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At least 55 records · Page 3

Mechanistic within-host mathematical model of inhalational anthrax

We present a mathematical model of the dynamics of Bacillus anthracis bacteria within the lymph nodes and blood of a host, following inhalation of an initial dose of spores. We also incorporate the dynamics of protective antigen, which is the binding component of the anthrax toxin produced by the bacteria. The model offers a mechanistic description of the early infection dynamics of inhalational anthrax, while its stochastic nature allows us to study the probabilities of different outcomes (for example, how likely it is that the infection will be cleared for a given inhaled dose of spores) in order to explain dose-response data for inhalational anthrax. The model is calibrated via a Bayesian approach, using in vivo data from New Zealand white rabbit and guinea pig infection studies, enabling within-host parameters to be estimated. We also leverage incubation-period data from the Sverdlovsk 1979 anthrax outbreak to show that the model can accurately describe human time-to-symptoms data under reasonable parameter regimes. Finally, we derive a simple approximate formula for the probability of symptom onset before time t, assuming that the number of inhaled spores has a Poisson distribution.

59 BASIC BIOLOGICAL SCIENCES↗

Technical Performance of Refractory Liners for Molten Chloride Salt Thermal Energy Storage Systems

A chloride-based molten-salt system that uses a ternary blend of MgCl2/KCl/NaCl is investigated to provide higher temperature thermal energy storage capability. Despite higher thermal stability, molten chlorides present several unique challenges, including the design of internal refractory-ceramic liners to prevent the corrosion and thermal stress of alloy tank shells. This work discusses issues and potential solutions related to containment of molten chloride salt, specifically the optimization of the refractory material at the molten salt interface (hot face). The down-selected hot face candidate limits permeation of salt through the material and forms a highly stable secondary surface phase in equilibrium with the molten salt. A mortar is created using the corrosion resistant hot face brick. Brick and mortar composite are subjected to mechanical stress/strain analysis, in order to calculate composite material properties and better inform thermomechanical models. The U.S. Department of Energy Generation 3 (DOE Gen3) program seeks to develop higher efficiency CSP plants that can provide cost-competitive, flexible power in the U.S. electric grid. The proposed Gen3 Liquid Pathway CSP plant closely resembles the configuration of current nitrate salt power towers with two-tank storage (Gen2). The differences between Gen2 and Gen3 include the types of compatible materials used in salt storage tank construction. Stainless steel loses strength at Gen3 temperatures, and although nickel superalloys would be capable of withstanding sustained high temperatures, these materials are prohibitively expensive at scale. Uninsulated tank shells also pose a significant risk as common steels are highly susceptible to chemical attack from molten chloride salt. To address these concerns, refractory-ceramic based containment materials are proposed to line the inside of the hot and cold storage tanks. In doing so, stainless or carbon steel shells may be used in construction depending on the level of insulation provided. The composition of the internal liner requires careful consideration to maximize the efficacy of multiple parameters including corrosion resistance, strength at operating temperature, durability, and cost. This is particularly true for the material at the interface with the salt, known as the "hot face", which is responsible for protecting the insulating layers between the tank shell and the hot face brick layer. The molten salt in this system is superheated over 300 °C above its freeze temperature. Therefore, unlike other industrial processes which use refractory-lined vessels, it is not expected that a freeze plane will develop in the hot face. Therefore, the hot face must be designed to withstand chemical corrosion and inhibit permeation of molten salt into the insulating layers. A down selection was performed to identify a hot face candidate best equipped to maintain thermal, mechanical, and chemical integrity when exposed to molten salt over extended periods of time. Long-duration chemical capability experiments were conducted with the down selected hot face refractory fully immersed in molten chloride salt for up to 3000 hours. The average salt penetration does not exceed 100 microns. When extrapolated to 20 and 30 years of continuous exposure, the expected salt penetration depth is approximately 2.0 mm and 2.9 mm, respectively. A magnesium-rich secondary phases develops at the salt/refractory interface. X-ray diffraction identifies the material as forsterite (Mg2SiO4), which is reported to form synthetically in molten chloride salt solutions. These results suggest the selected hot face will adequately inhibit salt permeation. While there is optimism that the hot face brick will inhibit salt permeation, mortar joints are typically the weakest point of a refractory brick liner. From a thermochemical perspective, differing thermal expansion coefficients may result in the mortar and brick to grow independent of each other, creating gaps through which molten salt can penetrate. To address this issue, NREL has developed an in-house mortar composed of the down selected hot face brick that has been shown to be compatible with the salt. Compressive stress/strain analyses have been performed on the brick/ mortar composites to generate stress/strain curves. Modulus of elasticity and Poisson's ratio of the composite may be calculated from the stress/strain curves, in order to provide more representative data to finite element mechanical models for accurate approximation of stress on the tank shell and the amount of thermal expansion expected within the tank liner.

