@article{21370, abstract = {Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning (ML) are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap encompasses key aspects of how ML is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of ML for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.}, author = {Volpe, Giovanni and Wählby, Carolina and Tian, Lei and Hecht, Michael and Yakimovich, Artur and Monakhova, Kristina and Waller, Laura and Sbalzarini, Ivo F. and Metzler, Christopher A. and Xie, Mingyang and Zhang, Kevin and Lenton, Isaac C and Rubinsztein-Dunlop, Halina and Brunner, Daniel and Bai, Bijie and Ozcan, Aydogan and Midtvedt, Daniel and Wang, Hao and Li, Tongyu and Sladoje, Nataša and Lindblad, Joakim and Smith, Jason T. and Ochoa, Marien and Barroso, Margarida and Intes, Xavier and Qiu, Tong and Yu, Li Yu and You, Sixian and Liu, Yongtao and Ziatdinov, Maxim A. and Kalinin, Sergei V. and Sheridan, Arlo and Manor, Uri and Nehme, Elias and Goldenberg, Ofri and Shechtman, Yoav and Moberg, Henrik K. and Langhammer, Christoph and Špačková, Barbora and Helgadottir, Saga and Midtvedt, Benjamin and Argun, Aykut and Thalheim, Tobias and Cichos, Frank and Bo, Stefano and Hubatsch, Lars and Pineda, Jesus and Manzo, Carlo and Bachimanchi, Harshith and Selander, Erik and Homs-Corbera, Antoni and Fränzl, Martin and De Haan, Kevin and Rivenson, Yair and Korczak, Zofia and Adiels, Caroline Beck and Mijalkov, Mite and Veréb, Dániel and Chang, Yu Wei and Pereira, Joana B. and Matuszewski, Damian and Kylberg, Gustaf and Sintorn, Ida Maria and Caicedo, Juan C. and Cimini, Beth A. and Lediju Bell, Muyinatu A. and Saraiva, Bruno M. and Jacquemet, Guillaume and Henriques, Ricardo and Ouyang, Wei and Le, Trang and Gómez-De-Mariscal, Estibaliz and Sage, Daniel and Muñoz-Barrutia, Arrate and Lindqvist, Ebba Josefson and Bergman, Johanna}, issn = {2515-7647}, journal = {Journal of Physics: Photonics}, number = {1}, publisher = {IOP Publishing}, title = {{Roadmap on deep learning for microscopy}}, doi = {10.1088/2515-7647/ae0fd1}, volume = {8}, year = {2026}, } @article{21470, abstract = {Despite its pivotal role in optical manipulation, high capacity communications, and quantum information, a general measure of orbital angular momentum (OAM) in structured light remains elusive. In optical fields, where multiple vortices coexist, the local nature of vortex OAM and the absence of a common rotation axis make the total OAM of the field difficult to quantify. Here, we introduce the R index—a metric that captures the intrinsic OAM content of any structured optical field, from pure Laguerre–Gaussian modes to arbitrary multi vortex superpositions. Not only does this metric quantify the total OAM, it also assesses field purity, providing insight into the fidelity and robustness of the OAM generation. By unifying OAM characterization into a single figure of merit, the R index enables direct comparison across diverse beam profiles and facilitates the identification of optimal configurations for both foundational studies and applied technologies.}, author = {Bahl, Monika and Koutentakis, Georgios and Maslov, Mikhail and Jungnickel, Tom and Gaßen, Timo and Lemeshko, Mikhail and Heckl, Oliver H.}, issn = {2515-7647}, journal = {Journal of Physics: Photonics}, number = {1}, publisher = {IOP Publishing}, title = {{The R-index: A universal metric for evaluating OAM content and mode purity in optical fields}}, doi = {10.1088/2515-7647/ae3506}, volume = {8}, year = {2026}, } @article{21469, abstract = {Terahertz (THz) spectroscopy is a powerful probe of low-energy excitations in complex materials. Extending it into the nonlinear regime broadens its scope and can provide valuable insight into interactions among these modes. However, interpreting nonlinear spectra is challenging because resonant features in this case do not always reflect intrinsic material dynamics. Here, we study nonlinear THz-induced Kerr effect in a generic material LaAlO3. After detailed analysis of temporal oscillations of the Kerr signal, we identify an 𝐸𝑔 Raman mode at 1.1 THz excited through a two-photon process, while two additional peaks (0.86 and 0.36 THz) arise from phase matching of the near-infrared probe beam with co- and counterpropagating THz pump fields, mediated by off-resonant electronic hyperpolarizability. These results demonstrate the crucial role of kinematic effects in shaping THz-induced Kerr response and establish a framework for interpreting nonlinear spectroscopies in complex materials.