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Large scale validation and uncertainty quantification are essential in the experimental design, control, and operations of fusion reactors. Reduced models and increasing computational power means that it is possible to run many simulations, yet setting up simulation runs remaining a time-consuming and error-prone process that involves many manual steps. duqtools is an open-source workflow tool written in Python for that addresses this bottleneck by automating the set up of new simulations. This enables uncertainty quantification and large scale validation of fusion energy modelling simulations. In this work, we demonstrate how duqtools can be used to set up and launch 2000 different simulations of plasma experiments to validate aspects of the JINTRAC modelling suite. With this large-scale validation we identified issues in preserving data consistency in model initialization of the current ($I(p)$) distribution. Furthermore, we used duqtools for sensitivity analysis on the QLKNN-jetexp-15D surrogate model to verify its correctness in multiple regimes.

Directed collective cell migration is central in morphogenesis, wound healing and cancer progression1,2. Although it is well-accepted that the molecular anisotropy of the micro-environment guides this migration3,4, its impact on the pattern of the cell flows remains largely unexplored. Studying confluent human bronchial epithelial cells (HBECs) in vitro, we show that subcellular microgrooves elicit a polar mode of collective migration in millimeter-long bidirectional lanes that are much wider than a cell size, even though cell flows are highly disordered on featureless surfaces 5. This directed flocking-like transition6,7 can be accounted for by a hydrodynamic theory of active polar fluids and corresponding numerical simulations. This model further predicts that anisotropic friction resulting from the grooves lowers the threshold of the transition, which we confirm experimentally. Therefore, microscopic anisotropy of the environment not only directs the collective motion of the cells in the easy direction, but also shapes the cell migration pattern. Flow patterns induced by collective contact guidance are thus markedly different from those induced by supracellular confinement8, demonstrating that all length-scales of the micro-environment must be considered in a comprehensive description of collective migration. Furthermore, artificial microtopographies designed from theoretical considerations can provide a rational strategy to direct cells to specific geometries and functions, which has broad implications, for instance, for tissue engineering strategies in organoid morphogenesis., Comment: Nature Physics, 2024

Quantum technology is predicted to have a significant impact on society once it matures. This study (n = 637 adults representative of the Dutch population) examined the effect of different frames on engagement - specifically, information seeking, internal efficacy, general interest and perceived knowledge - with quantum technology. The different frames were: enigmatic, explaining quantum physics, benefit, risk and balanced. Results indicated that framing quantum as enigmatic does not affect engagement, while explaining quantum physics positively influences general interest. Furthermore, emphasising a benefit of quantum technology increases participants' internal efficacy, whereas highlighting both a benefit and a risk of quantum technology decreases perceived knowledge. Based on these findings, we offer practical advice for science communicators in the field and suggest further research., Comment: 19 pages

In this era of non-fullerene acceptor (NFA) based organic solar cells, reducing voltage losses while maintaining high photocurrents is the holy grail of current research. Recent focus lies in understanding the manifold fundamental mechanisms in organic blends with minimal energy offsets - particularly the relationship between ionization energy offset ({\Delta}IE) and free charge generation. We quantitatively probe this relationship in multiple NFA-based blends by mixing Y5 and Y6 NFAs with PM6 of varying molecular weights, covering a 15% to 1% power conversion efficiency (PCE) range and a progression of {\Delta}IE. Spectroelectrochemistry reveals a critical {\Delta}IE of approximately 0.3 eV, below which the PCE sharply declines. Transient absorption spectroscopy consistently reveals that a smaller {\Delta}IE slows the dissociation of the NFA's local singlet exciton (LE) into free charges, albeit restorable by an electric field. Bias-dependent time delayed collection experiments quantify the free charge generation efficiency, while photoluminescence quantum efficiency measurements assess photocurrent loss from LE decay. Combined with transient photoluminescence experiments, we find that the decay of singlet excitons is the primary competition to free charge generation in low-offset NFA-based organic solar cells, with neither noticeable losses from charge-transfer (CT) decay nor evidence for LE-CT hybridization. Our experimental data align with Marcus theory calculations, supported by density functional theory simulations, for zero-field free charge generation and exciton decay efficiencies. We find that efficient photocurrent generation generally requires that the CT state is located below the LE, but that this restriction is lifted in systems with a small reorganization energy for charge transfer.

We propose and analyse numerical schemes for a system of quasilinear, degenerate evolution equations modelling biofilm growth as well as other processes such as flow through porous media and the spreading of wildfires. The first equation in the system is parabolic and exhibits degenerate and singular diffusion, while the second is either uniformly parabolic or an ordinary differential equation. First, we introduce a semi-implicit time discretisation that has the benefit of decoupling the equations. We prove the positivity, boundedness, and convergence of the time-discrete solutions to the time-continuous solution. Then, we introduce an iterative linearisation scheme to solve the resulting nonlinear time-discrete problems. Under weak assumptions on the time-step size, we prove that the scheme converges irrespective of the space discretisation and mesh. Moreover, if the problem is non-degenerate, the convergence becomes faster as the time-step size decreases. Finally, employing the finite element method for the spatial discretisation, we study the behaviour of the scheme, and compare its performance to other commonly used schemes. These tests confirm that the proposed scheme is robust and fast., Comment: 40 pages,7 figures, journal submission

