@article{12880, abstract = {Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.}, author = {Kaneshiro, Jeanae M. and Capitanio, Juliana S. and Hetzer, Martin W}, issn = {1949-1042}, journal = {Nucleus}, number = {1}, publisher = {Taylor & Francis}, title = {{Lamin B1 overexpression alters chromatin organization and gene expression}}, doi = {10.1080/19491034.2023.2202548}, volume = {14}, year = {2023}, } @article{12914, abstract = {We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier.}, author = {Suzuki, Fumika and Unruh, William G.}, issn = {2469-9934}, journal = {Physical Review A}, number = {4}, publisher = {American Physical Society}, title = {{Numerical quantum clock simulations for measuring tunneling times}}, doi = {10.1103/PhysRevA.107.042216}, volume = {107}, year = {2023}, } @article{12913, abstract = {The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices.}, author = {Díez-Mérida, J. and Díez-Carlón, A. and Yang, S. Y. and Xie, Y. M. and Gao, X. J. and Senior, Jorden L and Watanabe, K. and Taniguchi, T. and Lu, X. and Higginbotham, Andrew P and Law, K. T. and Efetov, Dmitri K.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene}}, doi = {10.1038/s41467-023-38005-7}, volume = {14}, year = {2023}, } @article{10550, abstract = {The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter.}, author = {Fellner, Klemens and Fischer, Julian L and Kniely, Michael and Tang, Bao Quoc}, issn = {1432-1467}, journal = {Journal of Nonlinear Science}, publisher = {Springer Nature}, title = {{Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion}}, doi = {10.1007/s00332-023-09926-w}, volume = {33}, year = {2023}, } @article{13043, abstract = {We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction of a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such cluster. This extends the two-dimensional construction to the three-dimensional case of surfaces meeting along triple junctions.}, author = {Hensel, Sebastian and Laux, Tim}, issn = {1463-9971}, journal = {Interfaces and Free Boundaries}, number = {1}, pages = {37--107}, publisher = {EMS Press}, title = {{Weak-strong uniqueness for the mean curvature flow of double bubbles}}, doi = {10.4171/IFB/484}, volume = {25}, year = {2023}, } @article{12912, abstract = {The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.}, author = {Schmid, Rochus and Cheng, Bingqing}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, number = {16}, publisher = {AIP Publishing}, title = {{Computing chemical potentials of adsorbed or confined fluids}}, doi = {10.1063/5.0146711}, volume = {158}, year = {2023}, } @article{12972, abstract = {Embroidery is a long-standing and high-quality approach to making logos and images on textiles. Nowadays, it can also be performed via automated machines that weave threads with high spatial accuracy. A characteristic feature of the appearance of the threads is a high degree of anisotropy. The anisotropic behavior is caused by depositing thin but long strings of thread. As a result, the stitched patterns convey both color and direction. Artists leverage this anisotropic behavior to enhance pure color images with textures, illusions of motion, or depth cues. However, designing colorful embroidery patterns with prescribed directionality is a challenging task, one usually requiring an expert designer. In this work, we propose an interactive algorithm that generates machine-fabricable embroidery patterns from multi-chromatic images equipped with user-specified directionality fields.We cast the problem of finding a stitching pattern into vector theory. To find a suitable stitching pattern, we extract sources and sinks from the divergence field of the vector field extracted from the input and use them to trace streamlines. We further optimize the streamlines to guarantee a smooth and connected stitching pattern. The generated patterns approximate the color distribution constrained by the directionality field. To allow for further artistic control, the trade-off between color match and directionality match can be interactively explored via an intuitive slider. We showcase our approach by fabricating several embroidery paths.}, author = {Liu, Zhenyuan and Piovarci, Michael and Hafner, Christian and Charrondiere, Raphael and Bickel, Bernd}, issn = {1467-8659}, journal = {Computer Graphics Forum}, keywords = {embroidery, design, directionality, density, image}, location = {Saarbrucken, Germany}, number = {2}, pages = {397--409}, publisher = {Wiley}, title = {{Directionality-aware design of embroidery patterns}}, doi = {10.1111/cgf.14770 }, volume = {42}, year = {2023}, } @article{13033, abstract = {Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.}, author = {Zavadakova, Anna and Vistejnova, Lucie and Belinova, Tereza and Tichanek, Filip and Bilikova, Dagmar and Mouton, Peter R.}, issn = {2045-2322}, journal = {Scientific Reports}, keywords = {Multidisciplinary}, number = {1}, publisher = {Springer Nature}, title = {{Novel stereological method for estimation of cell counts in 3D collagen scaffolds}}, doi = {10.1038/s41598-023-35162-z}, volume = {13}, year = {2023}, } @article{13095, abstract = {Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.