TY - JOUR AB - Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor. AU - Curk, Samo AU - Krausser, Johannes AU - Meisl, Georg AU - Frenkel, Daan AU - Linse, Sara AU - Michaels, Thomas C.T. AU - Knowles, Tuomas P.J. AU - Šarić, Anđela ID - 15001 IS - 7 JF - Proceedings of the National Academy of Sciences of the United States of America TI - Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites VL - 121 ER - TY - JOUR AB - The lattice Schwinger model, the discrete version of QED in 1 + 1 dimensions, is a well-studied test bench for lattice gauge theories. Here, we study the fractal properties of this model. We reveal the self-similarity of the ground state, which allows us to develop a recurrent procedure for finding the ground-state wave functions and predicting ground-state energies. We present the results of recurrently calculating ground-state wave functions using the fractal Ansatz and automized software package for fractal image processing. In certain parameter regimes, just a few terms are enough for our recurrent procedure to predict ground-state energies close to the exact ones for several hundreds of sites. Our findings pave the way to understanding the complexity of calculating many-body wave functions in terms of their fractal properties as well as finding new links between condensed matter and high-energy lattice models. AU - Petrova, Elena AU - Tiunov, Egor S. AU - Bañuls, Mari Carmen AU - Fedorov, Aleksey K. ID - 15002 IS - 5 JF - Physical Review Letters SN - 0031-9007 TI - Fractal states of the Schwinger model VL - 132 ER - TY - JOUR AB - In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation. AU - Agresti, Antonio AU - Veraar, Mark ID - 12485 JF - Probability Theory and Related Fields SN - 0178-8051 TI - The critical variational setting for stochastic evolution equations ER - TY - CONF AB - Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. In this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth. AU - Goranci, Gramoz AU - Henzinger, Monika H AU - Räcke, Harald AU - Sachdeva, Sushant AU - Sricharan, A. R. ID - 15008 SN - 1868-8969 T2 - 15th Innovations in Theoretical Computer Science Conference TI - Electrical flows for polylogarithmic competitive oblivious routing VL - 287 ER - TY - CONF AB - Traditional blockchains grant the miner of a block full control not only over which transactions but also their order. This constitutes a major flaw discovered with the introduction of decentralized finance and allows miners to perform MEV attacks. In this paper, we address the issue of sandwich attacks by providing a construction that takes as input a blockchain protocol and outputs a new blockchain protocol with the same security but in which sandwich attacks are not profitable. Furthermore, our protocol is fully decentralized with no trusted third parties or heavy cryptography primitives and carries a linear increase in latency and minimum computation overhead. AU - Alpos, Orestis AU - Amores-Sesar, Ignacio AU - Cachin, Christian AU - Yeo, Michelle X ID - 15007 SN - 1868-8969 T2 - 27th International Conference on Principles of Distributed Systems TI - Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks VL - 286 ER - TY - CONF AB - For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution. AU - Henzinger, Monika H AU - Saulpic, David AU - Sidl, Leonhard ID - 14769 T2 - 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments TI - Experimental evaluation of fully dynamic k-means via coresets ER - TY - JOUR AB - Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species. AU - Bett, Vincent K AU - Macon, Ariana AU - Vicoso, Beatriz AU - Elkrewi, Marwan N ID - 15009 IS - 1 JF - Genome Biology and Evolution TI - Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation VL - 16 ER - TY - JOUR AB - The impulsive limit (the “sudden approximation”) has been widely employed to describe the interaction between molecules and short, far-off-resonant laser pulses. This approximation assumes that the timescale of the laser-molecule interaction is significantly shorter than the internal rotational period of the molecule, resulting in the rotational motion being instantaneously “frozen” during the interaction. This simplified description of the laser-molecule interaction is incorporated in various theoretical models predicting rotational dynamics of molecules driven by short laser pulses. In this theoretical work, we develop an effective theory for ultrashort laser pulses by examining the full time-evolution operator and solving the time-dependent Schrödinger equation at the operator level. Our findings reveal a critical angular momentum, lcrit, at which the impulsive limit breaks down. In other words, the validity of the sudden approximation depends not only on the pulse duration but also on its intensity, since the latter determines how many angular momentum states are populated. We explore both ultrashort multicycle (Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce distinct effective potentials. We discuss the limitations of the impulsive limit and propose a method that rescales the effective matrix elements, enabling an improved and more accurate description of laser-molecule interactions. AU - Karle, Volker AU - Lemeshko, Mikhail ID - 15004 IS - 2 JF - Physical Review A SN - 2469-9926 TI - Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics VL - 109 ER - TY - DATA AB - Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species. AU - Elkrewi, Marwan N ID - 14705 KW - sex chromosome evolution KW - genome assembly KW - dosage compensation TI - Data from "Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation" ER - TY - JOUR AB - Magnetic frustration allows to access novel and intriguing properties of magnetic systems and has been explored mainly in planar triangular-like arrays of magnetic ions. In this work, we describe the phosphide Ce6Ni6P17, where the Ce+3 ions accommodate in a body-centered cubic lattice of Ce6 regular octahedra. From measurements of magnetization, specific heat, and resistivity, we determine a rich phase diagram as a function of temperature and magnetic field in which different magnetic phases are found. Besides clear evidence of magnetic frustration is obtained from entropy analysis. At zero field, a second-order antiferromagnetic transition occurs at TN1≈1 K followed by a first-order transition at TN2≈0.45 K. With magnetic field new magnetic phases appear, including a weakly first-order transition which ends in a classical critical point and a third magnetic phase. We also study the exact solution of the spin-1/2 Heisenberg model in an octahedron which allows us a qualitative understanding of the phase diagram and compare with the experimental results. AU - Franco, D. G. AU - Avalos, R. AU - Hafner, D. AU - Modic, Kimberly A AU - Prots, Yu AU - Stockert, O. AU - Hoser, A. AU - Moll, P. J.W. AU - Brando, M. AU - Aligia, A. A. AU - Geibel, C. ID - 15003 IS - 5 JF - Physical Review B SN - 2469-9950 TI - Frustrated magnetism in octahedra-based Ce6 Ni6 P17 VL - 109 ER - TY - JOUR AB - The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality. AU - Shimura, Yosuke AU - Godfrin, Clement AU - Hikavyy, Andriy AU - Li, Roy AU - Aguilera Servin, Juan L AU - Katsaros, Georgios AU - Favia, Paola AU - Han, Han AU - Wan, Danny AU - de Greve, Kristiaan AU - Loo, Roger ID - 15018 IS - 5 JF - Materials Science in Semiconductor Processing KW - Mechanical Engineering KW - Mechanics of Materials KW - Condensed Matter Physics KW - General Materials Science SN - 1369-8001 TI - Compressively strained epitaxial Ge layers for quantum computing applications VL - 174 ER - TY - CONF AB - Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach. AU - Kurtic, Eldar AU - Hoefler, Torsten AU - Alistarh, Dan-Adrian ID - 15011 T2 - Proceedings of Machine Learning Research TI - How to prune your language model: Recovering accuracy on the "Sparsity May Cry" benchmark VL - 234 ER - TY - JOUR AB - Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions. AU - Robin, Paul ID - 15024 IS - 6 JF - Journal of Chemical Physics SN - 0021-9606 TI - Correlation-induced viscous dissipation in concentrated electrolytes VL - 160 ER - TY - JOUR AB - We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble. AU - Erdös, László AU - McKenna, Benjamin ID - 15025 IS - 1B JF - Annals of Applied Probability SN - 1050-5164 TI - Extremal statistics of quadratic forms of GOE/GUE eigenvectors VL - 34 ER - TY - JOUR AB - The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM. AU - Adamowski, Maciek AU - Matijevic, Ivana AU - Friml, Jiří ID - 15033 JF - eLife KW - General Immunology and Microbiology KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Medicine KW - General Neuroscience SN - 2050-084X TI - Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery VL - 13 ER - TY - JOUR AB - In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication. AU - Csata, Eniko AU - Perez-Escudero, Alfonso AU - Laury, Emmanuel AU - Leitner, Hanna AU - Latil, Gerard AU - Heinze, Juerge AU - Simpson, Stephen AU - Cremer, Sylvia AU - Dussutour, Audrey ID - 14479 IS - 4 JF - Current Biology SN - 0960-9822 TI - Fungal infection alters collective nutritional intake of ant colonies VL - 34 ER - TY - JOUR AB - Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport. AU - Varshney, Atul AU - Ghazaryan, Areg AU - Volosniev, Artem ID - 15045 JF - Few-Body Systems KW - Atomic and Molecular Physics KW - and Optics SN - 1432-5411 TI - Classical ‘spin’ filtering with two degrees of freedom and dissipation VL - 65 ER - TY - JOUR AB - Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator. AU - Jin, Shuwei AU - Dai, Kunlun AU - Verstraten, Joris AU - Dixmerias, Maxime AU - Al Hyder, Ragheed AU - Salomon, Christophe AU - Peaudecerf, Bruno AU - de Jongh, Tim AU - Yefsah, Tarik ID - 15053 IS - 1 JF - Physical Review Research KW - General Physics and Astronomy SN - 2643-1564 TI - Multipurpose platform for analog quantum simulation VL - 6 ER - TY - JOUR AB - Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm. AU - Schauer, Alexandra AU - Pranjic-Ferscha, Kornelija AU - Hauschild, Robert AU - Heisenberg, Carl-Philipp J ID - 15048 IS - 4 JF - Development SN - 0950-1991 TI - Robust axis elongation by Nodal-dependent restriction of BMP signaling VL - 151 ER - TY - JOUR AB - Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity ( κL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower κL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications. AU - Cheng, Ruihuan AU - Zeng, Zezhu AU - Wang, Chen AU - Ouyang, Niuchang AU - Chen, Yue ID - 15052 IS - 5 JF - Physical Review B SN - 2469-9950 TI - Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites VL - 109 ER -