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DOE OSTI2025

Reweighting configurations generated by transferable, machine learned models for protein sidechain backmapping

Multiscale modeling requires the linking of models at different levels of detail, with the goal of gaining accelerations from lower fidelity models while recovering fine details from higher resolution models. Communication across resolutions is particularly important in modeling soft matter, where tight couplings exist between molecular-level details and mesoscale structures. While multiscale modeling of biomolecules has become a critical component in exploring their structure and self-assembly, backmapping from coarse-grained to fine-grained, or atomistic, representations presents a challenge, despite recent advances through machine learning. A major hurdle, especially for strategies utilizing machine learning, is that backmappings can only approximately recover the atomistic ensemble of interest. We demonstrate conditions for which backmapped configurations may be reweighted to exactly recover the desired atomistic ensemble. By training separate decoding models for each sidechain type, we develop an algorithm based on normalizing flows and geometric algebra attention to autoregressively propose backmapped configurations for any protein sequence. Critical for reweighting with modern protein force fields, our trained models include all hydrogen atoms in the backmapping and make probabilities associated with atomistic configurations directly accessible. We also demonstrate, however, that reweighting is extremely challenging despite state-of-the-art performance on recently developed metrics and generation of configurations with low energies in atomistic protein force fields. Through detailed analysis of configurational weights, we show that machine-learned backmappings must not only generate configurations with reasonable energies, but also correctly assign relative probabilities under the generative model. These are broadly important considerations in generative modeling of atomistic molecular configurations.

Monroe, Jacob I. [Univ. of Arkansas, Fayetteville,↗

NASA NTRS1974

A feasibility study of developing toroidal tanks for a spinning spacecraft. Part 2: Evaluation of fluid behavior in spinning toroidal tanks

An experimental program was conducted for the purpose of evaluating propellant behavior characteristics in spinning toroidal tanks. The effects of typical mission requirements, and related phenomena upon propellant slosh and settling, and orientation and stability of the ullage were investigated in a subscale model tank under both one-g and low-g acceleration environments. Specific conditions included were axial acceleration, spin rate, spinrate change, and spacecraft wobble, both singly and in combination. Methanol and water in combination with appropriate spin-rates and accelerations of the scale model system were used to simulate the behavior of fluorine, nitrogen tetroxide, monomethylhydrazine, and hydrazine. The experimental results indicate that no major fluid behavior problems would be encountered with the use of toroidal tanks containing any of the four propellants in a proposed spin-stabilized orbiter spacecraft.

Anderson, J. E.↗

NASA NTRS1985

Selection of a model of Earth's albedo radiation, practical calculation of its effect on the trajectory of a satellite

Theoretical models of Earth's albedo radiation was proposed. By comparing disturbing accelerations computed from a model to those measured in flight with the CACTUS Accelerometer, modified according to the results. Computation of the satellite orbit perturbations from a model is very long because for each position of this satellite the fluxes coming from each elementary surface of the terrestrial portion visible from the satellite must be summed. The speed of computation is increased ten times without significant loss of accuracy thanks to a stocking of some intermediate results. Now it is possible to confront the orbit perturbations computed from the selected model with the measurements of these perturbations found with satellite as LAGEOS.

Walch, J. J.↗

NASA NTRS1989

The effect of an unsteady three-dimensional wake on elastic blade-flapping eigenvalues in hover

This paper describes the formulation of a finite-state inflow model based on an acceleration potential and a helical wake geometry. The states of the model are coefficients of an inflow expansion in terms of a Fourier series (azimuthally) and of special polynomials (radially). The integrals over the wake are done in closed-form to obtain a set of ordinary differential equations for the inflow coefficients. The forcing functions for these equations are generalized forces which are integrals of the blade loading exactly as in structural dynamics. This model implicitly includes (for the hover case) Prandtl-Goldstein tip losses, dynamic inflow, and Theodorsen/Loewy lift deficiency. Thus, it is a fully three-dimensional unsteady wake model. Here, this model is coupled with elastic-blade equations in hover and eigenvalues are found. The results show that the three-dimensional wake has a large effect on the flap damping of all modes.

