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At least 595 records · Page 33

In vivo localization of iron starvation induced proteins under variable iron supplementation regimes in Phaeodactylum tricornutum

Abstract The model pennate diatom Phaeodactylum tricornutum is able to assimilate a range of iron sources. It therefore provides a platform to study different mechanisms of iron processing concomitantly in the same cell. In this study, we follow the localization of three iron starvation induced proteins (ISIPs) in vivo, driven by their native promoters and tagged by fluorophores in an engineered line of P. tricornutum . We find that the localization patterns of ISIPs are dynamic and variable depending on the overall iron status of the cell and the source of iron it is exposed to. Notwithstanding, a shared destination of the three ISIPs both under ferric iron and siderophore‐bound iron supplementation is a globular compartment in the vicinity of the chloroplast. In a proteomic analysis, we identify that the cell engages endocytosis machinery involved in the vesicular trafficking as a response to siderophore molecules, even when these are not bound to iron. Our results suggest that there may be a direct vesicle traffic connection between the diatom cell membrane and the periplastidial compartment (PPC) that co‐opts clathrin‐mediated endocytosis and the “cytoplasm to vacuole” (Cvt) pathway, for proteins involved in iron assimilation. Proteomics data are available via ProteomeXchange with identifier PXD021172. Highlight The marine diatom P. tricornutum engages a vesicular network to traffic siderophores and phytotransferrin from the cell membrane directly to a putative iron processing site in the vicinity of the chloroplast.

59 BASIC BIOLOGICAL SCIENCES↗

Thermal Gradient Effects on Local Hotspot Ignition in 1,3,5,7‐Tetranitro‐1,3,5,7‐tetrazocane (HMX)

Understanding hotspot ignition, growth, and criticality, as well as the timescales of each, is crucial for parameterizing mesoscale and continuum‐level models that rely on a statistical understanding of hotspots. However, these models often consider hotspots to have uniform temperatures or for hotspots of a given temperature and size to always behave the same. Therefore, using molecular dynamics simulations, we assess the influence of thermal distribution effects on hotspot local ignition and time to ignition in 1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocane (HMX) nanoscale hotspots. Finally, by assessing hotspots with a gradient driven from an initial two‐temperature core–shell setup, we show that small increases in the core temperature under a constant average temperature can lead to order‐of‐magnitude effects on reaction and local ignition timescales.

36 MATERIALS SCIENCE↗

A Deep Learning Approach for Detection and Localization of Leaf Anomalies

The detection and localization of possible diseases in crops are usually automated by resorting to supervised deep learning approaches. In this work, we tackle these goals with unsupervised models, by applying three different types of autoencoders to a specific open-source dataset of healthy and unhealthy pepper and cherry leaf images. CAE, CVAE and VQ-VAE autoencoders are deployed to screen unlabeled images of such a dataset, and compared in terms of image reconstruction, anomaly removal, detection and localization. The vector-quantized variational architecture turns out to be the best performing one with respect to all these targets.

Calabro', Davide↗

Local Poincaré algebra from quantum chaos

The local two-dimensional Poincaré algebra near the horizon of an eternal AdS black hole, or in proximity to any bifurcate Killing horizon, is generated by the Killing flow and outward null translations on the horizon. In holography, this local Poincaré algebra is reflected as a pair of unitary flows in the boundary Hilbert space whose generators under modular flow grow and decay exponentially with a maximal Lyapunov exponent. This is a universal feature of many geometric vacua of quantum gravity. To explain this universality, we show that a two-dimensional Poincaré algebra emerges in any quantum system that has von Neumann subalgebras associated with half-infinite modular time intervals (modular future and past subalgebras) in a limit analogous to the near-horizon limit. In ergodic theory, quantum dynamical systems with future or past algebras are called quantum K-systems. The surprising statement is that modular K-systems are always maximally chaotic. Interacting quantum systems in the thermodynamic limit and large N theories above the Hawking-Page phase transition are examples of physical theories with future/past subalgebras. We prove that the existence of (modular) future/past von Neumann subalgebras also implies a second law of (modular) thermodynamics and the exponential decay of (modular) correlators. We generalize our results from the modular flow to any dynamical flow with a positive generator and interpret the positivity condition as quantum detailed balance.

