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We present our implementation of non-reflecting boundary conditions in the magnetohydrodynamics (MHD) code LaRe3D. This implementation couples a characteristics-based boundary condition with a Lagrangian remap code, demonstrating the generality and flexibility of such non-reflecting boundary conditions for use with arbitrary grid-based MHD schemes. To test this implementation for perturbations on a background state, we present simulations of a hot sphere in an angled magnetic field. We then examine a series of simulations where we advect a spheromak through a non-reflecting boundary condition at four speeds related to the fast and slow magnetosonic speeds and the Alfven speed. We compare the behavior of these simulations to ground truth simulations run from the same initial condition on an extended grid that keeps the spheromak in the simulation volume at all times. We find that the non-reflecting boundary condition can lead to severe, physical differences developing between a simulation using a non-reflecting boundary and a ground truth simulation using a larger simulation volume. We conclude by discussing the origins of these differences., Comment: 32 pages, 13 figures, ApJ (accepted)

This paper details a significant milestone towards maturing a buoyant aerial robotic platform, or aerobot, for flight in the Venus clouds. We describe two flights of our subscale altitude-controlled aerobot, fabricated from the materials necessary to survive Venus conditions. During these flights over the Nevada Black Rock desert, the prototype flew at the identical atmospheric densities as 54 to 55 km cloud layer altitudes on Venus. We further describe a first-principle aerobot dynamics model which we validate against the Nevada flight data and subsequently employ to predict the performance of future aerobots on Venus. The aerobot discussed in this paper is under JPL development for an in-situ mission flying multiple circumnavigations of Venus, sampling the chemical and physical properties of the planet's atmosphere and also remotely sensing surface properties., Comment: Preprint submitted to AIAA Journal of Aircraft

We report a detailed investigation into the response of single BaTiO3 (BTO) nanocrystals under applied electric fields (E-field) using Bragg Coherent Diffraction Imaging (BCDI). Our study reveals pronounced domain wall migration and expansion of a sample measure in situ under applied electric field. The changes are most prominent at the surface of the nanocrystal, where the lack of external strain allows greater domain wall mobility. The observed domain shifts are correlated to the strength and orientation of the applied E-field, following a side-by-side domain model from Suzana et al. Notably, we identified a critical voltage threshold at +10 V, which leads to irreversible structural changes, suggesting plastic deformation. The findings highlight how surface effects and intrinsic defects contribute to the enhanced dielectric properties of BTO at the nanoscale, in contrast to bulk materials, where strain limits domain mobility. These findings deepen our understanding of nanoscale dielectric behaviour and inform the design of advanced nanoelectronic devices., Comment: 11 pages, 8 figures

Detecting non-classical light is a central requirement for photonics-based quantum technologies. Unrivaled high efficiencies and low dark counts have positioned superconducting nanowire single photon detectors (SNSPDs) as the leading detector technology for fiber and integrated photonic applications. However, a central challenge lies in their integration within photonic integrated circuits regardless of material platform or surface topography. Here, we introduce a method based on transfer printing that overcomes these constraints and allows for the integration of SNSPDs onto arbitrary photonic substrates. We prove this by integrating SNSPDs and showing through-waveguide single-photon detection in commercially manufactured silicon and lithium niobate on insulator integrated photonic circuits. Our method eliminates bottlenecks to the integration of high-quality single-photon detectors, turning them into a versatile and accessible building block for scalable quantum information processing., Comment: 11 pages, 12 figures

In this paper we prove a new characterization of the distinguished unipotent orbits of a connected reductive group over an algebraically closed field of characteristic 0. For classical groups we prove the characterization by a combinatorial computation, and for exceptional groups we check it with a computer. This characterization is needed in the theory of cuspidal sheaves on the stack of L-parameters in forthcoming work of the first two named authors., Comment: 23 pages, comments welcome!

The observation of unexpected polarisation textures such as vortices, skyrmions and merons in various oxide heterostructures has challenged the widely accepted picture of ferroelectric domain walls as being Ising-like. Bloch components in the 180{\deg} domain walls of PbTiO3 have recently been reported in PbTiO3/SrTiO3 superlattices and linked to domain wall chirality. While this opens exciting perspectives, the ubiquitous nature of this Bloch component remains to be further explored. In this work, we present a comprehensive investigation of domain walls in PbTiO3/SrTiO3 superlattices, involving a combination of first- and second-principles calculations, phase-field simulations, diffuse scattering calculations, and synchrotron based diffuse x-ray scattering. Our theoretical calculations highlight that the previously predicted Bloch polarisation in the 180{\deg} domain walls in PbTiO3/SrTiO3 superlattices might be more sensitive to the boundary conditions than initially thought and is not always expected to appear. Employing diffuse scattering calculations for larger systems we develop a method to probe the complex structure of domain walls in these superlattices via diffuse x-ray scattering measurements. Through this approach, we investigate depolarization-driven ferroelectric polarization rotation at the domain walls. Our experimental findings, consistent with our theoretical predictions for realistic domain periods, do not reveal any signatures of a Bloch component in the centres of the 180{\deg} domain walls of PbTiO3/SrTiO3 superlattices, suggesting that the precise nature of domain walls in the ultrathin PbTiO3 layers is more intricate than previously thought and deserves further attention.