Peters, David A.↗

DOE OSTI2020

Nanostructured Tube Wakefield Accelerator

Unprecedented $\rm TeVm^{-1}$ acceleration gradients are modeled to be realizable using a nonlinear surface crunch-in mode in nanostructured tubes. This mode is realizable using advances in nanofabrication and solid energy density attosecond bunch compression. Three dimensional computational and analytical modeling demonstrates GeV energy gain in sub-millimeter long tubes with effective wall densities $n_{\rm t}\sim10^{22-24}\rm cm^{-3}$ and hundreds of nanometer core radius when driven by submicron near solid electron beams, $n_{\rm b}\sim0.05n_{\rm t}$. Besides the many $\rm TVm^{-1}$ average gradients, strong self-focusing and nanomodulation of the beam which increases its peak density and the wakefield strength also opens up controlled high-energy photon production.

43 PARTICLE ACCELERATORS↗

NASA NTRS1993

The use of transition region characteristics to improve the numerical simulation of heat transfer in bypass transitional flows

A method is presented for improving the numerical prediction of bypass transition heat transfer on a flat plate in a high-disturbance environment with zero or favorable pressure gradient. The method utilizes low Reynolds number k-epsilon turbulence models in combination with the characteristic parameters of the transition region. The parameters representing the characteristics of the transition region used are the intermittency, transition length and turbulent spot properties. An analysis is made of the transition length in terms of turbulent spot variables. The nondimensional spot formation rate, required for the prediction of the transition length, is shown by the analysis to be a function of the spot spreading angle, the dimensionless spot velocity ratio and the dimensionless spot area ratio. The intermittency form of the k-epsilon equations were derived from conditionally averaged equations which have been shown to be an improvement over global-time-averaged equations for the numerical calculation of the transition region. The numerical predictions are in general good agreement with the experimental data and indicate the potential use of the method in accelerating flows. Turbulence models of the k-epsilon type are known to underpredict the transition length. The present work demonstrates how incorporating transition region characteristics improves the ability of two-equation turbulence models to simulate bypass transition for flat plates with potential application to turbine vanes and blades.

Simon, Frederick F.↗

NASA NTRS1985

Ultra high energy gamma rays, cosmic rays and neutrinos from accreting degenerate stars

Super-Eddington accretion for a recently proposed unipolar induction model of cosmic ray acceleration in accreting binary star systems containing magnetic white dwarfs or neutron stars is considered. For sufficiently high accretion rates and low magnetic fields, the model can account for: (1) acceleration of cosmic ray nuclei up to energies of 10 to the 19th power eV; (2) production of more or less normal solar cosmic ray composition; (3) the bulk of cosmic rays observed with energies above 1 TeV, and probably even down to somewhat lower energies as well; and (4) possibly the observed antiproton cosmic ray flux. It can also account for the high ultra high energy (UHE) gamma ray flux observed from several accreting binary systems (including Cygnus X-3), while allowing the possibility of an even higher neutrino flux from these sources, with L sub nu/L sub gamma is approximately 100.

Brecher, K.↗

NASA NTRS2001

Experimental and Numerical Investigation of Buoyancy Driven Convection During PDAMNA Thin Film Growth

This paper presents results from numerical simulations as well as laboratory experiments of buoyancy driven convection in an ampoule under varying heating and gravitational acceleration loadings. The modeling effort in this work resolves the large scale natural convective motion that occurs in the fluid during photodeposition of polydiacetelene films which is due to energy absorbed by the growth solution from a UV source. Consequently, the growth kinetics of the film are ignored in the model discussed here, and also a much simplified ampoule geometry is considered. The objective of this work is to validate the numerical prediction on the strength and structure of buoyancy driven convection that could occur under terrestrial conditions during nonlinear optical film growth. The validation is used to enable a reliable predictive capability on the nature and strength of the convective motion under low gravity conditions. The ampoule geometry is in the form of a parallelepiped with rectangular faces. The numerical results obtained from the solution to the Boussinesq equations show that natural convection will occur regardless of the orientation of the UV source with respect to the gravity vector. The least strong convective motion occurred with the UV beam directed at the top face of the parallelepiped. The strength of the convective motion was found to be almost linearly proportional to the total power of the UV source. Also, it was found that the strength of the convective motion decreased linearly with the gravity due to acceleration. The pattern of the convective flow on the other hand, depended on the source location.