}, author = {Shen, Chao and Frenzel, Maximilian and Maehrlein, Sebastian F. and Alpichshev, Zhanybek}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {10}, publisher = {American Physical Society}, title = {{Disentangling electronic and ionic nonlinear polarization effects in bulk THz Kerr response}}, doi = {10.1103/1c5k-9z82}, volume = {136}, year = {2026}, } @article{21472, abstract = {We study the ground state energy of a gas of spin 1/2 fermions with repulsive short-range interactions. We derive an upper bound that agrees, at low density e, with the Huang–Yang conjecture. The latter captures the first three terms in an asymptotic low-density expansion, and in particular the Huang–Yang correction term of order e^7/3. Our trial state is constructed using an adaptation of the bosonic Bogoliubov theory to the Fermi system, where the correlation structure of fermionic particles is incorporated by quasi-bosonic Bogoliubov transformations. In the latter, it is important to consider a modified zero-energy scattering equation that takes into account the presence of the Fermi sea, in the spirit of the Bethe–Goldstone equation.}, author = {Giacomelli, Emanuela L. and Hainzl, Christian and Nam, Phan Thành and Seiringer, Robert}, issn = {1097-0312}, journal = {Communications on Pure and Applied Mathematics}, publisher = {Wiley}, title = {{The Huang–Yang formula for the low-density Fermi gas: Upper bound}}, doi = {10.1002/cpa.70040}, year = {2026}, } @article{21473, abstract = {Physical exercise acutely improves hippocampus-dependent memory. Whereas animal studies have offered cellular- and synaptic-level accounts of these effects, human neuroimaging studies show that exercise improves hippocampal-cortical connectivity at the macroscale level. However, the neurophysiological basis of exercise-induced effects on hippocampal-cortical circuits remains unknown. Experimental evidence supports the idea that hippocampal sharp wave-ripples (SWR) play a critical role in learning and memory. Coupling between SWRs in the hippocampus and neocortex may reflect modulations in inter-regional connectivity required by mnemonic processes. Here, we examine the hypothesis that exercise modulates hippocampal-cortical ripple dynamics in the human brain. We performed intracranial recordings in epilepsy patients undergoing pre-surgical evaluation, during awake resting state, before and after an exercise session. Exercise increased ripple rate in the hippocampus. Exercise also enhanced the coupling and phase-synchrony between cortical ripples in the limbic and the default mode (DM) cortical networks and hippocampal SWRs. Further, a higher heart rate during exercise, reflecting exercise intensity, was related to a subsequent increase in resting state ripples across specific cortical networks, including the DM network. These results offer the first direct evidence that a single exercise session elicits changes in ripple events, a well-established neurophysiological marker of mnemonic processing. The characterisation and anatomical distribution of the described modulation points to hippocampal ripples as a potential mechanism by which exercise elicits its reported short-term effects in cognition.}, author = {Cardenas, Araceli R. and Ramirez Villegas, Juan F and Kovach, Christopher K. and Gander, Phillip E. and Cole, Rachel C. and Grossbach, Andrew J. and Kawasaki, Hiroto and Greenlee, Jeremy D.W. and Howard, Matthew A. and Nourski, Kirill V. and Banks, Matthew I. and Voss, Michelle W.}, issn = {2632-1297}, journal = {Brain Communications}, number = {2}, publisher = {Oxford University Press}, title = {{Exercise enhances hippocampal-cortical ripple interactions in the human brain}}, doi = {10.1093/braincomms/fcag041}, volume = {8}, year = {2026}, } @article{21471, author = {Backlund, Sofia Maria and Stankowski, Sean and Soler Schaller, Rosina Matilde}, issn = {1537-2197}, journal = {American Journal of Botany}, number = {3}, publisher = {Wiley}, title = {{Seeds as space-time travelers: How does evolution balance the joint benefits and trade-offs of dormancy and dispersal?