We characterize compatible families of real-rooted polynomials, allowing both positive and negative leading coefficients. Our characterization naturally generalizes the same-sign characterization used by Chudnovsky and Seymour in their famous 2007 paper proving the real-rootedness of independence polynomials of claw-free graphs, thus fully settling a question left open in their paper. Our methods are generally speaking elementary, utilizing mainly linear algebra and the established theory of interlacing polynomials, with a bit of invariant theory.

This short paper presents preliminary research on the Case-Enhanced Vision Transformer (CEViT), a similarity measurement method aimed at improving the explainability of similarity assessments for image data. Initial experimental results suggest that integrating CEViT into k-Nearest Neighbor (k-NN) classification yields classification accuracy comparable to state-of-the-art computer vision models, while adding capabilities for illustrating differences between classes. CEViT explanations can be influenced by prior cases, to illustrate aspects of similarity relevant to those cases.

Reliable control of quantum information in matter-based qubits requires precisely applied external fields, and unaccounted for spatial cross-talk of these fields between adjacent qubits leads to loss of fidelity. We report a CMOS foundry-produced, micro-fabricated silicon nitride (Si3N4) optical waveguide for addressing a chain of eight, unequally-spaced trapped barium ions with crosstalk compatible with scalable quantum information processing. The crosstalk mitigation techniques incorporated into the chip design result in a reduction of the measured optical field by at least 50.8(1.3) dB between adjacent waveguide outputs near 650 nm and similar behavior for devices designed for 493 nm and 585 nm. The waveguide outputs near 650 nm, along with a global laser near 493 nm were used to laser-cool a chain of eight barium-138 ions, and a camera imaged the resulting fluorescence at 493 nm., Comment: 9 pages, 7 figures

The type $A$ Kostant partition function is an important combinatorial object with various applications: it counts integer flows on the complete directed graph, computes Hilbert series of spaces of diagonal harmonics, and can be used to compute weight and tensor product multiplicities of representations. In this paper we study asymptotics of the Kostant partition function, improving on various previously known lower bounds and settling conjectures of O'Neill and Yip. Our methods build upon recent results and techniques of Br\"and\'en-Leake-Pak, who used Lorentzian polynomials and Gurvits' capacity method to bound the number of lattice points of transportation and flow polytopes. Finally, we also give new two-sided bounds using the Lidskii formulas from subdivisions of flow polytopes., Comment: 34 pages, 3 figures, and an appendix, v2. fixed typos and added a footnote about an announced improvement to Theorem 1.1 by Balashov, Bulavenko, and Molybog that we learned about after v1. was posted. v3. added a reference to the preprint of the aforementioned authors

We present the first results of three-dimensional (3D) numerical magnetohydrodynamic (MHD) simulations of the onset of magnetic reconnection via the tearing instability in dynamically thinning current sheets in the solar corona. In all our simulations, the onset of the non-linear tearing instability, which leads to the break-up of the thinning current sheet, does not occur until after the instability growth time becomes faster than the dynamic thinning time. Furthermore, as in previous 3D MHD simulations of static current sheets in the corona, for some parameters, the amount of magnetic shear is a fundamental switch-on parameter, which has consequences for coronal heating models. These results open up the possibility of using observable quantities of coronal current sheets to predict when they will break-up and release magnetic energy to power various energetic phenomena and/or heat the atmosphere.

Membraneless droplets formed through liquid-liquid phase separation (LLPS) play a crucial role in mRNA storage, enabling organisms to swiftly respond to environmental changes. However, the mechanisms underlying mRNA integration and protection within droplets remain unclear. Here, we unravel the role of bacterial aggresomes as stress granules (SGs) in safeguarding mRNA during stress. We discovered that upon stress onset, mobile mRNA molecules selectively incorporate into individual proteinaceous SGs based on length-dependent enthalpic gain over entropic loss. As stress prolongs, SGs undergo compaction facilitated by stronger non-specific RNA-protein interactions, thereby promoting recruitment of shorter RNA chains. Remarkably, mRNA ribonucleases are repelled from bacterial SGs, due to the influence of protein surface charge. This exclusion mechanism ensures the integrity and preservation of mRNA within SGs during stress conditions, explaining how mRNA can be stored and protected from degradation. Following stress removal, SGs facilitate mRNA translation, thereby enhancing cell fitness in changing environments. These droplets maintain mRNA physiological activity during storage, making them an intriguing new candidate for mRNA therapeutics manufacturing.