79 ASTRONOMY AND ASTROPHYSICS↗

Local SU(2) × U(1) quark flavor symmetry in the RS bulk

We propose a model of quark flavor based on an additional SU(2) × U(1) local symmetry in a warped extra dimensional bulk. In contrast to other works, we break the additional gauge symmetry in the bulk via two complex scalars which acquire bulk vevs, rather than relying on brane-localized symmetry breaking. A gauge-covariant Kaluza-Klein decomposition of a theory with a bulk spontaneously broken gauge symmetry is performed, and exact expressions for the bulk profiles of all physical particles in such systems are given. The SM quark masses and mixings are then recreated using gauge-covariant bulk quark mass terms and Yukawa-like couplings to the new bulk scalars. A numerical sampling of points in the model parameter space that recreate the quark masses and mixings is performed at a KK scale of M KK = 5 TeV. We then compute the ΔF = 2 4-quark operators arising from our new flavor gauge bosons and scalars, and those arising from Kaluza-Klein modes of SM gauge bosons. By decoupling one of our bulk scalar fields to all quark fields except the right-handed up-like sector, we find that it is possible to greatly suppress tree-level contributions to the highly constrained Kaon mixing parameters. Instead, the dominant constraints on the model emerge from neutral Bd and D meson mixing. These constraints are explored with our numerical sampling of the model parameter space, and the specific contribution of the new flavor gauge bosons and scalars is discussed. We find that for a significant range of realistic flavor gauge couplings, the new gauge bosons compete with the normally dominant gluon flavor-changing currents, but flavor-changing operators emerging from the bulk scalar fields are highly suppressed. Finally, we briefly comment on flavor constraints that are independent of the flavor gauge sector arising from the Z$\overline{b}$ L b L coupling and rare top decays.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Microscopic entropy of rotating electrically charged AdS 4 black holes from field theory localization

We employ supersymmetric localization to determine the exact partition function of 3d N = 2 gauge theories on a background given by a round S 2 fibered over a circle and certain complexified background fields. The Coulomb branch localization locus includes monopole configurations, and the partition function reduces to a matrix model. We consider the partition function of the ABJM theory on this background as an explicit case. We verify that the large-N limit of the ABJM theory partition function produces, in the Cardy limit, the entropy function of the dual rotating, electrically charged asymptotically AdS 4 supersymmetric black holes and thus provides a microscopic explanation for the Bekenstein-Hawking entropy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Kinetic mixing, dark photons and extra dimensions. Part III. Brane localized dark matter

Extra dimensions have proven to be a very useful tool in constructing new physics models. In earlier work, we began investigating toy models for the 5-D analog of the kinetic mixing/vector portal scenario where the interactions of dark matter, taken to be, e.g., a complex scalar, with the brane-localized fields of the Standard Model (SM) are mediated by a massive U(1) D dark photon living in the bulk. These models were shown to have many novel features differentiating them from their 4-D analogs and which, in several cases, avoided some well-known 4-D model building constraints. However, these gains were obtained at the cost of the introduction of a fair amount of model complexity, e.g., dark matter Kaluza-Klein excitations. In the present paper, we consider an alternative setup wherein the dark matter and the dark Higgs, responsible for U(1) D breaking, are both localized to the ‘dark’ brane at the opposite end of the 5-D interval from where the SM fields are located with only the dark photon now being a 5-D field. The phenomenology of such a setup is explored for both flat and warped extra dimensions and compared to the previous more complex models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Exploiting stochastic locality in lattice QCD: hadronic observables and their uncertainties

Abstract Because of the mass gap, lattice QCD simulations exhibit stochastic locality: distant regions of the lattice fluctuate independently. There is a long history of exploiting this to increase statistics by obtaining multiple spatially-separated samples from each gauge field; in the extreme case, we arrive at the master-field approach in which a single gauge field is used. Here we develop techniques for studying hadronic observables using position-space correlators, which are more localized, and compare with the standard time-momentum representation. We also adapt methods for estimating the variance of an observable from autocorrelated Monte Carlo samples to the case of correlated spatially-separated samples.

