@article{20546, abstract = {Rocky debris covers around 7.3 % of the global glacier area, influencing ice melt rates and the surface mass balance of glaciers, making the dynamics and hydrology of debris-covered glaciers distinct from those of clean-ice glaciers. Accurate representation of debris in models is challenging, as measurements of the physical properties and thickness of the supraglacial debris layer are scarce. Here, we compile a database of measured and reported bulk physical properties and layer thicknesses of supraglacial debris that we call the supraglacial Debris Database (DebDaB) and that is open to community submissions. The majority of the database (90 %) is compiled from 172 sources in the literature, and the remaining 10 % was previously unpublished. DebDaB contains 8741 data entries for supraglacial debris layer thickness, of which 1770 entries also include sub-debris ablation rates, 179 thermal conductivity of debris, 160 aerodynamic surface roughness length, 79 debris albedo, 59 debris emissivity, and 37 debris porosity. The data are distributed over 84 glaciers in 13 regions in the Global Terrestrial Network for Glaciers. We show regional differences in the distribution of debris thickness measurements in DebDaB and fit simplified Østrem curves to 19 glaciers with sufficient debris thickness and ablation data. The data in DebDaB can be used for energy balance, melt, and surface mass balance studies by incorporating site-specific debris properties or for evaluation of remote sensing estimates of debris thickness and surface roughness. They can also help future field campaigns on debris-covered glaciers by identifying observation gaps. DebDaB's uneven spatial coverage points to sampling biases in community efforts to observe debris-covered glaciers, with some regions (e.g. central Europe and South Asia) well-sampled but others having gaps with prevalent debris (e.g. the Andes and Alaska). Debris thickness measurements are mostly concentrated at lower elevations, leaving higher-elevation debris-covered areas undersampled and suggesting that our knowledge of debris properties might not be representative of all elevations. The aims of DebDaB, as an openly available dataset, are to evolve over time, to be updated, and to add to community submissions as new data on supraglacial properties become available. The data described in this paper can be accessed from Zenodo at https://doi.org/10.5281/zenodo.14224835 (Groeneveld et al., 2025).}, author = {Fontrodona-Bach, Adrià and Groeneveld, Lars and Miles, Evan and McCarthy, Michael and Shaw, Thomas and Melo Velasco, Juan Vicente and Pellicciotti, Francesca}, issn = {1866-3516}, journal = {Earth System Science Data}, number = {8}, pages = {4213--4234}, publisher = {Copernicus Publications}, title = {{DebDaB: A database of supraglacial debris thickness and physical properties}}, doi = {10.5194/essd-17-4213-2025}, volume = {17}, year = {2025}, } @misc{20547, abstract = {DebdaB is a database of measured and reported physical properties and thickness of supraglacial debris that is openly available and open to community submissions. The majority of the database (90%) is compiled from 172 sources in the literature, and the remaining 10% has not been published before. DebDaB contains 8,286 data entries for supraglacial debris thickness, of which 1,852 entries also include sub-debris ablation rates, 167 data entries of thermal conductivity of debris, 157 of aerodynamic surface roughness length, 77 of debris albedo, 56 of debris emissivity and 37 of debris porosity. The data are distributed over 83 glaciers in 13 regions in the Global Terrestrial Network for Glaciers. }, author = {Groeneveld, Lars and Fontrodona-Bach, Adrià and Miles, Evan and McCarthy, Michael and Melo Velasco, Juan Vicente and Shaw, Thomas and Pellicciotti, Francesca and Bauder, Andreas and Buri, Pascal and Kneib, Marin and Kumar, Amit and Mishra, Aditya and Petersen, lene and Renner, Roman and Schmid, Sandro}, publisher = {Zenodo}, title = {{DebDaB: A database of supraglacial debris thickness and physical properties}}, doi = {10.5281/ZENODO.14224835}, year = {2025}, } @article{20585, abstract = {Motivated by applications in medical sciences, we study finite chromatic sets in Euclidean space from a topological perspective. Based on the persistent homology for images, kernels and cokernels, we design provably stable homological quantifiers that describe the geometric micro- and macro-structure of how the color classes mingle. These can be efficiently computed using chromatic variants of Delaunay and alpha complexes, and code that does these computations is provided.