@inproceedings{22617, abstract = {Consider a 4-player version of Matching Pennies where a team of three players competes against the Devil. Each player simultaneously says "Heads" or "Tails". The team wins if all four choices match; otherwise the Devil wins. If all team players randomise independently, they win with probability 1/8; if all players share a common source of randomness, they win with probability 1/2. What happens when each pair of team players shares a source of randomness? Can the team do better than win with probability 1/4? The surprising (and nontrivial) answer is yes! We introduce Dicey Games, a formal framework motivated by the study of distributed systems with shared sources of randomness (of which the above example is a specific instance). We characterise the existence, representation and computational complexity of optimal strategies in Dicey Games, and we study the problem of allocating limited sources of randomness optimally within a team.}, author = {Brice, Leonard J and Henzinger, Thomas A and Thejaswini, K. S.}, booktitle = {41st Annual Symposium on Logic in Computer Science}, isbn = {9783959774345}, issn = {1868-8969}, keywords = {Concurrent games, Shared randomness, Topology, Algebraic Geometry}, location = {Lisbon, Portugal}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Dicey games: Shared sources of randomness in distributed systems}}, doi = {10.4230/LIPIcs.LICS.2026.23}, volume = {380}, year = {2026}, } @article{22614, abstract = {This study presents a sustainable and non-destructive recycling strategy for synthetic fibres, specifically polyethylene terephthalate (PET), polyamide 6 (PA6), polyamide 66 (PA66), and elastane (EL). Two deep eutectic solvents (DESs) were synthesised, enabling selective dissolution of EL without degrading the surrounding polymer matrices. The dissolved EL phase was subsequently recovered by centrifugation, demonstrating its potential for material reuse. Comprehensive characterisation confirmed that the process preserves fibre integrity. SEM imaging revealed no detectable changes in fibre morphology, while DSC and TGA analyses indicated that the thermal properties of both EL and synthetic polymers were preserved. ATR-FTIR spectroscopy verified the absence of measurable chemical modifications. Mechanical testing showed that solvent treatment did not compromise the tensile performance of PET, PA6, or PA66 fibres, confirming their suitability for fibre-to-fibre recycling. The recovered fibres were successfully re-extruded into continuous filaments, confirming their melt processability and enabling potential applications in textile yarns, technical fibres, nonwovens, and polymer components via melt-spinning or moulding. These results demonstrate that the proposed DES-based method offers a promising approach for the circular recycling of complex fibre blends and provides a viable pathway towards industrial implementation.}, author = {Depope, Nika and Depope, Al and Archodoulaki, Vasiliki Maria and Dabrowska, Alicja and Lendl, Bernhard and Mautner, Andreas and Ipsmiller, Wolfgang and Bartl, Andreas}, issn = {1879-2456}, journal = {Waste Management}, publisher = {Elsevier}, title = {{DES formulation for recycling synthetic fibre textile waste containing elastane}}, doi = {10.1016/j.wasman.2026.115736}, volume = {224}, year = {2026}, } @article{22406, abstract = {It is known that for a uniform morphic sequence 𝒖 =⟨𝑢𝑛⟩∞ 𝑛=0 and an algebraic number 𝛽 such that |𝛽| >1, the number [[𝒖]]𝛽 :=∑∞ 𝑛=0(𝑢𝑛/𝛽𝑛) either lies in ℚ⁡(𝛽) or is transcendental. In this paper, we show a similar rational–transcendental dichotomy for sequences defined by irreducible Pisot morphisms on binary alphabets. Subject to the Pisot conjecture (an irreducible Pisot morphism has pure discrete spectrum), we generalise the latter result to arbitrary finite alphabets. In certain cases, we are able to show transcendence of [[𝒖]]𝛽 outright. In particular, for 𝑘 ≥2, if 𝒖 is the k-Bonacci word, then [[𝒖]]𝛽 is transcendental.