@article{14603, abstract = {Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.}, author = {Reinhardt, Aleks and Chew, Pin Yu and Cheng, Bingqing}, issn = {1089-7690}, journal = {Journal of Chemical Physics}, number = {18}, publisher = {AIP Publishing}, title = {{A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals}}, doi = {10.1063/5.0173341}, volume = {159}, year = {2023}, } @article{14604, abstract = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.}, author = {Toups, Melissa A and Vicoso, Beatriz}, issn = {1558-5646}, journal = {Evolution}, number = {11}, pages = {2504--2511}, publisher = {Oxford University Press}, title = {{The X chromosome of insects likely predates the origin of class Insecta}}, doi = {10.1093/evolut/qpad169}, volume = {77}, year = {2023}, } @misc{14616, abstract = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.}, author = {Toups, Melissa A and Vicoso, Beatriz}, publisher = {Dryad}, title = {{The X chromosome of insects likely predates the origin of Class Insecta}}, doi = {10.5061/DRYAD.HX3FFBGKT}, year = {2023}, } @misc{14617, abstract = {Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.}, author = {Toups, Melissa A and Vicoso, Beatriz}, publisher = {Zenodo}, title = {{The X chromosome of insects likely predates the origin of Class Insecta}}, doi = {10.5281/ZENODO.8138705}, year = {2023}, } @misc{14619, abstract = {Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).}, author = {Cheng, Bingqing}, publisher = {Zenodo}, title = {{BingqingCheng/solubility: V1.0}}, doi = {10.5281/ZENODO.8398094}, year = {2023}, } @article{14564, abstract = {Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized.}, author = {Khouider, B. and GOSWAMI, BIDYUT B and Phani, R. and Majda, A. J.}, issn = {1942-2466}, journal = {Journal of Advances in Modeling Earth Systems}, keywords = {General Earth and Planetary Sciences, Environmental Chemistry, Global and Planetary Change}, number = {11}, publisher = {American Geophysical Union}, title = {{A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model}}, doi = {10.1029/2022ms003391}, volume = {15}, year = {2023}, } @article{12789, abstract = {Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.}, author = {Mujica, Nicolás and Waitukaitis, Scott R}, issn = {2470-0053}, journal = {Physical Review E}, number = {3}, publisher = {American Physical Society}, title = {{Accurate determination of the shapes of granular charge distributions}}, doi = {10.1103/PhysRevE.107.034901}, volume = {107}, year = {2023}, } @inproceedings{13238, abstract = {We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0. .}, author = {Schmid, Stefan and Svoboda, Jakub and Yeo, Michelle X}, booktitle = {SIROCCO 2023: Structural Information and Communication Complexity }, isbn = {9783031327322}, issn = {1611-3349}, location = {Alcala de Henares, Spain}, pages = {576--594}, publisher = {Springer Nature}, title = {{Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation}}, doi = {10.1007/978-3-031-32733-9_26}, volume = {13892}, year = {2023}, } @phdthesis{14506, abstract = {Payment channel networks are a promising approach to improve the scalability bottleneck of cryptocurrencies. Two design principles behind payment channel networks are efficiency and privacy. Payment channel networks improve efficiency by allowing users to transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding the lengthy process of consensus on the blockchain. Transacting over payment channel networks also improves privacy as these transactions are not broadcast to the blockchain. Despite the influx of recent protocols built on top of payment channel networks and their analysis, a common shortcoming of many of these protocols is that they typically focus only on either improving efficiency or privacy, but not both. Another limitation on the efficiency front is that the models used to model actions, costs and utilities of users are limited or come with unrealistic assumptions. This thesis aims to address some of the shortcomings of recent protocols and algorithms on payment channel networks, particularly in their privacy and efficiency aspects. We first present a payment route discovery protocol based on hub labelling and private information retrieval that hides the route query and is also efficient. We then present a rebalancing protocol that formulates the rebalancing problem as a linear program and solves the linear program using multiparty computation so as to hide the channel balances. The rebalancing solution as output by our protocol is also globally optimal. We go on to develop more realistic models of the action space, costs, and utilities of both existing and new users that want to join the network. In each of these settings, we also develop algorithms to optimise the utility of these users with good guarantees on the approximation and competitive ratios.}, author = {Yeo, Michelle X}, issn = {2663 - 337X}, pages = {162}, publisher = {Institute of Science and Technology Austria}, title = {{Advances in efficiency and privacy in payment channel network analysis}}, doi = {10.15479/14506}, year = {2023}, } @inproceedings{14490, abstract = {Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium.}, author = {Avarikioti, Zeta and Lizurej, Tomasz and Michalak, Tomasz and Yeo, Michelle X}, booktitle = {43rd International Conference on Distributed Computing Systems}, isbn = {9798350339864}, issn = {2575-8411}, location = {Hong Kong, China}, pages = {603--613}, publisher = {IEEE}, title = {{Lightning creation games}}, doi = {10.1109/ICDCS57875.2023.00037}, volume = {2023}, year = {2023}, } @phdthesis{12726, abstract = {Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self–sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub–population in the developing cortex.