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At least 217 records · Page 12

Encoding nonlinear and unsteady aerodynamics of limit cycle oscillations using nonlinear sparse Bayesian learning

This article investigates the applicability of a recently proposed, nonlinear sparse Bayesian learning (NSBL) algorithm to identify and estimate the complex aerodynamics of limit cycle oscillations. NSBL provides a semi-analytical framework for determining the data-optimal sparse model nested within a (potentially) over-parameterized model. This is particularly relevant to nonlinear dynamical systems where modelling approaches involve the use of physics-based and data-driven components. In such cases, the data-driven components, where analytical descriptions of the physical processes are not readily available, are often prone to overfitting, meaning that the empirical aspects of these models will often involve the calibration of an unnecessarily large number of parameters. While an overparameterized model may fit the observed data well, such models may be inadequate for making predictions in regimes that are different from those wherein the data were recorded. In view of this, it is desirable to not only calibrate the model parameters, but also identify the optimal compromise between data fit and model complexity. In this article, we exhibit the optimal model discovery for an aeroelastic system wherein the structural dynamics are well-known and described by a differential equation model, coupled with a semi-empirical aerodynamic model for laminar separation flutter, resulting in low-amplitude limit cycle oscillations (LCO). To illustrate the performance of the algorithm, in this article, we use synthetic data and demonstrate the ability of the algorithm to correctly rediscover the optimal model and model parameters, given a known data-generating model. The synthetic data are generated from a forward simulation of a known differential equation model with parameters selected so as to mimic the dynamics observed in wind-tunnel experiments. Subsequently, we demonstrate the performance of the algorithm for model selection using noisy LCO data from wind tunnel experiments. As there is no ground truth available for the experimental data case, we provide a comparison between NSBL and Bayesian model selection to validate the results, and demonstrate the use of NSBL as an efficient alternative to traditional methods.

97 MATHEMATICS AND COMPUTING↗

Simulated Weightlessness Alters Cardiomyocyte Structure and Transcriptional Regulation of Mediators Related to Immunity and Cardiovascular Disease

Spaceflight and the ensuing fluid shifts, together with an overall reduction in physical activity, lead to acute and latent effects on the cardiovascular system. This current study makes use of the rodent hindlimb unloading (HU) model to determine how factors such as sex, age, and duration of exposure impact cardiac responses to weightlessness. We hypothesize that extended exposure to simulated weightlessness and the ensuing recovery alters cardiac structure and expression of select genes, including those involved in redox signaling which together, negatively impact long-term cardiac tissue health. To begin to test this hypothesis, male and female rats underwent HU at various durations up to 90 days, with a subset reambulated after 90 days of HU. Physiological stress or contractility changes lead to alterations in ventricular cardiomyocyte size and ventricular wall thickness to adapt to greater functional demand and mitigate mechanical stress to ventricular tissue; under certain conditions, these changes also may mark progression to cardiac failure. Hence, left ventricular cardiomyocyte size (cardiomyocyte cross sectional area, CSA) was quantified to determine if HU leads to structural adaptation responses in cardiac tissue and if age and sex had any impact on this outcome. Cardiomyocyte CSA of older males (9 months) were altered by HU in a time-dependent manner, where HU led to decreases in CSA at 14 days and increases at 90 days. In contrast, younger males (3 months) did not show any changes at day 14 of HU. CSA of females (3 months) was increased in response to short-term HU (14 days) suggesting sex-dependence of structural changes. In older HU males, cardiomyocyte CSA was comparable to controls after 90 days of re-ambulation. Levels of the DNA oxidative damage marker, 8-hydroxydeoxyguanosine (8-OHdG) were greater in left ventricular tissue of females that underwent HU compared to sex-matched controls, while there were no such differences in older or younger males. To gain insight into the signals that drive cardiac adaptations to HU, global transcriptomic analysis (RNAseq) was performed on left ventricular tissue of older males that underwent 14 days of HU. Short-term simulated weightlessness led to differential expression of genes involved in immune and pro-inflammatory signaling. A subset of these genes play a role in autoimmune and cardiovascular disease and are targets of current drugs used to treat bradycardia, hypertension, atherosclerosis and rheumatoid arthritis, amongst others. Oxidative damage/redox signaling pathways were not enriched at the timepoint tested in older males. Since young females displayed greater oxidative damage to DNA, activation of oxidative stress responses at earlier or later time points cannot be ruled out. In summary, simulated weightlessness in adult rats caused changes in cardiomyocyte structure in a sex and age-dependent manner, and the transcriptional regulation of key mediators of immunity and cardiovascular disease, meriting further study to define cardiac risks for interplanetary travel of human crew. Our findings also confirm the value of the rat HU model for cardiac health and countermeasure research.