Physics↗

Local bilinear computation of Jacobi sets

Abstract We propose a novel method for the computation of Jacobi sets in 2D domains. The Jacobi set is a topological descriptor based on Morse theory that captures gradient alignments among multiple scalar fields, which is useful for multi-field visualization. Previous Jacobi set computations use piecewise linear approximations on triangulations that result in discretization artifacts like zig-zag patterns. In this paper, we utilize a local bilinear method to obtain a more precise approximation of Jacobi sets by preserving the topology and improving the geometry. Consequently, zig-zag patterns on edges are avoided, resulting in a smoother Jacobi set representation. Our experiments show a better convergence with increasing resolution compared to the piecewise linear method. We utilize this advantage with an efficient local subdivision scheme. Finally, our approach is evaluated qualitatively and quantitatively in comparison with previous methods for different mesh resolutions and across a number of synthetic and real-world examples.

97 MATHEMATICS AND COMPUTING↗

On the relationship between precipitation extreme and local temperature over eastern China based on convection permitting simulations: roles of different moisture processes and precipitation types

The Clausius–Clapeyron (CC) scaling, which indicates a roughly 7% increase in saturated water vapor per 1 °C increase in temperature, can serve as a strong constraint linking the intensity of precipitation extremes and local temperature. However, the relationship between precipitation extreme and local temperature (referred to as the PE-T relationship) does not always follow the CC scaling and is highly dependent on climate regimes. In this study, we investigated the impacts of different moisture processes and precipitation types on the PE-T relationship over eastern China during the summertime based on convection-permitting model simulations. Consistent with observations, the simulated intensity of precipitation extremes increases with temperature at a rate close to CC (double-CC) scaling below (above) 20 °C. When the temperature exceeds 25 °C, precipitation intensity starts to drop. Precipitation extremes are mainly contributed by the stratiform, MCS (i.e., mesoscale convective system) convective, and non-MCS convective precipitation at low (< 20 °C), medium (20–25 °C), and high (> 25 °C) temperatures, respectively, suggesting that the double-CC scaling occurs when convective types become dominant, while the negative scaling at high temperatures is attributed to the reduced horizontal scale of convection. Corresponding to the reduced intensity of precipitation at high temperatures, there are stronger divergence and subsidence in the low-level atmosphere, which is probably caused by the net cooling associated with the enhanced melting and evaporation of falling hydrometeors due to the lower relative humidity in the low-level atmosphere. Overall, our findings contribute to a deeper understanding of the temperature dependence of precipitation extremes in eastern China.

54 ENVIRONMENTAL SCIENCES↗

Revisiting the first Sandia Fracture Challenge with transient deformation heating and strain localization considerations

In this study, we present a systematic experimental study and accompanying theoretical analysis of the dependence of ductile fracture on strain localization, strain hardening rates, deformation-induced thermal softening, and transient heat conduction under spatially uniform as well as spatially heterogeneous deformation. Spatially uniform cases are studied via standard dogbone shaped specimens subject to uniaxial tension. Spatially heterogeneous deformation is studied via the so-called Sandia Fracture Challenge (SFC) specimen, which is a standard compact tension specimen modified with three machined holes in front of a blunt notch. We utilize the same precipitation hardened martensitic stainless steel used in the first SFC experiments, i.e. 15-5 PH with an H1075 heat treatment. We also study 15-5 PH in Condition A and with the H900 heat treatment, each of which has a different hardening behavior and ductility. We find that the ductility does not correlate with the deformation to first crack initiation in the SFC specimen. Instead, hardening rates are better correlated. Moreover, a re-examination finds that an accurate calibration of the hardening rates is strongly correlated with accurate blind predictions of ductile fracture in the SFC specimens. Given that thermal softening can greatly affect hardening rates, we provided a thermographic analysis of deformation-induced heating and transient heat transfer in both the dogbone shaped samples and the SFC specimens. Transient heating in stainless steels is found to have first-order effects on the strain at the onset of necking, strain to fracture, as well as strain localization and ductile fracture in complex geometries even under so-called quasi-static loading rates.

