@article{17535, abstract = {Supermassive black holes (SMBHs) with masses of ∼109 M⊙ within the first billion year of the universe challenge our conventional understanding of black hole formation and growth. One pathway to these SMBHs proposes that supermassive stars born in pristine atomic cooling haloes yield massive seed BHs evolving to these early SMBHs. This scenario leads to an overly massive BH galaxy (OMBG), in which the BH to stellar mass ratio is initially Mbh/M* ≥ 1, well in excess of the typical values of ∼10−3 at low redshifts. Previously, we have investigated two massive seed BH candidates from the Renaissance simulation and found that they remain outliers on the Mbh–M* relation until the OMBG merges with a much more massive halo at z = 8. In this work, we use Monte-Carlo merger trees to investigate the evolution of the Mbh–M* relation for 50 000 protogalaxies hosting massive BH seeds, across 10 000 trees that merge into a 1012 M⊙ halo at z = 6. We find that up to 60 per cent (depending on growth parameters) of these OMBGs remain strong outliers for several 100 Myr, down to redshifts detectable with JWST and with sensitive X-ray telescopes. This represents a way to diagnose the massive-seed formation pathway for early SMBHs. We expect to find ∼0.1–1 of these objects per JWST Near Infrared Camera (NIRCam) field per unit redshift at z ≳ 6. Recently detected SMBHs with masses of ∼107 M⊙ and low-inferred stellar-mass hosts may be examples of this population.}, author = {Scoggins, Matthew T and Haiman, Zoltán}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {4}, pages = {4584--4597}, publisher = {Oxford University Press}, title = {{Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio}}, doi = {10.1093/mnras/stae1449}, volume = {531}, year = {2024}, } @article{17545, abstract = {Self-lensing flares (SLFs) are expected to be produced once or twice per orbit by an accreting massive black hole binary (MBHB), if the eclipsing MBHBs are observed close to edge-on. SLFs can provide valuable electromagnetic (EM) signatures to accompany the gravitational waves (GWs) detectable by the upcoming Laser Interferometer Space Antenna (LISA). EM follow-ups are crucial for, e.g., sky-localization, and constraining the Hubble constant and the graviton mass. We use high-resolution two-dimensional viscous hydrodynamical simulations of a circumbinary disk (CBD) embedding a MBHB. We then use very high-cadence output of these hydrodynamical simulation inputs for a general-relativistic ray-tracing code to produce synthetic spectra and phase-folded light curves. Our main results show a significant periodic amplification of the flux with the characteristic shape of a sharp flare with a central dip, as the foreground black hole (BH) transits across the minidisk and shadow of the background BH, respectively. These corroborate previous conclusions based on the microlensing approximation and analytical toy models of the emission geometry. We also find that at lower inclinations, without some occlusion of the minidisk emission by the CBD, shocks from quasi-periodic mass-trading between the minidisks can produce bright flares which can mimic SLFs and could hinder their identification.}, author = {Krauth, Luke Major and Davelaar, Jordy and Haiman, Zoltán and Westernacher-Schneider, John Ryan and Zrake, Jonathan and MacFadyen, Andrew}, issn = {2470-0010}, journal = {Physical Review D}, number = {10}, publisher = {American Physical Society (APS)}, title = {{Self-lensing flares from black hole binaries: General-relativistic ray tracing of circumbinary accretion simulations}}, doi = {10.1103/physrevd.109.103014}, volume = {109}, year = {2024}, } @article{17546, abstract = {We show that gas disks around the components of an orbiting binary system (so-called minidisks) may be susceptible to a resonant instability that causes the minidisks to become significantly eccentric. Eccentricity is injected by, and also induces, regular impacts between the minidisks at roughly the orbital period of the binary. Such eccentric minidisks are seen in vertically integrated, two-dimensional simulations of a circular, equal-mass binary accreting from a circumbinary gas disk with a Γ-law equation of state. Minidisk eccentricity is suppressed by the use of an isothermal equation of state. However, the instability still operates and can be revealed in a minimal disk-binary simulation by removing the circumbinary disk and feeding the minidisks from the component