Surface acoustic wave devices are key components for processing radio frequency signals in wireless communication because these devices offer simultaneously high performance, compact size and low cost. The optimization of the device structure requires a quantitative understanding of energy conversion and loss mechanisms. Stroboscopic full-field diffraction x-ray microscopy studies of a prototypical one-port resonator device revealed the existence of unanticipated acoustic loss. A non-uniform acoustic excitation in the active area was responsible for the substantial end and side leakages observed at the design frequency. Quantitative analysis of the strain amplitude using a wave decomposition method allowed the determination of several key device parameters. This high-resolution spatiotemporal strain imaging technique is, more generally, suited for studying nanophononics, specifically when the feature size is smaller than optical wavelengths. The strain sensitivity allows precise measurement of acoustic waves with picometer-scale amplitude.

We propose a deep learning algorithm for the inpainting of Bragg Coherent Diffraction Imaging (BCDI) patterns affected by detector gaps. These regions of missing intensity can compromise the accuracy of reconstruction algorithms, inducing artifacts in the final result. It is thus desirable to restore the intensity in these regions in order to ensure more reliable reconstructions. The key aspect of our method lies in the choice of training the neural network with cropped sections of both experimental diffraction data and simulated data and subsequently patching the predictions generated by the model along the gap, thus completing the full diffraction peak. This provides us with more experimental training data and allows for a faster model training due to the limited size, while the neural network can be applied to arbitrarily larger BCDI datasets. Moreover, our method not only broadens the scope of application but also ensures the preservation of data integrity and reliability in the face of challenging experimental conditions., Comment: Main article + Supplemental Material

Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.

Observations have shown a clear association of filament/prominence eruptions with the emergence of magnetic flux in or near filament channels. Magnetohydrodynamic (MHD) simulations have been employed to systematically study the conditions under which such eruptions occur. These simulations to date have modeled filament channels as two-dimensional (2D) flux ropes or 3D uniformly sheared arcades. Here we present MHD simulations of flux emergence into a more realistic configuration consisting of a bipolar active region containing a line-tied 3D flux rope. We use the coronal flux-rope model of Titov et al. (2014) as the initial condition and drive our simulations by imposing boundary conditions extracted from a flux-emergence simulation by Leake et al. (2013). We identify three mechanisms that determine the evolution of the system: (i) reconnection displacing foot points of field lines overlying the coronal flux rope, (ii) changes of the ambient field due to the intrusion of new flux at the boundary, and (iii) interaction of the (axial) electric currents in the pre-existing and newly emerging flux systems. The relative contributions and effects of these mechanisms depend on the properties of the pre-existing and emerging flux systems. Here we focus on the location and orientation of the emerging flux relative to the coronal flux rope. Varying these parameters, we investigate under which conditions an eruption of the latter is triggered., Comment: 18 pages, 8 figures, accepted for publication by The Astrophysical Journal

We give simply exponential lower bounds on the probabilities of a given strongly Rayleigh distribution, depending only on its expectation. This resolves a weak version of a problem left open by Karlin-Klein-Oveis Gharan in their recent breakthrough work on metric TSP, and this resolution leads to a minor improvement of their approximation factor for metric TSP. Our results also allow for a more streamlined analysis of the algorithm. To achieve these new bounds, we build upon the work of Gurvits-Leake on the use of the productization technique for bounding the capacity of a real stable polynomial. This technique allows one to reduce certain inequalities for real stable polynomials to products of affine linear forms, which have an underlying matrix structure. In this paper, we push this technique further by characterizing the worst-case polynomials via bipartitioned forests. This rigid combinatorial structure yields a clean induction argument, which implies our stronger bounds. In general, we believe the results of this paper will lead to further improvement and simplification of the analysis of various combinatorial and probabilistic bounds and algorithms., Comment: ICALP 2024

We develop a general description of how information propagates through a magnetohydrodynamic (MHD) system based on the method of characteristics and use that to formulate numerical boundary conditions (BCs) that are intrinsically consistent with the MHD equations. Our formulation includes two major advances for simulations of the Sun. First, we derive data-driven BCs that optimally match the state of the plasma inferred from a time series of observations of a boundary (e.g., the solar photosphere). Second, our method directly handles random noise and systematic bias in the observations, and finds a solution for the boundary evolution that is strictly consistent with MHD and maximally consistent with the observations. We validate the method against a Ground Truth (GT) simulation of an expanding spheromak. The data-driven simulation can reproduce the GT simulation above the photosphere with high fidelity when driven at high cadence. Errors progressively increase for lower driving cadence until a threshold cadence is reached and the driven simulation can no longer accurately reproduce the GT simulation. However, our characteristic formulation of the BCs still requires adherence of the boundary evolution to the MHD equations even when the driven solution departs from the true solution in the driving layer. That increasing departure clearly indicates when additional information at the boundary is needed to fully specify the correct evolution of the system. The method functions even when no information about the evolution of some variables on the lower boundary is available, albeit with a further decrease in fidelity., Comment: Submitted for publication to the Astrophysical Journal; 77 pages, 12 figures