Tahimic, Candice↗

Physics-aware adaptive checkpointing with shadow systems for nonlinear PDE simulations

Large-scale simulations of nonlinear partial differential equations (PDEs) that exhibit strongly transient behavior and pattern-forming dynamics produce enormous amounts of data, which, even with modern storage systems, cannot be stored for later curation. Current I/O strategies either write dense time series of snapshots, which is often prohibitive in I/O and storage, or store a few checkpoints that enable restart but incur expensive recomputation cost and provide no control over post-restart error growth, especially when lossy compression is used. Moreover, most, if not all, existing strategies take no account of the actual physical state of the system. Here, we present a simple physics-aware I/O framework in which a low-cost shadow system adaptively triggers lossy checkpoints when the shadow system deviates from the fine-scale simulation. The shadow system can be a coarsened replica of the fine-scale simulation that evolves concurrently. This means that checkpoints are taken based on the physical state of the system: fewer checkpoints are triggered when the system is quiescent while more are taken when the system undergoes a rapid change. This type of behavior is observed in many systems such as Brusselator and FitzHugh–Nagumo. We illustrate that our framework maintains stable restarts, keeps fine-scale restart errors bounded by shadow errors, and reconstructs the time history with significantly lower error and storage than interpolating fixed-interval snapshots, with low-cost shadow replay and modest online synchronization overhead.

Gong, Qian [ORNL] (ORCID:0000000235704142)↗

Evolution of Thyroglobulin Loop Kinetics in EpCAM

Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

59 BASIC BIOLOGICAL SCIENCES↗

Integration of Electromagnetic Geophysics Forward Simulation in Coupled Flow and Geomechanics for Monitoring a Gas Hydrate Deposit Located in the Ulleung Basin, East Sea, Korea

We investigate the feasibility of electromagnetic (EM) geophysics methods to detect the dissociation of gas hydrate specifically from a gas hydrate deposit located in the Ulleung Basin, East Sea, Korea via an integrated flow-geomechanics-EM geophysics simulation. To this end, coupled flow and geomechanics simulation is first performed with the multiple porosity model employed, where a mixed formulation with the finite volume (FV) and finite element (FE) methods are taken for the flow and geomechanics, respectively. From the saturation and porosity fields obtained from the coupled flow and geomechanics, the electrical conductivity model is established for the EM simulation. Solving the partial differential equation of electrical diffusion which is linearized using the 3D finite element method (FEM), the EM fields are then computed. For numerical experiments, particularly two approaches in the configuration for the EM methods are compared in this contribution: the surface-to-surface and the surface-to-borehole methods. When the surface-to-surface EM method is employed, the EM is found to be less sensitive, implying low detectability. Especially for the short term of production, the low detectability is attributed to the similarity of electrical resistivity between the dissociated gas (CH4) and hydrate as well as the specific dissociation pattern within the intercalated composites of the field. On the other hand, when the surface-to-borehole EM method is employed, its sensitivity to capture the produced gas flow is improved, confirming its detectability in monitoring gas flow. Hence, the EM geophysics simulation integrated with coupled flow and geomechanics can be a potential tool for monitoring gas hydrate deposits.

depressurization↗

A relationship between peak temperature drop and velocity differential in a microburst

Results from numerical microburst simulations using the Terminal Area Simulation System (Proctor, 1987) are used to develop a relationship between wind velocity differential and peak temperature drop. The numerical model and the relationships derived from the model are described. The relationship between peak temperature drop and differential wind velocity is shown to be valid during microburst development, for all precipitation shaft intensities and diameters. It is found that the relationship is not valid for low-reflectivity microburst events or in the presence of ground-based stable layers. The use of the relationship in IR wind shear detection systems is considered.

Proctor, Fred H.↗

Differentiable Predictions for Large Scale Structure with SHAMNet

In simulation-based models of the galaxy-halo connection, theoretical predictions for galaxy clustering and lensing are typically made based on Monte Carlo realizations of a mock universe. In this paper, we use Subhalo Abundance Matching (SHAM) as a toy model to introduce an alternative to stochastic predictions based on mock population, demonstrating how to make simulation-based predictions for clustering and lensing that are both exact and differentiable with respect to the parameters of the model. Conventional implementations of SHAM are based on iterative algorithms such as Richardson-Lucy deconvolution; here we use the JAX library for automatic differentiation to train SHAMNet, a neural network that accurately approximates the stellar-to-halo mass relation (SMHM) defined by abundance matching. In our approach to making differentiable predictions of large-scale structure, we map parameterized PDFs onto each simulated halo, and calculate gradients of summary statistics of the galaxy distribution by using autodiff to propagate the gradients of the SMHM through the statistical estimators used to measure one- and two-point functions. Our techniques are quite general, and we conclude with an overview of how they can be applied in tandem with more complex, higher-dimensional models, creating the capability to make differentiable predictions for the multi-wavelength universe of galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Extremized nonlinear and linearized responses in soft metamaterials enabled by gradient-based design and grayscale digital light processing

