TY - GEN AB - Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1 AU - Sahu, Rishabh ID - 13122 TI - Entangling microwaves with light ER - TY - JOUR AB - Brachyury, a member of T-box gene family, is widely known for its major role in mesoderm specification in bilaterians. It is also present in non-bilaterian metazoans, such as cnidarians, where it acts as a component of an axial patterning system. In this study, we present a phylogenetic analysis of Brachyury genes within phylum Cnidaria, investigate differential expression and address a functional framework of Brachyury paralogs in hydrozoan Dynamena pumila. Our analysis indicates two duplication events of Brachyury within the cnidarian lineage. The first duplication likely appeared in the medusozoan ancestor, resulting in two copies in medusozoans, while the second duplication arose in the hydrozoan ancestor, resulting in three copies in hydrozoans. Brachyury1 and 2 display a conservative expression pattern marking the oral pole of the body axis in D. pumila. On the contrary, Brachyury3 expression was detected in scattered presumably nerve cells of the D. pumila larva. Pharmacological modulations indicated that Brachyury3 is not under regulation of cWnt signaling in contrast to the other two Brachyury genes. Divergence in expression patterns and regulation suggest neofunctionalization of Brachyury3 in hydrozoans. AU - Vetrova, Alexandra A. AU - Kupaeva, Daria M. AU - Kizenko, Alena AU - Lebedeva, Tatiana S. AU - Walentek, Peter AU - Tsikolia, Nikoloz AU - Kremnyov, Stanislav V. ID - 13166 JF - Scientific Reports TI - The evolutionary history of Brachyury genes in Hydrozoa involves duplications, divergence, and neofunctionalization VL - 13 ER - TY - JOUR AB - We consider the spin- 1 2 Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain. AU - Orlov, Pavel AU - Tiutiakina, Anastasiia AU - Sharipov, Rustem AU - Petrova, Elena AU - Gritsev, Vladimir AU - Kurlov, Denis V. ID - 13138 IS - 18 JF - Physical Review B SN - 2469-9950 TI - Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain VL - 107 ER - TY - JOUR AB - The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis–cortex and cortex–endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth. AU - Chen, C AU - Zhang, Y AU - Cai, J AU - Qiu, Y AU - Li, L AU - Gao, C AU - Gao, Y AU - Ke, M AU - Wu, S AU - Wei, C AU - Chen, J AU - Xu, T AU - Friml, Jiří AU - Wang, J AU - Li, R AU - Chao, D AU - Zhang, B AU - Chen, X AU - Gao, Z ID - 13213 IS - 3 JF - Plant Physiology SN - 0032-0889 TI - Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots VL - 192 ER - TY - JOUR AB - In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. As many different chemical compounds can induce this operon, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the processes of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was most heterogeneous within individual colonies for an intermediate value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype. AU - Guet, Calin C AU - Bruneaux, L AU - Oikonomou, P AU - Aldana, M AU - Cluzel, P ID - 12478 JF - Frontiers in Microbiology TI - Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression VL - 14 ER - TY - JOUR AB - The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases. AU - Michaels, Thomas C.T. AU - Qian, Daoyuan AU - Šarić, Anđela AU - Vendruscolo, Michele AU - Linse, Sara AU - Knowles, Tuomas P.J. ID - 13237 JF - Nature Reviews Physics TI - Amyloid formation as a protein phase transition VL - 5 ER - TY - JOUR AB - Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation. AU - Shamipour, Shayan AU - Hofmann, Laura AU - Steccari, Irene AU - Kardos, Roland AU - Heisenberg, Carl-Philipp J ID - 13229 IS - 6 JF - PLoS Biology TI - Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes VL - 21 ER - TY - JOUR AB - Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop an analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally. AU - Grosjean, Galien M AU - Waitukaitis, Scott R ID - 13197 IS - 6 JF - Physical Review Materials KW - Physics and Astronomy (miscellaneous) KW - General Materials Science SN - 2475-9953 TI - Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts VL - 7 ER - TY - JOUR AB - To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals. AU - Charlton, Julie A. AU - Mlynarski, Wiktor F AU - Bai, Yoon H. AU - Hermundstad, Ann M. AU - Goris, Robbe L.T. ID - 13230 IS - 6 JF - PLoS Computational Biology TI - Environmental dynamics shape perceptual decision bias VL - 19 ER - TY - JOUR AB - The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study. AU - Dormeshkin, Dmitri AU - Katsin, Mikalai AU - Stegantseva, Maria AU - Golenchenko, Sergey AU - Shapira, Michail AU - Dubovik, Simon AU - Lutskovich, Dzmitry AU - Kavaleuski, Anton AU - Meleshko, Alexander ID - 13232 IS - 6 JF - Vaccines TI - Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein VL - 11 ER - TY - JOUR AB - AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications. AU - Liu, Yu AU - Li, Mingquan AU - Wan, Shanhong AU - Lim, Khak Ho AU - Zhang, Yu AU - Li, Mengyao AU - Li, Junshan AU - Ibáñez, Maria AU - Hong, Min AU - Cabot, Andreu ID - 13235 IS - 12 JF - ACS Nano SN - 1936-0851 TI - Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance VL - 17 ER - TY - JOUR AB - We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles. AU - Schörner, Maximilian AU - Bethkenhagen, Mandy AU - Döppner, Tilo AU - Kraus, Dominik AU - Fletcher, Luke B. AU - Glenzer, Siegfried H. AU - Redmer, Ronald ID - 13231 IS - 6 JF - Physical Review E SN - 2470-0045 TI - X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula VL - 107 ER - TY - JOUR AB - We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters. AU - Agafonova, Sofya AU - Lemeshko, Mikhail AU - Volosniev, Artem ID - 13233 IS - 6 JF - Physical Review A SN - 2469-9926 TI - Finite-range bias in fitting three-body loss to the zero-range model VL - 107 ER - TY - JOUR AB - The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate. AU - Goswami, Bidyut B AU - An, Soon Il ID - 13256 JF - npj Climate and Atmospheric Science TI - An assessment of the ENSO-monsoon teleconnection in a warming climate VL - 6 ER - TY - JOUR AB - Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines. AU - De Castro Barbosa Rodrigues Barata, Carolina AU - Snook, Rhonda R. AU - Ritchie, Michael G. AU - Kosiol, Carolin ID - 13260 IS - 7 JF - Genome biology and evolution TI - Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura VL - 15 ER - TY - GEN AB - Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing. AU - Huber, Daniel AU - Pinsonneault, Marc AU - Beck, Paul AU - Bedding, Timothy R. AU - Joss Bland-Hawthorn, Joss Bland-Hawthorn AU - Breton, Sylvain N. AU - Bugnet, Lisa Annabelle AU - Chaplin, William J. AU - Garcia, Rafael A. AU - Grunblatt, Samuel K. AU - Guzik, Joyce A. AU - Hekker, Saskia AU - Kawaler, Steven D. AU - Mathis, Stephane AU - Mathur, Savita AU - Metcalfe, Travis AU - Mosser, Benoit AU - Ness, Melissa K. AU - Piro, Anthony L. AU - Serenelli, Aldo AU - Sharma, Sanjib AU - Soderblom, David R. AU - Stassun, Keivan G. AU - Stello, Dennis AU - Tayar, Jamie AU - Belle, Gerard T. van AU - Zinn, Joel C. ID - 13447 T2 - arXiv TI - Asteroseismology with the Roman galactic bulge time-domain survey ER - TY - THES AB - Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. Complex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. Cyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism. In summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function. AU - Kravchuk, Vladyslav ID - 12781 SN - 2663-337X TI - Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog ER - TY - THES AB - Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties. The focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks. AU - Peste, Elena-Alexandra ID - 13074 SN - 2663-337X TI - Efficiency and generalization of sparse neural networks ER - TY - THES AB - Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are established to determine cell fate and complex tissue patterns emerge to define structures such as limbs and vascular networks. Patterns are also seen in collectively migrating groups, for instance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through the local interaction of individual constituents or are dictated by higher level instructions is still an open question however there is evidence for the involvement of both types of process. Where patterns arise spontaneously there is a long standing interest in how far the interplay of mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation and signaling, contributes to the behaviour. This is because many systems are able to both chemically regulate mechanical force production and chemically sense mechanical deformation, forming mechano-chemical feedback loops which can potentially become unstable towards spatio and/or temporal patterning. We work with experimental collaborators to investigate the possibility that this type of interaction drives pattern formation in biological systems at different scales. We focus first on tissue-level ERK-density waves observed during the wound healing response across different systems where many previous studies have proposed that patterns depend on polarized cell migration and arise from a mechanical flocking-like mechanism. By combining theory with mechanical and optogenetic perturbation experiments on in vitro monolayers we instead find evidence for mechanochemical pattern formation involving only scalar bilateral feedbacks between ERK signaling and cell contraction. We perform further modeling and experiment to study how this instability couples with polar cell migration in order to produce a robust and efficient wound healing response. In a following chapter we implement ERK-density coupling and cell migration in a 2D active vertex model to investigate the interaction of ERK-density patterning with different tissue rheologies and find that the spatio-temporal dynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass transition. In a last chapter we move towards lower spatial scales in the context of subcellular patterning of the cell cytoskeleton where we investigate the transition between phases of spatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the dynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton and its activator). Experimental evidence supports an intrinsic chemical oscillator which we encode in a reaction model and couple to a contractile active gel description of the cell cortex. The model exhibits phases of chemical oscillations and contractile spatial patterning which reproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However, additional pharmacological perturbations to inhibit myosin contractility leaves the role of contractile instability unclear. We discuss alternative hypotheses and investigate the possibility of reaction-diffusion instability. AU - Boocock, Daniel R ID - 12964 SN - 2663-337X TI - Mechanochemical pattern formation across biological scales ER - TY - JOUR AB - The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons. AU - Brighi, Pietro AU - Ljubotina, Marko AU - Abanin, Dmitry A. AU - Serbyn, Maksym ID - 13963 IS - 5 JF - Physical Review B SN - 2469-9950 TI - Many-body localization proximity effect in a two-species bosonic Hubbard model VL - 108 ER -