}, author = {Cultrera di Montesano, Sebastiano and Draganov, Ondrej and Edelsbrunner, Herbert and Saghafian, Morteza}, issn = {2639-8001}, journal = {Foundations of Data Science}, pages = {30--62}, publisher = {American Institute of Mathematical Sciences}, title = {{Chromatic alpha complexes}}, doi = {10.3934/fods.2025003}, volume = {8}, year = {2025}, } @article{20586, abstract = {We present the discovery of deep, irregular, periodic transits toward the white dwarf ZTF J1944+4557 using follow-up time-series photometry and spectroscopy from Palomar, Keck, McDonald, Perkins, and Lowell observatories. We find a predominant period of 4.9704 hr, consistent with an orbit near the Roche limit of the white dwarf, with individual dips over 30% deep and lasting between 15 and 40 minutes. Similar to the first known white dwarf with transiting debris, WD 1145+017, the transit events are well-defined with prominent out-of-transit phases where the white dwarf appears unobscured. Spectroscopy concurrent with transit photometry reveals that the average Ca K equivalent width remains constant in and out of transit. The broadening observed in several absorption features cannot be reproduced by synthetic photospheric models, suggesting the presence of circumstellar gas. Simultaneous g + r- and g + i-band light curves from the CHIMERA instrument reveal no color dependence to the transit depths, requiring transiting dust grains to have sizes s ≳ 0.2 μm. The transit morphologies appear to be constantly changing at a rate faster than the orbital period. Overall transit activity varies in the system, with transit features completely disappearing during the seven months between our 2023 and 2024 observing seasons and then reappearing in 2025 March, still repeating at 4.9704 hr. Our observations of the complete cessation and resumption of transit activity provide a novel laboratory for constraining the evolution of disrupted debris and processes like disk exhaustion and replenishment timescales at white dwarfs.}, author = {Guidry, Joseph A. and Vanderbosch, Zachary P. and Hermes, J. J. and Veras, Dimitri and Hollands, Mark A. and Bhattacharjee, Soumyadeep and Caiazzo, Ilaria and El-Badry, Kareem and Kao, Malia L. and Ould Rouis, Lou Baya and Rodriguez, Antonio C. and Van Roestel, Jan}, issn = {1538-4357}, journal = {The Astrophysical Journal}, number = {2}, publisher = {IOP Publishing}, title = {{Transiting planetary debris near the Roche limit of a white dwarf on a 4.97 hr orbit—and its vanishing}}, doi = {10.3847/1538-4357/adfecb}, volume = {992}, year = {2025}, } @article{20588, abstract = {In this second paper on our variability survey of central stars of planetary nebulae (CSPNe) using the Zwicky Transient Facility (ZTF), we report 11 long-timescale variables with variability timescales ranging from months to years. We also present preliminary analyses based on spectroscopic and/or photometric follow-up observations for six of them. Among them is NGC 6833, which shows a 980 days periodic variability with strange characteristics: “triangle-shaped” brightening in r, i, and WISE bands but almost coincidental shallow dips in the g-band. The most plausible explanation is a wide binary with the photometric period being the orbital period. Long-period near-sinusoidal variability was detected in two other systems, NGC 6905 and Kn 26, with periods of 700 days and 230 days, respectively, making them additional wide-binary candidates. The latter also shows a short period at 1.18 hr. We then present CTSS 2 and K 3-5, which show brightening and significant reddening over the whole ZTF baseline. A stellar model fit to the optical spectrum of CTSS 2 reveals it to be one of the youngest post-AGB CSPNe known. Both show high-density emission-line cores. We propose these to be late-thermal-pulse candidates, currently evolving towards the AGB phase. We then present recent HST/COS ultraviolet spectroscopy of the known wide-binary candidate LoTr 1, showing that the hot star is a spectroscopic twin of the extremely hot white dwarf in UCAC2 46706450. Similar to this object, LoTr 1 also has a fast rotating wide subgiant companion. We suggest that the long photometric period of 11 yr is the binary orbital period. Finally, we briefly discuss the ZTF light curves of the remaining variables, namely Tan 2, K 3-20, WHTZ 3, Kn J1857+3931, and IPHAS J1927+0814. With these examples, we present the effectiveness of the von Neumann statistics and Pearson Skew-based metric space in searching for long-timescale variables.