}, author = {Kebis, Pavol and LUCA, FLORIAN and OUAKNINE, JOEL and SCOONES, ANDREW and WORRELL, JAMES}, issn = {1469-4417}, journal = {Ergodic Theory and Dynamical Systems}, keywords = {balanced-pair algorithm, Cobham’s conjecture, k-Bonacci words, Pisot conjecture, subspace theorem}, pages = {1--22}, publisher = {Cambridge University Press}, title = {{Transcendence for Pisot morphic words over an algebraic base}}, doi = {10.1017/etds.2026.10324}, year = {2026}, } @article{22615, abstract = {Background and Objectives: Anti-immunoglobulin-like cell adhesion molecule 5 (IgLON5) disease is a novel and poten- tially treatable entity. Therefore, it is important to recognize all clinical symptoms and di- agnostic clues. We specifically investigated neuromuscular signs and symptoms and muscle biopsy pathology, providing a link between IgLON5 and clinical features of myopathy. Methods: All patients diagnosed with anti-IgLON5 disease in the Netherlands between 2016 and 2023 were included. Serum and CSF samples were tested with immunohistochemistry on rat brain and in-house cell-based assay using live cells. Biopsies of the vastus lateralis muscle were performed in patients with neuromuscular signs and symptoms and analyzed in Vienna to- gether with 3 biopsies of non-Dutch patients sent to Vienna for second opinion. Results: Twenty patients with anti-IgLON5 disease were included (10 male, 50%). The median age at onset was 61.5 years (range 45–85), and the median time from onset to diagnosis was 30 months (range 3–280). Neuromuscular symptoms were present in over half of the patients (11/20), including proximal limb weakness (n = 11), axial weakness (n = 1), muscle atrophy (n = 6), and fasciculations (n = 5). All 12 muscle biopsies (9 from the Dutch cohort, 3 external) showed mild myopathic alterations, 2 additionally presented target fibers and fiber type grouping (compatible with neu- rogenic myopathy), and 3 patients showed immune cell infiltration. We found a strong upregulation of IgLON5 expression in muscle fibers in all patients and also in different muscle disease controls, while immunoreactivity in healthy control muscle was faint/absent. Discussion: Our data support that IgLON5 might play a role in muscle regeneration, which might result in proximal myopathy as a prominent clinical feature in anti-IgLON5 disease. This finding broadens the clinical phenotype of anti-IgLON5 disease and can be an important clue for earlier diagnosis and start of immunotherapy.}, author = {Crijnen, Yvette S. and Endmayr, Verena and Franken, Suzanne C. and Van Der Beek, Nadine A.M.E. and Louter, Maartje and Ströbel, Thomas and Gelpi, Ellen and Koneczny, Inga and Shigemoto, Ryuichi and Lewerenz, Jan and Högl, Birgit and Wanschitz, Julia V. and Hofstadt-Van Oy, Ulrich He and Van Steenhoven, Robin W. and Nagtzaam, Mariska M.P. and Kerstens, Jeroen and Brenner, Juliette and Bastiaansen, Anna E.M. and Verdijk, Robert M. and Van Den Bosch, Thierry P.P. and Schreurs, Marco and Veenbergen, Sharon and Verbeek, Marcel M. and Roelen, Dave L. and Guasp, Mar and Sillevis Smitt, Peter A.E. and Sabater, Lidia and De Vries, Juna M. and Höftberger, Romana and Titulaer, Maarten J.}, issn = {2332-7812}, journal = {Neurology, Neuroimmunology & Neuroinflammation}, number = {5}, pages = {e200525}, publisher = {Wolters Kluwer}, title = {{Muscle regeneration failure may lead to clinical features of myopathy in anti-IgLON5 disease}}, doi = {10.1212/NXI.0000000000200525}, volume = {13}, year = {2026}, } @article{22616, abstract = {Accretion disks in active galactic nuclei (AGN) are promising sites for mergers of stellar-mass black holes (BHs) detectable via gravitational waves (GWs). These environments facilitate both in situ formation and dynamical capture of compact objects and their subsequent mergers. The uncertain origin of GW events detected by LIGO, Virgo, and KAGRA motivates searching for accompanying electromagnetic (EM) signatures. Here, we investigate postmerger EM flares associated with jets launched from merger remnants, as well as from the shocked ambient gas as the jet breaks out of the disk. We find that jet breakout produces luminous gamma-ray emission, detectable with MeV-band telescopes. Cooling emission from a shocked circum-BH minidisk, winds, and background AGN disk peaks in the UV and optical, with durations ranging from about an hour to a month, and can be identified through year-long monitoring of ∼103 AGNs with luminosities ranging from ∼1044 to ∼1045 erg s−1. With a single set of parameters, this postmerger jet model produces gamma-ray, hard X-ray, and optical flares similar to those claimed to be associated with GW events. Furthermore, by incorporating a transition from a high- to low-angular-momentum accretion state after the merger, the model avoids excessive BH growth, alleviating tensions with hyper-Eddington accretion scenarios.