In this study, we develop a gradient-based design approach that exploits grayscale digital light processing (DLP) 3D printing for extremizing the nonlinear and linearized response of soft metamaterials — materials that harness engineered geometric instabilities to undergo large and programmable changes in configuration. Grayscale DLP approaches modulate local mechanical properties at the pixel scale by tuning the light intensity within a single grayscale image, unlocking an exceptionally large design space. To effectively navigate this space, we develop smooth mappings between local light intensity values and global quantities of interest that characterize the behavior of soft metamaterials. Enabling these smooth mappings are robust and differentiable nonlinear finite element simulations powered by a trust region solver. A PDE-constrained optimization problem is then solved to invert these mappings and produce light intensity distributions that endow the printed part with varying stiffness and flexibility in distinctive regions. It is shown that optimizing the distribution of soft and stiff phases throughout a metamaterial structure results in markedly different buckling and self-contact configurations to drive extremized nonlinear compression and linearized vibration responses. Optimized light intensity distributions are translated to grayscale images and directly used to print soft metamaterial samples, showing remarkable agreement between the buckling and self-contact response in simulated and measured deformed configurations.

Additive manufacturing↗

Multi-arrival infrasound from meteoroids: Fragmentation signatures versus propagation effects in a fine-scale layered atmosphere

Infrasonic signatures of meteoroid fragmentation are frequently ambiguous: do multiple arrivals signify a complex breakup or merely the distorting effects of a layered atmosphere? Resolving this ambiguity is critical for accurate energy estimates and source reconstruction. In this study, we address this challenge by analyzing a unique regional dataset of well-constrained meteoroid events observed by the Southern Ontario Meteor Network and the co-located Elginfield Infrasound Array. We employ pseudo-differential parabolic equation (PPE) simulations to quantify how fine-scale gravity-wave structures in the stratosphere and lower thermosphere modify acoustic waveforms at ranges <300 km. Our modeling reveals that while fine-scale layering can stretch signals and generate diffuse oscillatory tails, it does not produce discrete, high-amplitude pulse splitting at ranges below ∼140 km. By applying these results to the rare multi-arrival event 20060305, we demonstrate that its distinct double arrival at 100 km range is inconsistent with atmospheric multipathing and provides definitive evidence of separate fragmentation episodes. These findings establish new diagnostic criteria for separating source physics from propagation artifacts, improving the reliability of infrasound as a monitoring tool for natural bolides, space debris re-entries, and catastrophic launch failures.

79 ASTRONOMY AND ASTROPHYSICS↗

Half-life determination of heavy ions in a storage ring considering feeding and depleting background processes

Heavy-ion storage rings have relatively large momentum acceptance which allows for multiple ion species to circulate at the same time. This needs to be considered in radioactive decay measurements of highly charged ions, where atomic charge exchange reactions can significantly alter the intensities of parent and daughter ions. In this study, we investigate this effect using the decay curves of ion numbers in the recent 205 Tl 81+ bound-state beta decay experiment conducted using the Experimental Storage Ring at GSI Darmstadt. To understand the intricate dynamics of ion numbers, we present a set of differential equations that account for various atomic and nuclear reaction processes—bound state beta decay, atomic electron recombination and capture, and electron ionization. By incorporating appropriate boundary conditions, we develop a set of differential equations that accurately simulate the decay curves of various simultaneously stored ions in the storage ring: 205 Tl 81+ , 205 Pb 81+ , 205 Pb 82+ , 200 Hg 79+ , and 200 Hg 80+ . Through a quantitative comparison between simulations and experimental data, we provide insights into the detailed reaction mechanisms governing stored heavy ions within the storage ring. Our approach effectively models charge-changing processes, reduces the complexity of the experimental setup, and provides a simpler method for measuring the decay half-lives of highly charged ions in storage rings.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Performance Analysis of Speculative Parallel Adaptive Local Timestepping for Conservation Laws