}}, doi = {10.1002/ajb2.70175}, volume = {113}, year = {2026}, } @article{21481, abstract = {The Hα emission line in galaxies is a powerful tracer of their recent star formation activity. With the advent of JWST, we are now able to routinely observe Hα in galaxies at high redshift (z ≳ 3) and thus measure their star formation rates (SFRs). However, using classical SFR(Hα) calibrations to derive the SFRs leads to biased results because high-redshift galaxies are commonly characterized by low metallicities and bursty star formation histories, affecting the conversion factor between the Hα luminosity (LHα) and the SFR. We developed a set of new SFR(Hα) calibrations that allowed us to predict the SFRs of Hα-emitters at z ≳ 3 with very little error. We used the SPHINX cosmological simulations to select a sample of star-forming galaxies representative of the Hα-emitter population observed with JWST. We then derived linear corrections to the classical SFR(Hα) calibrations that took variations in the physical properties (e.g., stellar metallicities) among individual galaxies into account. We obtained two new SFR(Hα) calibrations that compared to the classical calibrations reduce the root mean squared error (RMSE) in the predicted SFRs by ΔRMSE ≈ 0.04 dex and ΔRMSE ≈ 0.06 dex, respectively. Using the recent JWST NIRCam/grism observations of Hα-emitters at z ∼ 6, we show that the new calibrations affect the high-redshift galaxy population statistics: (i) the estimated cosmic SFR density decreases by ΔρSFR ≈ 12%, and (ii) the observed slope of the star formation main sequence increases by Δ∂logSFR/∂logM★ = 0.08 ± 0.02.}, author = {Kramarenko, Ivan and Rosdahl, J. and Blaizot, J. and Matthee, Jorryt J and Katz, H. and Di Cesare, Claudia}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{H α as a tracer of star formation in the SPHINX cosmological simulations}}, doi = {10.1051/0004-6361/202557114}, volume = {707}, year = {2026}, } @article{21480, abstract = {We present and test a protocol to learn the matrix-product operator (MPO) representation of an experimentally prepared quantum state. The protocol takes as input classical shadows corresponding to local randomized measurements, and outputs the tensors of an MPO maximizing a suitably defined fidelity with the experimental state. The tensor optimization is carried out sequentially, similarly to the well-known density matrix renormalization group algorithm. Our approach is provably efficient under certain technical conditions expected to be met in short-range correlated states and in typical noisy experimental settings. Under the same conditions, we also provide an efficient scheme to estimate fidelities between the learned and the experimental states. We experimentally demonstrate our protocol by learning entangled quantum states of up to N = 96 qubits in a superconducting quantum processor. Our method upgrades classical shadows to large-scale quantum computation and simulation experiments.}, author = {Votto, Matteo and Ljubotina, Marko and Lancien, Cécilia and Cirac, J. Ignacio and Zoller, Peter and Serbyn, Maksym and Piroli, Lorenzo and Vermersch, Benoît}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {9}, publisher = {American Physical Society}, title = {{Learning mixed quantum states in large-scale experiments}}, doi = {10.1103/rbg2-f61m}, volume = {136}, year = {2026}, } @article{21482, abstract = {Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly and is highly relevant in material design and biology. Here, we show that specific but promiscuous short-range binding interactions make it possible to economically assemble linear filaments of user-defined length. Our approach leads to independent control over the mean and width of the filament size distribution and allows us to smoothly explore design trade-offs between assembly quality (spread in size) and cost (number of particle species). We employ a simple hierarchical assembly protocol to minimize assembly times and show that multiple stages of hierarchy make it possible to extend our approach to the assembly of higher-dimensional structures. Our work provides a conceptually simple solution to size control that is applicable to a broad range of systems, from DNA nanoparticles to supramolecular polymers and beyond.