}, author = {Troussicot, Laura and Vallet, Alicia and Molin, Mikael and Burmann, Björn M. and Schanda, Paul}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {19}, pages = {10700–10711}, publisher = {American Chemical Society}, title = {{Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR}}, doi = {10.1021/jacs.3c01200}, volume = {145}, year = {2023}, } @article{13042, abstract = {Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant. We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s. for c>20, thus extending a result of Frieze and the author to smaller values of c. Thereafter, for c>20, we determine the limit of the probability that G(n, c/n)contains cycles of every length between the length of its shortest and its longest cycles as n→∞.}, author = {Anastos, Michael}, issn = {1077-8926}, journal = {Electronic Journal of Combinatorics}, number = {2}, publisher = {Electronic Journal of Combinatorics}, title = {{A note on long cycles in sparse random graphs}}, doi = {10.37236/11471}, volume = {30}, year = {2023}, } @misc{12820, abstract = {Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. This data repository contains NMR data presented in the associated manuscript}, author = {Schanda, Paul}, publisher = {Institute of Science and Technology Austria}, title = {{Research data of the publication "Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR"}}, doi = {10.15479/AT:ISTA:12820}, year = {2023}, } @article{13092, abstract = {There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe.}, author = {Nan, Bingfei and Song, Xuan and Chang, Cheng and Xiao, Ke and Zhang, Yu and Yang, Linlin and Horta, Sharona and Li, Junshan and Lim, Khak Ho and Ibáñez, Maria and Cabot, Andreu}, issn = {1944-8252}, journal = {ACS Applied Materials and Interfaces}, number = {19}, pages = {23380–23389}, publisher = {American Chemical Society}, title = {{Bottom-up synthesis of SnTe-based thermoelectric composites}}, doi = {10.1021/acsami.3c00625}, volume = {15}, year = {2023}, } @article{13094, abstract = {Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states.}, author = {Azadbakht, Ali and Meadowcroft, Billie and Varkevisser, Thijs and Šarić, Anđela and Kraft, Daniela J.}, issn = {1530-6992}, journal = {Nano Letters}, number = {10}, pages = {4267–4273}, publisher = {American Chemical Society}, title = {{Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles}}, doi = {10.1021/acs.nanolett.3c00375}, volume = {23}, year = {2023}, } @article{13093, abstract = {The direct, solid state, and reversible conversion between heat and electricity using thermoelectric devices finds numerous potential uses, especially around room temperature. However, the relatively high material processing cost limits their real applications. Silver selenide (Ag2Se) is one of the very few n-type thermoelectric (TE) materials for room-temperature applications. Herein, we report a room temperature, fast, and aqueous-phase synthesis approach to produce Ag2Se, which can be extended to other metal chalcogenides. These materials reach TE figures of merit (zT) of up to 0.76 at 380 K. To improve these values, bismuth sulfide (Bi2S3) particles also prepared in an aqueous solution are incorporated into the Ag2Se matrix. In this way, a series of Ag2Se/Bi2S3 composites with Bi2S3 wt % of 0.5, 1.0, and 1.5 are prepared by solution blending and hot-press sintering. The presence of Bi2S3 significantly improves the Seebeck coefficient and power factor while at the same time decreasing the thermal conductivity with no apparent drop in electrical conductivity. Thus, a maximum zT value of 0.96 is achieved in the composites with 1.0 wt % Bi2S3 at 370 K. Furthermore, a high average zT value (zTave) of 0.93 in the 300–390 K range is demonstrated.}, author = {Nan, Bingfei and Li, Mengyao and Zhang, Yu and Xiao, Ke and Lim, Khak Ho and Chang, Cheng and Han, Xu and Zuo, Yong and Li, Junshan and Arbiol, Jordi and Llorca, Jordi and Ibáñez, Maria and Cabot, Andreu}, issn = {2637-6113}, journal = {ACS Applied Electronic Materials}, publisher = {American Chemical Society}, title = {{Engineering of thermoelectric composites based on silver selenide in aqueous solution and ambient temperature}}, doi = {10.1021/acsaelm.3c00055}, year = {2023}, } @article{13091, abstract = {We use a function field version of the Hardy–Littlewood circle method to study the locus of free rational curves on an arbitrary smooth projective hypersurface of sufficiently low degree. On the one hand this allows us to bound the dimension of the singular locus of the moduli space of rational curves on such hypersurfaces and, on the other hand, it sheds light on Peyre’s reformulation of the Batyrev–Manin conjecture in terms of slopes with respect to the tangent bundle.