@article{18848, abstract = {Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases.}, author = {Ocampo, Rodrigo Fregoso and Bravo, Jack Peter Kelly and Dangerfield, Tyler L. and Nocedal, Isabel and Jirde, Samatar A. and Alexander, Lisa M. and Thomas, Nicole C. and Das, Anjali and Nielson, Sarah and Johnson, Kenneth A. and Brown, Christopher T. and Butterfield, Cristina N. and Goltsman, Daniela S.A. and Taylor, David W.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{DNA targeting by compact Cas9d and its resurrected ancestor}}, doi = {10.1038/s41467-024-55573-4}, volume = {16}, year = {2025}, } @article{18849, abstract = {Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks.}, author = {Sokolowski, Thomas R and Gregor, Thomas and Bialek, William and Tkačik, Gašper}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {1}, publisher = {National Academy of Sciences}, title = {{Deriving a genetic regulatory network from an optimization principle}}, doi = {10.1073/pnas.2402925121}, volume = {122}, year = {2025}, } @article{18850, abstract = {Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.}, author = {Perkins, Mindy Liu and Crocker, Justin and Tkačik, Gašper}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {1}, publisher = {National Academy of Sciences}, title = {{Chromatin enables precise and scalable gene regulation with factors of limited specificity}}, doi = {10.1073/pnas.2411887121}, volume = {122}, year = {2025}, } @article{18851, abstract = {We present volume-limited samples of cataclysmic variables (CVs) and AM CVn binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray + optical color–color diagram (the "X-ray Main Sequence"). This tool identifies all CV subtypes, including magnetic and low-accretion rate systems, in contrast to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also present CV candidates out to 300 pc and 1000 pc. We discovered two previously unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030 erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7 ± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the solar neighborhood. Our uniform selection method also allows us to place meaningful estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3. Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively. This work, through a novel discovery technique, shows that the observed number densities of CVs and AM CVns, as well as the fraction of period bouncers, are still in tension with population synthesis estimates.}, author = {Rodriguez, Antonio C. and El-Badry, Kareem and Suleimanov, Valery and Pala, Anna F. and Kulkarni, Shrinivas R. and Gaensicke, Boris and Mori, Kaya and Rich, R. Michael and Sarkar, Arnab and Bao, Tong and De Oliveira, Raimundo Lopes and Ramsay, Gavin and Szkody, Paula and Graham, Matthew and Prince, Thomas A. and Caiazzo, Ilaria and Vanderbosch, Zachary P. and Roestel, Jan Van and Das, Kaustav K. and Qin, Yu Jing and Kasliwal, Mansi M. and Wold, Avery and Groom, Steven L. and Reiley, Daniel and Riddle, Reed}, issn = {0004-6280}, journal = {Publications of the Astronomical Society of the Pacific}, number = {1}, publisher = {IOP Publishing}, title = {{Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities}}, doi = {10.1088/1538-3873/ada185}, volume = {137}, year = {2025}, } @article{18852, abstract = {Recent observations have found a growing number of hypervelocity stars with speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear supernovae in white dwarf binaries. Most of the observed hypervelocity runaways in this class display a surprising inflated structure: their current radii are roughly an order of magnitude greater than they would have been as white dwarfs filling their Roche lobe. While many simulations exist studying the dynamical phase leading to supernova detonation in these systems, no detailed calculations of the long-term structure of the runaways have yet been performed. We used an existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary as a starting point for the evolution of these stars with the one-dimensional stellar evolution code MESA. We show that the supernova shock is not energetic enough to inflate the white dwarf over timescales longer than a few thousand years, significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙ away, our models do not experience significant interior heating, and all contract back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed inflated states requires either an additional source of significant heating or some other physics that is not yet accounted for in the subsequent evolution.}, author = {Bhat, Aakash and Bauer, Evan B. and Pakmor, Rüdiger and Shen, Ken J. and Caiazzo, Ilaria and Rajamuthukumar, Abinaya Swaruba and El-Badry, Kareem and Kerzendorf, Wolfgang E.