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At least 811 records · Page 45

Communication: Distinguishing between short-time non-Fickian diffusion and long-time Fickian diffusion for a random walk on a crowded lattice

The motion of cells and molecules through biological environments is often hindered by the presence of other cells and molecules. A common approach to modeling this kind of hindered transport is to examine the mean squared displacement (MSD) of a motile tracer particle in a lattice-based stochastic random walk in which some lattice sites are occupied by obstacles. Unfortunately, stochastic models can be computationally expensive to analyze because we must average over a large ensemble of identically prepared realizations to obtain meaningful results. To overcome this limitation we describe an exact method for analyzing a lattice-based model of the motion of an agent moving through a crowded environment. Using our approach we calculate the exact MSD of the motile agent. Our analysis confirms the existence of a transition period where, at first, the MSD does not follow a power law with time. However, after a sufficiently long period of time, the MSD increases in proportion to time. This latter phase corresponds to Fickian diffusion with a reduced diffusivity owing to the presence of the obstacles. Our main result is to provide a mathematically motivated, reproducible, and objective estimate of the amount of time required for the transport to become Fickian. Our new method to calculate this crossover time does not rely on stochastic simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DNA molecules deviate from shortest trajectory when driven through hydrogel

Dynamic fluorescence-based single-molecule imaging of $λ$-DNA molecules driven through agarose hydrogels by DC electric fields reveals that passage through the hydrogel (98.5% water content) induces mobility orthogonal to the external field. Tortuous paths followed by the DNA molecules, which are heavily entangled in the hydrogel mesh as their contour length is nearly 100 times the hydrogel mesh size of 200 nm, cause them to appear to diffuse orthogonal to the driving force. The higher the driving field, from 2 to 16 V/cm, the higher the off-axis dispersion is, over the same time interval. In this work we measure the off-axis displacement distribution over 3 orders of magnitude of probability density and find a master curve after normalizing for time (t) elapsed, but the power of time for normalizing increases with the external field, from t 0.25 to t 0.6 with increasing field. Comparing trajectories over the same distance traveled in the electric field direction, we observe whereas for the highest field strengths DNA molecules come closest to taking the shortest trajectory between two points in space, deviations from the shortest trajectory grow larger and larger (up to 40% larger) as one approaches the case of small yet finite external field strength.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Detecting hidden transient events in noisy nonlinear time-series

The information impulse function (IIF), running Variance, and local Hölder Exponent are three conceptually different time-series evaluation techniques. These techniques examine time-series for local changes in information content, statistical variation, and point-wise smoothness, respectively. Using simulated data emulating a randomly excited nonlinear dynamical system, this study interrogates the utility of each method to correctly differentiate a transient event from the background while simultaneously locating it in time. Computational experiments are designed and conducted to evaluate the efficacy of each technique by varying pulse size, time location, and noise level in time-series. Our findings reveal that, in most cases, the first instance of a transient event is more easily observed with the information-based approach of IIF than with the Variance and local Hölder Exponent methods. While our study highlights the unique strengths of each technique, the results suggest that very robust and reliable event detection for nonlinear systems producing noisy time-series data can be obtained by incorporating the IIF into the analysis.

42 ENGINEERING↗

Radiation burnthrough measurements to infer opacity at conditions close to the solar radiative zone–convective zone boundary

Recent measurements at the Sandia National Laboratory of the x-ray transmission of iron plasma have inferred opacities much higher than predicted by theory, which casts doubt on modeling of iron x-ray radiative opacity at conditions close to the solar convective zone-radiative zone boundary. An increased radiative opacity of the solar mixture, in particular iron, is a possible explanation for the disagreement in the position of the solar convection zone-radiative zone boundary as measured by helioseismology and predicted by modeling using the most recent photosphere analysis of the elemental composition. In this report we present data from radiation burnthrough experiments, which do not support a large increase in the opacity of iron at conditions close to the base of the solar convection zone and provide a constraint on the possible values of both the mean opacity and the opacity in the x-ray range of the Sandia experiments. The data agree with opacity values from current state-of-the-art opacity modeling using the CASSANDRA opacity code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Staircases of passive and active scalar concentration in cellular flow

This paper develops a unified model for staircase formation in both passive and active scalar systems, building upon prior numerical studies by offering new heuristic and physical insights. While prior studies primarily reported numerical results, they did not explore the underlying unifying physics that governs both types of scalar transport; this work addresses that gap by identifying shared mechanisms across both cases. Results of studies of passive and active scalar staircase formation in cellular flows are presented. Staircase formation in cellular flows occurs due to the interplay of fast mixing within cells and slow transport across the inter-cell boundary. The cell boundary emerges as a de facto transport barrier. Special attention is focused on the effects of cellular fluctuations and noise upon staircase structure. A forced, fluctuating vortex array model is used to drive the underlying flow structure. Cellular Peclet number and staircase profile curvature are identified as figures-of-merit to quantify the resiliency of layering. These are related to simple, multi-scatterer scalar random walk models. Results for Peclet number and curvature scaling with flow excitation are presented. We also study staircases of magnetic potential evolving in two-dimensional magnetohydrodynamics as examples of layering of active scalar concentration. Formation of magnetic potential staircases is indeed observed. Flux expulsion inhibits the intercellular transport of magnetic potential and strengthens staircase barriers. Magnetic staircases can be supported against resistive decay by magnetic potential noise forcing. Implications for staircase formation in magnetic confinement experiments are discussed.

