@article{17291, abstract = {Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13Csingle bond13C and heteronuclear 1Hsingle bond15N, 1Hsingle bond13C and 15Nsingle bond13C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3–4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples.}, author = {Vallet, Alicia and Ayala, Isabel and Perrone, Barbara and Hassan, Alia and Simorre, Jean-Pierre and Bougault, Catherine and Schanda, Paul}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, publisher = {Elsevier}, title = {{MAS NMR experiments of corynebacterial cell walls: Complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments}}, doi = {10.1016/j.jmr.2024.107708}, volume = {364}, year = {2024}, } @misc{17344, abstract = {This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. }, author = {Surendranadh, Parvathy and Sachdeva, Himani}, publisher = {Institute of Science and Technology Austria}, title = {{Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'}}, doi = {10.15479/AT:ISTA:17344}, year = {2024}, } @article{17480, abstract = {One of the most promising approaches towards large-scale quantum computation uses devices based on many Josephson junctions. Yet, even today, open questions regarding the single junction remain unsolved, such as the detailed understanding of the quantum phase transitions, the coupling of the Josephson junction to the environment or how to improve the coherence of a superconducting qubit. Here we design and build an engineered on-chip reservoir connected to a Josephson junction that acts as an efficient bolometer for detecting the Josephson radiation under non-equilibrium, that is, biased conditions. The bolometer converts the a.c. Josephson current at microwave frequencies up to about 100 GHz into a temperature rise measured by d.c. thermometry. A circuit model based on realistic parameter values captures both the current–voltage characteristics and the measured power quantitatively. The present experiment demonstrates an efficient, wide-band, thermal detection scheme of microwave photons and provides a sensitive detector of Josephson dynamics beyond the standard conductance measurements.}, author = {Karimi, Bayan and Steffensen, Gorm Ole and Higginbotham, Andrew P and Marcus, Charles M. and Levy Yeyati, Alfredo and Pekola, Jukka P.}, issn = {1748-3395}, journal = {Nature Nanotechnology}, pages = {1613--1618}, publisher = {Springer Nature}, title = {{Bolometric detection of Josephson radiation}}, doi = {10.1038/s41565-024-01770-7}, volume = {19}, year = {2024}, } @inbook{18167, abstract = {Holdase chaperones are essential in the mitochondrial membrane-protein biogenesis as they stabilize preproteins and keep them in an import-competent state as they travel through the aqueous cytosol and intermembrane space. The small TIM chaperones of the mitochondrial intermembrane space function within a fine balance of client promiscuity and high affinity binding, while being also able to release their client proteins without significant energy barrier to the downstream insertases/translocases. The tendency of the preproteins to aggregate and the dynamic nature of the preprotein—chaperone complexes makes the preparation of these complexes challenging. Here we present two optimized methods for complex formation of highly hydrophobic precursor proteins and chaperones: a pull-down approach and an in-vitro translation strategy. In the former, attaching the client protein to an affinity resin keeps the individual client protein copies apart from each other and decreases the client self-aggregation probability, thereby favouring complex formation. In the latter approach, a purified chaperone, added to the cell-free protein synthesis, captures the nascent precursor protein. The choice of method will depend on the desired client-chaperone complex amount, or the need for specific labeling scheme.}, author = {Guillerm, Undina and Sučec, Iva and Schanda, Paul}, booktitle = {Methods in Enzymology}, issn = {0076-6879}, pages = {391--422}, publisher = {Elsevier}, title = {{Generation of TIM chaperone substrate complexes}}, doi = {10.1016/bs.mie.2024.07.051}, volume = {707}, year = {2024}, } @unpublished{20701, abstract = {A Proof of Exponentiation (PoE) allows a prover to efficiently convince a verifier that 𝑦 = 𝑥 𝑒 in some group of unknown order. PoEs are the basis for practical constructions of Verifiable Delay Functions (VDFs), which, in turn, are important for various higher-level protocols in distributed computing. In applications such as distributed consensus, many PoEs are generated regularly, motivating protocols for secure aggregation of batches of statements into a few statements to improve the efficiency for both parties. Rotem (TCC 2021) recently presented two such generic batch PoEs. In this work, we introduce two batch PoEs that outperform both proposals of Rotem and we evaluate their practicality. First, we show that the two batch PoEs of Rotem can be combined to improve the overall efficiency by at least a factor of two. Second, we revisit the work of Bellare, Garay, and Rabin (EUROCRYPT 1998) on batch verification of digital signatures and show that, under the low order assumption, their bucket test can be securely adapted to the setting of groups of unknown order. The resulting batch PoE quickly outperforms the state of the