With recent advances in Generative AI, it is becoming easier to automatically manipulate 3D models. However, current methods tend to apply edits to models globally, which risks compromising the intended functionality of the 3D model when fabricated in the physical world. For example, modifying functional segments in 3D models, such as the base of a vase, could break the original functionality of the model, thus causing the vase to fall over. We introduce a method for automatically segmenting 3D models into functional and aesthetic elements. This method allows users to selectively modify aesthetic segments of 3D models, without affecting the functional segments. To develop this method we first create a taxonomy of functionality in 3D models by qualitatively analyzing 1000 models sourced from a popular 3D printing repository, Thingiverse. With this taxonomy, we develop a semi-automatic classification method to decompose 3D models into functional and aesthetic elements. We propose a system called Style2Fab that allows users to selectively stylize 3D models without compromising their functionality. We evaluate the effectiveness of our classification method compared to human-annotated data, and demonstrate the utility of Style2Fab with a user study to show that functionality-aware segmentation helps preserve model functionality.

The thickness of current sheets is extremely important, especially as it relates to the onset of fast magnetic reconnection. Onset determines how much magnetic free energy can build up in a field before it is explosively released. This has implications for many phenomena on the Sun and throughout the universe, including the heating of the solar corona. Significant effort has been devoted to the question of whether equilibrium current sheets in realistic geometries have finite or zero thickness. Using a simple force balance analysis, we show why current sheets without a guide field (2D) and with a guide field that is invariant in the guide field direction (2.5D) cannot be in equilibrium if they have both finite thickness and finite length. We then estimate the conditions under which the tension of a curved line-tied guide field can facilitate equilibrium in 3D sheets that are finite in all dimensions. Finally, we argue that some quasi-statically evolving current sheets undergoing slow stressing (e.g., when the coronal magnetic field is subjected to photospheric boundary driving) may reach a critical shear, at which point they lose equilibrium, spontaneously collapse, and reconnect. The critical shear is generally consistent with the heating requirements of solar active regions., Comment: 15 pages, 5 figures, accepted by Frontiers in Physics

Controlling large-scale many-body quantum systems at the level of single photons and single atomic systems is a central goal in quantum information science and technology. Intensive research and development has propelled foundry-based silicon-on-insulator photonic integrated circuits to a leading platform for large-scale optical control with individual mode programmability. However, integrating atomic quantum systems with single-emitter tunability remains an open challenge. Here, we overcome this barrier through the hybrid integration of multiple InAs/InP microchiplets containing high-brightness infrared semiconductor quantum dot single photon emitters into advanced silicon-on-insulator photonic integrated circuits fabricated in a 300~mm foundry process. With this platform, we achieve single photon emission via resonance fluorescence and scalable emission wavelength tunability through an electrically controlled non-volatile memory. The combined control of photonic and quantum systems opens the door to programmable quantum information processors manufactured in leading semiconductor foundries., Comment: 9 pages, 4 figures

Physics of Life research in the UK is proving to be transformative to scientific insight and translational impact, but challenges remain. Here I discuss its disruptive potential and the barriers to interdisciplinary research seen through the lens of the activities of one of its pioneers, Tom McLeish, FRS.

We investigate six operations on chemical reaction networks, all of which have been proven to preserve important dynamical properties, namely, the capacity for nondegenerate multistationarity (multiple steady states) and periodic orbits. Both multistationarity and periodic orbits are properties that are known to be precluded when the deficiency (a nonnegative integer associated to a network) is zero. It is therefore natural to conjecture that the deficiency never decreases when any of the six aforementioned network operations are performed. We prove that this is indeed the case, and moreover, we characterize the numerical difference in deficiency after performing each network operation., Comment: Reorganized Section 3, improved exposition throughout, made several edits in response to referee suggestions

Inspired by the theory of hyperbolic polynomials and Hodge theory, we develop the theory of Lorentzian polynomials on cones. This notion captures the Hodge-Riemann relations of degree zero and one. Motivated by fundamental properties of volume polynomials of Chow rings of simplicial fans, we define a class of multivariate polynomials which we call hereditary polynomials. We give a complete and easily checkable characterization of hereditary Lorentzian polynomials. This characterization is used to give elementary and simple proofs of the Heron-Rota-Welsh conjecture for the characteristic polynomial of a matroid, and the Alexandrov-Fenchel inequalities for convex bodies. We then characterize Chow rings of simplicial fans which satisfy the Hodge-Riemann relations of degree zero and one, and we prove that this property only depends on the support of the fan. Several different characterizations of Lorentzian polynomials on cones are provided.