}, author = {Bhattacharjee, Soumyadeep and Reindl, Nicole and Bond, Howard E. and Werner, Klaus and Zeimann, Gregory R. and Jones, David and El-Badry, Kareem and Mackensen, Nina and Chornay, Nicholas and Kulkarni, S. R. and Caiazzo, Ilaria and Van Roestel, Jan and Rodriguez, Antonio C. and Prince, Thomas A. and Rusholme, Ben and Laher, Russ R. and Smith, Roger}, issn = {1538-3873}, journal = {Publications of the Astronomical Society of the Pacific}, number = {10}, publisher = {IOP Publishing}, title = {{Variability of central stars of planetary nebulae with the Zwicky Transient Facility. II. Long-timescale variables including wide binary and late thermal pulse candidates}}, doi = {10.1088/1538-3873/ae051e}, volume = {137}, year = {2025}, } @article{20589, abstract = {Context. This paper investigates the star formation histories (SFHs) of a sample of massive galaxies (M⋆ ≥ 1010 M⊙) in the redshift range 1 < z < 4.5. Methods. We analyzed spectro-photometric data, combining broadband photometry from HST and JWST with low-resolution grism spectroscopy from JWST/NIRISS, obtained as part of the MIRI Deep Imaging Survey program. SFHs were derived through spectral energy distribution fitting using two independent codes, BAGPIPES and synthesizer, under various SFH assumptions. This approach enables a comprehensive assessment of the biases introduced by different modeling choices. Results. The inclusion of NIRISS spectroscopy, even with its low resolution, significantly improves constraints on key physical parameters, such as the mass-weighted stellar age (tM) and formation redshift (zform), by narrowing their posterior distributions. The massive galaxies in our sample exhibit rapid stellar mass assembly, forming 50% of their mass between 3 ≤ z ≤ 9. The highest inferred formation redshifts are compatible with elevated star formation efficiencies (ϵ) at early epochs. Nonparametric SFHs generally imply an earlier and slower mass assembly compared to parametric forms, highlighting the sensitivity of inferred formation timescales to the chosen SFH model–particularly for galaxies at z < 2. We find that quiescent galaxies are, on average, older (tM ∼ 1.1 Gyr) and assembled more rapidly at earlier times than their star-forming counterparts. These findings support the “downsizing” scenario, in which more massive and passive systems form earlier and more efficiently.}, author = {Annunziatella, M. and P’Erez-Gonz’Alez, P. G. and Álvarez-Márquez, J. and Costantin, L. and Iani, Edoardo and Labiano, Unknown and Rinaldi, P. and Boogaard, L. and Meyer, R. A. and Östlin, G. and Colina, L. and Melinder, J. and Jermann, I. and Gillman, S. and Langeroodi, D. and Hjorth, J. and Alonso-Herrero, A. and Eckart, A. and Walter, F. and Van Der Werf, P. P. and Bik, A. and Peißker, F. and Caputi, K. I. and García-Marín, M. and Wright, G. and Greve, T. R.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{MIDIS: Unveiling the star formation history in massive galaxies at 1 < z < 4.5 with spectro-photometric analysis}}, doi = {10.1051/0004-6361/202453298}, volume = {702}, year = {2025}, } @article{20590, abstract = {Moist convection is a fundamental process occurring in the Earth's atmosphere. It plays a central role in the weather and climate of the Tropics, where, to first order, the heating of the atmosphere by convection is in balance with the cooling of the atmosphere by the emission of radiation to outer space. In this study, we use a cloud-resolving model in radiative–convective equilibrium with an imposed constant rate of radiative cooling and study the response of moist convection to varying this rate of radiative cooling. In particular, we study two types of simulation: varying air temperature (VAT) simulations, where the air temperature is allowed to adjust to the imposed radiative cooling, and constant air temperature (CAT) simulations, where the surface temperature is tuned to ensure that the atmospheric temperature profile in the domain