positions. Minidisk eccentricity is also suppressed when the gravitational softening length is large (≳4% of the binary semimajor axis), suggesting that its absence could be an artifact of widely adopted numerical approximations; a follow-up study in three dimensions with well-resolved, geometrically thin minidisks (aspect ratios ≲0.02) may be needed to assess whether eccentric minidisks can occur in real astrophysical environments. If they can, the electromagnetic signature may be important for discriminating between binary and single black hole scenarios for quasiperiodic oscillations in active galactic nuclei; in turn, this might aid in targeted searches with pulsar timing arrays for individual supermassive black hole binary sources of low-frequency gravitational waves.}, author = {Westernacher-Schneider, John Ryan and Zrake, Jonathan and MacFadyen, Andrew and Haiman, Zoltán}, issn = {0004-637X}, journal = {The Astrophysical Journal}, number = {1}, publisher = {American Astronomical Society}, title = {{Eccentric minidisks in accreting binaries}}, doi = {10.3847/1538-4357/ad1a17}, volume = {962}, year = {2024}, } @article{17590, abstract = {Close encounters between stellar-mass black holes (BHs) and stars occur frequently in dense star clusters and in the disks of active galactic nuclei. Recent studies have shown that in highly eccentric close encounters, the star can be tidally disrupted by the BH in a microtidal disruption event (microTDE), resulting in rapid mass accretion and possibly bright electromagnetic signatures. Here we consider a scenario in which the star might approach the stellar-mass BH in a gradual, nearly circular inspiral, under the influence of dynamical friction in a circum-binary gas disk or three-body interactions in a star cluster. We perform hydrodynamics simulations of this scenario using the smoothed particle hydrodynamics code PHANTOM. We find that under certain circumstances (for initial eccentricity e0 ≳ 0.4 and penetration factor β = 1, or e0 < 0.4 and β ≲ 0.67), the mass of the star is slowly stripped away by the BH. We call this gradual tidal disruption a "tidal-peeling event." Additionally, we discover that some low-eccentricity microTDEs (e0 < 0.4 and β = 1) are a new form of fast luminous transients similar to parabolic microTDEs. Depending on the initial distance and eccentricity of the encounter, these low-eccentricity microTDEs might exhibit significant accretion rates and orbital evolution distinct from those of a typical (eccentric) microTDE.}, author = {Xin, Chengcheng and Haiman, Zoltán and Perna, Rosalba and Wang, Yihan and Ryu, Taeho}, issn = {0004-637X}, journal = {The Astrophysical Journal}, number = {2}, publisher = {American Astronomical Society}, title = {{“Tidal Peeling Events”: Low-eccentricity tidal disruption of a star by a stellar-mass black hole}}, doi = {10.3847/1538-4357/ad11d3}, volume = {961}, year = {2024}, } @inproceedings{17634, abstract = {System behaviors are traditionally evaluated through binary classifications of correctness, which do not suffice for properties involving quantitative aspects of systems and executions. Quantitative automata offer a more nuanced approach, mapping each execution to a real number by incorporating weighted transitions and value functions generalizing acceptance conditions. In this paper, we introduce QuAK, the first tool designed to automate the analysis of quantitative automata. QuAK currently supports a variety of quantitative automaton types, including Inf, Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision procedures for problems such as emptiness, universality, inclusion, equivalence, as well as for checking whether an automaton is safe, live, or constant. Additionally, QuAK is able to compute extremal values when possible, construct safety-liveness decompositions, and monitor system behaviors. We demonstrate the effectiveness of QuAK through experiments focusing on the inclusion, constant-function check, and monitoring problems.}, author = {Chalupa, Marek and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation}, isbn = {9783031753862}, issn = {1611-3349}, location = {Crete, Greece}, pages = {3--20}, publisher = {Springer Nature}, title = {{QuAK: Quantitative Automata Kit}}, doi = {10.1007/978-3-031-75387-9_1}, volume = {15222}, year = {2024}, } @phdthesis{17850, abstract = {Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data. In this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design.