art in the expected number of group multiplications with the growing number of instances, and it decreases the cost of batching by an order of magnitude already for hundreds of thousands of instances. Importantly, it is the first batch PoE that significantly decreases both the proof size and complexity of verification. Our experimental evaluations show that even a nonoptimized implementation achieves such improvements, which would match the demands of real-life systems requiring large-scale PoE processing. Finally, even though our proof techniques are conceptually similar to Rotem, we give an improved analysis of the application of the low order assumption towards secure batching of PoE instances, resulting in a tight reduction, which is important when setting the security parameter in practice.}, author = {Hoffmann, Charlotte and Hubáček, Pavel and Ivanova, Svetlana}, booktitle = {Cryptology ePrint Archive}, publisher = {International Association for Cryptologic Research}, title = {{Practical batch proofs of exponentiation}}, year = {2024}, } @unpublished{19425, abstract = {We demonstrate that periodically driven quantum rotors provide a promising and broadly applicable platform to implement multi-gap topological phases, where groups of bands can acquire topological invariants due to non-Abelian braiding of band degeneracies. By adiabatically varying the periodic kicks to the rotor we find nodal-line braiding, which causes sign flips of topological charges of band nodes and can prevent them from annihilating, indicated by non-zero values of the %non-Abelian patch Euler class. In particular, we report on the emergence of an anomalous Dirac string phase arising in the strongly driven regime, a truly out-of-equilibrium phase of the quantum rotor. This phase emanates from braiding processes involving all (quasienergy) gaps and manifests itself with edge states at zero angular momentum. Our results reveal direct applications in state-of-the-art experiments of quantum rotors, such as linear molecules driven by periodic far-off-resonant laser pulses or artificial quantum rotors in optical lattices, whose extensive versatility offers precise modification and observation of novel non-Abelian topological properties. }, author = {Karle, Volker and Lemeshko, Mikhail and Bouhon, Adrien and Slager, Robert-Jan and Ünal, F. Nur}, booktitle = {arXiv}, title = {{Anomalous multi-gap topological phases in periodically driven quantum rotors}}, doi = {10.48550/arXiv.2408.16848}, year = {2024}, } @article{19051, abstract = {This paper corrects an error in an earlier work of the author.}, author = {Browning, Timothy D}, issn = {1687-0247}, journal = {International Mathematics Research Notices}, number = {13}, pages = {10165--10168}, publisher = {Oxford University Press}, title = {{The polynomial sieve and equal sums of like polynomials}}, doi = {10.1093/imrn/rnae066}, volume = {2024}, year = {2024}, } @unpublished{20071, abstract = {Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take "infinite values".}, author = {Dvorak, Martin and Kolmogorov, Vladimir}, booktitle = {arXiv}, keywords = {Farkas lemma, linear programming, extended reals, calculus of inductive constructions}, title = {{Duality theory in linear optimization and its extensions -- formally verified}}, doi = {10.48550/arXiv.2409.08119}, year = {2024}, } @unpublished{19545, abstract = {We prove the Eigenstate Thermalisation Hypothesis for Wigner matrices uniformly in the entire spectrum, in particular near the spectral edges, with a bound on the fluctuation that is optimal for any observable. This complements earlier works of Cipolloni et. al. (Comm. Math. Phys. 388, 2021; Forum Math., Sigma 10, 2022) and Benigni et. al. (Comm. Math. Phys. 391, 2022; arXiv: 2303.11142) that were restricted either to the bulk of the spectrum or to special observables. As a main ingredient, we prove a new multi-resolvent local law that optimally accounts for the edge scaling.}, author = {Cipolloni, Giorgio and Erdös, László and Henheik, Sven Joscha}, booktitle = {arXiv}, title = {{Eigenstate thermalisation at the edge for Wigner matrices}}, doi = {10.48550/arXiv.2309.05488}, year = {2024}, } @unpublished{19550, abstract = {We introduce a multi-band BCS free energy functional and prove that for a multi-band superconductor the effect of inter-band coupling can only increase the critical temperature, irrespective of its attractive or repulsive nature and its strength. Further, for weak coupling and weaker inter-band coupling, we prove that the dependence of the increase in critical temperature on the inter-band coupling is (1) linear, if there are two or more equally strongly superconducting bands, or (2) quadratic, if there is only one dominating band.