - Genetics (clinical)
KW - Genetics
KW - Molecular Biology
KW - Molecular Medicine
SN - 1756-994X
TI - Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity
VL - 15
ER -
TY - JOUR
AB - We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.
AU - Makatura, Liane
AU - Wang, Bohan
AU - Chen, Yi-Lu
AU - Deng, Bolei
AU - Wojtan, Christopher J
AU - Bickel, Bernd
AU - Matusik, Wojciech
ID - 14628
IS - 5
JF - ACM Transactions on Graphics
KW - Computer Graphics and Computer-Aided Design
SN - 0730-0301
TI - Procedural metamaterials: A unified procedural graph for metamaterial design
VL - 42
ER -
TY - GEN
AB - Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression.
AU - Tluckova, Katarina
AU - Testa Salmazo, Anita P
AU - Bernecky, Carrie A
ID - 14644
TI - Mechanism of mammalian transcriptional repression by noncoding RNA
ER -
TY - JOUR
AB - We investigate spin-charge separation of a spin-
1
2
Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom.
AU - Becker, J. M.
AU - Koutentakis, Georgios
AU - Schmelcher, P.
ID - 14658
IS - 4
JF - Physical Review Research
SN - 2643-1564
TI - Spin-charge correlations in finite one-dimensional multiband Fermi systems
VL - 5
ER -
TY - JOUR
AB - We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures.
AU - Volosniev, Artem
AU - Bighin, Giacomo
AU - Santos, Luis
AU - Peña Ardila, Luisllu A.
ID - 14650
IS - 6
JF - SciPost Physics
KW - General Physics and Astronomy
SN - 2542-4653
TI - Non-equilibrium dynamics of dipolar polarons
VL - 15
ER -
TY - JOUR
AB - Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.
AU - Kluibenschedl, Florian
AU - Ploner, Anna
AU - Meisenbichler, Christina
AU - Konrat, Robert
AU - Müller, Thomas
ID - 14653
JF - International Journal of Mass Spectrometry
SN - 1387-3806
TI - Advanced motion tracking for interactive mass spectrometry imaging (IMSI)
VL - 495
ER -
TY - GEN
AB - In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that new born neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.
AU - Bose, Mahima
AU - Suresh, Varun
AU - Mishra, Urvi
AU - Talwar, Ishita
AU - Yadav, Anuradha
AU - Biswas, Shiona
AU - Hippenmeyer, Simon
AU - Tole, Shubha
ID - 14647
T2 - bioRxiv
TI - Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway
ER -
TY - JOUR
AB - The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.
AU - Sorichetti, Valerio
AU - Lenz, Martin
ID - 14655
IS - 22
JF - Physical Review Letters
SN - 0031-9007
TI - Transverse fluctuations control the assembly of semiflexible filaments
VL - 131
ER -
TY - JOUR
AB - The classical Steinitz theorem states that if the origin belongs to the interior of the convex hull of a set 𝑆⊂ℝ𝑑, then there are at most 2𝑑 points of 𝑆 whose convex hull contains the origin in the interior. Bárány, Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem. Let 𝑄 be a convex polytope in ℝ𝑑 containing the standard Euclidean unit ball 𝐁𝑑. Then there exist at most 2𝑑 vertices of 𝑄 whose convex hull 𝑄′ satisfies 𝑟𝐁𝑑⊂𝑄′ with 𝑟⩾𝑑−2𝑑. They conjectured that 𝑟⩾𝑐𝑑−1∕2 holds with a universal constant 𝑐>0. We prove 𝑟⩾15𝑑2, the first polynomial lower bound on 𝑟. Furthermore, we show that 𝑟 is not greater than 2/√𝑑.
AU - Ivanov, Grigory
AU - Naszódi, Márton
ID - 14660
JF - Bulletin of the London Mathematical Society
SN - 0024-6093
TI - Quantitative Steinitz theorem: A polynomial bound
ER -
TY - JOUR
AB - So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function.
AU - Chintaluri, Chaitanya
AU - Vogels, Tim P
ID - 14666
IS - 48
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species
VL - 120
ER -
TY - JOUR
AB - Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.
AU - Nardin, Michele
AU - Csicsvari, Jozsef L
AU - Tkačik, Gašper
AU - Savin, Cristina
ID - 14656
IS - 48
JF - The Journal of Neuroscience
TI - The structure of hippocampal CA1 interactions optimizes spatial coding across experience
VL - 43
ER -
TY - JOUR
AB - Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident.