We report on a study of the Multiview Observatory for Solar Terrestrial Science (MOST) mission that will provide comprehensive imagery and time series data needed to understand the magnetic connection between the solar interior and the solar atmosphere/inner heliosphere. MOST will build upon the successes of SOHO and STEREO missions with new views of the Sun and enhanced instrument capabilities. This article is based on a study conducted at NASA Goddard Space Flight Center that determined the required instrument refinement, spacecraft accommodation, launch configuration, and flight dynamics for mission success. MOST is envisioned as the next generation great observatory positioned to obtain three-dimensional information of large-scale heliospheric structures such as coronal mass ejections, stream interaction regions, and the solar wind itself. The MOST mission consists of 2 pairs of spacecraft located in the vicinity of Sun-Earth Lagrange points L4 (MOST1, MOST3) and L5 (MOST2 and MOST4). The spacecraft stationed at L4 (MOST1) and L5 (MOST2) will each carry seven remote-sensing and three in-situ instrument suites, including a novel radio package known as the Faraday Effect Tracker of Coronal and Heliospheric structures (FETCH). MOST3 and MOST4 will carry only the FETCH instruments and are positioned at variable locations along the Earth orbit up to 20{\deg} ahead of L4 and 20{\deg} behind L5, respectively. FETCH will have polarized radio transmitters and receivers on all four spacecraft to measure the magnetic content of solar wind structures propagating from the Sun to Earth using the Faraday rotation technique. The MOST mission will be able to sample the magnetized plasma throughout the Sun-Earth connected space during the mission lifetime over a solar cycle., Comment: 42 pages, 19 figures, 8 tables, to appear in J. Atmospheric and Solar Terrestrial Physics

The Theory of Functional Connections (TFC) is most often used for constraints over the field of real numbers. However, previous works have shown that it actually extends to arbitrary fields. The evidence for these claims is restricting oneself to the field of real numbers is unnecessary because all of the theorems, proofs, etc. for TFC apply as written to fields in general. Here, that notion is taken a step further, as fields themselves are unnecessarily restrictive. The theorems, proofs, etc. of TFC apply to vector spaces, not just fields. Moreover, the inputs of the functions/constraints do not even need to be restricted to vector spaces; they can quite literally be anything. In this note, the author shows the more general inputs/outputs of the various symbols that comprise TFC. Examples with accompanying, open-access Python code are included to aid the reader's understanding., Comment: 6 pages

The condensation of Rubisco holoenzymes and linker proteins into 'pyrenoids', a crucial super-charger of photosynthesis in algae, is qualitatively understood in terms of 'sticker-and-spacer' theory. We derive semi-analytical partition sums for small Rubisco:linker aggregates, which enable the calculation of both dilute-phase titration curves and dimerisation diagrams. By fitting the titration curves to Surface Plasmon Resonance and Single-Molecule Fluorescence Microscopy data, we extract the molecular properties needed to predict dimerisation diagrams. We use these to estimate typical concentrations for condensation, and successfully compare these to microscopy observations., Comment: v2: correction in the single-Rubisco calculations; v3: added single-Rubisco experimental work; v4: model and experiments extended to describe Rubisco condensation

A book embedding of a complete graph is a spatial embedding whose planar projection has the vertices located along a circle, consecutive vertices are connected by arcs of the circle, and the projections of the remaining "interior" edges in the graph are straight line segments between the points on the circle representing the appropriate vertices. A random embedding of a complete graph can be generated by randomly assigning relative heights to these interior edges. We study a family of two-component links that arise as the realizations of pairs of disjoint cycles in these random embeddings of graphs. In particular, we show that the distribution of linking numbers can be described in terms of Eulerian numbers. Consequently, the mean of the squared linking number over all random embeddings is $\frac{i}{6}$, where $i$ is the number of interior edges in the cycles. We also show that the mean of the squared linking number over all pairs of $n$-cycles in $K_{2n}$ grows linearly in $n$., Comment: 17 pages

We give a method for computing asymptotic formulas and approximations for the volumes of spectrahedra, based on the maximum-entropy principle from statistical physics. The method gives an approximate volume formula based on a single convex optimization problem of minimizing $-\log \det P$ over the spectrahedron. Spectrahedra can be described as affine slices of the convex cone of positive semi-definite (PSD) matrices, and the method yields efficient deterministic approximation algorithms and asymptotic formulas whenever the number of affine constraints is sufficiently dominated by the dimension of the PSD cone. Our approach is inspired by the work of Barvinok and Hartigan who used an analogous framework for approximately computing volumes of polytopes. Spectrahedra, however, possess a remarkable feature not shared by polytopes, a new fact that we also prove: central sections of the set of density matrices (the quantum version of the simplex) all have asymptotically the same volume. This allows for very general approximation algorithms, which apply to large classes of naturally occurring spectrahedra. We give two main applications of this method. First, we apply this method to what we call the "multi-way Birkhoff spectrahedron" and obtain an explicit asymptotic formula for its volume. This spectrahedron is the set of quantum states with maximal entanglement (i.e., the quantum states having univariant quantum marginals equal to the identity matrix) and is the quantum analog of the multi-way Birkhoff polytope. Second, we apply this method to explicitly compute the asymptotic volume of central sections of the set of density matrices.