41 EE - Solar Energy Technologies Office (EE-4S)↗

A weighted Shifted Boundary Method for free surface flow problems

The Shifted Boundary Method (SBM) belongs to the class of unfitted (or immersed, or embedded) finite element methods and was recently introduced for the Poisson, linear advection/diffusion, Stokes, Navier-Stokes, acoustics, and shallow-water equations. By reformulating the original boundary value problem over a surrogate (approximate) computational domain, the SBM avoids integration over cut cells and the associated problematic issues regarding numerical stability and matrix conditioning. Accuracy is maintained by modifying the original boundary conditions using Taylor expansions. Hence the name of the method, that shifts the location and values of the boundary conditions. In this article, we extend the SBM to the simulation of incompressible Navier-Stokes flows with moving free-surfaces, by appropriately weighting its variational form with the elemental volume fraction of active fluid. This approach prevents spurious pressure oscillations in time, which would otherwise be produced if the total active fluid volume were to change abruptly over a time step. In fact, the proposed weighted SBM method induces small mass (i.e., volume) conservation errors, which converge quadratically in the case of piecewise-linear finite element interpolations, as the grid is refined. Finally, we present an extensive set of two- and three-dimensional tests to demonstrate the robustness and accuracy of the method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Towards Automated Reasoning Chains for Verification of LLM-Generated Scientific Code

With the rise of Large Language Model (LLM) generated code, including in domains like scientific computing, ensuring not only syntactical, but also mathematical correctness, has become a critical task. Traditional formal methods approaches often struggle with the ambiguity of floating-point code, and full symbolic execution is extremely costly and limited. We propose a chain-of-reasoning approach that iteratively lifts basic semantics from code into the SPIRAL system and then establishes numerical equivalency to the desired mathematical operation. Here, we leverage the ample mathematical knowledge already formalized in SPIRAL to enable the system to recognize not just different implementations of the same algorithm but fully separate approaches to solving the given problem. The chain establishes tight error bounds on the output of given code with respect to the true continuous solution it approximates, quantifying all sources of error. We demonstrate this approach by establishing the correctness of a pseudospectral solver for a simple 1-dimensional Poisson problem.

Oschatz, Quentin [Carnegie Mellon University,Pitts↗

Voltage-Dependent First-Principles Simulation of Insertion of Chloride Ions into Al/Al 2 O 3 Interfaces Using the Quantum Continuum Approximation

Experiments have shown that pitting corrosion can develop in aluminum surfaces at potentials > − 0.5 V relative to the standard hydrogen electrode (SHE). Until recently, the onset of pitting corrosion in aluminum has not been rigorously explored at an atomistic scale because of the difficulty of incorporating a voltage into density functional theory (DFT) calculations. We introduce the Quantum Continuum Approximation (QCA) which self-consistently couples explicit DFT calculations of the metal-insulator and insulator-solution interfaces to continuum Poisson-Boltzmann electrostatic distributions describing the bulk of the insulating region. By decreasing the number of atoms necessary to explicitly simulate with DFT by an order of magnitude, QCA makes the first-principles prediction of the voltage of realistic electrochemical interfaces feasible. After developing this technique, we apply QCA to predict the formation energy of chloride atoms inserting into oxygen vacancies in Al(111)/α-Al 2 O 3 (0001) interfaces as a function of applied voltage. We predict that chloride insertion is only favorable in systems with a grain boundary in the Al 2 O 3 for voltages > − 0.2 V (SHE). Here our results roughly agree with the experimentally demonstrated onset of corrosion, demonstrating QCA's utility in modeling realistic electrochemical systems at reasonable computational cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reassessment of Birch's Law on hcp‐Fe From Ultrasonic Sound Velocity Measurement and Implications on the Velocity Profiles of Earth's Inner Core