AU - Tkadlec, Josef
AU - Kaveh, Kamran
AU - Chatterjee, Krishnendu
AU - Nowak, Martin A.
ID - 14657
IS - 208
JF - Journal of the Royal Society, Interface
TI - Evolutionary dynamics of mutants that modify population structure
VL - 20
ER -
TY - JOUR
AB - The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts “on demand”.
AU - Hema, Kuntrapakam
AU - Grommet, Angela B.
AU - Białek, Michał J.
AU - Wang, Jinhua
AU - Schneider, Laura
AU - Drechsler, Christoph
AU - Yanshyna, Oksana
AU - Diskin-Posner, Yael
AU - Clever, Guido H.
AU - Klajn, Rafal
ID - 14664
IS - 45
JF - Journal of the American Chemical Society
SN - 0002-7863
TI - Guest encapsulation alters the thermodynamic landscape of a coordination host
VL - 145
ER -
TY - JOUR
AB - As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity.
AU - Zhao, Jinyan
AU - Yao, Zihao
AU - Bunting, Rhys
AU - Hu, P.
AU - Wang, Jianguo
ID - 14663
IS - 22
JF - ACS Catalysis
TI - Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles
VL - 13
ER -
TY - JOUR
AB - For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum.
AU - Erdös, László
AU - Ji, Hong Chang
ID - 14667
IS - 4
JF - Annales de l'institut Henri Poincare (B) Probability and Statistics
SN - 0246-0203
TI - Functional CLT for non-Hermitian random matrices
VL - 59
ER -
TY - JOUR
AB - We consider a class of polaron models, including the Fröhlich model, at zero total
momentum, and show that at sufficiently weak coupling there are no excited eigenvalues below
the essential spectrum.
AU - Seiringer, Robert
ID - 14662
IS - 3
JF - Journal of Spectral Theory
SN - 1664-039X
TI - Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling
VL - 13
ER -
TY - JOUR
AB - In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli.
AU - Gupta, Shyam Lal
AU - Singh, Saurabh
AU - Kumar, Sumit
AU - Anupam, Unknown
AU - Thakur, Samjeet Singh
AU - Kumar, Ashish
AU - Panwar, Sanjay
AU - Diwaker, D.
ID - 14652
JF - Physica B: Condensed Matter
SN - 0921-4526
TI - Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys
VL - 674
ER -
TY - JOUR
AB - Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis.
AU - Scarpetta, Silvia
AU - Morrisi, Niccolò
AU - Mutti, Carlotta
AU - Azzi, Nicoletta
AU - Trippi, Irene
AU - Ciliento, Rosario
AU - Apicella, Ilenia
AU - Messuti, Giovanni
AU - Angiolelli, Marianna
AU - Lombardi, Fabrizio
AU - Parrino, Liborio
AU - Vaudano, Anna Elisabetta
ID - 12487
IS - 10
JF - iScience
TI - Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture
VL - 26
ER -
TY - JOUR
AB - Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force.
Results: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on.
Conclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk.
AU - Metzler, Sina
AU - Kirchner, Jessica
AU - Grasse, Anna V
AU - Cremer, Sylvia
ID - 12696
JF - BMC Ecology and Evolution
SN - 2730-7182
TI - Trade-offs between immunity and competitive ability in fighting ant males
VL - 23
ER -
TY - JOUR
AB - Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment.
AU - Salerno, Franco
AU - Guyennon, Nicolas
AU - Yang, Kun
AU - Shaw, Thomas
AU - Lin, Changgui
AU - Colombo, Nicola
AU - Romano, Emanuele
AU - Gruber, Stephan
AU - Bolch, Tobias
AU - Alessandri, Andrea
AU - Cristofanelli, Paolo
AU - Putero, Davide
AU - Diolaiuti, Guglielmina
AU - Tartari, Gianni
AU - Verza, Gianpietro
AU - Thakuri, Sudeep
AU - Balsamo, Gianpaolo
AU - Miles, Evan S.
AU - Pellicciotti, Francesca
ID - 14659
JF - Nature Geoscience
SN - 1752-0894
TI - Local cooling and drying induced by Himalayan glaciers under global warming
VL - 16
ER -
TY - JOUR
AB - AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators.
AU - Zhang, Danyang
AU - Lape, Remigijus
AU - Shaikh, Saher A.
AU - Kohegyi, Bianka K.