Antar, Basil N.↗

NASA NTRS1993

The abundances of hydrogen, helium, oxygen, and iron accelerated in large solar particle events

Energy spectra measured in 10 large flares with the University of Maryland/Max-Planck-Institut sensors on ISEE I and Goddard Space Flight Center sensors on IMP 8 allowed us to determine the average H, He, O, and Fe abundances as functions of energy in the range of about 0.3-80 MeV/nucleon. Model fits to the spectra of individual events using the predictions of a steady state stochastic acceleration model with rigidity-dependent diffusion provided a means of interpolating small portions of the energy spectra not measured with the instrumentation. Particles with larger mass-to-charge ratios were relatively less abundant at higher energies in the flare-averaged composition. The Fe/O enhancement at low SEP energies was less than the Fe/O ratios observed in He-3-rich flares. Unlike the SEP composition averaged above 5 MeV/nucleon, the average SEP abundances above 0.3 MeV/nucleon were similar to the average solar wind.

Mazur, J. E.↗

NASA NTRS2011

Prognostics of Power Mosfets Under Thermal Stress Accelerated Aging Using Data-Driven and Model-Based Methodologies

An approach for predicting remaining useful life of power MOSFETs (metal oxide field effect transistor) devices has been developed. Power MOSFETs are semiconductor switching devices that are instrumental in electronics equipment such as those used in operation and control of modern aircraft and spacecraft. The MOSFETs examined here were aged under thermal overstress in a controlled experiment and continuous performance degradation data were collected from the accelerated aging experiment. Dieattach degradation was determined to be the primary failure mode. The collected run-to-failure data were analyzed and it was revealed that ON-state resistance increased as die-attach degraded under high thermal stresses. Results from finite element simulation analysis support the observations from the experimental data. Data-driven and model based prognostics algorithms were investigated where ON-state resistance was used as the primary precursor of failure feature. A Gaussian process regression algorithm was explored as an example for a data-driven technique and an extended Kalman filter and a particle filter were used as examples for model-based techniques. Both methods were able to provide valid results. Prognostic performance metrics were employed to evaluate and compare the algorithms.

Electrolytic capacitors↗

DOE OSTI2023

A simple, flexible technique for RF cavity wake-field calculations

It is typical in the accelerator field to model machine components, especially RF cavities, as parallel RLC resonators. In the interest of simulating and diagnosing beam instabilities, knowledge of the time-domain voltage waveform over an equivalent resonator by a bunch current often proves useful. This waveform may be found by convolving the bunch current with the RLC resonator impulse response. While analytical and quasi-analytical expressions are available in this regime for common distributions such as the Gaussian, analogous results for less standard distributions are difficult to obtain using direct methods, which opens the door for the development of a more generalized technique. In this paper, a formulation is created that allows for the simple computation of the time-domain voltage waveform of and RLC resonator. The formulation uses the Cauchy Residue Theorem to extract the convolution result from the Fourier Domain, and it only requires that the current distribution Fourier Transform be holomorphic and known at one specific evaluation point. This greatly simplifies the computation of the time domain voltage for a large amount of bunch distributions both common and uncommon.