}, author = {Hübl, Maximilian and Goodrich, Carl Peter}, issn = {2643-1564}, journal = {Physical Review Research}, publisher = {American Physical Society}, title = {{Entropic size control of self-assembled filaments}}, doi = {10.1103/68rs-3qgn}, volume = {8}, year = {2026}, } @article{21485, abstract = {Insulating oxides are among the most abundant solid materials in the universe1,2,3. Of the many ways in which they influence natural phenomena, perhaps the most consequential is their capacity to transfer electrical charge during contact4,5,6,7,8,9,10—which occurs even between samples of the same oxide—yet the symmetry-breaking parameter that causes this remains unidentified11,12. Here we show that adventitious carbonaceous molecules adsorbed from the environment are the symmetry-breaking factor in same-material oxide contact electrification (CE). We use acoustic levitation to measure charge exchange between a sphere and a plate composed of identical amorphous silicon dioxide (SiO2). Although charging polarity is random for co-prepared samples, we control it with baking or plasma treatment. Observing the charge-exchange relaxation afterwards, we see dynamics over a timescale of hours and connect this directly to the presence of adventitious carbon with time-of-flight mass spectrometry, low-energy ion scattering and infrared spectroscopy. Going further, we confirm that adventitious carbon can even determine charge exchange among different oxides. Our results identify the symmetry-breaking parameter that causes insulating oxides to exchange charge in settings ranging from desert sands4 to volcanic plumes5,6, while simultaneously highlighting an overlooked factor in CE more broadly.}, author = {Grosjean, Galien M and Ostermann, Markus and Sauer, Markus and Hahn, Michael and Pichler, Christian M. and Fahrnberger, Florian and Pertl, Felix and Balazs, Daniel and Link, Mason M. and Kim, Seong H. and Schrader, Devin L. and Blanco, Adriana and Gracia, Francisco and Mujica, Nicolás and Waitukaitis, Scott R}, issn = {1476-4687}, journal = {Nature}, number = {8106}, pages = {626--631}, publisher = {Springer Nature}, title = {{Adventitious carbon breaks symmetry in oxide contact electrification}}, doi = {10.1038/s41586-025-10088-w}, volume = {651}, year = {2026}, } @article{21490, abstract = {Auxin canalization is a self-organizing process that governs the flexible formation of vasculature by reinforcing the formation of auxin transport channels. A key prerequisite is the feedback between auxin signaling and directional auxin transport, mediated by PIN transporters. Despite the developmental importance of canalization, the molecular components linking auxin perception to the regulation of PIN auxin transporters remain poorly understood. Here, we identify TOW, a novel and essential component of auxin canalization that links intracellular auxin signaling with cell surface auxin perception. TOW is regulated downstream of TIR1/AFB-Aux/IAA-WRKY23 transcriptional auxin signaling. tow mutants exhibit defects in regeneration and de novo vasculature formation, along with impaired formation of polarized, PIN-expressing auxin channels. At the subcellular level, these mutants display disrupted auxin-induced PIN polarization and altered PIN endocytic trafficking dynamics. TOW localizes predominantly to the plasma membrane, where it interacts with receptor-like kinases involved in auxin canalization, including the TMK1 auxin co-receptor and the CAMEL-CANAR complex. TOW promotes PIN interaction with these kinases and stabilizes PINs at the cell surface. Together, our findings identify TOW as a molecular link between intracellular and cell surface auxin signaling mechanisms that converge on PIN trafficking and polarity, providing new insights into how auxin signaling regulates directional auxin transport for the self-organizing formation of vasculature during flexible plant development.}, author = {Li, Mingyue and Rydza, Nikola and Mazur, Ewa and Molnar, Gergely and Nodzyński, Tomasz and Friml, Jiří}, issn = {0960-9822}, journal = {Current Biology}, number = {6}, pages = {1468--1480.e6}, publisher = {Elsevier}, title = {{Receptor-like-kinase-interacting protein TOW stabilizes PIN transporters for auxin canalization}}, doi = {10.1016/j.cub.2026.02.023}, volume = {36}, year = {2026}, } @article{21488, abstract = {Human height is a model for the genetic analysis of complex traits, and recent studies suggest the presence of thousands of common genetic variant associations and hundreds of low-frequency/rare variants. Here, we develop a new algorithmic paradigm based on approximate message passing (genomic vector approximate message passing [gVAMP]) for identifying DNA sequence variants associated with complex traits and common diseases in large-scale whole-genome sequencing (WGS) data. We show that gVAMP accurately localizes associations to variants with the correct frequency and position in the DNA, outperforming existing fine-mapping methods in selecting the appropriate genetic variants within WGS data. We then apply gVAMP to jointly model the relationship of tens of millions of WGS variants with human height in hundreds of thousands of UK Biobank individuals. We identify 59 rare variants and gene burden scores alongside many hundreds of DNA regions containing common variant associations and show that understanding the genetic basis of complex traits will require the joint analysis of hundreds of millions of variables measured on millions of people. The polygenic risk scores obtained from gVAMP have high accuracy (including a prediction accuracy of ∼46% for human height) and outperform current methods for downstream tasks such as mixed linear model association testing across 13 UK Biobank traits. In conclusion, gVAMP offers a scalable foundation for a wider range of analyses in WGS data.