}, author = {Tagawa, Hiromichi and Haiman, Zoltán and Kimura, Shigeo S. and Yesuf, Hassen M. and Guo, Hengxiao}, issn = {1538-4357}, journal = {The Astrophysical Journal}, number = {2}, publisher = {IOP Publishing}, title = {{Electromagnetic flares from compact-object mergers in active galactic nucleus disks: Signatures and predictions}}, doi = {10.3847/1538-4357/ae7d29}, volume = {1006}, year = {2026}, } @article{22620, abstract = {Development depends on precise shaping of molecular gradients, but how natural selection acts to establish precision is unknown. Here, we analyze genes that control differences in the gradient of yellow flower color between two varieties of snapdragon (Antirrhinum). We show that these differences depend, in part, on cis-regulatory variation in the pigment biosynthetic gene, FLAVIA (FLA). FLA interacts multiplicatively with three other loci, one of which is a trans-acting regulator of FLA, to further shape the yellow gradient. All the loci exhibit clines at a hybrid zone, with widths that correlate with phenotypic effect, showing how selection can hone gradient shape with remarkable precision by acting on cis and trans variation at multiple loci.}, author = {Bradley, Desmond and Boell, Louis and Richardson, Daniel and Copsey, Lucy and Whibley, Annabel and Xu, Ting and Zhang, Yu’E and Xue, Yongbiao and Field, David and Coen, Enrico}, issn = {2375-2548}, journal = {Science Advances}, number = {29}, pages = {1--11}, publisher = {AAAS}, title = {{Shaping of developmental gradients through selection on multiple loci in Antirrhinum}}, doi = {10.1126/sciadv.adx2011}, volume = {12}, year = {2026}, } @article{22619, abstract = {Planar germanium is currently the only semiconducting platform where high-coherence spin qubits and proximity-induced superconductivity have each been demonstrated. Recent research into spin qubits in Ge/SiGe heterostructures has focused on increasing the thickness of the SiGe capping layer, reporting improvements in the electrostatic noise levels. Meanwhile, heterostructures with thinner capping layers remain rather unexplored, despite the potential advantages for proximity-induced superconductivity. Here, we study a Ge/SiGe heterostructure with a thin SiGe cap d - 4nm and investigate its viability to host low-noise quantum dots. To keep the thermal budget compatible with superconducting layers, low-temperature oxide deposition processes were developed and implemented for the gate dielectrics. The charge noise level of the fabricated devices is estimated to be 1.8  +- 1.0 μeV/ square HZ⁠, comparable to devices fabricated on shallow heterostructures (⁠ d - 20nm⁠) with high-temperature deposited oxides. Low charge noise levels, together with the straightforward integration of superconductors, make this heterostructure an attractive platform for prototyping hybrid semiconducting–superconducting devices.}, author = {Borovkov, Maksim and Schell, Yona A and Sokolova, Dina and Roux, Kevin Etienne Robert and Falthansl-Scheinecker, Paul and Fabris, Giorgio and Shah, Devashish C and Saez Mollejo, Jaime and Previdi, Rodolfo and Taha, Inas and Genç, Aziz and Arbiol, Jordi and Calcaterra, Stefano and Oliveira, Afonso De Cerdeira and Chrastina, Daniel and Isella, Giovanni and Bubis, Anton and Katsaros, Georgios}, issn = {1077-3118}, journal = {Applied Physics Letters}, number = {3}, publisher = {AIP Publishing}, title = {{Low-noise quantum dots in ultra-shallow Ge/SiGe heterostructures for prototyping hybrid semiconducting–superconducting devices}}, doi = {10.1063/5.0333142}, volume = {129}, year = {2026}, } @article{22618, abstract = {We use a function field version of the circle method to prove that a positive proportion of elements in 𝔽𝑞⁡[𝑡] are representable as a sum of three cubes of minimal degree from 𝔽𝑞⁡[𝑡], assuming a suitable form of the Ratios Conjecture and that char⁡(𝔽𝑞) >3. The analogue of this conjecture for quadratic Dirichlet L-functions is known for large fixed q, via recent developments in homological stability.}, author = {Browning, Timothy D and Glas, Jakob and Wang, Victor}, issn = {2050-5094}, journal = {Forum of Mathematics Sigma}, publisher = {Cambridge University Press}, title = {{Sums of three cubes over a function field}}, doi = {10.1017/fms.2026.10259}, volume = {14}, year = {2026}, } @misc{22242, abstract = {This deposit contains the data and analysis code accompanying the publication "Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting–Superconducting Devices" (Borovkov et al.). The deposit includes the raw transport and current-noise measurements of three gate-defined quantum-dot devices as QCodes SQLite databases, the master table of the charge-noise (flank-method) analysis with the pointers linking every analyzed PSD trace to the raw data, the toy-model noise simulation datasets behind the supplementary figures, the archived analysis figures (PSD fits and lever-arm extractions), and the Python code reproducing the full analysis and all figures. The code is also maintained at https://github.com/ISTA-Nanoelectronics/noise_paper_public; instructions are provided in the README files.