Quantum technology is expected to have an impact on society. Scientists warn against the use of certain frames because they may create barriers to effective science communication. We studied 385 Dutch newspaper articles for the use of these frames. Newspapers commonly explained quantum concepts when mentioning quantum technology. They also regularly framed quantum technology as beneficial and enigmatic, often in prominent positions of the articles. The economic development/competitiveness frame, the social progress frame and the risk frame were less common. Although these frames are only potential barriers, we encourage journalists to weigh them when communicating about quantum technology., Comment: 33 pages, 6 figures

State-of-the-art computational methods combined with common idealized structural models provide an incomplete understanding of experiments on real nanostructures, since manufacturing introduces unavoidable deviations from the design. We propose to close this knowledge gap by using the real structure of a manufactured crystal as input in computations to obtain a realistic comparison with observations on the same nanostructure. We demonstrate this approach on the structure of a real silicon inverse woodpile photonic bandgap crystal, obtained by previous synchrotron X-ray imaging. A 2D part of the dataset is selected and processed into a computational mesh suitable for a Discontinuous Galerkin Finite Element Method (DGFEM) to compute optical transmission spectra that are compared to those of a utopian crystal, i.e., a hypothetical model crystal with the same filling fraction where all pores are identical and circular. The nanopore shapes in the real crystal differ in a complex way from utopian pores, leading to a complex transmission spectrum with significant frequency speckle in and beyond the gap. The utopian model provides only a limited understanding of the spectrum: while it accurately predicts low frequency finite-size fringes and the lower band edge, the upper band edge is off, it completely misses the presence of speckle, the domination of speckle above the gap, and possible Anderson localized states in the gap. Moreover, unlike experiments where only external probes are available, numerical methods allow to study all fields everywhere. While the pore shapes hardly affect the fields at low frequency, major differences occur at high frequency such as localized fields deep inside the real crystal. In summary, using only external measurements and utopian models may give an erroneous picture of the fields and the LDOS inside a real crystal, which is remedied by our new approach., Comment: 24 pages, 10 figures, including 1 supplement

Given a family of varieties over the projective line, we study the density of fibres that are everywhere locally soluble in the case that components of higher multiplicity are allowed. We use log geometry to formulate a new sparsity criterion for the existence of everywhere locally soluble fibres and formulate new conjectures that generalise previous work of Loughran-Smeets. These conjectures involve geometric invariants of the associated multiplicity orbifolds on the base of the fibration in the spirit of Campana. We give evidence for the conjectures using Chebotarev's theorem and sieve methods., Comment: 44 pages

Calcium carbonate (CaCO3), the most abundant biogenic mineral on earth, plays a crucial role in various fields. Of the four polymorphs, calcite, aragonite, vaterite, and amorphous CaCO3, vaterite is the most enigmatic one due to an ongoing debate regarding its structure that has persisted for nearly a century. In this work, based on systematic transmission electron microscopy characterizations, elaborate crystallographic analysis and machine learning aided molecular dynamics simulations with ab initio accuracy, we reveal that vaterite can be regarded as a polytypic structure. The basic phase is a monoclinic lattice possessing pseudohexagonal symmetry. Direct imaging and atomic-scale simulations provide evidence that a single grain of vaterite can have three orientation variants. Additionally, we find that vaterite undergoes a second-order phase transition. These atomic scale insights provide a comprehensive understanding of the structure of vaterite and offer new perspectives on the biomineralization process of calcium carbonate.

Graph Anomaly Detection (GAD) is a technique used to identify abnormal nodes within graphs, finding applications in network security, fraud detection, social media spam detection, and various other domains. A common method for GAD is Graph Auto-Encoders (GAEs), which encode graph data into node representations and identify anomalies by assessing the reconstruction quality of the graphs based on these representations. However, existing GAE models are primarily optimized for direct link reconstruction, resulting in nodes connected in the graph being clustered in the latent space. As a result, they excel at detecting cluster-type structural anomalies but struggle with more complex structural anomalies that do not conform to clusters. To address this limitation, we propose a novel solution called GAD-NR, a new variant of GAE that incorporates neighborhood reconstruction for graph anomaly detection. GAD-NR aims to reconstruct the entire neighborhood of a node, encompassing the local structure, self-attributes, and neighbor attributes, based on the corresponding node representation. By comparing the neighborhood reconstruction loss between anomalous nodes and normal nodes, GAD-NR can effectively detect any anomalies. Extensive experimentation conducted on six real-world datasets validates the effectiveness of GAD-NR, showcasing significant improvements (by up to 30% in AUC) over state-of-the-art competitors. The source code for GAD-NR is openly available. Importantly, the comparative analysis reveals that the existing methods perform well only in detecting one or two types of anomalies out of the three types studied. In contrast, GAD-NR excels at detecting all three types of anomalies across the datasets, demonstrating its comprehensive anomaly detection capabilities., Comment: Accepted at the 17th ACM International Conference on Web Search and Data Mining (WSDM-2024)