Here, we performed in situ X-ray diffraction and ultrasonic sound velocity measurements on hcp-Fe up to 15 GPa, 873 K in a multi-anvil apparatus. The elastic moduli and their pressure and temperature derivatives were determined by fitting the velocity and density data to the third-order finite strain equations, yielding K S0 = 169.0(57) GPa, K$^{′}_{S0}$ = 5.4(6), (∂K S /∂T) P = −0.031(3) GPa/K, G 0 = 104.5(27) GPa, G$^{′}_{0}$ = 1.7(2), (∂G/∂T) P = −0.060(2) GPa/K. Within the experimental P-T range, we find significant temperature effect on the density-velocity (ρ − V P or S ) relations and caution the use of the temperature-independent Birch's law for extrapolation to core conditions. Furthermore, temperature-induced velocity decrease is more significant in V S than in V P , offering a possible explanation for the high Poisson's ratio in the core. Extrapolations based on our results together with previous experimental data suggest that V P of hcp-Fe aligns with PREM at Earth's core conditions, while Vs and density are approximately 10% and 2.7% higher than PREM, respectively.

36 MATERIALS SCIENCE↗

Near-zero photon bioimaging by fusing deep learning and ultralow-light microscopy

Enhancing the reliability and reproducibility of optical microscopy by reducing specimen irradiance continues to be an important biotechnology target. As irradiance levels are reduced, however, the particle nature of light is heightened, giving rise to Poisson noise, or photon sparsity that restricts only a few (0.5%) image pixels to comprise a photon. Photon sparsity can be addressed by collecting approximately 200 photons per pixel; this, however, requires long acquisitions and, as such, suboptimal imaging rates. Here, we introduce near-zero photon bioimaging, a method that operates at kHz rates and 10,000-fold lower irradiance than standard microscopy. To achieve this level of performance, we uniquely combined a judiciously designed epifluorescence microscope enabling ultralow background levels and AI that learns to reconstruct biological images from as low as 0.01 photons per pixel. We demonstrate that near-zero photon bioimaging captures the structure of multicellular and subcellular features with high fidelity, including features represented by nearly zero photons. Beyond optical microscopy, the near-zero photon bioimaging paradigm can be applied in remote sensing, covert applications, and biomedical imaging that utilize damaging or quantum light.

AI↗

The concept of spin ice graphs and a field theory for their charges

Originally detected in rare earth pyrochlores, spin ice physics is now being artificially extended to a variety of geometries that control collective behavior and exotic properties, making graph theory their proper framework. We relate spin ice notions, such as ice rule, ice manifold, Coulomb phases, charges, and monopoles, to graph-theoretical notions, such as balance, in/out-degrees, and Euler paths. We then propose a field-theoretical treatment in which topological charges and monopoles are the degrees of freedom, while the binary spins are subsumed in an entropic interaction among charges. We show that for a spin ice on a graph in a Gaussian approximation, the kernel of the entropic interaction is the inverse of the graph Laplacian, and we compute screening functions from the graph spectra as Green operators for the screened Poisson problem on a graph. We then apply the treatment to star graphs, tournaments, cycles, and regular spin ice in different dimensions. Our aim is twofold: to set spin ice physics in a proper graph setting, where only topological rather than geometrical notions hold, and to invite graph theorists to contribute their powerful tools to the field of spin ice.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Universal behavior in fragmenting brittle, isotropic solids across material properties