}, author = {Borovkov, Maksim}, publisher = {Institute of Science and Technology Austria}, title = {{Low-Noise Quantum Dots in Ultra-Shallow Ge/SiGe Heterostructures for Prototyping Hybrid Semiconducting-Superconducting Devices}}, doi = {10.15479/AT-ISTA-22242}, year = {2026}, } @article{22645, abstract = {Nanocrystal superlattices are commonly formed by changing concentration, solvent conditions, or particle surface chemistry. Although effective, these approaches alter multiple contributions to the interparticle potential simultaneously, making it difficult to isolate the interactions responsible for ordering or to control assembly in chemically complex environments. Here, we show that oligomeric species present in a nanocrystal reaction medium drive superlattice formation through a depletion mechanism. Using PbTe nanocrystals as a model system, we identify Pb–oleate oligomers in the crude reaction mixture, characterize their solution structure, and quantify their contribution to the interparticle potential, establishing depletion as the dominant short-range interaction governing spontaneous body-centered cubic superlattice formation. We then confirm the depletion origin of ordering by showing that varying depletant concentration predictably shifts the order–disorder boundary and produces a thermally reversible transition between dispersed and ordered states ─ behavior that is inconsistent with van der Waals or ligand-mediated mechanisms but is a direct consequence of depletion control. Having established and validated the mechanism, we demonstrate that the same depletion framework can be deliberately activated in purified dispersions and transferred across nanocrystal systems of different composition and shape, including anisotropic and binary assemblies. These results establish precursor-derived depletion as a general and chemically grounded mechanism for nanocrystal superlattice formation, and show that collective ordering can be programmed through the surrounding medium rather than through particle surface modification.}, author = {Lee, Seungho and Balazs, Daniel and Rayaroth Puthiyaveettil, Aiswarya and Horta, Sharona and Goodrich, Carl Peter and Engel, Michael and Cherniukh, Ihor and Ibáñez, Maria}, issn = {1520-5126}, journal = {Journal of the AmericanChemical Society}, number = {29}, pages = {31245--31252}, publisher = {American Chemical Society}, title = {{Reaction medium asan architect of nanocrystal superlattices}}, doi = {10.1021/jacs.6c07859}, volume = {148}, year = {2026}, } @article{22642, abstract = {Continuously operating atom-light interfaces represent a key prerequisite for steady-state quantum sensors and efficient quantum processors. Here, we demonstrate continuous accumulation of sub-Doppler-cooled atoms in a shallow intracavity dipole trap, realizing this regime. The key ingredient is a light-shift manipulation that creates spatially varying cooling parameters, enabling efficient capture and accumulation of atoms within a cavity mode. Demonstrated with rubidium atoms, a continuous flux from a source cell is funneled through the magneto-optical trap into the cavity mode, where the atoms are cooled and maintained below 10µK in steady state without time-sequenced operation. We characterize the resulting continuously maintained ensemble of millions of atoms and its collective coupling to the cavity field, establishing a route toward continuously operated cavity-QED systems and long-duration atomic and hybrid quantum sensors.}, author = {Gheorghita, Edward-Fulbright and Wald, Sebastian and Pupić, Andrea and Hosten, Onur}, issn = {2469-9934}, journal = {Physical Review A}, number = {2}, publisher = {American Physical Society}, title = {{Continuous accumulation of cold atoms in an optical cavity}}, doi = {10.1103/71f2-sq4p}, volume = {114}, year = {2026}, } @article{22647, abstract = {Within the plant endomembrane system, the vesicle coat protein clathrin localizes to the plasma membrane (PM) and the trans-Golgi Network/early endosome (TGN/EE). While the role of clathrin in endocytosis at the PM is well established, its function at TGN/EE, presumably in late secretion (trafficking from the TGN/EE to the cell surface) or en route to the vacuole, is debated. Similarly debated are potential homeostatic mechanisms balancing the trafficking routes, especially endocytosis and late secretion. We address these questions in Arabidopsis thaliana using conditional silencing of CLATHRIN HEAVY CHAIN (CHC), conditional overexpression of the clathrin uncoating factor AUXILIN-LIKE1, and secretory mutants. CHC silencing interferes with trafficking of cargoes destined for the apoplast and the PM, supporting a function of clathrin in late secretion. The secretory cargoes become abnormally rerouted from the TGN/EE to the vacuole. Unlike CHC silencing, overexpression of AUXILIN-LIKE1 selectively inhibits clathrin-mediated endocytosis while secretion continues normally at early points of induction. Conversely, secretory mutants exhibit a reduced PM recruitment of clathrin, and variably, of the TPLATE endocytic component. Together, our data show a role of clathrin in secretion and suggest secretion as a fundamental trafficking process to which endocytosis is adjusted by a weak homeostatic mechanism.