Compression of micro-pillars is followed in situ by a quick nano-focused X-ray scanning microscopy technique combined with three-dimensional reciprocal space mapping. Compared to other attempts using 2 X-ray nanobeams, it avoids any motion or vibration that would lead to a destruction of the sample. The technique consists of scanning both the energy of the incident nano-focused X-ray beam and the in-plane translations of the focusing optics along the X-ray beam. Here, we demonstrate the approach by imaging the strain and lattice orientation of Si micro-pillars and their pedestals during in situ compression. Varying the energy of the incident beam instead of rocking the sample and mapping the focusing optics instead of moving the sample supplies a vibration-free measurement of the reciprocal space maps without removal of the mechanical load. The maps of strain and lattice orientation are in good agreement with the ones recorded by ordinary rocking-curve scans. Variable-wavelength quick scanning X-ray microscopy opens the route for in situ strain and tilt mapping towards more diverse and complex materials environments, especially where sample manipulation is difficult.

Monolithic integration of quantum dot (QD) gain materials onto Si photonic platforms via direct epitaxial growth is a promising solution for on-chip light sources. Recent developments have demonstrated superior device reliability in blanket hetero-epitaxy of III-V devices on Si at elevated temperatures. Yet, thick, defect management epi designs prevent vertical light coupling from the gain region to the Si-on-Insulator (SOI) waveguides. Here, we demonstrate the first electrically pumped QD lasers grown on a 300 mm patterned (001) Si wafer with a butt-coupled configuration by molecular beam epitaxy (MBE). Unique growth and fabrication challenges imposed by the template architecture have been resolved, contributing to continuous wave lasing to 60 {\deg}C and a maximum double-side output power of 126.6 mW at 20 {\deg}C with a double-side wall plug efficiency of 8.6%. The potential for robust on-chip laser operation and efficient low-loss light coupling to Si photonic circuits makes this heteroepitaxial integration platform on Si promising for scalable and low-cost mass production., Comment: 11 pages including references, 6 figures

Solar eruptive events such as coronal mass ejections and eruptive flares are frequently associated with the emergence of magnetic flux from the convection zone into the corona. We use three dimensional magnetohydrodynamic numerical simulations to study the interaction of coronal magnetic fields with emerging flux and determine the conditions that lead to eruptive activity. A simple parameter study is performed, varying the relative angle between emerging magnetic flux and a pre-existing coronal dipole field. We find that in all cases, the emergence results in a sheared magnetic arcade that transitions to a twisted coronal flux rope via low-lying magnetic reconnection. This structure, however, is constrained by its own outer field, and so is non-eruptive in the absence of reconnection with the overlying coronal field. The amount of this overlying reconnection is determined by the relative angle between the emerged and pre-existing fields. The reconnection between emerging and pre-existing fields is necessary to generate sufficient expansion of the emerging structure so that flare-like reconnection below the coronal flux rope becomes strong enough to trigger its release. Our results imply that the relative angle is the key parameter in determining whether the resultant active regions exhibit eruptive behavior, and is thus a potentially useful candidate for predicting eruptions in newly emerging active regions. More generally, our results demonstrate that the detailed interaction between the convection zone/photosphere and the corona must be calculated self-consistently in order to model solar eruptions accurately.

As computing resource demands continue to escalate in the face of big data, cloud-connectivity and the internet of things, it has become imperative to develop new low-power, scalable architectures. Neuromorphic photonics, or photonic neural networks, have become a feasible solution for the physical implementation of efficient algorithms directly on-chip. This application is primarily due to the linear nature of light and the scalability of silicon photonics, specifically leveraging the wide-scale complementary metal-oxide-semiconductor (CMOS) manufacturing infrastructure used to fabricate microelectronics chips. Current neuromorphic photonic implementations stem from two paradigms: wavelength coherent and incoherent. Here, we introduce a novel architecture that supports coherent and incoherent operation to increase the capability and capacity of photonic neural networks with a dramatic reduction in footprint compared to previous demonstrations. As a proof-of-principle, we experimentally demonstrate simple addition and subtraction operations on a foundry-fabricated silicon photonic chip. Additionally, we experimentally validate an on-chip network to predict the logical 2-bit gates AND, OR, and XOR to accuracies of $96.8\%, 99\%,$ and $98.5\%$, respectively. This architecture is compatible with highly wavelength parallel sources, enabling massively scalable photonic neural networks.