}, author = {Gonzalez Somermeyer, Louisa}, issn = {2663-337X}, pages = {89}, publisher = {Institute of Science and Technology Austria}, title = {{Fitness landscapes of orthologous green fluorescent proteins}}, doi = {10.15479/at:ista:17850}, year = {2024}, } @article{17852, abstract = {Metal-metal contacts, though not yet widely realized, may provide exciting opportunities to serve as tunable and functional interfaces in single-molecule devices. One of the simplest components which might facilitate such binding interactions is the ferrocene group. Notably, direct bonds between the ferrocene iron center and metals such as Pd or Co have been demonstrated in molecular complexes comprising coordinating ligands attached to the cyclopentadienyl rings. Here, we demonstrate that ferrocene-based single-molecule devices with Fe-Au interfacial contact geometries form at room temperature in the absence of supporting coordinating ligands. Applying a photoredox reaction, we propose that ferrocene only functions effectively as a contact group when oxidized, binding to gold through a formal Fe3+ center. This observation is further supported by a series of control measurements and density functional theory calculations. Our findings extend the scope of junction contact chemistries beyond those involving main group elements, lay the foundation for light switchable ferrocene-based single-molecule devices, and highlight new potential mechanistic function(s) of unsubstituted ferrocenium groups in synthetic processes.}, author = {Lee, Woojung and Li, Liang and Camarasa-Gómez, María and Hernangómez-Pérez, Daniel and Roy, Xavier and Evers, Ferdinand and Inkpen, Michael S. and Venkataraman, Latha}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions}}, doi = {10.1038/s41467-024-45707-z}, volume = {15}, year = {2024}, } @article{17853, abstract = {Single-molecule one-dimensional topological insulator (1D TI) is a class of molecular wires that exhibit increasing conductance with wire length. This unique trend is due to the coupling between the two low-lying topological edge states of 1D TIs described by the Su–Schrieffer–Heeger model. In principle, this quantum phenomenon within 1D TIs can be utilized to achieve long-range gating in molecular conductors. Here, we study electron transport through a single-edge state of doubly oxidized oligophenylene bis(triarylamine) to understand the effect of the edge state coupling on conductance. We find that conductance is elevated by approximately 1 order of magnitude compared to a control molecule with the same conductance pathway. Density function theory calculations further support that the increase in conductance is due to the interaction between the edge states of 1D TIs. This work demonstrates a new gating paradigm in molecular electronics, while also providing a deeper understanding of how edge states interact and affect electron transport within 1D TIs.}, author = {Li, Liang and Louie, Shayan and Orchanian, Nicholas M. and Nuckolls, Colin and Venkataraman, Latha}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {24}, pages = {16920--16925}, publisher = {American Chemical Society}, title = {{Long-range gating in single-molecule one-dimensional topological insulators}}, doi = {10.1021/jacs.4c05699}, volume = {146}, year = {2024}, } @article{17854, abstract = {As social media platforms continue to grow in popularity, there is an increasing need for science outreach teams to bring STEM content to the virtual landscape. Here, we highlight the use of short-form videos on our TikTok channel─@IvyLeagueScience─as a new way to approach science outreach. Through a combination of content production and data analytics, we were able to build an online platform with >150k followers, 3.6 million likes, and 18 million views. By bringing science to social media, we engage with students across the world, allowing them to experience science-based content. In this case study, we hope to encourage other scientific outreach teams to employ social media as a means of increasing visibility of scientists and STEM careers.