42 ENGINEERING↗

Nonoverlapping Localized Exponential Time Differencing Methods for Diffusion Problems

In this paper, we propose nonoverlapping localized exponential time differencing (ETD) methods for diffusion problems. The model time-dependent diffusion equation is first reformulated on subdomains based on the nonoverlapping domain decomposition, in which Neumann boundary conditions are imposed on the interfaces for the subdomain problems and Dirichlet type conditions are enforced to form a space-time interface problem. After spatial discretization by standard central finite differences and temporal integration with the first or second order ETD methods, the fully discrete interface problem is obtained. Such an interface problem is then solved iteratively either at each time step or over the whole time interval: the former involves the solution of stationary problems in each subdomain at each iteration while the latter involves the solution of time-dependent subdomain problems at each iteration. For both approaches, we prove that localized ETD solutions conserve mass exactly and converge in time to the exact space semidiscrete solution. Numerical experiments in two dimensions are also presented to illustrate the performance of the proposed methods.

Mass conservation↗

Parametric reduced-order modeling for component-oriented treatment and localized nonlinear feature inclusion

Abstract We propose coupling a physics-based reduction framework with a suited response decomposition technique to derive a component-oriented reduction (COR) approach, which is suitable for assembly systems featuring localized nonlinearities. Dependencies on influencing parameters are injected into the reduced-order model (ROM), thus ensuring robustness and validity over a domain of parametric inputs, while capturing nonlinear effects. The implemented approach employs individual component modes to capture localized features while additionally relying on reduced modes of a global nature to approximate the system’s dynamics accurately. The global modes are derived from a linear monolithic system, defined as a result of a coordinate separation scheme, which permits the proposed COR-ROM to naturally couple the response between linear and nonlinear subdomains. The derived low-order representation utilizes a proper orthogonal decomposition projection and is additionally reinforced with the inclusion of a hyper-reduction technique to capture the underlying high-fidelity model response while providing accelerated computations. The resulting approach is exemplified in the synthetic case studies of a four-story shear frame with multiple nonlinear regions driven by hysteresis and a large-scale kingpin connection featuring plasticity.

Vlachas, Konstantinos (ORCID:000000029124219X)↗

Anomalous X-Ray Scattering and Extended X-Ray Absorption Fine Structure Study of the Local Structure of CrFeCoNiMo x (x = 0.11, 0.18, and 0.23) High-Entropy Alloys

Anomalous x-ray scattering (AXS) and extended x-ray absorption fine structure (EXAFS) were used to determine the local structure of Mo in CrFeCoNiMo x (x = 0.11, 0.18, and 0.23), a high-entropy alloy with a face-centered cubic (FCC) lattice. No superlattice peaks were observed down to the 10 -4 intensity level. This observation along with the nearly constant decrease of the FCC diffraction peaks above the Mo K absorption edge suggests that Mo atoms have no preferred site occupancy in the FCC lattice. Modeling of the EXAFS data suggests a local chemical order in CrFeCoNiMo x , where in Mo-rich samples (e.g., x = 0.23), Mo atoms are preferably surrounded by lighter atoms, such as Cr.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Investigating the Interaction Between Circulating Tumor Cells and Local Hydrodynamics via Experiment and Simulations

Introduction: The biological and mechanical properties of circulating tumor cells (CTCs) in combination with the hemodynamics affect the preference of metastatic sites in the vasculature. Despite the extensive literature on the effects of biological properties on cell adhesion, the effects of hydrodynamic forces on primary attachment remains an active area of research. Here, using simulations in conjunction with experimentation, we provide new insight into the interplay of CTCs dynamics and local hydrodynamics. Methods: A flow experiment of CTC attachment was performed within a bioprinted, double branching endothelialized vessel. Simulations of fluid flow and CTC transport in the reconstructed and idealized bifurcated vessel were respectively performed by HARVEY, our in-house massively parallel computational fluid dynamics solver. HARVEY is based on the lattice Boltzmann and finite element methods to model the fluid and cells dynamics. The immersed boundary method is employed for resolving the fluid–structure interaction. Results: CTC attachment was quantified experimentally at all regions of the complex vessel. The results demonstrate a clear preference for CTCs to attach at the branch points. To elucidate the effect of the vessel topology on the location of attachment, a fluid-only simulation was performed assessing the differences in the hydrodynamics along the vessel. CTC transport in idealized bifurcated vessels was subsequently studied to examine the effects of cell deformability on the local hydrodynamics patterns and, thus, the preference of attachment sites. Conclusions: The current work provides evidence on the correlation of the hydrodynamics forces arising from the vessel topology and CTC properties on the attachment regions.