}, author = {Adamowski, Maciek and Gackowski, Adam and Matijevic, Ivana and Alotaibi, Saqer S. and Friml, Jiří}, issn = {1469-8137}, journal = {New Phytologist}, publisher = {Wiley}, title = {{The role of clathrin in post‐Golgi secretion in plant cells}}, doi = {10.1111/nph.71454}, year = {2026}, } @article{22639, abstract = {We present an abstract Dyson expansion for perturbations that are merely relatively form-bounded, and apply it to the polaron problem. For a large class of polaron-type models, including the Fröhlich and Nelson models, we prove that the vacuum expectation value of the heat semi-group is a completely monotone function of the square of the total momentum. Consequently, the ground-state energy is a concave function of the square of the momentum, a result recently proved for the Fröhlich model in [14] using a probabilistic approach via Wiener integrals.}, author = {Desio, Davide and Seiringer, Robert}, issn = {1573-0530}, journal = {Letters in Mathematical Physics}, number = {4}, publisher = {Springer Nature}, title = {{Dyson expansion for form-bounded perturbations and applications to the polaron problem}}, doi = {10.1007/s11005-026-02107-2}, volume = {116}, year = {2026}, } @article{22638, abstract = {The one-bond proton-carbon coupling constant (1JCH) is an insightful probe of carbohydrate configuration. Equatorial and axial protons at the C1 position typically exhibit distinct 1JCH values, enabling NMR measurements to distinguish α- and β-configurations in carbohydrates. In principle, such measurements could provide insights into carbohydrates in the cell walls of intact microbes. However, traditionally, these measurements are performed by solution NMR with carbohydrates that were extracted, solubilized and fractionated, leaving the biological relevance of the measurements uncertain. Here, we demonstrate that 1H-detected solid-state NMR with fast magic-angle spinning allows quantitative measurements of 1JCH couplings for mobile capsular polysaccharides, directly on submilligram amounts of pathogenic cells. Our approach is demonstrated on intact cells of the pathogenic yeast Cryptococcus neoformans. High-resolution proton-detected spectra enabled the determination of coupling constants for five mobile polysaccharide units of the cryptococcal capsule, revealing their native configurations and confirming previous solution NMR-based anomeric configuration assignments.}, author = {Lends, Alons and Lamon, Gaelle and Vallet, Alicia and Grélard, Axelle and Morvan, Estelle and Aimanianda, Vishukumar and Schanda, Paul and Loquet, Antoine}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {27}, pages = {28037--28042}, publisher = {American Chemical Society}, title = {{On-cell detection of polysaccharide one-bond1Jch couplings by proton-detected solid-state NMR}}, doi = {10.1021/jacs.6c06064}, volume = {148}, year = {2026}, } @article{22644, abstract = {We analyze the average behavior of various arithmetic functions at the values of degree 𝑑 binary forms ordered by height, with probability 1. This approach yields averaged versions of the Chowla conjecture and the Bateman–Horn conjecture for random binary forms. Furthermore, we show that the rational Hasse principle holds for almost all Châtelet varieties defined by a fixed norm form of degree 𝑒 and by varying binary forms of fixed degree 𝑑, provided 𝑒 divides 𝑑. This proves an average version of a conjecture of Colliot-Thélène.