}, author = {Depope, Al and Bajzik, Jakub and Mondelli, Marco and Robinson, Matthew Richard}, issn = {2666-979X}, journal = {Cell Genomics}, publisher = {Elsevier}, title = {{Joint modeling of whole-genome sequencing data for human height via approximate message passing}}, doi = {10.1016/j.xgen.2026.101162}, year = {2026}, } @article{21484, abstract = {An individual's phenotype reflects a complex interplay of the direct effects of their DNA, epigenetic modifications of their DNA induced by their parents, and indirect effects of their parents' DNA. Here, we derive how the genetic variance within a population is changed under the influence of indirect maternal, paternal and parent-of-origin effects under random mating. We also consider indirect effects of a sibling, in particular how the genetic variance is altered when looking at the phenotypic difference between two siblings. The calculations are then extended to include assortative mating (AM), which alters the variance by inducing increased homozygosity and correlations within and across loci. AM likely leads to covariance of parental genetic effects, a measure of the similarity of parents in the indirect effects they have on their children. We propose that this assortment for parental characteristics, where biological parents create similar environments for their children, can create shared parental effects across traits and the appearance of cross-trait AM. Our theory shows how the resemblance among relatives increases under both AM, indirect and parent-of-origin effects. When our model is used to predict correlations among relatives in human height, we find that explaining the patterns observed in real data requires both indirect genetic effects and assortative mating. The degree to which direct, indirect and epigenetic effects shape the phenotypic variance of complex traits remains an open question that requires large-scale family data to be resolved.}, author = {Krätschmer, Ilse and Robinson, Matthew Richard}, issn = {1943-2631}, journal = {Genetics}, publisher = {Oxford University Press}, title = {{A quantitative genetic model for indirect genetic effects and genomic imprinting under random and assortative mating}}, doi = {10.1093/genetics/iyag042}, year = {2026}, } @article{21486, abstract = {Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analyzed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find that the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on Muller element F (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.}, author = {Layana Franco, Lorena Alexandra and Toups, Melissa A and Vicoso, Beatriz}, issn = {2056-3744}, journal = {Evolution Letters}, publisher = {Oxford University Press}, title = {{Causes and consequences of sex-chromosome turnovers in Diptera}}, doi = {10.1093/evlett/qrag003}, year = {2026}, } @misc{21137, author = {Naik, Suyash}, publisher = {Institute of Science and Technology Austria}, title = {{Data associated with Keratins coordinate tissue spreading }}, doi = {10.15479/AT-ISTA-21137}, year = {2026}, } @article{21489, abstract = {We study Kirillov algebras attached to minuscule highest weight representations of semisimple Lie algebras. They can be viewed as equivariant cohomology algebras of partial flag varieties. Real structures on the varieties then induce involutions of these algebras. We describe how these involutions act on the spectra of minuscule Kirillov algebras, and model the fixed points via the equivariant cohomology of real partial flag varieties. We then use this model to characterise freeness of the fixed point coordinate ring over the appropriate base. As an application, we recover a q = -1 phenomenon of Stembridge in the minuscule case by geometric means.