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, number = {1}, publisher = {EDP Sciences}, title = {{Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries}}, doi = {10.1051/0004-6361/202451371}, volume = {693}, year = {2025}, } @article{18853, abstract = {Electrolyte additives are extensively validated effective in mitigating dendrite growth and parasitic reactions in aqueous zinc-ion batteries (AZIBs). Nonetheless, the mechanisms by which additives influence the formation and characteristics of the inorganic solid–electrolyte interphase (SEI) are not yet fully elucidated. Herein, we investigate how Zn(CF3COO)2 additives influence solvation structure and elucidate the mechanism by which these additives promote the dual reduction of anions. Through cryo-transmission electron microscopy analysis, we identified the SEI as a highly amorphous ZnS/ZnF2 phase. This amorphous hybrid SEI demonstrates exceptional stability, mechanical robustness, and high Zn2+ conductivity, effectively mitigating parasitic reactions and enhancing Zn plating/stripping reversibility. Even under elevated current densities, the Zn anode exhibits ultra-stable longevity and ultra-high reversibility. This study provides a comprehensive understanding of the intrinsic mechanisms governing solvation structure modulation that lead to the formation of amorphous hybrid SEI, underscoring their efficacy in enhancing the performance and durability of AZIBs.}, author = {Zeng, Guifang and Sun, Qing and Horta, Sharona and Martínez-Alanis, Paulina R. and Wu, Peng and Li, Jing and Wang, Shang and Ibáñez, Maria and Tian, Yanhong and Ci, Lijie and Cabot, Andreu}, issn = {1754-5706}, journal = {Energy and Environmental Science}, number = {4}, pages = {1683--1695}, publisher = {Royal Society of Chemistry}, title = {{Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode}}, doi = {10.1039/d4ee03750b}, volume = {18}, year = {2025}, } @article{18854, abstract = {Context. One of the surprising early findings with JWST has been the discovery of a strong “roll-over” or a softening of the absorption edge of Lyα in a large number of galaxies at z ≳ 6, in addition to systematic offsets from photometric redshift estimates and fundamental galaxy scaling relations. This has been interpreted as strong cumulative damped Lyα absorption (DLA) wings from high column densities of neutral atomic hydrogen (H I), signifying major gas accretion events in the formation of these galaxies. Aims. To explore this new phenomenon systematically, we assembled the JWST/NIRSpec PRImordial gas Mass AssembLy (PRIMAL) legacy survey of 584 galaxies at z = 5.0 − 13.4, designed to study the physical properties and gas in and around galaxies during the reionization epoch. Methods. We characterized this benchmark sample in full and spectroscopically derived the galaxy redshifts, metallicities, star formation rates, and ultraviolet (UV) slopes. We defined a new diagnostic, the Lyα damping parameter DLyα, to measure and quantify the net effect of Lyα emission strength, the H I fraction in the intergalactic medium, or the local H I column density for each source. The JWST-PRIMAL survey is based on the spectroscopic DAWN JWST Archive (DJA-Spec). We describe DJA-Spec in this paper, detailing the reduction methods, the post-processing steps, and basic analysis tools. All the software, reduced spectra, and spectroscopically derived quantities and catalogs are made publicly available in dedicated repositories. Results. We find that the fraction of galaxies showing strong integrated DLAs with NHI > 1021 cm−2 only increases slightly from ≈60% at z ≈ 6 up to ≈65 − 90% at z > 8. Similarly, the prevalence and prominence of Lyα emission is found to increase with decreasing redshift, in qualitative agreement with previous observational results. Strong Lyα emitters (LAEs) are predominantly found to be associated with low-metallicity and UV faint galaxies. By contrast, strong DLAs are observed in galaxies with a variety of intrinsic physical properties, but predominantly at high redshifts and low metallicities. Conclusions. Our results indicate that strong DLAs likely reflect a particular early assembly phase of reionization-era galaxies, at which point they are largely dominated by pristine H I gas accretion. At z = 8 − 10, this gas gradually cools and forms into stars that ionize their local surroundings, forming large ionized bubbles and producing strong observed Lyα emission at z < 8.}, author = {Heintz, K. E. and Brammer, G. B. and Watson, D. and Oesch, P. A. and Keating, L. C. and Hayes, M. J. and Abdurro'Uf, Unknown and Arellano-Córdova, K. Z. and Carnall, A. C. and Christiansen, C. R. and Cullen, F. and Davé, R. and Dayal, P. and Ferrara, A. and Finlator, K. and Fynbo, J. P.U. and Flury, S. R. and Gelli, V. and Gillman, S. and Gottumukkala, R. and Gould, K. and Greve, T. R. and Hardin, S. E. and Hsiao, T. Y.Y. and Hutter, A. and Jakobsson, P. and Killi, M. and Khosravaninezhad, N. and Laursen, P. and Lee, M. M. and Magdis, G. E. and Matthee, Jorryt J and Naidu, R. P. and Narayanan, D. and Pollock, C. and Prescott, M. K.M. and Rusakov, V. and Shuntov, M. and Sneppen, A. and Smit, R. and Tanvir, N. R. and Terp, C. and Toft, S. and Valentino, F. and Vijayan, A. P. and Weaver, J. R. and Wise, J. H. and Witstok, J.