AU - Watson, Jake
AU - Cais, Ondrej
AU - Nakagawa, Terunaga
AU - Greger, Ingo H.
ID - 12786
JF - Nature Communications
TI - Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics
VL - 14
ER -
TY - DATA
AB - See Readme File for further information.
AU - Cremer, Sylvia
ID - 12693
TI - Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males
ER -
TY - JOUR
AB - Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways.
AU - Xu, Jiayuan
AU - Liu, Nana
AU - Polemiti, Elli
AU - Garcia-Mondragon, Liliana
AU - Tang, Jie
AU - Liu, Xiaoxuan
AU - Lett, Tristram
AU - Yu, Le
AU - Nöthen, Markus M.
AU - Feng, Jianfeng
AU - Yu, Chunshui
AU - Marquand, Andre
AU - Schumann, Gunter
AU - Walter, Henrik
AU - Heinz, Andreas
AU - Ralser, Markus
AU - Twardziok, Sven
AU - Vaidya, Nilakshi
AU - Serin, Emin
AU - Jentsch, Marcel
AU - Hitchen, Esther
AU - Eils, Roland
AU - Taron, Ulrike Helene
AU - Schütz, Tatjana
AU - Schepanski, Kerstin
AU - Banks, Jamie
AU - Banaschewski, Tobias
AU - Jansone, Karina
AU - Christmann, Nina
AU - Meyer-Lindenberg, Andreas
AU - Tost, Heike
AU - Holz, Nathalie
AU - Schwarz, Emanuel
AU - Stringaris, Argyris
AU - Neidhart, Maja
AU - Nees, Frauke
AU - Siehl, Sebastian
AU - A. Andreassen, Ole
AU - T. Westlye, Lars
AU - Van Der Meer, Dennis
AU - Fernandez, Sara
AU - Kjelkenes, Rikka
AU - Ask, Helga
AU - Rapp, Michael
AU - Tschorn, Mira
AU - Böttger, Sarah Jane
AU - Novarino, Gaia
AU - Marr, Lena
AU - Slater, Mel
AU - Viapiana, Guillem Feixas
AU - Orosa, Francisco Eiroa
AU - Gallego, Jaime
AU - Pastor, Alvaro
AU - Forstner, Andreas
AU - Hoffmann, Per
AU - M. Nöthen, Markus
AU - J. Forstner, Andreas
AU - Claus, Isabelle
AU - Miller, Abbi
AU - Heilmann-Heimbach, Stefanie
AU - Sommer, Peter
AU - Boye, Mona
AU - Wilbertz, Johannes
AU - Schmitt, Karen
AU - Jirsa, Viktor
AU - Petkoski, Spase
AU - Pitel, Séverine
AU - Otten, Lisa
AU - Athanasiadis, Anastasios Polykarpos
AU - Pearmund, Charlie
AU - Spanlang, Bernhard
AU - Alvarez, Elena
AU - Sanchez, Mavi
AU - Giner, Arantxa
AU - Hese, Sören
AU - Renner, Paul
AU - Jia, Tianye
AU - Gong, Yanting
AU - Xia, Yunman
AU - Chang, Xiao
AU - Calhoun, Vince
AU - Liu, Jingyu
AU - Thompson, Paul
AU - Clinton, Nicholas
AU - Desrivieres, Sylvane
AU - H. Young, Allan
AU - Stahl, Bernd
AU - Ogoh, George
ID - 13168
JF - Nature Medicine
SN - 1078-8956
TI - Effects of urban living environments on mental health in adults
VL - 29
ER -
TY - CONF
AB - 3D printing based on continuous deposition of materials, such as filament-based 3D printing, has seen widespread adoption thanks to its versatility in working with a wide range of materials. An important shortcoming of this type of technology is its limited multi-material capabilities. While there are simple hardware designs that enable multi-material printing in principle, the required software is heavily underdeveloped. A typical hardware design fuses together individual materials fed into a single chamber from multiple inlets before they are deposited. This design, however, introduces a time delay between the intended material mixture and its actual deposition. In this work, inspired by diverse path planning research in robotics, we show that this mechanical challenge can be addressed via improved printer control. We propose to formulate the search for optimal multi-material printing policies in a reinforcement
learning setup. We put forward a simple numerical deposition model that takes into account the non-linear material mixing and delayed material deposition. To validate our system we focus on color fabrication, a problem known for its strict requirements for varying material mixtures at a high spatial frequency. We demonstrate that our learned control policy outperforms state-of-the-art hand-crafted algorithms.