is constant. We recover the previously known result that, in response to increasing radiative cooling, the area of convection expands rapidly, while the intensity of convection does not change. We find that this response is explained by the increased boundary-layer variability in simulations with greater radiative cooling, which compensates for the decreasing temperature by adding a larger initial velocity close to the cloud base. We also propose a fundamental scaling of the non-dimensional cumulus mass flux in moist convection, which is robust across models of different complexity. We aim to bridge the gap between highly idealised prototypes of moist convection, such as the “Rainy–Bénard convection” introduced by Vallis et al., and comprehensive cloud-resolving models.}, author = {Agasthya, Lokahith N and Muller, Caroline J}, issn = {1477-870X}, journal = {Quarterly Journal of the Royal Meteorological Society}, publisher = {Wiley}, title = {{Moist convection and radiative cooling: Dynamical response and scaling}}, doi = {10.1002/qj.70044}, year = {2025}, } @article{20591, abstract = {In this paper we derive estimates for the Hessian of the logarithm (log-Hessian) for solutions to the heat equation. For initial data in the form of log-Lipschitz perturbation of strongly log-concave measures, the log-Hessian admits an explicit, uniform (in space) lower bound. This yields a new estimate for the Lipschitz constant of a transport map pushing forward the standard Gaussian to a measure in this class. On the other hand, we show that assuming only fast decay of the tails of the initial datum does not suffice to guarantee uniform log-Hessian upper bounds.}, author = {Brigati, Giovanni and Pedrotti, Francesco}, issn = {1083-589X}, journal = {Electronic Communications in Probability}, publisher = {Institute of Mathematical Statistics}, title = {{Heat flow, log-concavity, and Lipschitz transport maps}}, doi = {10.1214/25-ECP717}, volume = {30}, year = {2025}, } @inproceedings{20592, abstract = {Filtering-based probabilistic numerical solvers for ordinary differential equations (ODEs), also known as ODE filters, have been established as efficient methods for quantifying numerical uncertainty in the solution of ODEs. In practical applications, however, the underlying dynamical system often contains uncertain parameters, requiring the propagation of this model uncertainty to the ODE solution. In this paper, we demonstrate that ODE filters, despite their probabilistic nature, do not automatically solve this uncertainty propagation problem. To address this limitation, we present a novel approach that combines ODE filters with numerical quadrature to properly marginalize over uncertain parameters, while accounting for both parameter uncertainty and numerical solver uncertainty. Experiments across multiple dynamical systems demonstrate that the resulting uncertainty estimates closely match reference solutions. Notably, we show how the numerical uncertainty from the ODE solver can help prevent overconfidence in the propagated uncertainty estimates, especially when using larger step sizes. Our results illustrate that probabilistic numerical methods can effectively quantify both numerical and parametric uncertainty in dynamical systems. }, author = {Yao, Dingling and Tronarp, Filip and Bosch, Nathanael}, booktitle = {Proceedings of the 1st International Conference on Probabilistic Numerics}, issn = {2640-3498}, location = {Sophia Antipolis, France}, publisher = {ML Research Press}, title = {{Propagating model uncertainty through filtering-based probabilistic numerical ODE solvers}}, volume = {271}, year = {2025}, } @article{20593, abstract = {“Quasi-solid-state” conversion mechanisms using sparingly solvating electrolytes (SPSEs) bridge the gap between traditional solid–liquid–solid and solid-state sulfur conversion in lithium–sulfur (Li–S) batteries. Although these terms are commonly used, their precise distinctions and impacts on key performance metrics, such as rate capability, energy density, and capacity fading, remain poorly understood. In this work, we employ operando small- and wide-angle X-ray scattering alongside cryogenic transmission electron microscopy (cryo-TEM) to compare Li–S batteries in sparingly solvating and solvating ether-based electrolytes. We find that, unlike solvating electrolytes, SPSEs lead to an extended presence of lithium sulfide during cycling, coexisting with sulfur at a 50% state of charge and beyond. In the charged state, solid sulfur is present in its amorphous form inside the carbon black nanopores. These findings indicate that the limited solubility confines polysulfides in regions near the carbon surface, where these polysulfides enable conversion between the coexisting solid discharge and charge product.