Stable simulation of conservation laws, such as those used to model fluid dynamics and plasma physics applications, requires the satisfaction of the so-called Courant-Friedrichs-Lewy condition. By allowing regions of the mesh to advance with different timesteps that locally satisfy this stability constraint, significant work reduction can be attained when compared to a time integration scheme using a single timestep size. However, parallelizing this algorithm presents considerable difficulty. Since the stability condition depends on the state of the system, dependencies become dynamic and potentially non-local. In this article, we present an adaptive local timestepping algorithm using an optimistic (Timewarp-based) parallel discrete event simulation. We introduce waiting heuristics to limit misspeculation and a semi-static load balancing scheme to eliminate load imbalance as parts of the mesh require finer or coarser timesteps. Last, we outline an interface for separating the physics of the specific conservation law from the temporal integration allowing for productive adoption of our proposed algorithm. We present a misspeculation study for three conservation laws, demonstrating both the productivity of the local timestepping API, for which 74% of the lines of code are reused across different conservation laws, and the robustness of the waiting heuristics—at most 1.5% of element updates are rolled back. Our performance studies demonstrate up to a 2.8× speedup versus a baseline unoptimized local timestepping approach, a 4x improvement in per-node throughput compared to an MPI parallelization of synchronous timestepping, and scalability up to 3,072 cores on NERSC’s Cori Haswell partition.

97 MATHEMATICS AND COMPUTING↗

Whole cell simulator

A whole cell model (WCM) is a comprehensive multi-scale computational model representing all the known biochemical processes in a cell. It relies on a variety of intracellular pathway models and omics data. This computational framework enables seamless integration of diverse simulation methods used in WCM such as stochastic simulation algorithm (SSA), ordinary differential equations (ODE), flux balance analysis (FBA), and logic-based approaches. These methods run simultaneously, not only for whole pathways but also for subsets of reactions. Furthermore, we aim to enable dynamic switching between the methods when beneficial. Is

GEORGAKOUDIS, GIORGIS↗

Cardiovascular system simulation in biomedical engineering education.

Use of complex cardiovascular system models, in conjunction with a large hybrid computer, in biomedical engineering courses. A cardiovascular blood pressure-flow model, driving a compartment model for the study of dye transport, was set up on the computer for use as a laboratory exercise by students who did not have the computer experience or skill to be able to easily set up such a simulation involving some 27 differential equations running at 'real time' rate. The students were given detailed instructions regarding the model, and were then able to study effects such as those due to septal and valve defects upon the pressure, flow, and dye dilution curves. The success of this experiment in the use of involved models in engineering courses was such that it seems that this type of laboratory exercise might be considered for use in physiology courses as an adjunct to animal experiments.

Rideout, V. C.↗

Methods for study of cardiovascular adaptation of small laboratory animals during exposure to altered gravity

Several new techniques are reported for studying cardiovascular circulation in small laboratory animals kept in metabolic chambers. Chronical cannulation, miniaturized membrane type heart-lung machines, a prototype walking chamber, and a fluorocarbon immersion method to simulate weightlessness are outlined. Differential hypothermia work on rat cancers provides localized embedding of radionuclides and other chemotherapeutical agents in tumors and increases at the same time blood circulation through the warmed tumor as compared to the rest of the cold body. Some successful clinical applications of combined chemotherapy and differential hypothermia in skin cancer, mammary tumors, and brain gliomas are described.

Popovic, V.↗

Mapping implicit spectral methods to distributed memory architectures

Spectral methods were proven invaluable in numerical simulation of PDEs (Partial Differential Equations), but the frequent global communication required raises a fundamental barrier to their use on highly parallel architectures. To explore this issue, a 3-D implicit spectral method was implemented on an Intel hypercube. Utilization of about 50 percent was achieved on a 32 node iPSC/860 hypercube, for a 64 x 64 x 64 Fourier-spectral grid; finer grids yield higher utilizations. Chebyshev-spectral grids are more problematic, since plane-relaxation based multigrid is required. However, by using a semicoarsening multigrid algorithm, and by relaxing all multigrid levels concurrently, relatively high utilizations were also achieved in this harder case.

Overman, Andrea L.↗

Turbulent convection with overshooting - Reynolds stress approach

The Reynolds stress formalism is adopted to treat turbulent convection. This methodology is reviewed, and it is suggested that it may prove very useful to treat stellar and accretion disk turbulent convection, as well as in the construction of the subgrid models needed in large eddy simulations. A set of differential equations that yield the mean and turbulent quantities such as convective fluxes, turbulent viscosity, and turbulent conductivity is presented.

Canuto, V. M.↗