A bonded particle model is used to explore how variations in the material properties of brittle, isotropic solids affect critical behavior in fragmentation. To control material properties, a model is proposed which includes breakable two- and three-body particle interactions to calibrate elastic moduli and mode I and mode II fracture toughnesses. In the quasistatic limit, fragmentation leads to a power-law distribution of grain sizes which is truncated at a maximum grain mass that grows as a nontrivial power of system size. In the high-rate limit, truncation occurs at a mass that decreases as a power of increasing rate. A scaling description is used to characterize this behavior by collapsing the mean-square grain mass across rates and system sizes. Consistent scaling persists across all material properties studied, although there are differences in the evolution of grain size distributions with strain as the initial number of grains at fracture and their subsequent rate of production depend on Poisson's ratio. Importantly, this evolving granular structure is found to induce a unique rheology where the ratio of the shear stress to pressure, an internal friction coefficient, decays approximately as the logarithm of increasing strain rate. The stress ratio also decreases at all rates with increasing strain as fragmentation progresses and depends on elastic properties of the solid.

36 MATERIALS SCIENCE↗

Exponential Runge-Kutta Parareal for non-diffusive equations

Parareal is a well-known parallel-in-time algorithm that combines a coarse and fine propagator within a parallel iteration. It allows for large-scale parallelism that leads to significantly reduced computational time compared to serial time-stepping methods. However, like many parallel-in-time methods it can fail to converge when applied to non-diffusive equations such as hyperbolic systems or dispersive nonlinear wave equations. Here, this paper explores the use of exponential integrators within the Parareal iteration. Exponential integrators are particularly interesting candidates for Parareal because of their ability to resolve fast-moving waves, even at the large stepsizes used by coarse propagators. This work begins with an introduction to exponential Parareal integrators followed by several motivating numerical experiments involving the nonlinear Schrödinger equation. These experiments are then analyzed using linear analysis that approximates the stability and convergence properties of the exponential Parareal iteration on nonlinear problems. The paper concludes with two additional numerical experiments involving the dispersive Kadomtsev-Petviashvili equation and the hyperbolic Vlasov-Poisson equation. These experiments demonstrate that exponential Parareal methods offer improved time-to-solution compared to serial exponential integrators when solving certain non-diffusive equations.

97 MATHEMATICS AND COMPUTING↗

Analysis of overlapping count data

Counts of a specific characteristic were obtained within regions defined on an object that was manufactured in a proprietary setting. The count regions were altered during production and resulted in misaligned or overlapping count data. A closed-formula maximum likelihood estimator (MLE) of the new region means is derived using all of the available count data and an independent Poisson model. The MLE is shown to be preferable to estimators constructed using generalized linear models for the overlapping data setting. This closed-form estimator extends to over-dispersed overlapping count data as the quasi-MLE and also performs well with correlated overlapping count data. Standard errors for the estimator are approximated and are validated with a simulation study. Additionally, the methods are extended to overlapping multinomial data. Illustrative examples of the methods are provided throughout the paper and are reproducible with the supplemental R code. Additionally, proofs of the paper’s results are also included in the supplemental material.

97 MATHEMATICS AND COMPUTING↗

A soft departure from jamming: the compaction of deformable granular matter under high pressures

Here, the high-pressure compaction of three-dimensional granular packings is simulated using a bonded particle model (BPM) to capture linear elastic deformation. In the model, grains are represented by a collection of point particles connected by bonds. A simple multibody interaction is introduced to control Poisson's ratio and the arrangement of particles on the surface of a grain is varied to model both high- and low-frictional grains. At low pressures, the growth in packing fraction and coordination number follows the expected behavior near jamming and exhibit friction dependence. As the pressure increases, deviations from the low-pressure power-law scaling emerge after the packing fraction grows by approximately 0.1 and results from simulations with different friction coefficients converge. These results are compared to predictions from traditional discrete element method simulations which, depending on the definition of packing fraction and coordination number, may only differ by a factor of two. As grains deform under compaction, the average volumetric strain and asphericity, a measure of the change in the shape of grains, are found to grow as power laws and depend heavily on the Poisson's ratio of the constituent solid. Larger Poisson's ratios are associated with less volumetric strain and more asphericity and the apparent power-law exponent of the asphericity may vary. The elastic properties of the packed grains are also calculated as a function of packing fraction. In particular, we find the Poisson's ratio near jamming is 1/2 but decreases to around 1/4 before rising again as systems densify.