}, author = {Dutta, Pronoy and Von Mentlen, Jean Marc and Mondal, Soumyadip and Kostoglou, Nikolaos and Wilts, Bodo D. and Freunberger, Stefan Alexander and Zickler, Gregor A. and Prehal, Christian}, issn = {2380-8195}, journal = {ACS Energy Letters}, pages = {5722--5732}, publisher = {American Chemical Society}, title = {{Bridging solution and solid-state mechanism: Confined quasi-solid-state conversion in Li–S batteries}}, doi = {10.1021/acsenergylett.5c02093}, volume = {10}, year = {2025}, } @article{20594, abstract = {(Scanning) transmission electron microscopy ((S)TEM) has significantly advanced materials science but faces challenges in correlating precise atomic structure information with the functional properties of devices due to its time-intensive nature. To address this, an analytical workflow is introduced for the holistic characterization, modelling, and simulation of device heterostructures. This workflow automates the experimental (S)TEM data analysis, providing an in-depth characterization of crystallographic information, 3D orientation, elemental composition, and strain distribution. It reduces a process that typically takes days for a trained human into an automatic routine solved in minutes. Utilizing a physics-guided artificial intelligence model, it generates representative descriptions of materials and samples. The workflow culminates in creating digital twins of systems limited with at least one axis of translational invariance –3D finite element and atomic models of millions of atoms–enabling simulations that provide crucial insights into device behavior in practical applications. Demonstrated with SiGe planar heterostructures for scalable spin qubits, the workflow links digital twins to theoretical properties, revealing how atomic structure impacts materials and functional properties such as spatially-resolved phononic or electronic characteristics, or (inverse) spin orbit lengths. The versatility of the workflow is demonstrated through its application to a wide array of materials systems, device configurations, and sample morphologies.}, author = {Botifoll, Marc and Pinto-Huguet, Ivan and Rotunno, Enzo and Galvani, Thomas and Coll, Catalina and Kavkani, Payam Habibzadeh and Spadaro, Maria Chiara and Niquet, Yann Michel and Eriksen, Martin Børstad and Martí-Sánchez, Sara and Katsaros, Georgios and Scappucci, Giordano and Krogstrup, Peter and Isella, Giovanni and Cabot, Andreu and Merino, Gonzalo and Ordejón, Pablo and Roche, Stephan and Grillo, Vincenzo and Arbiol, Jordi}, issn = {1521-4095}, journal = {Advanced Materials}, publisher = {Wiley}, title = {{Artificial intelligence-assisted workflow for transmission electron microscopy: From data analysis automation to materials knowledge unveiling}}, doi = {10.1002/adma.202506785}, year = {2025}, } @article{20603, abstract = {We study the growth of sumsets A+B⊂S⊂G, where S does not contain an arithmetic progression of length 2k+1, and where G is a commutative group, in which every nonzero element has an order of at least 2k+1. More specifically, we show the following: if A,B⊂G are sets such that A+B does not contain an arithmetic progression of length 2k+1, then |A+B|≥|A|2k−13k−2|B|k3k−2. As an application we derive upper bounds on the cardinality of the summands in sumsets A+B+C contained in the set of t-th powers, where t≥2 is an integer. In particular, we show that min(|A|,|B|,|C|)≪(logN)4/5 for t=2, and min(|A|,|B|,|C|)≪t(logN)1/2 for t≥3.