}, author = {Henheik, Sven Joscha and Langmann, Edwin and Lauritsen, Asbjørn Bækgaard}, booktitle = {arXiv}, title = {{Multi-band superconductors have enhanced critical temperatures}}, doi = {10.48550/arXiv.2409.17297}, year = {2024}, } @unpublished{19547, abstract = {For correlated real symmetric or complex Hermitian random matrices, we prove that the local eigenvalue statistics at any cusp singularity are universal. Since the density of states typically exhibits only square root edge or cubic root cusp singularities, our result completes the proof of the Wigner-Dyson-Mehta universality conjecture in all spectral regimes for a very general class of random matrices. Previously only the bulk and the edge universality were established in this generality [arXiv:1804.07744], while cusp universality was proven only for Wigner-type matrices with independent entries [arXiv:1809.03971, arXiv:1811.04055]. As our main technical input, we prove an optimal local law at the cusp using the Zigzag strategy, a recursive tandem of the characteristic flow method and a Green function comparison argument. Moreover, our proof of the optimal local law holds uniformly in the spectrum, thus also re-establishing universality of the local eigenvalue statistics in the previously studied bulk [arXiv:1705.10661] and edge [arXiv:1804.07744] regimes.}, author = {Erdös, László and Henheik, Sven Joscha and Riabov, Volodymyr}, booktitle = {arXiv}, title = {{Cusp universality for correlated random matrices}}, doi = {10.48550/arXiv.2410.06813}, year = {2024}, } @unpublished{19551, abstract = {We introduce a notion of a \emph{local gap} for interacting many-body quantum lattice systems and prove the validity of response theory and Kubo's formula for localized perturbations in such settings. On a high level, our result shows that the usual spectral gap condition, concerning the system as a whole, is not a necessary condition for understanding local properties of the system. More precisely, we say that an equilibrium state ρ0 of a Hamiltonian H0 is locally gapped in Λgap⊂Λ, whenever the Liouvillian −i[H0,⋅] is almost invertible on local observables supported in Λgap when tested in ρ0. To put this into context, we provide other alternative notions of a local gap and discuss their relations. The validity of response theory is based on the construction of \emph{non-equilibrium almost stationary states} (NEASSs). By controlling locality properties of the NEASS construction, we show that response theory holds to any order, whenever the perturbation \(\epsilon V\) acts in a region which is further than |logϵ| away from the non-gapped region Λ∖Λgap.}, author = {Henheik, Sven Joscha and Wessel, Tom}, booktitle = {arXiv}, title = {{Response theory for locally gapped systems}}, doi = {10.48550/arXiv.2410.10809}, year = {2024}, } @article{15359, abstract = {Molecular dynamics (MD) simulations play an important role in understanding and engineering heat transport properties of complex materials. An essential requirement for reliably predicting heat transport properties is the use of accurate and efficient interatomic potentials. Recently, machine-learned potentials (MLPs) have shown great promise in providing the required accuracy for a broad range of materials. In this mini-review and tutorial, we delve into the fundamentals of heat transport, explore pertinent MD simulation methods, and survey the applications of MLPs in MD simulations of heat transport. Furthermore, we provide a step-by-step tutorial on developing MLPs for highly efficient and predictive heat transport simulations, utilizing the neuroevolution potentials as implemented in the GPUMD package. Our aim with this mini-review and tutorial is to empower researchers with valuable insights into cutting-edge methodologies that can significantly enhance the accuracy and efficiency of MD simulations for heat transport studies.}, author = {Dong, Haikuan and Shi, Yongbo and Ying, Penghua and Xu, Ke and Liang, Ting and Wang, Yanzhou and Zeng, Zezhu and Wu, Xin and Zhou, Wenjiang and Xiong, Shiyun and Chen, Shunda and Fan, Zheyong}, issn = {1089-7550}, journal = {Journal of Applied Physics}, number = {16}, publisher = {AIP Publishing}, title = {{Molecular dynamics simulations of heat transport using machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution potentials}}, doi = {10.1063/5.0200833}, volume = {135}, year = {2024}, } @article{17278, abstract = {An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult due to the complexities and convergence problems of Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes, or lack thereof, in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes and reveal that they tend to form when the mixture components have similar boiling points and strong interactions.}, author = {Wang, Xiaoyu and Cheng, Bingqing}, issn = {1089-7690}, journal = {Journal of Chemical Physics}, number = {3}, publisher = {AIP Publishing}, title = {{Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures}}, doi = {10.1063/5.0217232}, volume = {161}, year = {2024}, } @misc{22234, abstract = {Lists of nontrivial integral points on some (families of) cubic surfaces. (2024-07-18)}, author = {Browning, Timothy D and Sutherland, Andrew}, publisher = {Göttingen Research Online Data}, title = {{Data and code for: Integral points on cubic surfaces: heuristics and numerics}}, doi = {10.25625/4FLFH8}, year = {2024}, } @unpublished{19063, abstract = {Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed. }, author = {Zverev, Egor and Abdelnabi, Sahar and Tabesh, Soroush and Fritz, Mario and Lampert, Christoph}, booktitle = {arXiv}, title = {{Can LLMs separate instructions from data? And what do we even mean by that?