60 APPLIED LIFE SCIENCES↗

Transfer learning for probabilistic localization of hidden cracks in concrete structures

Abstract The utility of discriminative supervised learning models built using multiple training-data sources is investigated for hidden crack localization in concrete. Feed-forward neural network (FFNN) is chosen as the model architecture, and transfer learning is used to assimilate the information obtained from different sources (computational physics simulations and laboratory experiments). The labeled training data consists of values of a damage index and the known locations of hidden cracks. The classification models need to learn how the presence of damage (hidden cracks) affects the damage index at different sensors for different test conditions. To this end, diagnostic FFNN models are built by sequentially adding and training new hidden layers to assimilate labeled information from computer models (different model geometries, test conditions, crack lengths, crack locations) and laboratory experiments on a plain cement slab. These transfer learning-based models are then used to localize damage in concrete specimens that reflect real-world conditions (i.e., specimens with steel reinforcement and randomly distributed aggregate). The actual damage state in these specimens is determined by extracting cores and performing petrographic studies on the extracted cores. The damage probability estimated by transfer learning-based models is compared with the petrographic damage rating index (DRI) to identify the most suitable approach to train the diagnostic models. The transfer learning-based diagnostic methodology shows promise and could be used in various structural health monitoring applications, where sufficient labeled data are typically not available from a single data source.

Miele, S.↗

Grain boundary strain as a determinant of localized sink efficiency

The opportunity to achieve radiation tolerance in crystalline materials hinges on understanding the structure and response of grain boundary sinks to irradiation. A common descriptor of grain boundary efficiency as a defect sink is the denuded zone, which is a defect free zone adjacent to the grain boundary dictated by its ability to absorb radiation induced defects. This descriptor is often used at the mesoscale, which requires an averaging of absorption events. In this paper, we resolve the defect sink efficiency as a function of interfacial strain with respect to grain boundary character, and correlate high levels of grain boundary strain to an enhanced absorption efficiency. Here, we also introduce a key relationship between localized strain in proximity with the grain boundary sink and the variation absorption efficiency associated with these regions, revealing the pitfalls of averaging absorption events along a grain boundary, and presenting a path forward toward improved models for denuded zones and localized grain boundary absorption phenomena.

36 MATERIALS SCIENCE↗

Grain incompatibility determines the local structure of amorphous grain boundary complexions

Amorphous grain boundary complexions lack long-range crystalline order but are not featureless, as distinct gradients in structural short-range order have been reported through their thickness. In this work, we test the hypothesis that the distribution of short-range order is determined by the confining crystals using atomistic simulations of both Cu-Zr bicrystals and a random polycrystal. Voronoi polyhedra with structures similar to that of perfect face-centered cubic serve as signatures of high structural order and are only found at the amorphous-crystalline transition regions. The density of the ordered structural motifs within a specific amorphous-crystalline transition region is found to not be directly determined by the orientation and symmetry of the grain which touches it, but rather by the incompatibility between the two confining grains. Further, ordered polyhedra density is found to be inversely related to grain incompatibility, meaning that large incompatibilities between the confining crystals lead to less order in the amorphous-crystalline transition region. The finding that the entire grain-film-grain system must be considered to understand local structure unequivocally demonstrates that amorphous complexions are not simply a collection of independent phases which happen to nucleate at a grain boundary. Rather, an amorphous grain boundary complexion is a single entity that finds a local equilibrium configuration.

36 MATERIALS SCIENCE↗