}, author = {Elsholtz, Christian and Ruzsa, Imre Z. and Wurzinger, Lena}, issn = {1730-6264}, journal = {Acta Arithmetica}, pages = {289--303}, publisher = {Institute of Mathematics}, title = {{Sumset growth in progression-free sets}}, doi = {10.4064/aa250115-14-7}, volume = {220}, year = {2025}, } @article{20604, abstract = {Entry into and exit from cellular quiescence require dynamic adjustments in nutrient acquisition, yet the mechanisms by which quiescent cells downregulate amino acid (AA) transport remain poorly understood. Here we show that cells entering quiescence selectively target plasma membrane-resident amino acid transporters for endocytosis and lysosomal degradation. This process matches amino acid uptake with reduced translational demand and promotes survival during extended periods of quiescence. Mechanistically, we identify the α-arrestin TXNIP as a key regulator of this metabolic adaptation, since it mediates the endocytosis of the SLC7A5-SLC3A2 (LAT1-4F2hc) AA transporter complex in response to reduced AKT signaling. To promote transporter ubiquitination, TXNIP interacts with NEDD4L and other HECT-type ubiquitin ligases. Loss of TXNIP disrupts this regulation, resulting in dysregulated amino acid uptake, sustained mTORC1 signaling, and ultimately cell death under prolonged quiescence. The characterization of a novel TXNIP loss-of-function variant in a patient with a severe metabolic disease further supports its role in nutrient homeostasis and human health. Together, these findings highlight TXNIP’s central role in controlling nutrient acquisition and metabolic plasticity with implications for quiescence biology and diseases.}, author = {Kahlhofer, Jennifer and Marchet, Nikolas and Zubak, Kristian and Seifert, Brigitta and Hotze, Madlen and Egger-Hörschinger, Anna-Sophia and Kucej, Lucija and Manzl, Claudia and Weyer, Yannick and Weys, Sabine and Offterdinger, Martin and Herzog, Sebastian and Reiterer, Veronika and Volani, Chiara and Kwiatkowski, Marcel and Wortmann, Saskia B and Nemati, Siamak and Mayr, Johannes A and Zschocke, Johannes and Radlinger, Bernhard and Thedieck, Kathrin and Kremser, Leopold and Sarg, Bettina and Huber, Lukas A and Farhan, Hesso and de Araujo, Mariana E G and Kaser, Susanne and Scholl-Bürgi, Sabine and Karall, Daniela and Teis, David}, issn = {1460-2075}, journal = {The EMBO Journal}, pages = {7119--7153}, publisher = {Embo Press}, title = {{TXNIP mediates LAT1/SLC7A5 endocytosis to limit amino acid uptake in cells entering quiescence}}, doi = {10.1038/s44318-025-00608-9}, volume = {44}, year = {2025}, } @inproceedings{20610, abstract = {Markov decision processes (MDPs) are a fundamental model of decision making which exhibit non-deterministic choice as well as probabilistic uncertainty. Traditionally, verification assumes exact knowledge of the probabilities that govern the behaviour of an MDP. However, this assumption often is unrealistic, e.g. when modelling cyber-physical systems or biological processes. There, we can employ statistical model checking (SMC) to obtain an estimate of the MDP’s value (e.g. the maximal probability of reaching a goal state) that is close to the true value with high confidence (probably approximately correct). Model-based SMC algorithms sample the MDP and build a model of it by estimating all transition probabilities, essentially for every transition answering the question: “What are the odds?” However, so far the statistical methods employed by state-of-the-art SMC verification algorithms are quite naive or even compromise the correctness guarantees. Our first contribution is to survey, categorize, and analyse statistical methods, identifying those few that are most efficient and that provide suitable guarantees for the verification setting. Secondly, we propose improvements that exploit structural knowledge of the MDP. Both contributions generalize to many types of problem statements as they are largely independent of the setting. Moreover, our experimental evaluation shows that they lead to significant gains, reducing the number of samples that an SMC algorithm has to collect by up to two orders of magnitude.}, author = {Meggendorfer, Tobias and Weininger, Maximilian and Wienhöft, Patrick}, booktitle = {Second International Joint Conference on QEST+FORMATS}, isbn = {9783032057914}, issn = {1611-3349}, location = {Aarhus, Denmark}, pages = {195--218}, publisher = {Springer Nature}, title = {{What are the odds? Improving statistical model checking of Markov decision processes}}, doi = {10.1007/978-3-032-05792-1_11}, volume = {16143}, year = {2025}, } @article{20628, abstract = {The realistic simulation of sand, soil, powders, rubble piles, and large collections of rigid bodies is a common and important problem in the fields of computer graphics, computational physics, and engineering. Direct simulation of these individual bodies quickly becomes