}, author = {Browning, Timothy D and Sawin, Will}, issn = {1944-7833}, journal = {Algebra and Number Theory}, number = {3}, pages = {719--748}, publisher = {Mathematical Sciences Publishers}, title = {{Free rational curves on low degree hypersurfaces and the circle method}}, doi = {10.2140/ant.2023.17.719}, volume = {17}, year = {2023}, } @article{13117, abstract = {The ability to control the direction of scattered light is crucial to provide flexibility and scalability for a wide range of on-chip applications, such as integrated photonics, quantum information processing, and nonlinear optics. Tunable directionality can be achieved by applying external magnetic fields that modify optical selection rules, by using nonlinear effects, or interactions with vibrations. However, these approaches are less suitable to control microwave photon propagation inside integrated superconducting quantum devices. Here, we demonstrate on-demand tunable directional scattering based on two periodically modulated transmon qubits coupled to a transmission line at a fixed distance. By changing the relative phase between the modulation tones, we realize unidirectional forward or backward photon scattering. Such an in-situ switchable mirror represents a versatile tool for intra- and inter-chip microwave photonic processors. In the future, a lattice of qubits can be used to realize topological circuits that exhibit strong nonreciprocity or chirality.}, author = {Redchenko, Elena and Poshakinskiy, Alexander V. and Sett, Riya and Zemlicka, Martin and Poddubny, Alexander N. and Fink, Johannes M}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Tunable directional photon scattering from a pair of superconducting qubits}}, doi = {10.1038/s41467-023-38761-6}, volume = {14}, year = {2023}, } @article{13106, abstract = {Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification.}, author = {Sahu, Rishabh and Qiu, Liu and Hease, William J and Arnold, Georg M and Minoguchi, Y. and Rabl, P. and Fink, Johannes M}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6646}, pages = {718--721}, publisher = {American Association for the Advancement of Science}, title = {{Entangling microwaves with light}}, doi = {10.1126/science.adg3812}, volume = {380}, year = {2023}, } @article{13129, abstract = {We study the representative volume element (RVE) method, which is a method to approximately infer the effective behavior ahom of a stationary random medium. The latter is described by a coefficient field a(x) generated from a given ensemble ⟨⋅⟩ and the corresponding linear elliptic operator −∇⋅a∇. In line with the theory of homogenization, the method proceeds by computing d=3 correctors (d denoting the space dimension). To be numerically tractable, this computation has to be done on a finite domain: the so-called representative volume element, i.e., a large box with, say, periodic boundary conditions. The main message of this article is: Periodize the ensemble instead of its realizations. By this, we mean that it is better to sample from a suitably periodized ensemble than to periodically extend the restriction of a realization a(x) from the whole-space ensemble ⟨⋅⟩. We make this point by investigating the bias (or systematic error), i.e., the difference between ahom and the expected value of the RVE method, in terms of its scaling w.r.t. the lateral size L of the box. In case of periodizing a(x), we heuristically argue that this error is generically O(L−1). In case of a suitable periodization of ⟨⋅⟩ , we rigorously show that it is O(L−d). In fact, we give a characterization of the leading-order error term for both strategies and argue that even in the isotropic case it is generically non-degenerate. We carry out the rigorous analysis in the convenient setting of ensembles ⟨⋅⟩ of Gaussian type, which allow for a straightforward periodization, passing via the (integrable) covariance function. This setting has also the advantage of making the Price theorem and the Malliavin calculus available for optimal stochastic estimates of correctors. We actually need control of second-order correctors to capture the leading-order error term. This is due to inversion symmetry when applying the two-scale expansion to the Green function. As a bonus, we present a stream-lined strategy to estimate the error in a higher-order two-scale expansion of the Green function.}, author = {Clozeau, Nicolas and Josien, Marc and Otto, Felix and Xu, Qiang}, issn = {1615-3383}, journal = {Foundations of Computational Mathematics}, publisher = {Springer Nature}, title = {{Bias in the representative volume element method: Periodize the ensemble instead of its realizations}}, doi = {10.1007/s10208-023-09613-y}, year = {2023}, } @misc{13124, abstract = {This dataset comprises all data shown in the figures of the submitted article "Tunable directional photon scattering from a pair of superconducting qubits" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.}, author = {Redchenko, Elena and Poshakinskiy, Alexander and Sett, Riya and Zemlicka, Martin and Poddubny, Alexander and Fink, Johannes M}, publisher = {Zenodo}, title = {{Tunable directional photon scattering from a pair of superconducting qubits}}, doi = {10.5281/ZENODO.7858567}, year = {2023}, } @misc{13122, abstract = {Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1}, author = {Sahu, Rishabh}, publisher = {Zenodo}, title = {{Entangling microwaves with light}}, doi = {10.5281/ZENODO.7789417}, year = {2023}, }