@article{12832, abstract = {The development of cost-effective, high-activity and stable bifunctional catalysts for the oxygen reduction and evolution reactions (ORR/OER) is essential for zinc–air batteries (ZABs) to reach the market. Such catalysts must contain multiple adsorption/reaction sites to cope with the high demands of reversible oxygen electrodes. Herein, we propose a high entropy alloy (HEA) based on relatively abundant elements as a bifunctional ORR/OER catalyst. More specifically, we detail the synthesis of a CrMnFeCoNi HEA through a low-temperature solution-based approach. Such HEA displays superior OER performance with an overpotential of 265 mV at a current density of 10 mA/cm2, and a 37.9 mV/dec Tafel slope, well above the properties of a standard commercial catalyst based on RuO2. This high performance is partially explained by the presence of twinned defects, the incidence of large lattice distortions, and the electronic synergy between the different components, being Cr key to decreasing the energy barrier of the OER rate-determining step. CrMnFeCoNi also displays superior ORR performance with a half-potential of 0.78 V and an onset potential of 0.88 V, comparable with commercial Pt/C. The potential gap (Egap) between the OER overpotential and the ORR half-potential of CrMnFeCoNi is just 0.734 V. Taking advantage of these outstanding properties, ZABs are assembled using the CrMnFeCoNi HEA as air cathode and a zinc foil as the anode. The assembled cells provide an open-circuit voltage of 1.489 V, i.e. 90% of its theoretical limit (1.66 V), a peak power density of 116.5 mW/cm2, and a specific capacity of 836 mAh/g that stays stable for more than 10 days of continuous cycling, i.e. 720 cycles @ 8 mA/cm2 and 16.6 days of continuous cycling, i.e. 1200 cycles @ 5 mA/cm2.}, author = {He, Ren and Yang, Linlin and Zhang, Yu and Wang, Xiang and Lee, Seungho and Zhang, Ting and Li, Lingxiao and Liang, Zhifu and Chen, Jingwei and Li, Junshan and Ostovari Moghaddam, Ahmad and Llorca, Jordi and Ibáñez, Maria and Arbiol, Jordi and Xu, Ying and Cabot, Andreu}, issn = {2405-8297}, journal = {Energy Storage Materials}, number = {4}, pages = {287--298}, publisher = {Elsevier}, title = {{A CrMnFeCoNi high entropy alloy boosting oxygen evolution/reduction reactions and zinc-air battery performance}}, doi = {10.1016/j.ensm.2023.03.022}, volume = {58}, year = {2023}, } @article{12833, abstract = {The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.}, author = {Biniaz, Ahmad and Jain, Kshitij and Lubiw, Anna and Masárová, Zuzana and Miltzow, Tillmann and Mondal, Debajyoti and Naredla, Anurag Murty and Tkadlec, Josef and Turcotte, Alexi}, issn = {1365-8050}, journal = {Discrete Mathematics and Theoretical Computer Science}, number = {2}, publisher = {EPI Sciences}, title = {{Token swapping on trees}}, doi = {10.46298/DMTCS.8383}, volume = {24}, year = {2023}, } @article{12836, abstract = {Coherent control and manipulation of quantum degrees of freedom such as spins forms the basis of emerging quantum technologies. In this context, the robust valley degree of freedom and the associated valley pseudospin found in two-dimensional transition metal dichalcogenides is a highly attractive platform. Valley polarization and coherent superposition of valley states have been observed in these systems even up to room temperature. Control of valley coherence is an important building block for the implementation of valley qubit. Large magnetic fields or high-power lasers have been used in the past to demonstrate the control (initialization and rotation) of the valley coherent states. Here, the control of layer–valley coherence via strong coupling of valley excitons in bilayer WS2 to microcavity photons is demonstrated by exploiting the pseudomagnetic field arising in optical cavities owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The use of photonic structures to generate pseudomagnetic fields which can be used to manipulate exciton-polaritons presents an attractive approach to control optical responses without the need for large magnets or high-intensity optical pump powers.