36 MATERIALS SCIENCE↗

Baryon-Interacting Dark Matter: heating dark matter and the emergence of galaxy scaling relations

The empirical scaling relations observed in disk galaxies remain challenging for models of galaxy formation. The most striking among these is the Mass Discrepancy-Acceleration Relation (MDAR), which encodes both a tight baryonic Tully-Fisher relation (BTFR) and the observed diversity of galaxy rotation curves through the central surface density relation (CSDR). Building on our earlier work [1], we propose here that the MDAR is the result of interactions between baryons and ‘Baryon-Interacting Dark Matter’ (BIDM), which heat up the dark matter. Following a bottom-up, hydrodynamical approach, we find that the MDAR follows if: i) the BIDM equation of state approximates that of an ideal gas; ii) the BIDM relaxation time is order the Jeans time; iii) the heating rate is inversely proportional to the BIDM density. Remarkably, under these assumptions the set of hydrodynamical equations together with Poisson’s equation enjoy an anisotropic scaling symmetry. In the BIDM-dominated regime, this gives rise to an enhanced symmetry which fully captures the low-acceleration limit of the MDAR. We then show that, assuming a cored pseudo-isothermal profile at equilibrium, this set of equations gives rise to parameters reproducing the MDAR. Specifically, in the flat part of the rotation curve the asymptotic rotational velocity matches the parametric dependence of the BTFR. Moreover, in the central region of high-surface brightness galaxies, the profile reproduces the CSDR. Finally, by studying the time-dependent approach to equilibrium, we derive a global combination of the BTFR and CSDR, which matches the expectations in low surface-brightness galaxies. The form of the heating rate also makes model-independent predictions for various cosmological observables. We argue that our scenario satisfies existing observational constraints, and, intriguingly, offers a possible explanation to the EDGES anomaly.

79 ASTRONOMY AND ASTROPHYSICS↗

A new method for solving the linearized 1D Vlasov–Poisson system yielding a new class of solutions

We describe a new method for solving the linearized 1D Vlasov–Poisson system by using properties of Cauchy-type integrals. Our method remedies critical flaws of the two standard methods, reveals a previously unrecognized Gaussian-in-time-like decay, and can also account for an externally applied electric field. The Landau approximation involves deforming the Bromwich contour around the poles closest to the real axis due to the analytically continued dielectric function, finding the long-time behavior for a stable system: Landau damping. Jackson's generalization encircles all poles while sending the contour to infinity, assuming its contribution vanishes, which is not true in general. This gives incorrect solutions for physically reasonable configurations and can exhibit pathological behavior, of which we show examples. The van Kampen method expresses the solution for a stable equilibrium as a continuous superposition of waves, resulting in an opaque integral. Case's generalization includes unstable systems and predicts a decaying discrete mode for each growing discrete mode, an apparent contradiction to both the Jackson solution and ours. We show, without imposing additional constraints, that the decaying modes are never present in the time evolution due to an exact cancellation with part of the continuum. Our solution is free of integral expressions, is obtained using algebra and Laurent series expansions, does not rely on analytic continuations, and results in a correct asymptotically convergent form in the case of infinite sums. The analysis used can be readily applied in higher-dimensional, electromagnetic systems and also provides a new technique for evaluating certain inverse Laplace transforms.