}, author = {Prindle, Claudia R. and Orchanian, Nicholas M. and Venkataraman, Latha and Nuckolls, Colin}, issn = {1938-1328}, journal = {Journal of Chemical Education}, number = {3}, pages = {1319--1324}, publisher = {American Chemical Society}, title = {{Short-form videos as an emerging social media tool for STEM edutainment}}, doi = {10.1021/acs.jchemed.3c01185}, volume = {101}, year = {2024}, } @article{17855, abstract = {Biased metal–molecule–metal junctions emit light through electroluminescence, a phenomenon at the intersection of molecular electronics and nanoplasmonics. This can occur when the junction plasmon mode is excited by inelastic electron current fluctuations. Here, we simultaneously measure the conductance and electroluminescence intensity from single-molecule junctions with time resolution in a solution environment at room temperature. We use current versus bias data to determine the molecular junction transport parameters and then relate these to the expected current shot noise. We find that the electroluminescence signal accurately matches the theoretical prediction of shot-noise-driven emission in a large fraction of the molecular junctions studied. This introduces a novel experimental method for qualitatively estimating finite-frequency shot noise in single-molecule junctions under ambient conditions. We further demonstrate that electroluminescence can be used to obtain the level alignment of the frontier orbital dominating transport in the molecular junction.}, author = {Paoletta, Angela L. and Venkataraman, Latha}, issn = {1530-6984}, journal = {Nano Letters}, number = {6}, pages = {1931--1935}, publisher = {American Chemical Society}, title = {{Determining transmission characteristics from shot-noise-driven electroluminescence in single-molecule junctions}}, doi = {10.1021/acs.nanolett.3c04207}, volume = {24}, year = {2024}, } @article{17856, abstract = {The successful incorporation of molecules as active circuit elements relies on the ability to tune their electronic properties through chemical design. A synthetic strategy that has been used to manipulate and gate circuit conductance involves attaching a pendant substituent along the molecular conduction pathway. However, such a chemical gate has not yet been shown to significantly modify conductance. Here, we report a novel series of triarylmethylium and triangulenium carbocations gated by different substituents coupled to the delocalized conducting orbitals on the molecular backbone through a Fano resonance. By changing the pendant substituents to modulate the position of the Fano resonance and its coupling to the conducting orbitals, we can regulate the junction conductance by a remarkable factor of 450. This work thus provides a new design principle to enable effective chemical gating of single-molecule devices toward effective molecular transistors.}, author = {Prindle, Claudia R. and Shi, Wanzhuo and Li, Liang and Dahl Jensen, Jesper and Laursen, Bo W. and Steigerwald, Michael L. and Nuckolls, Colin and Venkataraman, Latha}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {6}, pages = {3646--3650}, publisher = {American Chemical Society}, title = {{Effective gating in single-molecule junctions through fano resonances}}, doi = {10.1021/jacs.3c14226}, volume = {146}, year = {2024}, } @article{17857, abstract = {Gold–dithiol molecular junctions have been studied both experimentally and theoretically. However, the nature of the gold–thiolate bond as it relates to the solvent has seldom been investigated. It is known that solvents can impact the electronic structure of single-molecule junctions, but the correlation between the solvent and dithiol-linked single-molecule junction conductance is not well understood. We study molecular junctions formed with thiol-terminated phenylenes from both 1-chloronaphthalene and 1-bromonaphthalene solutions. We find that the most probable conductance and the distribution of conductances are both affected by the solvent. First-principles calculations show that junction conductance depends on the binding configurations (adatom, atop, and bridge) of the thiolate on the Au surface, as has been shown previously. More importantly, we find that brominated solvents can restrict the binding of thiols to specific Au sites. This mechanism offers new insight into the effects of the solvent environment on covalent bonding in molecular junctions.