In spite of the nanoscale and single-molecule insights into how nucleoid associated proteins (NAPs) interact with DNA, their role in modulating the mesoscale viscoelasticity of the entangled genome in vivo has been overlooked so far. By combining microrheology and molecular dynamics simulation we find that the important NAP called Integration Host Factor (IHF) lowers the viscosity of entangled $\lambda$DNA 20-fold at physiological concentrations and stoichiometries. We argue that IHF may act as a "genomic fluidiser", reducing the effective viscosity of the nucleoid $\sim$200-fold. Our results suggest a previously unappreciated key role of IHF in regulating DNA dynamics and re-organisation in vivo

Early Career Researcher (ECR) development is a dynamic challenge that tensions the urge to perform ground-breaking research against an ultimate practical aspiration of establishing an acceptable level of job security. There is no typical career path for an ECR, least of all in the area of the Physics of Life or Biophysics/Biological Physics. Being explicitly interdisciplinary across the physical-life sciences interface presents more opportunities for a multiplicity of career trajectories through different home academic institutions and departments, as well as offering a broader range of alternative future career trajectories in non-academic sectors. That said, there are key common features, such as the transient nature of fixed-term postdoc contracts, the substantial research and domestic challenges that these present, and the often overwhelming pressures of the realities of competition in the job market. In this short article I outline the key challenges to ECRs in the Physics of Life and discuss simple strategies to manage and potentially overcome them.

Harnessing the full complexity of optical fields requires complete control of all degrees-of-freedom within a region of space and time -- an open goal for present-day spatial light modulators (SLMs), active metasurfaces, and optical phased arrays. Here, we solve this challenge with a programmable photonic crystal cavity array enabled by four key advances: (i) near-unity vertical coupling to high-finesse microcavities through inverse design, (ii) scalable fabrication by optimized, 300 mm full-wafer processing, (iii) picometer-precision resonance alignment using automated, closed-loop "holographic trimming", and (iv) out-of-plane cavity control via a high-speed micro-LED array. Combining each, we demonstrate near-complete spatiotemporal control of a 64-resonator, two-dimensional SLM with nanosecond- and femtojoule-order switching. Simultaneously operating wavelength-scale modes near the space- and time-bandwidth limits, this work opens a new regime of programmability at the fundamental limits of multimode optical control., Comment: 25 pages, 20 figures

Surface strain is widely used in gas phase catalysis and electrocatalysis to control the binding energies of adsorbates on metal surfaces. However, $in$ $situ$ or $operando$ strain measurements are experimentally challenging, especially on nanomaterials. Here, we take advantage of the 4$^{th}$ generation Extremely Brilliant Source at the European Synchrotron Radiation Facility (ESRF-EBS, Grenoble, France) to quantify the distribution of strain inside a Pt nanoparticle, and to determine its morphology in an electrochemical environment. Our results show for the first time evidence of heterogeneous and potential-dependent strain distribution between highly-coordinated ({100} and {111} facets) and under-coordinated atoms (edges and corners) as well as evidence of strain propagation from the surface to the bulk of the nanoparticle. These results provide dynamic structural insights to better simulate and design efficient nanocatalysts for energy storage and conversion applications.

Results from 2.5D and 3D studies of the onset and development of the tearing instability are presented, using high fidelity resistive MHD simulations. A limited parameter study of the strength of the reconnecting field (or shear angle) was performed. An initially simple 1D equilibrium was used, consisting of a modified force-free current sheet, with periodic boundary conditions in all directions. In all cases, the linear and non-linear evolution led to a primary current sheet between two large flux ropes. The global reconnection rate during this later stage was analyzed in all simulations. It was found that in 2.5D the primary current sheet fragmented due to plasmoids, and as expected, the global reconnection rate, calculated using multiple methods, increases with the strength of the reconnecting field due to a stronger Alfv\'{e}n speed. In 3D, the presence of interacting oblique modes of the tearing instability complicates the simple 2.5D picture, entangling the magnetic field of the inflow and introducing a negative effect on the reconnection rate. The two competing effects of stronger Alfv\'{e}n speed and entangling, which both increase with the strength of the reconnecting field, resulted in a decrease in the reconnection rate with increasing reconnecting field. For all simulations, the 3D rates were less than in 2.5D, but suggest that as one goes to weak reconnecting field (or strong guide field), the system becomes more 2.5D like and the 2.5D and 3D rates converge. These results have relevance to situations like nano-flare heating and flare current sheets in the corona., Comment: 15 pages, 10 figures

The RecA protein and RecBCD complex are key bacterial components for the maintenance and repair of DNA, RecBCD a helicase-nuclease that uses homologous recombination to resolve double-stranded DNA breaks and also facilitating decoration of single-stranded DNA with RecA to form RecA filaments, a vital step in the double-stranded break DNA repair pathway. However, questions remain about the mechanistic roles of RecA and RecBCD in live cells. Here, we use millisecond super-resolved fluorescence microscopy to pinpoint the spatial localization of fluorescent reporters of RecA and the RecB at physiological levels of expression in individual live Escherichia coli cells. By introducing the DNA crosslinker mitomycin C, we induce DNA damage and quantify the resulting changes in stoichiometry, copy number and molecular mobilities of RecA and RecB. We find that both proteins accumulate in molecular hotspots to effect repair, resulting in RecA filamental stoichiometries equivalent to several hundred molecules that act largely in RecA tetramers before DNA damage, but switch to approximately hexameric subunits when mature filaments are formed. Unexpectedly, we find that the physiologically predominant form of RecB is a dimer.