}, author = {Elkner, Mischa M}, issn = {1531-586X}, journal = {Transformation Groups}, publisher = {Springer Nature}, title = {{On involutions of minuscule Kirillov algebras induced by real structures}}, doi = {10.1007/s00031-026-09958-y}, year = {2026}, } @phdthesis{21393, abstract = {This thesis documents a voyage towards truth and beauty via formal verification of theorems. To this end, we develop libraries in Lean 4 that present definitions and results from diverse areas of MathematiCS (i.e., Mathematics and Computer Science). The aim is to create code that is understandable, believable, useful, and elegant. The code should stand for itself as much as possible without a need for documentation; however, this text redundantly documents our code artifacts and provides additional context that isn’t present in the code. This thesis is written for readers who know Lean 4 but are not familiar with any of the topics presented. We manifest truth and beauty in three formalized areas of MathematiCS. We formalize general grammars in Lean 4 and use grammars to show closure of the class of type-0 languages under four operations; union, reversal, concatenation, and the Kleene star. Our second stop is the theory of optimization. Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take “infinite values”. Additionally, we develop the basics of the theory of optimization in terms of the framework called General-Valued Constraint Satisfaction Problems, and we prove that, if a Rational-Valued Constraint Satisfaction Problem template has symmetric fractional polymorphisms of all arities, then its basic LP relaxation is tight. Our third stop is matroid theory. Seymour’s decomposition theorem is a hallmark result in matroid theory, presenting a structural characterization of the class of regular matroids. We aim to formally verify Seymour’s theorem in Lean 4. First, we build a library for working with totally unimodular matrices. We define binary matroids and their standard representations, and we prove that they form a matroid in the sense how Mathlib defines matroids. We define regular matroids to be matroids for which there exists a full representation rational matrix that is totally unimodular, and we prove that all regular matroids are binary. We define 1-sum, 2-sum, and 3 sum of binary matroids as specific ways to compose their standard representation matrices. We prove that the 1-sum, the 2-sum, and the 3-sum of regular matroids are a regular matroid, which concludes the composition direction of the Seymour’s theorem. The (more difficult) decomposition direction remains unproved. In the pursuit of truth, we focus on identifying the trusted code in each project and presenting it faithfully. We emphasize the readability and believability of definitions rather than choosing definitions that are easier to work with. In search for beauty, we focus on the philosophical framework of Roger Scruton, who emphasizes that beauty is not a mere decoration but, most importantly, beauty is the means for shaping our place in the world and a source of redemption, where it can be viewed as a substitute for religion.}, author = {Dvorak, Martin}, isbn = {978-3-99078-074-9}, issn = {2663-337X}, pages = {160}, publisher = {Institute of Science and Technology Austria}, title = {{Pursuit of truth and beauty in Lean 4 : Formally verified theory of grammars, optimization, matroids}}, doi = {10.15479/AT-ISTA-21393}, year = {2026}, } @article{21501, abstract = {Kinetically constrained models were originally introduced to capture slow relaxation in glassy systems, where dynamics are hindered by local constraints instead of energy barriers. Their quantum counterparts have recently drawn attention for exhibiting highly degenerate eigenstates at zero energy—known as zero modes—stemming from chiral symmetry. Yet, the structure and implications of these zero modes remain poorly understood. In this work, we focus on the properties of the zero mode subspace in quantum kinetically constrained models with a U(1) particle-conservation symmetry. We use the U(1) East, which lacks inversion symmetry, and the inversion-symmetric U(1) East-West models to illustrate our two main results. First, we observe that the simultaneous presence of constraints and chiral symmetry generally leads to a parametric increase in the number of zero modes due to the fragmentation of the many-body Hilbert space into disconnected sectors. Second, we generalize the concept of compact localized states from single-particle physics and introduce the notion of collective bound states, a special kind of nonergodic eigenstates that are robust to enlarging the