Control theory↗

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

It is not known how life originated. It is thought that prebiotic processes were able to synthesize short random polymers. However, then, how do short-chain molecules spontaneously grow longer? Also, how would random chains grow more informational and become autocatalytic (i.e., increasing their own concentrations)? We study the folding and binding of random sequences of hydrophobic ( H ) and polar ( P ) monomers in a computational model. We find that even short hydrophobic polar ( HP ) chains can collapse into relatively compact structures, exposing hydrophobic surfaces. In this way, they act as primitive versions of today’s protein catalysts, elongating other such HP polymers as ribosomes would now do. Such foldamer catalysts are shown to form an autocatalytic set, through which short chains grow into longer chains that have particular sequences. An attractive feature of this model is that it does not overconverge to a single solution; it gives ensembles that could further evolve under selection. This mechanism describes how specific sequences and conformations could contribute to the chemistry-to-biology (CTB) transition.

36 MATERIALS SCIENCE↗

Cosmological fluctuations of a random field and radiation fluid

A generalization of the random fluid hydrodynamic fluctuation theory due to Landau and Lifshitz is applied to describe cosmological fluctuations in systems with radiation and scalar fields. The viscous pressures, parametrized in terms of the bulk and shear viscosity coefficients, and the respective random fluctuations in the radiation fluid are combined with the stochastic and dissipative scalar evolution equation. This results in a complete set of equations describing the perturbations in both scalar and radiation fluids. These derived equations are then studied, as an example, in the context of warm inflation. Similar treatments can be done for other cosmological early universe scenarios involving thermal or statistical fluctuations.

79 ASTRONOMY AND ASTROPHYSICS↗

Sensitivity Enhancement and Random Telegraph Noise in Magnetic Tunnel Junctions with Compensated Anisotropy

We demonstrate the manipulation of perpendicular magnetic anisotropy (PMA) in magnetic tunnel junctions (MTJs) by varying the layer stacks and temperature. PMA is tuned to compensate the shape anisotropy, giving a nonhysteretic magnetic response, a noteworthy sensitivity enhancement, and a field detectability of 1.8 nT/$\sqrt{Hz}$ at 100 kHz. Such a method is further exemplified in multiple MTJs, providing a solution to obtain desired sensitivities and operating temperatures. Additionally, the electronic noise of this MTJ is revealed as a random telegraph noise (RTN) due to a generation-recombination process. In conclusion, the observed voltage-dependent RTN could potentially be applied to true random number generators.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Odd Diffusivity of Chiral Random Motion

Diffusive transport is characterized by a diffusivity tensor which may, in general, contain both a symmetric and an antisymmetric component. Although the latter is often neglected, we derive Green-Kubo relations showing it to be a general characteristic of random motion breaking time-reversal and parity symmetries, as encountered in chiral active matter. In analogy with the odd viscosity appearing in chiral active fluids, we term this component the odd diffusivity. Furthermore, we show how odd diffusivity emerges in a chiral random walk model, and demonstrate the applicability of the Green-Kubo relations through molecular dynamics simulations of a passive tracer particle diffusing in a chiral active bath.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

UQ Toolkit v 2.0

The Uncertainty Quantification (UQ) Toolkit is a software library for the characterizaton and propagation of uncertainties in computational models. For the characterization of uncertainties, Bayesian inference tools are provided to infer uncertain model parameters, as well as Bayesian compressive sensing methods for discovering sparse representations of high-dimensional input-output response surfaces, and also Karhunen-Loève expansions for representing stochastic processes. Uncertain parameters are treated as random variables and represented with Polynomial Chaos expansions (PCEs). The library implements several spectral basis function types (e.g. Hermite basis functions in terms of Gaussian random variables or Legendre basis functions in terms of uniform random variables) that can be used to represent random variables with PCEs. For propagation of uncertainty, tools are provided to propagate PCEs that describe the input uncertainty through the computational model using either intrusive methods (Galerkin projection of equations onto basis functions) or non-intrusive methods (perform deterministic operation at sampled values of the random values and project the obtained results onto basis functions).