expensive, so we often approximate the entire group as a continuum material that can be more easily computed using tools for solving partial differential equations, like the material point method (MPM). In this paper, we present a method for automatically extracting continuum material properties from a collection of rigid bodies. We use numerical homogenization with periodic boundary conditions to simulate an effectively infinite number of rigid bodies in contact. We then record the effective stress-strain relationships from these simulations and convert them into elastic properties and yield criteria for the continuum simulations. Our experiments validate existing theoretical models like the Mohr-Coulomb yield surface by extracting material behaviors from a collection of spheres in contact. We further generalize these existing models to more exotic materials derived from diverse and non-convex shapes. We observe complicated jamming behaviors from non-convex grains, and we introduce a new material model for materials with extremely high levels of internal friction and cohesion. We simulate these new continuum models using MPM with an improved return mapping technique. The end result is a complete system for turning an input rigid body simulation into an efficient continuum simulation with the same effective mechanical properties.}, author = {Chen, Yi-Lu and Ly, Mickaël and Wojtan, Christopher J}, issn = {1557-7368}, journal = {ACM Transactions on Graphics}, location = {Hong Kong, China}, number = {6}, publisher = {Association for Computing Machinery}, title = {{Numerical homogenization of sand from grain-level simulations}}, doi = {10.1145/3763344}, volume = {44}, year = {2025}, } @article{20635, abstract = {Plants have evolved sophisticated mechanisms to adapt to environmental changes, with root gravitropism playing a pivotal role in nutrient and water acquisition. Our study reveals that SnRK2 kinases (SnRK2.2 and SnRK2.3) are critical regulators of root gravitropism through their direct phosphorylation of the auxin transporter PIN2 at S259. We demonstrate that SnRK2s-mediated phosphorylation modulates both the polar localization and transport activity of PIN2. Importantly, SnRK2s function antagonistically to the AGCVIII kinase PID, which phosphorylates PIN2 at a distinct site (S258), establishing a regulatory balance essential for adaptive root growth. Structural modeling and phosphorylation assays further suggest that SnRK2s-mediated phosphorylation at S259 sterically hinders access of PID to S258, providing a mechanistic basis for their antagonistic relationship. These findings uncover a novel regulatory mechanism, by which plants fine-tune root developmental programs to adapt to environmental stimuli, highlighting the evolutionary significance of multilayered kinase-mediated regulation in plant adaptation.}, author = {Sheng, F and Gao, Y and Wang, Y and Li, Y and Zhang, JA and Zhang, Z and Qin, X and Zhang, S and Song, W and Li, J and Guo, Y and Friml, Jiří and Gong, Z and Zhang, Q and Zhang, J}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {39}, pages = {e2512274122}, publisher = {National Academy of Sciences}, title = {{Antagonistic SnRK2 and PID kinases' action on auxin transport-mediated root gravitropism}}, doi = {10.1073/pnas.2512274122}, volume = {122}, year = {2025}, } @article{20636, abstract = {The versatile and pivotal roles of the phytohormone auxin in regulating plant growth and development are typically linked to its directional transport, relying on the polarized PIN-FORMED (PIN) auxin exporters at the plasma membrane (PM). For decades, auxin has been proposed to promote PIN polarization, generating self-regulatory feedback mediating much of plant development, but mechanistic insight into this regulation is lacking. Here, we uncover an auxin-induced protein complex at the PM, containing auxin co-receptors transmembrane kinases (TMKs) and PIN1 auxin exporter, as the core machinery that underlies this feedback regulation. Auxin promotes PIN1 phosphorylation by TMKs, modulating PIN1 polarization and transport activity. We also provide evidence that PIN1-exported extracellular auxin is crucial for TMK activation and cell elongation, thus forming the simplest two-element self-regulatory feedback circuit. Thus, these findings offer direct mechanistic insights into a potential self-organizing circuit for auxin signaling and transport to ensure proper plant development in Arabidopsis.