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4}}, doi = {10.1051/0004-6361/202450243}, volume = {693}, year = {2025}, } @article{18855, abstract = {A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n]. Two important parameters are the partition function, which is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the vector of pre-image counts c_x=|H^-1(x)|. We develop black-box sampling algorithms to estimate the counts roughly Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions, where q = (log Z(β_max))/Z(β_min) (ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate all values of the partition function using Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions. This improves over a prior algorithm of Huber (2015) which computes a single point estimate Z(β_max) and which uses a slightly larger amount of samples. We show matching lower bounds, demonstrating this complexity is optimal as a function of n and q up to logarithmic terms.}, author = {Harris, David G. and Kolmogorov, Vladimir}, issn = {1549-6333}, journal = {ACM Transactions on Algorithms}, number = {1}, publisher = {Association for Computing Machinery}, title = {{Parameter estimation for Gibbs distributions}}, doi = {10.1145/3685676}, volume = {21}, year = {2025}, } @article{18866, abstract = {Using JWST Near Infrared Camera (NIRCam) images of the globular cluster 47,Tucanæ, (or NGC,104), taken at two epochs just 7 months apart, we derived proper-motion membership down to F322W2 ∼ 27. We identified an intriguing feature at the very low-mass end of the main sequence, around ∼ 0.08,M_⋅, at magnitudes F322W2 ∼ 24 and m_ F150W2 ∼ 25. This feature, dubbed 'kink', is characterized by a prominent discontinuity in the slope of the main sequence. A similar discontinuity is seen in theoretical isochrones with oxygen-poor chemistries, related to the rapid onset of absorption. We therefore hypothesize that the cluster hosts disproportionately more oxygen-poor stars near the bottom of the main sequence compared to the upper main sequence and the red giant branch. Our results show no strong or conclusive evidence of a rise in the brown dwarf luminosity function at faint magnitudes, in contrast to previous findings likely affected by faint red background galaxies. In our analysis, we accounted for this contamination by using proper motion membership.}, author = {Scalco, M. and Gerasimov, R. and Bedin, L. R. and Vesperini, E. and Correnti, M. and Nardiello, D. and Burgasser, A. and Richer, H. and Caiazzo, Ilaria and Heyl, J. and Libralato, M. and Anderson, J. and Griggio, M.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, publisher = {EDP Sciences}, title = {{JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition}}, doi = {10.1051/0004-6361/202452907}, volume = {694}, year = {2025}, } @article{18878, abstract = {Thermoelectric (TE) materials, with the ability to convert heat into electrical energy, can generate micro-electrical fields at electronic interfaces with biological systems, making them applicable in electric-catalyzing as nanozymes, and modulate the infected microenvironment of skin wounds. Thereby, by harnessing temperature differences in vitro or in vivo, TE nanomaterials can provide antimicrobial reactive oxygen species (ROS) by catalyzing redox reactions, thereby accelerating wound healing by suppressing infection. However, despite their promising potential, there is still a lack of comprehensive understanding of the antimicrobial mechanisms, biocompatibility, and practical applications of TE nanomaterials in wound healing, as this is a newly-emerged sub-area of energy-related biomedical applications. This review aims to address this gap by highlighting the emerging progress of TE materials in wound healing, clarifying their mechanism and advances, emphasizing their potential challenges for commercialization and clinical use, and proposing novel design strategies of TE nanomaterials for effective antibacterial performance.}, author = {Jia, Shiyu and Qi, Cai and Xu, Shengduo and Yang, Lei and Sun, Qiang}, issn = {1005-0302}, journal = {Journal of Materials Science and Technology}, number = {08}, pages = {212--226}, publisher = {Elsevier}, title = {{Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing}}, doi = {10.1016/j.jmst.2024.11.039}, volume = {225}, year = {2025}, } @article{18879, abstract = {Our brain has remarkable computational power, generating sophisticated behaviors, storing memories over an individual’s lifetime, and producing higher cognitive functions. However, little of our neuroscience knowledge covers the human brain. Is this organ truly unique, or is it a scaled version of the extensively studied rodent brain? Combining multicellular patch-clamp recording with expansion-based superresolution microscopy and full-scale modeling, we determined the cellular and microcircuit properties of the human hippocampal CA3 region, a fundamental circuit for memory storage. In contrast to neocortical networks, human hippocampal CA3 