Safta, Cosmin↗

Observing Profiles of Derived Kinematic Field Quantities Using a Network of Profiling Sites

Abstract Observations of thermodynamic and kinematic parameters associated with derivatives of the thermodynamics and wind fields, namely, advection, vorticity, divergence, and deformation, can be obtained by applying Green’s theorem to a network of observing sites. The five nodes that comprise the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) profiling network, spaced 50–80 km apart, are used to obtain measurements of these parameters over a finite region. To demonstrate the applicability of this technique at this location, it is first applied to gridded model output from the High-Resolution Rapid Refresh (HRRR) numerical weather prediction model, using profiles from the locations of ARM network sites, so that values calculated from this method can be directly compared to finite difference calculations. Good agreement is found between both approaches as well as between the model and values calculated from the observations. Uncertainties for the observations are obtained via a Monte Carlo process in which the profiles are randomly perturbed in accordance with their known error characteristics. The existing size of the ARM network is well suited to capturing these parameters, with strong correlations to model values and smaller uncertainties than a more closely spaced network, yet it is small enough that it avoids the tendency for advection to go to zero over a large area.

54 ENVIRONMENTAL SCIENCES↗

Virtual Growth of SRF Materials

Niobium's native surface oxide affects SRF cavity and superconducting qubit performance, motivating interest in controlling its crystalline structure. We combine a literature-derived machine-learning analysis with temperature-dependent XRD to study crystalline ordering in Nb2O5. Random Forest models, trained on 74 processing conditions from 17 papers and validated by leave-one-group-out cross-validation, predicted broad crystallinity outcomes well (balanced accuracy 0.809), but struggled with specific polymorph identity (0.577). Annealing temperature was the dominant predictor across all targets; oxygen partial pressure showed negligible importance, reflecting narrow literature coverage rather than physical irrelevance. Temperature-dependent XRD on anodized and H2O2-treated Niobium showed structural evolution consistent with the machine learning predictions. Our model and overall approach provide a data-driven framework for identifying and optimizing conditions that promote crystallization in initially amorphous oxides. This framework can guide the selection of growth and post-annealing conditions for Nb surfaces by narrowing the experimental parameter space, thereby reducing trial-and-error efforts in developing oxide structures relevant to SRF applications.

Tilkin, Anthony [Fermilab]↗

Simulation-Based Improvement in the Models for Tool-Inventory Management at Manufacturing Plants

Tool-inventory management at manufacturing plants is of great theoretical and practical importance. The main management problem here is that it is impossible to take precise account of all the changes in the tool stock for the basic production process. The relevant dynamics may be random as a consequence of the simultaneous action of several factors. In the present work, attention focuses on statistical modeling, which allows many factors to be taken into account and permits the creation of a more precise model of planning, production, and tool consumption at an industrial enterprise.

42 ENGINEERING↗

Impact of Erbium Doping in the Structural and Magnetic Properties of the Anisotropic and Frustrated SrYb 2 O 4 Antiferromagnet

We present a systematic study of the structural and magnetic properties of a series of powder samples of SrYb 2-x Er x O 4 with different Yb/Er concentrations. Magnetometry and neutron diffraction have been used to study the magnetic ground states of the compound series, while inelastic neutron scattering was used to investigate the crystal field excitations for a chosen concentration. These results show that the crystal structure remains the same for all compositions, while the lattice parameters increase linearly with the Er content. All compounds showed some type of magnetic transition below 1 K, however, both the magnetic structure and nature of the phase transition vary throughout the series. The samples present a non-collinear magnetic structure with the moments lying on the ab plane for low Er content. For high Er content, the magnetic structure is collinear with the moments aligned along the c-axis. A critical concentration is found where there is a bifurcation between zero-field and field-cooled magnetic susceptibility. This irreversible process could be due to the random mixture of single-ion magnetic anisotropies.

36 MATERIALS SCIENCE↗

STOCHASTIC TRANSIENTS AS A SOURCE OF QUASI-PERIODIC PROCESSES IN THE SOLAR ATMOSPHERE

Solar dynamics and turbulence occur at all heights of the solar atmosphere and could be described as stochastic processes. We propose that finite-lifetime transients recurring at a certain place could trigger quasi-periodic processes in the associated structures. In this study, we developed a mathematical model for finite-lifetime and randomly occurring transients, and found that quasi-periodic processes with periods longer than the timescale of the transients, are detectable intrinsically in the form of trains. We simulate their propagation in an empirical solar atmospheric model with chromosphere, transition region, and corona. We found that, due to the filtering effect of the chromospheric cavity, only the resonance period of the acoustic resonator is able to propagate to the upper atmosphere; such a scenario is applicable to slow magnetoacoustic waves in sunspots and active regions. If the thermal structure of the atmosphere is less wild and acoustic resonance does not take place, the long-period oscillations could propagate to the upper atmosphere. Such a case would be more likely to occur in polar plumes.

79 ASTRONOMY AND ASTROPHYSICS↗

The data-handling problem with television recording of spectra.

A television tube is a useful way to record a many-element picture such as is obtained from an echelle spectrograph. The signal on the tube target is scanned and relayed to the data-processing center where it must be reconstituted into the scene that was present in the focal plane of the spectrograph camera. A typical television frame will contain four million bits of information which must be processed to remove transmission errors and random noise pulses, to remove periodic noise, to correct for optical and electrical distortion, to remove sensitivity variations across the face of the tube, to calibrate from the photoelectrons back to incident energy, and to provide a wavelength scale. Results of a study of these problems is presented.

Underhill, A. B.↗