Physics↗

Randomized probe imaging through deep k-learning

Randomized probe imaging (RPI) is a single-frame diffractive imaging method that uses highly randomized light to reconstruct the spatial features of a scattering object. The reconstruction process, known as phase retrieval, aims to recover a unique solution for the object without measuring the far-field phase information. Typically, reconstruction is done via time-consuming iterative algorithms. In this work, we propose a fast and efficient deep learning based method to reconstruct phase objects from RPI data. The method, which we call deep k-learning, applies the physical propagation operator to generate an approximation of the object as an input to the neural network. This way, the network no longer needs to parametrize the far-field diffraction physics, dramatically improving the results. Deep k-learning is shown to be computationally efficient and robust to Poisson noise. The advantages provided by our method may enable the analysis of far larger datasets in photon starved conditions, with important applications to the study of dynamic phenomena in physical science and biological engineering.

Guo, Zhen (ORCID:0000000213473451)↗

Multimode theory of electron hole transverse instability

We present Vlasov–Poisson three-dimensional linear stability analysis of an initially planar electron hole structure, solving for the distribution function by integration along unperturbed orbits. The non-sinusoidal potential perturbation shape (parallel to $B$ ) is expanded in eigenfunctions of the adiabatic Poisson operator, generalizing the prior assumption of a rigid shift of the equilibrium. We show that the shiftmode is then modified by a second discrete mode plus an integral over a continuum of wave-like modes. A rigorous treatment shows that the continuum can be approximated effectively by a single mode that satisfies the external wave dispersion relation, thus making the perturbation a weighted sum of three modes. We find numerically the solution for the complex instability frequency, and the corresponding three mode amplitudes determining the perturbation eigenmode. This multimode analysis refines the accuracy of the prior single-mode results, giving slightly higher growth rates at most parameters, as expected from the extra mode shape freedom. Oscillating modes near stability boundaries have larger mode distortions which help explain particle-in-cell simulations that observe instability up to ${\sim }20$ % beyond the prior shiftmode thresholds, and narrowing of the perturbation. At high magnetic field, the multimode analysis predicts a reduction of the already small growth rate.

Physics↗

A Hybrid Method for Tensor Decompositions that Leverages Stochastic and Deterministic Optimization

In this paper, we propose a hybrid method that uses stochastic and deterministic search to compute the maximum likelihood estimator of a low-rank count tensor with Poisson loss via state-of-theart local methods. Our approach is inspired by Simulated Annealing for global optimization and allows for fine-grain parameter tuning as well as adaptive updates to algorithm parameters. We present numerical results that indicate our hybrid approach can compute better approximations to the maximum likelihood estimator with less computation than the state-of-the-art methods by themselves.

97 MATHEMATICS AND COMPUTING↗

Physics-based adaptivity of a spectral method for the Vlasov–Poisson equations based on the asymmetrically-weighted Hermite expansion in velocity space

We propose a spectral method for the 1D-1V Vlasov–Poisson system where the discretization in velocity space is based on asymmetrically-weighted Hermite functions, dynamically adapted via a scaling α and shifting u of the velocity variable. Specifically, at each time instant an adaptivity criterion selects new values of α and u based on the numerical solution of the discrete Vlasov–Poisson system obtained at that time step. Once the new values of the Hermite parameters α and u are fixed, the Hermite expansion is updated and the discrete system is further evolved for the next time step. The procedure is applied iteratively over the desired temporal interval. The key aspects of the adaptive algorithm are: the map between approximation spaces associated with different values of the Hermite parameters that preserves total mass, momentum and energy; and the adaptivity criterion to update α and u based on physics considerations relating the Hermite parameters to the average velocity and temperature of each plasma species. For the discretization of the spatial coordinate, we rely on Fourier functions and use the implicit midpoint rule for time stepping. The resulting numerical method possesses intrinsically the property of fluid-kinetic coupling, where the low-order terms of the expansion are akin to the fluid moments of a macroscopic description of the plasma, while kinetic physics is retained by adding more spectral terms. Moreover, the scheme features conservation of total mass, momentum and energy associated in the discrete, for periodic boundary conditions. A set of numerical experiments confirms that the adaptive method outperforms the non-adaptive one in terms of accuracy and stability of the numerical solution.

97 MATHEMATICS AND COMPUTING↗