@article{22406, abstract = {It is known that for a uniform morphic sequence š’– =āŸØš‘¢š‘›āŸ©āˆž š‘›=0 and an algebraic number š›½ such that |š›½| >1, the number [[š’–]]š›½ :=āˆ‘āˆž š‘›=0(š‘¢š‘›/š›½š‘›) either lies in ā„šā”(š›½) or is transcendental. In this paper, we show a similar rationalā€“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 [[š’–]]š›½ outright. In particular, for š‘˜ ā‰„2, if š’– is the k-Bonacci word, then [[š’–]]š›½ 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, Cobhamā€™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{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 1.8ā€‰ +-ā€‰1.0ā€‰Ī¼eV/ square HZā , comparable to devices fabricated on shallow heterostructures (ā  d - 20nmā ) 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 semiconductingā€“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 GenƧ, 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 semiconductingā€“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 š”½š‘žā”[š‘”] are representable as a sum of three cubes of minimal degree from š”½š‘žā”[š‘”], assuming a suitable form of the Ratios Conjecture and that charā”(š”½š‘ž) >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 Semiconductingā€“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 Pbā€“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 orderā€“disorder boundary and produces a thermally reversible transition between dispersed and ordered states ā”€ 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 IbƔƱez, 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 10ĀµK 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, JiÅ™Ć­}, issn = {1469-8137}, journal = {New Phytologist}, publisher = {Wiley}, title = {{The role of clathrin in postā€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 Frƶhlich 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 Frƶhlich 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{22644, abstract = {We analyze the average behavior of various arithmetic functions at the values of degree š‘‘ binary forms ordered by height, with probability 1. This approach yields averaged versions of the Chowla conjecture and the Batemanā€“Horn conjecture for random binary forms. Furthermore, we show that the rational Hasse principle holds for almost all ChĆ¢telet varieties defined by a fixed norm form of degree š‘’ and by varying binary forms of fixed degree š‘‘, provided š‘’ divides š‘‘. This proves an average version of a conjecture of Colliot-ThĆ©lĆØne.}, 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, MickaĆ«l 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{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 BĆ¼schl, Christoph and LadstƤtter, Sabrina and Oliveira, BĆ”rbara 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, Jƶrg 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 ā€“ 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}, } @misc{21145, 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 and Chipot, Christophe}, publisher = {Institute of Science and Technology Austria}, title = {{Additional Data for "Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes"}}, doi = {10.15479/AT-ISTA-21145}, year = {2026}, } @article{22663, abstract = {The detection of strong, large-scale magnetic fields at the surfaces of the oldest white dwarfs might point toward a hidden internal magnetic field slowly rising to the surface. In addition, strong magnetic fields have recently been measured through asteroseismology in the radiative interiors of red giant stars, the progenitors of white dwarfs. To investigate the potential connection between these observations, we revisited the fossil field framework using asteroseismic detections to constrain the strength of such magnetic fields as red giants evolve into the white dwarf stage. We assumed that the magnetic field was either created during the core convection on the main sequence or that it fills the radiative interior as the star evolves on the red giant branch. From these initial conditions, we evolved the magnetic flux, allowing for magnetic diffusion along the evolution of a modeled 1.5 MāŠ™ star. We find that measured field strengths in red giants attributed to the hydrogen-burning shell are compatible with the field amplitudes and emergence timescales of magnetized white dwarfs. On the contrary, magnetic fields generated solely from a convective-core dynamo on the main sequence and detectable on the red giant branch would be buried too deep in the star and would not match the breakout timescales or the field strengths of magnetic white dwarfs. Therefore, for us to connect magnetic fields observed along the late evolution of stars via a fossil field we would need to find a broadly magnetized internal radiative zone on the red giant branch.}, author = {Einramhof, Lukas and Bugnet, Lisa Annabelle and Calcaferro, L. M. and Barrault, Lucas and Das, S. B.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{Magneto-archeology of white dwarfs}}, doi = {10.1051/0004-6361/202659069}, volume = {708}, year = {2026}, } @phdthesis{22626, author = {Fiedler, Christine}, isbn = {978-3-99078-086-2}, issn = {2663-337X}, pages = {141}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanistic insight into solution-processed p-type tin chalcogenides as a basis for designing their n-type analogs}}, doi = {10.15479/AT-ISTA-22626}, year = {2026}, } @inproceedings{22299, abstract = {The depth poset of a filtered Lefschetz complex reflects the dependencies between the cancellations of different shallow birth-death pairs. Using the fast algorithms for computing the depth poset in [Edelsbrunner et al., 2026] and for updating the persistence diagram under transpositions in [Cohen-Steiner et al., 2006], we give a complete case analysis of how transpositions of cells in the filter affect the depth poset. In addition, we present statistics on the depth poset for random point data and its sensitivity to the transpositions that occur in random straight-line homotopies.