}, author = {Diao, Yijie}, issn = {1469-509X}, journal = {Glasgow Mathematical Journal}, pages = {1--34}, publisher = {Cambridge University Press}, title = {{Liouville function, von Mangoldt function, and norm forms at random binary forms}}, doi = {10.1017/s0017089526101074}, year = {2026}, } @article{21923, abstract = {The appearance of simulated natural phenomena heavily depends on the way surfaces are textured. However, applying texture maps to dynamic deformable surfaces presents a significant challenge, due to ever-shifting differences in length scales involved. When these surfaces move and advect the texture along with them, their final appearance degrades as deformed regions dramatically distort their texture map. Modifications to the texture directly at the pixel level in response to the deformation may introduce ghosting artifacts and look unnatural. In the real world, the appearance of surface details on a deforming material changes through the interplay of physical processes such as rupturing, exposure of internal structure, or wrinkling. Motivated by these behaviors, in this work we explore how physical principles can guide the texturing methods based on the measure of surface deformation. We present two novel wave-based procedural texturing algorithms which reproduce common physical properties like advection and self-similarity, enabling the plausible animation of deforming objects with extreme texture map distortions. Our algorithms are fully procedural, require no actual physics simulation, and store no state or history of deformation besides the input UV map, making them highly parallelizable on the GPU and efficient enough for real-time applications. We show the versatility of the method by animating physical phenomena with extreme deformations such as flowing lava, stretching putty and outpouring sludge.}, author = {Kalinov, Aleksei and Ly, Mickaël and Hafner, Christian and Wojtan, Christopher J}, issn = {0730-0301}, journal = {ACM Transactions on Graphics}, keywords = {Procedural animation}, location = {Los Angeles, CA, United States}, number = {4}, publisher = {Association for Computing Machinery}, title = {{Physics-inspired procedural texturing of extremely deformable surfaces}}, doi = {10.1145/3811353}, volume = {45}, year = {2026}, } @article{22363, abstract = {Eukaryotic gene regulation relies on stochastic yet controlled promoter switching, in which genes transition between transcriptionally active and inactive states. Despite the molecular complexity of this process, recent studies have revealed a surprising invariance of the “switching correlation time” (TC)—the characteristic decay time of the autocorrelation function of promoter activity fluctuations—across gene expression levels in multiple genes and organisms. A biophysically plausible explanation for this invariance has so far been lacking. Here, we show that this empirical constraint imposes stringent requirements on minimal yet realistic models of transcriptional regulation. Specifically, reproducing TC–invariance requires regulatory architectures with at least four internal states and nonequilibrium dynamics that break detailed balance. Using Bayesian inference on Drosophila gap gene expression data, we demonstrate that such models i) quantitatively reproduce the observed TC–invariance, ii) remain robust to parameter perturbations, and iii) maximize information transmission from transcription factor concentration to gene expression. Remarkably, the TC-invariant modulation strategy we identify as optimal closely parallels contemporary control-theoretic results on the modulation of stochastic switching systems. Taken together, our results suggest that eukaryotic transcriptional regulation operates in a nonequilibrium regime to balance precision, reaction-rate limitations, and energy dissipation, thereby achieving near-optimal information transmission under fundamental physical constraints.}, author = {Zoller, Benjamin and Benichou, Alexis and Gregor, Thomas and Tkačik, Gašper}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {28}, publisher = {National Academy of Sciences}, title = {{Invariant nonequilibrium dynamics in gene regulation optimize information flow}}, doi = {10.1073/pnas.2524855123}, volume = {123}, year = {2026}, } @article{22295, abstract = {Despite the functional diversity of over 100 causal genes1,2,3, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD.}, author = {Schwarz, Lena A and Dotter, Christoph and Isaev, Sergey and Lisi, Michela and Malzl, Daniel and Büschl, Christoph and Ladstätter, Sabrina and Oliveira, Bárbara and Barel, Matteo and Basilico, Bernadette and Chintaluri, Chaitanya and Gorkiewicz, Sarah and Goudarzi, Mohammad and Belinova, Tereza and Reichl, Stephan and Sendžikaitė, Gintarė and Arcot Jayaram, Satish and Koppensteiner, Peter and Sommer, Christoph M and Vogels, Tim P and Menche, Jörg and Adameyko, Igor and Kharchenko, Peter Vasili and Bock, Christoph and Novarino, Gaia}, issn = {1476-4687}, journal = {Nature}, publisher = {Springer Nature}, title = {{Cortical development dynamics across autism spectrum disorder mouse models}}, doi = {10.1038/s41586-026-10679-1}, year = {2026}, } @article{22268, abstract = {AlphaFold3 predicts highly accurate protein structures from sequence but tends to collapse to a single dominant conformation, even when