}, author = {Riedl, Michael}, issn = {2663-337X}, pages = {260}, publisher = {Institute of Science and Technology Austria}, title = {{Synchronization in collectively moving active matter}}, doi = {10.15479/at:ista:12726}, year = {2023}, } @phdthesis{14530, abstract = {Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. }, author = {Riedl, Michael}, issn = {2663 - 337X}, keywords = {Synchronization, Collective Movement, Active Matter, Cell Migration, Active Colloids}, pages = {260}, publisher = {Institute of Science and Technology Austria}, title = {{Synchronization in collectively moving active matter}}, doi = {10.15479/14530}, year = {2023}, } @phdthesis{14547, abstract = {Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation. Despite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood. In this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. The second focuses on a technological application, a gate-tunable Josephson parametric amplifier. In the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well. We embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance. The behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \pm ip$ pairing in InAs. Measuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory. We observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory. In contrast, the data can be captured quantitatively by fitting to a two-component model. We find the evidence of the intraband $p \pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\mathrm{T}$. From the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined. By systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle. Strong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data. In the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element. The device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator. By applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz. Modelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage. We observed gate-tunable Kerr nonlinearity qualitatively in line with expectation. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency. In general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared. The noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier. As a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account. We found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier.}, author = {Phan, Duc T}, issn = {2663 - 337X}, keywords = {superconductor-semiconductor, superconductivity, Al, InAs, p-wave, superconductivity, JPA, microwave}, pages = {80}, publisher = {Institute of Science and Technology Austria}, title = {{Resonant microwave spectroscopy of Al-InAs}}, doi = {10.15479/14547}, year = {2023}, } @article{13264, abstract = {We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency. }, author = {Phan, Duc T and Falthansl-Scheinecker, Paul and Mishra, Umang and Strickland, W. M. and Langone, D. and Shabani, J. and Higginbotham, Andrew P}, issn = {2331-7019}, journal = {Physical Review Applied}, number = {6}, publisher = {American Physical Society}, title = {{Gate-tunable superconductor-semiconductor parametric amplifier}}, doi = {10.1103/PhysRevApplied.19.064032}, volume = {19}, year = {2023}, } @unpublished{14591, abstract = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.}, author = {Gnyliukh, Nataliia and Johnson, Alexander J and Nagel, Marie-Kristin and Monzer, Aline and Hlavata, Annamaria and Isono, Erika and Loose, Martin and Friml, Jiří}, booktitle = {bioRxiv}, title = {{Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants}}, doi = {10.1101/2023.10.09.561523}, year = {2023}, } @article{14639, abstract = {Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship. Methods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity. Results: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy. Conclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”.}, author = {Lin, Sheng-Jia and Vona, Barbara and Lau, Tracy and Huang, Kevin and Zaki, Maha S. and Aldeen, Huda Shujaa and Karimiani, Ehsan Ghayoor and Rocca, Clarissa and Noureldeen, Mahmoud M. and Saad, Ahmed K. and Petree, Cassidy and Bartolomaeus, Tobias and Abou Jamra, Rami and Zifarelli, Giovanni and Gotkhindikar, Aditi and Wentzensen, Ingrid M. and Liao, Mingjuan and Cork, Emalyn Elise and Varshney, Pratishtha and Hashemi, Narges and Mohammadi, Mohammad Hasan and Rad, Aboulfazl and Neira, Juanita and Toosi, Mehran Beiraghi and Knopp, Cordula and Kurth, Ingo and Challman, Thomas D. and Smith, Rebecca and Abdalla, Asmahan and Haaf, Thomas and Suri, Mohnish and Joshi, Manali and Chung, Wendy K. and Moreno-De-Luca, Andres and Houlden, Henry and Maroofian, Reza and Varshney, Gaurav K.}, issn = {1756-994X}, journal = {Genome Medicine}, keywords = {Genetics (clinical), Genetics, Molecular Biology, Molecular Medicine}, publisher = {Springer Nature}, title = {{Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity}}, doi = {10.1186/s13073-023-01258-4}, volume = {15}, year = {2023}, } @article{14628, abstract = {We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration.}, author = {Makatura, Liane and Wang, Bohan and Chen, Yi-Lu and Deng, Bolei and Wojtan, Christopher J and Bickel, Bernd and Matusik, Wojciech}, issn = {0730-0301}, journal = {ACM Transactions on Graphics}, keywords = {Computer Graphics and Computer-Aided Design}, number = {5}, publisher = {Association for Computing Machinery}, title = {{Procedural metamaterials: A unified procedural graph for metamaterial design}}, doi = {10.1145/3605389}, volume = {42}, year = {2023}, } @unpublished{14644, abstract = {Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression.}, author = {Tluckova, Katarina and Testa Salmazo, Anita P and Bernecky, Carrie A}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanism of mammalian transcriptional repression by noncoding RNA}}, doi = {10.15479/AT:ISTA:14644}, year = {2023}, } @article{14658, abstract = {We investigate spin-charge separation of a spin- 1 2 Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom.}, author = {Becker, J. M. and Koutentakis, Georgios and Schmelcher, P.}, issn = {2643-1564}, journal = {Physical Review Research}, number = {4}, publisher = {American Physical Society}, title = {{Spin-charge correlations in finite one-dimensional multiband Fermi systems}}, doi = {10.1103/PhysRevResearch.5.043039}, volume = {5}, year = {2023}, } @article{14650, abstract = {We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures.}, author = {Volosniev, Artem and Bighin, Giacomo and Santos, Luis and Peña Ardila, Luisllu A.}, issn = {2542-4653}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {6}, publisher = {SciPost Foundation}, title = {{Non-equilibrium dynamics of dipolar polarons}}, doi = {10.21468/scipostphys.15.6.232}, volume = {15}, year = {2023}, }