}, author = {Dalmieda, Johnson and Shi, Wanzhuo and Li, Liang and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {2}, pages = {703--707}, publisher = {American Chemical Society}, title = {{Solvent-mediated modulation of the Au–S bond in dithiol molecular junctions}}, doi = {10.1021/acs.nanolett.3c04058}, volume = {24}, year = {2024}, } @article{17859, abstract = {The electrostatic environment around nanoscale molecular junctions modulates charge transport; solvents alter this environment. Methods to directly probe solvent effects require correlating measurements of the local electrostatic environment with charge transport across the metal–molecule–metal junction. Here, we measure the conductance and current–voltage characteristics of molecular wires using a scanning tunneling microscope–break junction (STM-BJ) setup in two commonly used solvents. Our results show that the solvent environment induces shifts in molecular conductance, which we quantify, but more importantly we find that the solvent also impacts the magnitude of current rectification in molecular junctions. By incorporating electrochemical impedance spectroscopy into the STM-BJ setup, we measure the capacitance of the dipole layer formed at the metal–solvent interface and show that rectification can be correlated with solvent capacitance. These results provide a method of quantifying the impact of the solvent environment and a path toward improved environmental control of molecular devices.}, author = {Shi, Wanzhuo and Greenwald, Julia E. and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {30}, pages = {9283--9288}, publisher = {American Chemical Society}, title = {{Impact of solvent electrostatic environment on molecular junctions probed via electrochemical impedance spectroscopy}}, doi = {10.1021/acs.nanolett.4c02103}, volume = {24}, year = {2024}, } @article{17885, abstract = {The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.}, author = {Kofler, Lisa and Grundmann, Lorenz and Gerhalter, Magdalena and Prattes, Michael and Merl-Pham, Juliane and Zisser, Gertrude and Grishkovskaya, Irina and Hodirnau, Victor-Valentin and Vareka, Martin and Breinbauer, Rolf and Hauck, Stefanie M. and Haselbach, David and Bergler, Helmut}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation}}, doi = {10.1038/s41467-024-51754-3}, volume = {15}, year = {2024}, } @article{17886, abstract = {Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatially-embedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: (1) the network distribution of neuronal excitability, (2) the distribution of connections between neurons of the network, and (3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models.}, author = {Zendrikov, Dmitrii and Paraskevov, Alexander}, issn = {1879-2782}, journal = {Neural Networks}, publisher = {Elsevier}, title = {{The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks}}, doi = {10.1016/j.neunet.2024.106589}, volume = {180}, year = {2024}, } @article{17887, abstract = {We show convergence of the Navier-Stokes/Allen-Cahn system to a classical sharp interface model for the two-phase flow of two viscous incompressible fluids with same viscosities in a smooth bounded domain in two and three space dimensions as long as a smooth solution of the limit system exists. Moreover, we obtain error estimates with the aid of a relative entropy method. Our results hold provided that the mobility mε>0 in the Allen-Cahn equation tends to zero in a subcritical way, i.e., mε=m0εβ for some β∈(0,2) and m0>0 . The proof proceeds by showing via a relative entropy argument that the solution to the Navier-Stokes/Allen-Cahn system remains close to the solution of a perturbed version of the two-phase flow problem, augmented by an extra mean curvature flow term mεHΓt in the interface motion. In a second step, it is easy to see that the solution to the perturbed problem is close to the original two-phase flow.}, author = {Abels, Helmut and Fischer, Julian L and Moser, Maximilian}, issn = {1432-0673}, journal = {Archive for Rational Mechanics and Analysis}, number = {5}, publisher = {Springer Nature}, title = {{Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system}}, doi = {10.1007/s00205-024-02020-9}, volume = {248}, year = {2024}, } @article{17888, abstract = {Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models. Objectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns. Methods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales. Results: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected. Conclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies.}, author = {Pocull Belles, Guillem and Baskett, Carina and Barton, Nicholas H}, issn = {1572-9761}, journal = {Landscape Ecology}, number = {9}, publisher = {Springer Nature}, title = {{Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects}}, doi = {10.1007/s10980-024-01899-9}, volume = {39}, year = {2024}, } @article{17889, abstract = {The increasingly neutral intergalactic gas at z > 6 impacts the Lyman-α (Lyα) flux observed from galaxies. One luminous galaxy, COLA1, stands out because of its unique double-peaked Lyα line at z = 6.6, unseen in any simulation of reionization. Here, we present JWST/NIRCam wide-field slitless spectroscopy in a 21 arcmin2 field centered on COLA1. We find 141 galaxies spectroscopically selected through the [O III] doublet at 5.35 < z < 6.95, with 40 of these sources showing Hβ. For COLA1, we additionally detect [O III]4363 as well as Hγ. We measure a systemic redshift of z = 6.5917 for COLA1, confirming the classical double-peak nature of the Lyα profile. This implies that it resides in a highly ionized bubble and that it is leaking ionizing photons with a high escape fraction of fesc(LyC) = 20–50%, making it a prime laboratory to study Lyman continuum escape in the Epoch of Reionization. COLA1 shows all the signs of a prolific ionizer with a Lyα escape fraction of 81 ± 5%, Balmer decrement indicating no dust, a steep UV slope (βUV = −3.2 ± 0.4), and a star-formation surface density ≳10× that of typical galaxies at similar redshift. We detect five galaxies in COLA1’s close environment (Δz < 0.02). Exploiting the high spectroscopic completeness inherent to grism surveys, and using mock simulations that fully mimic the selection function, we show that the number of detected companions is very typical for a normal similarly UV-bright (MUV ∼ −21.3) galaxy – that is, the ionized bubble around COLA1 is unlikely to be due to an excessively large over-density. Instead, the measured ionizing properties suggest that COLA1 by itself might be powering the bubble required to explain its double-peaked Lyα profile (Rion ≈ 0.7 pMpc), with only minor contributions from detected neighbors (−19.5 ≲ MUV ≲ −17.5).}, author = {Torralba-Torregrosa, Alberto and Matthee, Jorryt J and Naidu, Rohan P. and Mackenzie, Ruari and Pezzulli, Gabriele and Hutter, Anne and Arnalte-Mur, Pablo and Gurung-López, Siddhartha and Tacchella, Sandro and Oesch, Pascal and Kashino, Daichi and Conroy, Charlie and Sobral, David}, issn = {1432-0746}, journal = {Astronomy and Astrophysics}, publisher = {EDP Sciences}, title = {{Anatomy of an ionized bubble: NIRCam grism spectroscopy of the z = 6.6 double-peaked Lyman- α emitter COLA1 and its environment}}, doi = {10.1051/0004-6361/202450318}, volume = {689}, year = {2024}, } @article{17891, abstract = {Abstract Methods used in topological data analysis naturally capture higher-order interactions in point cloud data embedded in a metric space. This methodology was recently extended to data living in an information space, by which we mean a space measured with an information theoretical distance. One such setting is a finite collection of discrete probability distributions embedded in the probability simplex measured with the relative entropy (Kullback–Leibler divergence). More generally, one can work with a Bregman divergence parameterized by a different notion of entropy. While theoretical algorithms exist for this setup, there is a paucity of implementations for exploring and comparing geometric-topological properties of various information spaces. The interest of this work is therefore twofold. First, we propose the first robust algorithms and software for geometric and topological data analysis in information space. Perhaps surprisingly, despite working with Bregman divergences, our design reuses robust libraries for the Euclidean case. Second, using the new software, we take the first steps towards understanding the geometric-topological structure of these spaces. In particular, we compare them with the more familiar spaces equipped with the Euclidean and Fisher metrics.}, author = {Edelsbrunner, Herbert and Ölsböck, Katharina and Wagner, Hubert}, issn = {1099-4300}, journal = {Entropy}, number = {8}, publisher = {MDPI}, title = {{Understanding higher-order interactions in information space}}, doi = {10.3390/e26080637}, volume = {26}, year = {2024}, } @article{17892, abstract = {Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)⁢(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate.}, author = {Olmeda, Fabrizio and Rulands, Steffen}, issn = {2470-0053}, journal = {Physical Review E}, number = {2}, publisher = {American Physical Society}, title = {{Field theory of enzyme-substrate systems with restricted long-range interactions}}, doi = {10.1103/PhysRevE.110.024404}, volume = {110}, year = {2024}, }