system size. We formulate sufficient criteria for their existence, arguing that the degenerate zero mode subspace plays a central role, and demonstrate bound states in both example models and in a two-dimensional model, the U(1) North-East, and in the pairflip model, a system without particle conservation. Our results motivate a systematic study of bound states and their relation to ergodicity breaking, transport, and other properties of quantum kinetically constrained models. }, author = {Nicolau Jimenez, Eulalia and Ljubotina, Marko and Serbyn, Maksym}, issn = {2691-3399}, journal = {PRX Quantum}, publisher = {American Physical Society}, title = {{Fragmentation, zero modes, and collective bound states in constrained models}}, doi = {10.1103/sl79-1xgb}, volume = {7}, year = {2026}, } @article{21503, abstract = {Currently, pharmacogenetics relies on partially annotated star alleles, leaving novel variants and complex haplotypes uninterpretable. Computational scoring frameworks could overcome these limitations. Here, we comprehensively evaluated the ability of existing (CADD, FATHMM-XF, PROVEAN, MutationAssessor, SIFT, PhyloP100, APF, APF2) and novel (PharmGScore and PharmMLScore) variant effect predictors to assess pharmacogenetic alleles in multiple scenarios. Altogether we analyzed 541 PharmVar alleles, high‑throughput CYP2C9 and CYP2C19 mutational maps, and 200 642 UK Biobank exomes linked with health records containing antidepressant treatment outcomes. Many evaluated tools, especially ensemble frameworks, matched or exceeded star allele classifications (ROC‑AUC up to 0.85 for allele definitions, 0.95 in vitro; TPR up to 0.99 for exomes) and accurately predicted severe antidepressant adverse events for carriers of deleterious variants in CYP2C19 (OR 1.20–1.35). Our findings show that computational predictors deliver star allele accuracy while overcoming their limitations. With additional validation, computational tools could enhance clinical decision frameworks by enabling continuous scoring, incorporating previously unknown variants, and providing genome-wide applicability.}, author = {Hajto, Jacek and Piechota, Marcin and Krätschmer, Ilse and Konowalska, Paula and Boyle, Gabriel E. and Fowler, Douglas M. and Borczyk, Malgorzata and Korostynski, Michal}, issn = {1473-1150}, journal = {Pharmacogenomics Journal}, number = {2}, publisher = {Springer Nature}, title = {{Computational variant predictors for pharmacogenomics: From evaluation of single alleles to assessment of adverse drug reactions to antidepressants}}, doi = {10.1038/s41397-026-00399-0}, volume = {26}, year = {2026}, } @article{21509, abstract = {Chromatin remodeling complexes mobilize nucleosomes and promote transcription factor (TF) binding. Using ensemble and single-molecule assays combined with cryo-electron microscopy (cryo-EM), we studied the interaction between pioneer TFs OCT4–SOX2 and the human BRG1/BRM-associated factor (BAF) complex on nucleosomes. BAF engages TF-bound substrates in two orientations, placing OCT4–SOX2 at either the remodeler ENTRY or EXIT site. At the ENTRY site, OCT4–SOX2 initially coexists with BAF without structural interference. However, continued DNA translocation is expected to cause collisions with bound TFs, which can trigger remodeling direction reversals or may induce TF dissociation. To accommodate TFs at the EXIT site, BAF undergoes structural rearrangements, and ensemble assays reveal a nucleosome subpopulation translocating away from TF-binding sites. Moreover, single-molecule experiments show that nucleosome-bound BAF frequently changes remodeling direction, and we identify an ADP-bound remodeler conformation as a potential intermediate. Together, these findings reveal key aspects of the conformational dynamics and remodeling outcomes underlying BAF processing of TF-bound nucleosomes.}, author = {Weiss, Joscha and Vecchia, Luca and Domjan, David and Cavadini, Simone and Sabantsev, Anton and Kempf, Georg and Pathare, Ganesh R. and Brackmann, Klaus and Michael, Alicia and Kater, Lukas and Hietter-Pfeiffer, Eric and Haddawi, Mina and Kuber, Urja P. and Mühlhäusser, Sandra and Grand, Ralph S. and Stadler, Michael B. and Deindl, Sebastian and Thomä, Nicolas H.}, issn = {1097-2765}, journal = {Molecular Cell}, number = {4}, pages = {625--639.e8}, publisher = {Elsevier}, title = {{The human BAF chromatin remodeler processes nucleosomes bound by pioneer transcription factors OCT4–SOX2}}, doi = {10.1016/j.molcel.2026.01.021}, volume = {86}, year = {2026}, }