}, author = {Edelsbrunner, Herbert and Lipiński, Michał and Mrozek, Marian and Soriano Trigueros, Manuel and Zimin, Fedor}, booktitle = {42nd International Symposium on Computational Geometry}, isbn = {9783959774185}, issn = {1868-8969}, keywords = {Algebraic topology, Lefschetz complexes, persistent homology, vines and vineyards, birth-death pairs, shallow pairs, relations, partial orders, transpositions, Theory of computation ā†’ Computational geometry}, location = {New Brunswick, NJ, United States}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum fĆ¼r Informatik}, title = {{The depth poset under transpositions in the filter}}, doi = {10.4230/LIPICS.SOCG.2026.41}, volume = {367}, year = {2026}, } @inproceedings{22717, abstract = {We study concurrent graph games where n players cooperate against an opponent to reach a set of target states. Unlike traditional settings, we study distributed randomisation: team players do not share a source of randomness, and their private random sources are hidden from the opponent and from each other. We show that memoryless strategies are sufficient for the threshold problem (deciding whether there is a strategy for the team that ensures winning with probability that exceeds a threshold), a result that not only places the problem in the Existential Theory of the Reals (ER) but also enables the construction of value iteration algorithms. We additionally show that the threshold problem is NP-hard. For the almost-sure reachability problem, we prove NP-completeness. We introduce Individually Randomised Alternating-time Temporal Logic (IRATL). This logic extends the standard ATL framework to reason about probability thresholds, with semantics explicitly designed for coalitions that lack a shared source of randomness. On the practical side, we implement and evaluate a solver for the threshold and almost-sure problem based on the algorithms that we develop.}, author = {Brice, Leonard J and Henzinger, Thomas A and Montaseri, Alipasha and Shafiee, Ali and Thejaswini, K. S.}, booktitle = {38th International Conference on Computer Aided Verification}, isbn = {9783032325181}, issn = {1611-3349}, location = {Lisbon, Portugal}, pages = {215--236}, publisher = {Springer Nature}, title = {{Randomise alone, reach asĀ aĀ team}}, doi = {10.1007/978-3-032-32519-8_12}, volume = {16682}, year = {2026}, } @inproceedings{22722, abstract = {The local structure of a protein strongly impacts its function and interactions with other molecules. Representing local biomolecular environments remains a key challenge while applying machine learning approaches over protein structures. The structural and chemical variability of these environments makes them challenging to model, and performing representation learning on these objects remains largely under-explored. In this work, we propose representations for local protein environments that leverage intermediate features from machine learning force fields (MLFFs). We extensively benchmark state-of-the-art MLFFs, comparing their performance across latent spaces and downstream tasks, and show that their embeddings capture local structural (e.g., secondary motifs) and chemical features (e.g., amino acid identity and protonation state), organizing protein environments into a structured manifold. We show that these representations enable zero-shot generalization and transfer across diverse downstream tasks. As a case study, we build a physics-informed, uncertainty-aware chemical shift predictor that achieves state-of-the-art accuracy in biomolecular NMR spectroscopy. Our results establish MLFFs as general-purpose, reusable representation learners for protein modeling, opening new directions in representation learning for structured physical systems. Code and data are available at https://github.com/mb012/MLFF_representation. }, author = {Bojan, Meital I and Vedula, Sanketh and Maddipatla, Sai A and Sellam, Nadav E and Rzayev, Anar and Napoli, Federico and Schanda, Paul and Bronstein, Alexander}, booktitle = {14th International Conference on Learning Representations}, location = {Rio de Janeiro, Brazil}, pages = {100760--100799}, title = {{Representing local protein environments with machine learning force fields}}, volume = {2026}, year = {2026}, } @article{22720, abstract = {Circadian clocks underlie daily rhythms in physiology by coordinating temporal patterns of gene expression and protein function throughout the body. At the core of this system in mammals is CLOCK/BMAL1, a ubiquitously expressed heterodimeric transcription factor complex that orchestrates tissue-specific circadian gene expression. The basis for this specificity remains unclear, but tissue-specific interactions at chromatin could provide one. Here we used chromatin immunoprecipitation coupled to mass spectrometry to map CLOCK/BMAL1-associated protein complexes on chromatin in mouse liver, kidney and lung. We detected 1,510 associated proteins, most of which were tissue-specific and not explained by protein abundance. Among these, we identified the homeodomain transcription factors PROX1, HNF1B and HOXA5 as tissue-enriched interactors that bind BMAL1, co-occupy most BMAL1 genomic sites and establish organ-restricted circadian transcription. Our findings demonstrate that tissue-specific transcription factors confer cellular identity on the core clock, thereby contributing to organ-specific patterns of rhythmic gene expression.}, author = {Aygenli, Fatih and Huschet, Lukas A. and Popp, Tanja and Ribeiro, Andrea and Barkhatova, Darina and Jouffe, CĆ©line and Trozzo, Ricardo and Menet, Jerome S. and Rad, Roland and Dyar, Kenneth A. and Lech, Maciej and Straub, Tobias and Michael, Alicia and Robles, Maria S.}, issn = {1476-4679}, journal = {Nature Cell Biology}, publisher = {Springer Nature}, title = {{CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators}}, doi = {10.1038/s41556-026-02041-4}, year = {2026}, }