}, author = {Huang, R and Wang, J and Chang, M and Tang, W and Yu, Y and Zhang, Y and Peng, Y and Wang, Y and Guo, Y and Lu, T and Cao, Y and Zhou, Y and Zhang, Q and Huang, Y and Wu, A and Ren, L and Gallei, Michelle C and Dong, J and Chen, H and He, J and Wen, M and Friml, Jiří and Sun, L and Xiong, Y and Yang, Z and Xu, T}, issn = {1878-1551}, journal = {Developmental Cell}, pages = {S1534--5807(25)00569--6}, publisher = {Elsevier}, title = {{TMK-PIN1 drives a short self-organizing circuit for auxin export and signaling in Arabidopsis}}, doi = {10.1016/j.devcel.2025.09.009}, year = {2025}, } @misc{20641, abstract = {Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labeling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions. }, author = {Becker, Lea Marie and Schanda, Paul}, publisher = {Institute of Science and Technology Austria}, title = {{Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes"}}, doi = {10.15479/AT-ISTA-20641}, year = {2025}, } @inproceedings{20648, abstract = {Polynomial quantified entailments with existentially and universally quantified variables arise in many problems of verification and program analysis. We present PolyQEnt which is a tool for solving polynomial quantified entailments in which variables on both sides of the implication are real valued or unbounded integers. Our tool provides a unified framework for polynomial quantified entailment problems that arise in several papers in the literature. Our experimental evaluation over a wide range of benchmarks shows the applicability of the tool as well as its benefits as opposed to simply using existing SMT solvers to solve such constraints.}, author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Kafshdar Goharshadi, Ehsan and Karrabi, Mehrdad and Saadat, Milad and Seeliger, Maximilian and Zikelic, Dorde}, booktitle = {23rd International Symposium on Automated Technology for Verification and Analysis}, isbn = {9783032087065}, issn = {1611-3349}, location = {Bengaluru, India}, pages = {411--424}, publisher = {Springer Nature}, title = {{PolyQEnt: A polynomial quantified entailment solver}}, doi = {10.1007/978-3-032-08707-2_19}, volume = {16145}, year = {2025}, } @article{20649, abstract = {Ionized proximity zones around luminous quasars provide a unique laboratory to characterize the Lyα emission lines from z > 6 galaxies without significant attenuation from the intergalactic medium (IGM). However, Lyα line measurements for galaxies within high-redshift quasars’ proximity zones have been rare so far. Here we present deep spectroscopic observations obtained with the NIRSpec/Micro-Shutter Assembly (MSA) instrument on the James Webb Space Telescope of galaxies in two z > 6 quasar fields. We measure the Lyα line fluxes for 50 galaxies at 6 < z < 7 with UV absolute magnitude M UV < −19 (median M UV = −19.97), among which 15 are located near the luminous quasars, i.e., within Δv < 2500 km s−1. We find that galaxies near the quasars show significant flux blueward of the systemic Lyα wavelength, and have higher Lyα equivalent width compared to galaxies at similar redshifts that are not located within the quasars’ environment. Our result indicates little or no redshift evolution for the Lyα emitter fraction from z ∼ 6.4 to z ∼ 5. Leveraging the low IGM opacity in the quasars’ vicinity, we evaluate the Lyα escape fraction (f esc Ly α) of high-redshift galaxies. Our analysis suggests that galaxies at 〈z〉 ≈ 6.4 have an average f esc Ly α = 0.14 ± 0.04. This value is consistent with reionization models where the Lyman continuum escape fraction is low ( fescLyC ≲ 0.1 ) for luminous galaxies, and where the most luminous galaxies have only a minor contribution to the total ionizing photon budget. © 2025. The Author(s). Published by the American Astronomical Society.}, author = {Yue, Minghao and Eilers, Anna Christina and Matthee, Jorryt J and Naidu, Rohan P. and Bordoloi, Rongmon and Davies, Frederick B. and Hennawi, Joseph F. and Kashino, Daichi and Mackenzie, Ruari and Simcoe, Robert A.}, issn = {2041-8213}, journal = {The Astrophysical Journal Letters}, number = {1}, publisher = {IOP Publishing}, title = {{Escape fractions from unattenuated Lyα emitters around luminous z > 6 quasars}}, doi = {10.3847/2041-8213/ae0e0e}, volume = {993}, year = {2025}, }