}}, doi = {10.48550/arXiv.2403.06833}, year = {2024}, } @article{17161, abstract = {Dynamic processes in molecules can occur on a wide range of timescales, and it is important to understand which timescales of motion contribute to different parameters used in dynamics measurements. For spin relaxation, this can easily be understood from the sampling frequencies of the spectral-density function by different relaxation-rate constants. In addition to data from relaxation measurements, determining dynamically averaged anisotropic interactions in magic-angle spinning (MAS) solid-state NMR allows for better quantification of the amplitude of molecular motion. For partially averaged anisotropic interactions, the relevant timescales of motion are not so clearly defined. Whether the averaging depends on the experimental methods (e.g., pulse sequences) or conditions (e.g., MAS frequency, magnitude of anisotropic interaction, radio-frequency field amplitudes) is not fully understood. To investigate these questions, we performed numerical simulations of dynamic systems based on the stochastic Liouville equation using several experiments for recoupling the dipolar coupling, chemical-shift anisotropy or quadrupolar coupling. As described in the literature, the transition between slow motion, where parameters characterizing the anisotropic interaction are not averaged, and fast motion, where the tensors are averaged leading to a scaled anisotropic quantity, occurs over a window of motional rate constants that depends mainly on the strength of the interaction. This transition region can span 2 orders of magnitude in exchange-rate constants (typically in the microsecond range) but depends only marginally on the employed recoupling scheme or sample spinning frequency. The transition region often coincides with a fast relaxation of coherences, making precise quantitative measurements difficult. Residual couplings in off-magic-angle experiments, however, average over longer timescales of motion. While in principle one may gain information on the timescales of motion from the transition area, extracting such information is hampered by low signal-to-noise ratio in experimental spectra due to fast relaxation that occurs in the same region.}, author = {Aebischer, Kathrin and Becker, Lea Marie and Schanda, Paul and Ernst, Matthias}, issn = {2699-0016}, journal = {Magnetic Resonance}, number = {1}, pages = {69--86}, publisher = {Copernicus Publications}, title = {{Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR}}, doi = {10.5194/mr-5-69-2024}, volume = {5}, year = {2024}, } @misc{22906, author = {Aebischer, Kathrin}, publisher = {Repository}, title = {{Evaluating the motional time scales contributing to averaged anisotropic interactions in MAS solid-state NMR}}, doi = {10.3929/ethz-b-000666765}, year = {2024}, } @article{18603, abstract = {It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the rodent hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.}, author = {Kim, Olena and Okamoto, Yuji and Kaufmann, Walter and Brose, Nils and Shigemoto, Ryuichi and Jonas, Peter M}, issn = {1545-7885}, journal = {PLoS Biology}, number = {11}, publisher = {Public Library of Science}, title = {{Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons}}, doi = {10.1371/journal.pbio.3002879}, volume = {22}, year = {2024}, } @misc{18296, abstract = {It is widely believed that information storage in neuronal circuits involves nanoscopic structural changes at synapses, resulting in the formation of synaptic engrams. However, direct evidence for this hypothesis is lacking. To test this conjecture, we combined chemical potentiation, functional analysis by paired pre-postsynaptic recordings, and structural analysis by electron microscopy (EM) and freeze-fracture replica labeling (FRL) at the murine hippocampal mossy fiber synapse, a key synapse in the trisynaptic circuit of the hippocampus. Biophysical analysis of synaptic transmission revealed that forskolin-induced chemical potentiation increased the readily releasable vesicle pool size and vesicular release probability by 146% and 49%, respectively. Structural analysis of mossy fiber synapses by EM and FRL demonstrated an increase in the number of vesicles close to the plasma membrane and the number of clusters of the priming protein Munc13-1, indicating an increase in the number of both docked and primed vesicles. Furthermore, FRL analysis revealed a significant reduction of the distance between Munc13-1 and CaV2.1 Ca2+ channels, suggesting reconfiguration of the channel-vesicle coupling nanotopography. Our results indicate that presynaptic plasticity is associated with structural reorganization of active zones. We propose that changes in potential nanoscopic organization at synaptic vesicle release sites may be correlates of learning and memory at a plastic central synapse.}, author = {Kim, Olena}, keywords = {Hippocampal mossy fiber synapses, short-term potentiation, long-term potentiation, presynaptic plasticity, electron microscopy, freeze-fracture replica labeling, paired recordings, forskolin, cyclic adenosine monophosphate (cAMP), protein kinase A (PKA), neuromodulation, synaptic vesicle pools, presynaptic Ca2+ channels, Munc13, docking, priming, active zone}, publisher = {Institute of Science and Technology Austria}, title = {{Presynaptic cAMP-PKA-mediated potentiation induces reconfiguration of synaptic vesicle pools and channel-vesicle coupling at hippocampal mossy fiber boutons}}, doi = {10.15479/AT:ISTA:18296}, year = {2024}, }