AU - Liao, Kang
AU - Tricard, Thibault
AU - Piovarci, Michael
AU - Seidel, Hans-Peter
AU - Babaei, Vahid
ID - 12976
KW - reinforcement learning
KW - deposition
KW - control
KW - color
KW - multi-filament
SN - 1050-4729
T2 - 2023 IEEE International Conference on Robotics and Automation
TI - Learning deposition policies for fused multi-material 3D printing
VL - 2023
ER -
TY - JOUR
AB - Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization.
AU - Gert, Krista R.B.
AU - Panser, Karin
AU - Surm, Joachim
AU - Steinmetz, Benjamin S.
AU - Schleiffer, Alexander
AU - Jovine, Luca
AU - Moran, Yehu
AU - Kondrashov, Fyodor
AU - Pauli, Andrea
ID - 13164
JF - Nature Communications
TI - Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries
VL - 14
ER -
TY - JOUR
AB - Let P be a nontorsion point on an elliptic curve defined over a number field K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that every term of the sequence of the Bn has a primitive divisor for n greater than an effectively computable constant that we will explicitly compute. This constant will depend only on the model defining the curve.
AU - Verzobio, Matteo
ID - 12313
IS - 2
JF - Pacific Journal of Mathematics
TI - Some effectivity results for primitive divisors of elliptic divisibility sequences
VL - 325
ER -
TY - JOUR
AB - We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes.
AU - Dello Schiavo, Lorenzo
AU - Lytvynov, Eugene
ID - 13145
JF - Electronic Communications in Probability
TI - A Mecke-type characterization of the Dirichlet–Ferguson measure
VL - 28
ER -
TY - JOUR
AB - We 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 R n such that any point in R n 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 derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory.
AU - Zhang, Yihan
AU - Vatedka, Shashank
ID - 12838
IS - 7
JF - IEEE Transactions on Information Theory
SN - 0018-9448
TI - Multiple packing: Lower bounds via infinite constellations
VL - 69
ER -
TY - CONF
AB - A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox.
AU - Henzinger, Thomas A
AU - Karimi, Mahyar
AU - Kueffner, Konstantin
AU - Mallik, Kaushik
ID - 13228
SN - 9781450372527
T2 - FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency
TI - Runtime monitoring of dynamic fairness properties
ER -
TY - JOUR
AB - Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.
AU - Benedikter, Niels P
AU - Porta, Marcello
AU - Schlein, Benjamin
AU - Seiringer, Robert
ID - 13225
IS - 4
JF - Archive for Rational Mechanics and Analysis
SN - 0003-9527
TI - Correlation energy of a weakly interacting Fermi gas with large interaction potential
VL - 247
ER -
TY - JOUR
AB - We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion.
AU - Bossmann, Lea
AU - Petrat, Sören P
ID - 13226
IS - 4
JF - Letters in Mathematical Physics
SN - 0377-9017
TI - Weak Edgeworth expansion for the mean-field Bose gas
VL - 113
ER -
TY - JOUR
AB - Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis.
AU - Hassani, Farid
AU - Peruzzo, Matilda
AU - Kapoor, Lucky
AU - Trioni, Andrea
AU - Zemlicka, Martin
AU - Fink, Johannes M
ID - 13227
JF - Nature Communications
TI - Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours
VL - 14
ER -
TY - CONF
AB - We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm.
AU - Xu, Yizhou
AU - Hou, Tian Qi
AU - Liang, Shan Suo
AU - Mondelli, Marco
ID - 13321
SN - 9798350301496
T2 - 2023 IEEE Information Theory Workshop
TI - Approximate message passing for multi-layer estimation in rotationally invariant models
ER -
TY - JOUR
AB - In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality.
AU - Zhong, Fanchao
AU - Xu, Yonglai
AU - Zhao, Haisen
AU - Lu, Lin
ID - 13265
IS - 3
JF - ACM Transactions on Graphics
SN - 0730-0301
TI - As-Continuous-As-Possible extrusion-based fabrication of surface models
VL - 42
ER -
TY - JOUR
AB - Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes.
AU - Volberg, Alexander
AU - Zhang, Haonan
ID - 13318
JF - Mathematische Annalen
SN - 0025-5831
TI - Noncommutative Bohnenblust–Hille inequalities
ER -