We give a short proof of the log-concavity of the coefficients of the reduced characteristic polynomial of a matroid. The proof uses an extension of the theory of Lorentzian polynomials to convex cones, and reproves the Hodge-Riemann relations of degree one for the Chow ring of a matroid.

In the last few years, the notion of symmetry has provided a powerful and essential lens to view several optimization or sampling problems that arise in areas such as theoretical computer science, statistics, machine learning, quantum inference, and privacy. Here, we present two examples of nonconvex problems in optimization and sampling where continuous symmetries play -- implicitly or explicitly -- a key role in the development of efficient algorithms. These examples rely on deep and hidden connections between nonconvex symmetric manifolds and convex polytopes, and are heavily generalizable. To formulate and understand these generalizations, we then present an introduction to Lie theory -- an indispensable mathematical toolkit for capturing and working with continuous symmetries. We first present the basics of Lie groups, Lie algebras, and the adjoint actions associated with them, and we also mention the classification theorem for Lie algebras. Subsequently, we present Kostant's convexity theorem and show how it allows us to reduce linear optimization problems over orbits of Lie groups to linear optimization problems over polytopes. Finally, we present the Harish-Chandra and the Harish-Chandra--Itzykson--Zuber (HCIZ) formulas, which convert partition functions (integrals) over Lie groups into sums over the corresponding (discrete) Weyl groups, enabling efficient sampling algorithms., Comment: This article is to supplement the talks by the authors at the Bootcamp in the semester on Geometric Methods for Optimization and Sampling at the Simons Institute for the Theory of Computing

Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical perturbation is due to molecular machines such as topoisomerases which must stretch and twist DNA as part of various functions including DNA repair and replication. While the broad-scale mechanical response of nucleic acids to tension and torsion is well characterized, detail at the single base pair level is beyond the limits of even super-resolution imaging. Here, we present a straightforward, flexible, and extensible umbrella-sampling protocol to twist and stretch nucleic acids in silico using the popular biomolecular simulation package Amber -- though the principles we describe are applicable also to other packages such as GROMACS. We discuss how to set up the simulation system, decide forcefields and solvation models, and equilibrate. We then introduce the torsionally-constrained stretching protocol, and finally we present some analysis techniques we have used to characterize structural motif formation. Rather than define forces or fictional pseudoatoms, we instead define a fixed translation of specified atoms between each umbrella sampling step, which allows comparison with experiment without needing to estimate applied forces by simply using the fractional end-to-end displacement as a comparison metric. We hope that this easy to implement solution will be valuable for interrogating optical and magnetic tweezers data on nucleic acids at base pair resolution.

Here we describe the coupled standardisation of two complementary fluorescence imaging techniques and apply it to liquid-liquid phase separated condensates formed from an EGFP fluorescent reporter of Flowering Control Locus A (FCA), a protein that associates with chromosomal DNA in plants during epigenetic regulation of the flowering process. First, we use home-built single-molecule Slimfield microscopy to establish a fluorescent protein standard. This sample comprises live yeast cells expressing Mig1 protein, a metabolic regulator which localises to the nucleus under conditions of high glucose, fused to the same type of EGFP label as for the FCA fusion construct. Then we employ commercial confocal AiryScan microscopy to study the same standard. Finally, we demonstrate how to quantify FCA-EGFP nuclear condensates in intact root tips at rapid timescales and apply this calibration. This method is a valuable approach to obtaining single-molecule precise stoichiometry and copy number estimates of protein condensates that are integrated into the chromosome architecture of plants, using confocal instrumentation that lacks de facto single-molecule detection sensitivity.

Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear how these events are coordinated and how they integrate with regulation of molecular crowding. We use the budding yeast Saccharomyces cerevisiae as a model system to study these questions using recent progress in optical fluorescence microscopy and crowding sensing probe technology. We used a F\"{o}rster Resonance Energy Transfer (FRET) based sensor, illuminated by confocal microscopy for high throughput analyses and Slimfield microscopy for single-molecule resolution, to quantify molecular crowding. We determine crowding in response to cellular growth of both mother and daughter cells, in addition to osmotic stress, and reveal hot spots of crowding across the bud neck in the burgeoning daughter cell. This crowding might be rationalized by the packing of inherited material, like the vacuole, from mother cells. We discuss recent advances in understanding the role of crowding in cellular regulation and key current challenges and conclude by presenting our recent advances in optimizing FRET-based measurements of crowding whilst simultaneously imaging a third color, which can be used as a marker that labels organelle membranes. Our approaches can be combined with synchronised cell populations to increase experimental throughput and correlate molecular crowding information with different stages in the cell cycle.