displayed sparse connectivity, providing a circuit architecture that maximizes associational power. Human synapses showed unique reliability, high precision, and long integration times, exhibiting both species- and circuit-specific properties. Together with expanded neuronal numbers, these circuit characteristics greatly enhanced the memory storage capacity of CA3. Our results reveal distinct microcircuit properties of the human hippocampus and begin to unravel the inner workings of our most complex organ. }, author = {Watson, Jake and Vargas Barroso, Victor M and Morse, Rebecca and Navas Olivé, Andrea C and Tavakoli, Mojtaba and Danzl, Johann G and Tomschik, Matthias and Rössler, Karl and Jonas, Peter M}, issn = {1097-4172}, journal = {Cell}, number = {2}, pages = {501--514.e18}, publisher = {Elsevier}, title = {{Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory}}, doi = {10.1016/j.cell.2024.11.022}, volume = {188}, year = {2025}, } @article{18880, abstract = {In this paper, we provide a rate of convergence for a version of the Carathéodory convergence for the multiple SLE model with a Dyson Brownian motion driver towards its hydrodynamic limit, for β=1 and β=2. The results are obtained by combining techniques from the field of Schramm–Loewner Evolutions with modern techniques from random matrices. Our approach shows how one can apply modern tools used in the proof of universality in random matrix theory to the field of Schramm–Loewner Evolutions.}, author = {Campbell, Andrew J and Luh, Kyle and Margarint, Vlad}, issn = {2010-3271}, journal = {Random Matrices: Theory and Application}, number = {1}, publisher = {World Scientific Publishing}, title = {{Rate of convergence in multiple SLE using random matrix theory}}, doi = {10.1142/S201032632450028X}, volume = {14}, year = {2025}, } @article{18881, abstract = {The determination of the intrinsic properties of solid active material candidates is essential for their performance optimization. However, macroscopic electrodes and related analytical techniques show challenges concerning the number of additional influencing parameters. We explore recessed microelectrodes (rME) as a platform that allows for a binder-free investigation of Prussian Blue analogues (PBA), a family of promising battery materials. The enhanced diffusion using microelectrochemical tools is indispensable to assess the intrinsic material performance, overcoming the limitation of cation diffusion from the electrolyte to the solid interface during (dis)charging cycles and allowing the investigation of limiting steps in the coupled ion-electron transfer process. The intrinsic electrochemical performance of PBAs was studied in a three-electrode configuration by means of cyclic voltammetry and galvanostatic (dis)charging in aqueous Na+-containing electrolyte. We extended the evaluation to the role of the electrolyte on the performance of cathodic and anodic processes of a Mn-based PBA. Ex-situ and operando chemical characterization were coupled to support the microelectrochemical results.}, author = {Jiyane, Nomnotho and Santana Santos, Carla and Echevarria Poza, Igor and Palacios Corella, Mario and Abdillah Mahbub, Muhammad Adib and Marin-Tajadura, Gimena and Quast, Thomas and Ibáñez, Maria and Ventosa, Edgar and Schuhmann, Wolfgang}, issn = {2566-6223}, journal = {Batteries & Supercaps}, number = {3}, publisher = {Wiley}, title = {{Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application}}, doi = {10.1002/batt.202400743}, volume = {8}, year = {2025}, } @article{18882, abstract = {Ternary liquid-like thermoelectric materials have garnered significant attention due to their ultra-low lattice thermal conductivity. Among these, Ag8SnSe6 stands out for its exceptionally low sound velocity and thermal conductivity. However, the inherent poor electrical conductivity and suboptimal thermoelectric properties of Ag8SnSe6 necessitate further improvement. Here, a novel approach is initiated to enhance the thermoelectric properties of Ag8SnSe6 by combining low-dimensionalization with intrinsic doping. For the first time, this work successfully synthesizes single-phase Ag8SnSe6 nanocrystals, ≈10 nm in size, with the correct phase and composition using a robust and reliable colloidal method. This approach represents a significant improvement over previous reports on this material. Reducing the crystal domains of Ag8SnSe6 to the nanoscale induces quantum confinement effects, increasing the density of states near the Fermi surface. It also introduces additional grain boundaries, which lower the lattice thermal conductivity and simplify structural design. Moreover, incorporating small amounts of Sn nanopowder into the Ag8SnSe6 nanocrystals before consolidation further enhances the thermoelectric performance. Sn acts as a donor dopant, increasing the electronic concentration while at the same time improving their mobility by reducing interface barriers, thus significantly improving the material transport properties. Additionally, the presence of Sn leads to the formation of point defects, dislocations, and secondary phases, which increase phonon scattering and further reduce the thermal conductivity. Through this synergistic optimization, the figure of merit shows a significant increase across a wide temperature range. Overall, a strategy is presented for the controlled preparation of Ag8SnSe6 nanocrystals, the decoupling of their electrical and thermal transport, and the practical application of this material to thermoelectric single-leg modules.