the underlying structure is inherently heterogeneous. Moreover, its predictions are oblivious to experimental conditions that can alter local sequence conformation. In this work, we show that AlphaFold3 can be guided to match data obtained by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and cryogenic electron microscopy (cryo-EM) experiments and combinations thereof. Our approach can also incorporate data that explicitly report on dynamics, such as site-resolved order parameters. We demonstrate that this methodology generates compact structural ensembles whose ensemble-averaged observables agree with experiment, with fewer distance restraint violations than traditionally resolved NMR structures and with unmodeled alternate conformations uncovered in electron density. This methodology paves the way for experimentally aware predictive models that generate structural ensembles consistent with the measurements, potentially over multiple modalities, and that can be further refined toward thermodynamically grounded ensembles by incorporating energetics.}, author = {Maddipatla, Sai A and Sellam, Nadav E and Bojan, Meital I and Masalitin, Vova and Vedula, Sanketh and Schanda, Paul and Marx, Ailie and Bronstein, Alexander}, issn = {1546-1696}, journal = {Nature Biotechnology}, publisher = {Springer Nature}, title = {{Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles}}, doi = {10.1038/s41587-026-03166-5}, year = {2026}, } @phdthesis{22334, abstract = {Characterizing protein dynamics at the atomic level is essential for our understanding of biological mechanisms. Whether it is to facilitate metabolite transport, catalyze reactions, transmit signals, or regulate metabolism – proteins are constantly in motion and sample multiple conformational states to fulfill their function. Nuclear magnetic resonance (NMR) spectroscopy is particularly well suited to elucidate the dynamics of biomolecules on their complex free-energy landscape. In particular, solid-state magic-angle spinning (MAS) NMR enables the study of large molecular assemblies, protein crystals, or insoluble proteins at atomic resolution without an inherent molecular size limitation. MAS NMR experiments to probe protein dynamics are extremely versatile and sensitive to motional timescales from picoseconds to seconds. Over the past decades, technological advances, developments in experimental design, and new isotope-labeling approaches have further expanded the possibilities of this technique and significantly improved the accuracy of the determined motional parameters. Functionally important sites of proteins often contain aromatic residues. Their side-chain motions have therefore long served as valuable indicators of mechanistically relevant dynamics in NMR studies. In this thesis, site-specifically labeled aromatic residues act as sensitive reporters for MAS NMR studies of protein dynamics. The first part addresses how different environments impact side-chain motion by probing ring flips of phenylalanines and tyrosines in crystalline proteins and amyloid fibrils. It provides important insights for the analysis of dynamics obtained in non-native protein environments and emphasizes the complex factors that determine the timescale of internal dynamics. In the second part, the focus shifts towards methodological questions regarding the investigation of protein dynamics by 19F MAS NMR. The fluorine nucleus exhibits promising characteristics for NMR studies but also presents significant challenges, which is why the full methodological potential of 19F MAS NMR has not been fully realized yet. This work demonstrates that paramagnetic doping can considerably reduce the measurement time and improve the sensitivity of fluorinated samples. Finally, 19F MAS NMR is evaluated as a tool for studying protein side-chain dynamics on the example of tryptophans. The results illustrate the challenges in analyzing such experiments and lay the foundation for further development of 19F MAS NMR relaxation studies. Taken together, this thesis highlights the potential of combining specific isotope labeling, MAS NMR, and complementary methods such as crystallography and computational simulations to elucidate internal protein dynamics. The further development of such integrative approaches will be crucial to improving our understanding of complex mechanisms and protein function. }, author = {Becker, Lea Marie}, isbn = {978-3-99078-084-8}, issn = {2663-337X}, pages = {205}, publisher = {Institute of Science and Technology Austria}, title = {{Exploring protein dynamics using specific labeling approaches for solid-state MAS NMR}}, doi = {10.15479/AT-ISTA-22334}, year = {2026}, }