}, author = {Khatoniar, Mandeep and Yama, Nicholas and Ghazaryan, Areg and Guddala, Sriram and Ghaemi, Pouyan and Majumdar, Kausik and Menon, Vinod}, issn = {2195-1071}, journal = {Advanced Optical Materials}, number = {13}, publisher = {Wiley}, title = {{Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities}}, doi = {10.1002/adom.202202631}, volume = {11}, year = {2023}, } @article{12837, abstract = {As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.}, author = {Bocanegra, Laura and Singh, Amrita and Hannezo, Edouard B and Zagórski, Marcin P and Kicheva, Anna}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1050--1058}, publisher = {Springer Nature}, title = {{Cell cycle dynamics control fluidity of the developing mouse neuroepithelium}}, doi = {10.1038/s41567-023-01977-w}, volume = {19}, year = {2023}, } @article{12838, abstract = {We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L – 1 balls of radius √ nN around points in C . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory.}, author = {Zhang, Yihan and Vatedka, Shashank}, issn = {1557-9654}, journal = {IEEE Transactions on Information Theory}, number = {7}, pages = {4513--4527}, publisher = {IEEE}, title = {{Multiple packing: Lower bounds via infinite constellations}}, doi = {10.1109/TIT.2023.3260950}, volume = {69}, year = {2023}, } @article{12839, abstract = {Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport.}, author = {Ljubotina, Marko and Desaules, Jean Yves and Serbyn, Maksym and Papić, Zlatko}, issn = {2160-3308}, journal = {Physical Review X}, number = {1}, publisher = {American Physical Society}, title = {{Superdiffusive energy transport in kinetically constrained models}}, doi = {10.1103/PhysRevX.13.011033}, volume = {13}, year = {2023}, } @unpublished{12846, abstract = {We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.}, author = {Chern, Albert and Ishida, Sadashige}, booktitle = {arXiv}, title = {{Area formula for spherical polygons via prequantization}}, doi = {10.48550/arXiv.2303.14555}, year = {2023}, } @inproceedings{12854, abstract = {The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis. At SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.}, author = {Chalupa, Marek and Henzinger, Thomas A}, booktitle = {Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783031308192}, issn = {1611-3349}, location = {Paris, France}, pages = {535--540}, publisher = {Springer Nature}, title = {{Bubaak: Runtime monitoring of program verifiers}}, doi = {10.1007/978-3-031-30820-8_32}, volume = {13994}, year = {2023}, } @inproceedings{12856, abstract = {As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both. We present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems. We implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.}, author = {Chalupa, Marek and Mühlböck, Fabian and Muroya Lei, Stefanie and Henzinger, Thomas A}, booktitle = {Fundamental Approaches to Software Engineering}, isbn = {9783031308253}, issn = {1611-3349}, location = {Paris, France}, pages = {260--281}, publisher = {Springer Nature}, title = {{Vamos: Middleware for best-effort third-party monitoring}}, doi = {10.1007/978-3-031-30826-0_15}, volume = {13991}, year = {2023}, } @inproceedings{12859, abstract = {Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this "universal" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an "interaction matrix", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10).}, author = {Bombari, Simone and Kiyani, Shayan and Mondelli, Marco}, booktitle = {Proceedings of the 40th International Conference on Machine Learning}, location = {Honolulu, HI, United States}, pages = {2738--2776}, publisher = {ML Research Press}, title = {{Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels}}, volume = {202}, year = {2023}, } @article{12861, abstract = {The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight," have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations.}, author = {Schmid, Laura and Ekbatani, Farbod and Hilbe, Christian and Chatterjee, Krishnendu}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Quantitative assessment can stabilize indirect reciprocity under imperfect information}}, doi = {10.1038/s41467-023-37817-x}, volume = {14}, year = {2023}, } @article{12862, abstract = {Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings.}, author = {Safavi, Shervin and Panagiotaropoulos, Theofanis I. and Kapoor, Vishal and Ramirez Villegas, Juan F and Logothetis, Nikos K. and Besserve, Michel}, issn = {1553-7358}, journal = {PLoS Computational Biology}, number = {4}, publisher = {Public Library of Science}, title = {{Uncovering the organization of neural circuits with Generalized Phase Locking Analysis}}, doi = {10.1371/journal.pcbi.1010983}, volume = {19}, year = {2023}, } @article{12863, abstract = {In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.}, author = {Filipović Marijić, Vlatka and Krasnici, Nesrete and Valić, Damir and Kapetanović, Damir and Vardić Smrzlić, Irena and Jordanova, Maja and Rebok, Katerina and Ramani, Sheriban and Kostov, Vasil and Nastova, Rodne and Dragun, Zrinka}, issn = {1614-7499}, journal = {Environmental Science and Pollution Research}, pages = {63510--63521}, publisher = {Springer Nature}, title = {{Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish}}, doi = {10.1007/s11356-023-26844-2}, volume = {30}, year = {2023}, } @inbook{12866, abstract = {Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation. Decades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain.}, author = {Currin, Christopher and Beyer, Chad}, booktitle = {Encyclopedia of Child and Adolescent Health}, editor = {Halpern-Felsher, Bonnie}, isbn = {9780128188736}, pages = {86--98}, publisher = {Elsevier}, title = {{Altered childhood brain development in autism and epilepsy}}, doi = {10.1016/b978-0-12-818872-9.00129-1}, year = {2023}, } @misc{12869, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. }, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, publisher = {Institute of Science and Technology Austria}, title = {{Research data for: A stochastic cellular automaton model of culture formation}}, doi = {10.15479/AT:ISTA:12869}, year = {2023}, } @article{12876, abstract = {Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only. Results: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data.}, author = {Beneš, Nikola and Brim, Luboš and Huvar, Ondřej and Pastva, Samuel and Šafránek, David}, issn = {1367-4811}, journal = {Bioinformatics}, number = {4}, publisher = {Oxford Academic}, title = {{Boolean network sketches: A unifying framework for logical model inference}}, doi = {10.1093/bioinformatics/btad158}, volume = {39}, year = {2023}, } @article{12877, abstract = {We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table.}, author = {De Simoi, Jacopo and Kaloshin, Vadim and Leguil, Martin}, issn = {1432-1297}, journal = {Inventiones Mathematicae}, pages = {829--901}, publisher = {Springer Nature}, title = {{Marked Length Spectral determination of analytic chaotic billiards with axial symmetries}}, doi = {10.1007/s00222-023-01191-8}, volume = {233}, year = {2023}, } @article{12878, abstract = {Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components.}, author = {Jiang, Lihui and Yao, Baolin and Zhang, Xiaoyan and Wu, Lixia and Fu, Qijing and Zhao, Yiting and Cao, Yuxin and Zhu, Ruomeng and Lu, Xinqi and Huang, Wuying and Zhao, Jianping and Li, Kuixiu and Zhao, Shuanglu and Han, Li and Zhou, Xuan and Luo, Chongyu and Zhu, Haiyan and Yang, Jing and Huang, Huichuan and Zhu, Zhengge and He, Xiahong and Friml, Jiří and Zhang, Zhongkai and Liu, Changning and Du, Yunlong}, issn = {1365-313X}, journal = {Plant Journal}, number = {1}, pages = {155--174}, publisher = {Wiley}, title = {{Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth}}, doi = {10.1111/tpj.16218}, volume = {115}, year = {2023}, } @article{12879, abstract = {Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations.}, author = {Chen, Ke and Kunkel, Christian and Cheng, Bingqing and Reuter, Karsten and Margraf, Johannes T.}, issn = {2041-6539}, journal = {Chemical Science}, publisher = {Royal Society of Chemistry}, title = {{Physics-inspired machine learning of localized intensive properties}}, doi = {10.1039/d3sc00841j}, year = {2023}, } @article{12880, abstract = {Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.}, author = {Kaneshiro, Jeanae M. and Capitanio, Juliana S. and Hetzer, Martin W}, issn = {1949-1042}, journal = {Nucleus}, number = {1}, publisher = {Taylor & Francis}, title = {{Lamin B1 overexpression alters chromatin organization and gene expression}}, doi = {10.1080/19491034.2023.2202548}, volume = {14}, year = {2023}, }