}, author = {Zhao, Xueke and Li, Mengyao and Jia, Mochen and Fiedler, Christine and Nan, Bingfei and Yang, Dongwen and Li, Lei and Yuan, Zicheng and Song, Hongzhang and Liu, Yu and Ibáñez, Maria and Wang, Ziyu and Shan, Chongxin and Cabot, Andreu}, issn = {1616-3028}, journal = {Advanced Functional Materials}, number = {24}, publisher = {Wiley}, title = {{Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance}}, doi = {10.1002/adfm.202421449}, volume = {35}, year = {2025}, } @misc{18886, abstract = {Research Data for publication 'Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors'}, author = {Janik, Marian}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for publication 'Strong charge-photon coupling in planar germanium enabled by granular aluminium superinductors'}}, doi = {10.15479/AT:ISTA:18886}, year = {2025}, } @article{18892, abstract = {Sick individuals often conceal their disease status to group members, thereby preventing social exclusion or aggression. Here we show by behavioural, chemical, immunological and infection load analyses that sick ant pupae instead actively emit a chemical signal that in itself is sufficient to trigger their own destruction by colony members. In our experiments, this altruistic disease-signalling was performed only by worker but not queen pupae. The lack of signalling by queen pupae did not constitute cheating behaviour, but reflected their superior immune capabilities. Worker pupae suffered from extensive pathogen replication whereas queen pupae were able to restrain their infection. Our data suggest the evolution of a finely-tuned signalling system in which it is not the induction of an individual’s immune response, but rather its failure to overcome the infection, that triggers pupal signalling for sacrifice. This demonstrates a balanced interplay between individual and social immunity that efficiently achieves whole-colony health.}, author = {Dawson, Erika and Hönigsberger, Michaela and Kampleitner, Niklas and Grasse, Anna V and Lindorfer, Lukas and Robb, Jennifer and Beikzadeh Abbasi, Farnaz and Strahodinsky, Florian and Leitner, Hanna and Rajendran, Harikrishnan and Schmitt, Thomas and Cremer, Sylvia}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Altruistic disease signalling in ant colonies}}, doi = {10.1038/s41467-025-66175-z}, volume = {16}, year = {2025}, } @article{18936, abstract = {A major obstacle to predictive understanding of evolution stems from the complexity of biological systems, which prevents detailed characterization of key evolutionary properties. Here, we highlight some of the major sources of complexity that arise when relating molecular mechanisms to their evolutionary consequences and ask whether accounting for every mechanistic detail is important to accurately predict evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial promoter regulated by 2 proteins, allowing us to connect any promoter genotype to 6 phenotypes that capture the dynamics of gene expression following an environmental switch. Accounting for the mechanisms that govern how this system works enabled us to provide an in-depth picture of how regulated bacterial promoters might evolve. More importantly, we used the model to explore which factors that contribute to the complexity of this system are essential for understanding its evolution, and which can be simplified without information loss. We found that several key evolutionary properties—the distribution of phenotypic and fitness effects of mutations, the evolutionary trajectories during selection for regulation—can be accurately captured without accounting for all, or even most, parameters of the system. Our findings point to the need for a mechanistic approach to studying evolution, as it enables tackling biological complexity and in doing so improves the ability to predict evolutionary outcomes.}, author = {Grah, Rok and Guet, Calin C and Tkačik, Gašper and Lagator, Mato}, issn = {1943-2631}, journal = {Genetics}, number = {2}, publisher = {Oxford University Press}, title = {{Linking molecular mechanisms to their evolutionary consequences: a primer}}, doi = {10.1093/genetics/iyae191}, volume = {229}, year = {2025}, } @article{18960, abstract = {The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter.}, author = {Brückner, David and Hannezo, Edouard B}, issn = {1943-0264}, journal = {Cold Spring Harbor Perspectives in Biology}, number = {4}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Tissue active matter: Integrating mechanics and signaling into dynamical models}}, doi = {10.1101/cshperspect.a041653}, volume = {17}, year = {2025}, } @phdthesis{18979, abstract = {Topological Data Analysis (TDA) is a discipline utilizing the mathematical field of topology to study data, most prominently collections of point sets. This thesis summarizes three projects related to computations in TDA. The first one establishes a variant of TDA for chromatic point sets, where each point is given a color. For example, we are given positions of cells within a tumor microenvironment, and color the cancerous cells red, and the immune cells blue. The aim is then to give a quantitative description of how the two or more sets of points spatially interact. Building on image, kernel and cokernel variants of persistent homology, we suggest six-packs of persistent diagrams as such a descriptor. We describe a construction of a chromatic alpha complex, which enables efficient computation of several variants of the six-packs. We give topological descriptions of natural subcomplexes of the chromatic alpha complex, and show that the radii of the simplices form a discrete Morse function. Finally, we provide an implementation of the presented chromatic TDA pipeline. The second part aims to translate a powerful tool of sheaf theory to elementary terms using labeled matrices. The goal is to enable their use in computational settings. We show that derived categories of sheaves over finite posets have, up to isomorphism, unique objects---minimal injective resolutions---and give a concrete algorithm to compute them. We further describe simple algorithms to compute derived pushforwards and pullbacks for monotonic maps, and their proper variants for inclusions, and demonstrate their tractability by providing an implementation. Finally, we suggest a discrete definition of microsupport and show desirable properties inspired by discrete Morse theory. In the last part, we present a collection of observations about collapses. We give a characterization of collapsibility in terms of unitriangular submatrices of the boundary matrix, a cotree-tree decomposition, and the optimal solution to a variant of the Procrustes problem. We establish relation between dual collapses and relative Morse theory and pose several open questions. Finally, focusing on complexes embedded in the three-dimensional Euclidean space, we describe a relation between the collapsibility and the triviality of a polygonal knot.}, author = {Draganov, Ondrej}, issn = {2663-337X}, keywords = {topological data analysis, chromatic point set, alpha complex, persistent homology, six pack, sheaf, microlocal discrete Morse, injective resolution, collapse, knot, discrete Morse theory}, pages = {140}, publisher = {Institute of Science and Technology Austria}, title = {{Structures and computations in topological data analysis}}, doi = {10.15479/at:ista:18979}, year = {2025}, } @article{18984, abstract = {Although planets have been found orbiting binary systems, whether they can survive binary interactions is debated. While the tightest-orbit binaries should host the most dynamically stable and long-lived circumbinary planetary systems, they are also the systems that are expected to experience mass transfer, common envelope evolution, or stellar mergers. In this study, we explore the effect of stable non-conservative mass transfer on the dynamical evolution of circumbinary planets. We present a new script that seamlessly integrates binary evolution data from the 1D binary stellar evolution code MESA into the N-body simulation code REBOUND. This integration framework enables a comprehensive examination of the dynamical evolution of circumbinary planets orbiting mass-transferring binaries, while simultaneously accounting for the detailed stellar structure evolution. In addition, we introduce a recalibration method to mitigate numerical errors from updates of binary properties during the system's dynamical evolution. We construct a reference binary model in which a 2.21M⊙ star loses its hydrogen-rich envelope through non-conservative mass transfer to the 1.76M⊙ companion star, creating a 0.38M⊙ subdwarf. We find the tightest stable orbital separation for circumbinary planets to be ≃2.5 times the binary separation after mass transfer. Accounting for tides by using the interior stellar structure, we find that tidal effects become apparent after the rapid mass transfer phase and start to fade away during the latter stage of the slow mass transfer phase. Our research provides a new framework for exploring circumbinary planet dynamics in interacting binary systems.}, author = {Xing, Zepei and Torres Rodriguez, Santiago and Götberg, Ylva Louise Linsdotter and Trani, Alessandro A. and Korol, Valeriya and Cuadra, Jorge}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {1}, pages = {285--292}, publisher = {Oxford University Press}, title = {{Combining REBOUND and MESA: Dynamical evolution of planets orbiting interacting binaries}}, doi = {10.1093/mnras/stae2820}, volume = {537}, year = {2025}, }