43 PARTICLE ACCELERATORS↗

NASA NTRS1947

Acceleration Measurements During Landing in Rough Water of a 1/7-Scale Dynamic Model of Grumman XJR2F-1 Amphibian - Langley Tank Model 212, TED No. NACA 2378

Tests of a 1/7 size model of the Grumman XJR2F-1 amphibian were made in Langley tank no.1 to examine the landing behavior in rough water and to measure the normal and angular accelerations experienced by the model during these landings. All landings were made normal to the direction of wave advance, a condition assumed to produce the greatest accelerations. Wave heights of 4.4 and 8.0 inches (2.5 and 4.7 ft, full size) were used in the tests and the wave lengths were varied between 10 and 50 feet (70 and 350 ft, full size). Maximum normal accelerations of about 6.5g were obtained in 4.4 inch waves and 8.5g were obtained in 8.0 inch waves. A maximum angular acceleration corresponding to 16 radians per second per second, full size, was obtained in the higher waves. The data indicate that the airplane will experience its greatest accelerations when landing in waves of about 20 feet (140 ft, full size) in length.

Land, Norman S.↗

DOE OSTI2025

Bayesian Calibration of Stochastic Agent Based Model via Random Forest

Agent-based models (ABM) provide an excellent framework for modeling outbreaks and interventions in epidemiology by explicitly accounting for diverse individual interactions and environments. However, these models are usually stochastic and highly parametrized, requiring precise calibration for predictive performance. When considering realistic numbers of agents and properly accounting for stochasticity, this high-dimensional calibration can be computationally prohibitive. This paper presents a random forest-based surrogate modeling technique to accelerate the evaluation of ABMs and demonstrates its use to calibrate an epidemiological ABM named CityCOVID via Markov chain Monte Carlo (MCMC). The technique is first outlined in the context of CityCOVID's quantities of interest, namely hospitalizations and deaths, by exploring dimensionality reduction via temporal decomposition with principal component analysis (PCA) and via sensitivity analysis. The calibration problem is then presented, and samples are generated to best match COVID-19 hospitalization and death numbers in Chicago from March to June in 2020. Further, these results are compared with previous approximate Bayesian calibration (IMABC) results, and their predictive performance is analyzed, showing improved performance with a reduction in computation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Fuel Injection Dynamics and Composition Effects on RDE Performance

Rotating detonation engines (RDEs) provide a promising route to substantially increasing cycle efficiency in stationary gas turbines. Much of this increase relies on the ability to achieve consistent pressure gain within the combustor. In particular, the design of injectors that feed fuel and air into the detonation channel plays a crucial role. Such injectors have to ensure proper mixing of fuel and oxidizer, while minimizing backflow of detonation products into the feed plenums, and reduce susceptibility to the complex wave structures that exist within the combustor. From a practical perspective, such RDEs also need to operate with variable fuel composition. When fuel mixtures with components that possess vastly different oxidation pathways and time-scales are used, there could be additional losses through deflagrative burning instead of detonation-driven heat release. Such sensitivity to the complete flow path is akin to the physics of thermoacoustic instabilities in conventional gas turbines. In this sense, RDEs pose a unique research challenge: the performance of the device relies on the small-scale heat release process, which is highly dependent on the flow interactions within the full-scale system. As a result, canonical flow configurations, instrumented with detailed diagnostics or modeled using high-fidelity tools, but only focus on the small-scale processes will not contain the key system-level interactions. At the same time, macroscopic measurements and models that only capture system-level performance will not provide insight into the key sources of pressure losses. These couplings and sensitivities provide a formidable challenge to both experimental and simulation studies of the effects Thus, a joint experimental/computational program designed specifically to address these challenges was undertaken in this program. The focus of this program was on two key topics: a) the interaction between injector flow and the overall wave dynamics within the combustor, and b) the deflagration/detonation structure in multi-component fuels that are of practical interest. Both topics involve interaction of small-scale heat release processes with the geometry-dependent wave structure. Studies focused on the study of full-scale RDE systems, based on a 6-inch conventional annular geometry. Experimentally RDEs were studied using a combination of diagnostics. A combination of optical diagnostics and aero-thermo-acoustic analysis based on a combination of spectral and mode decomposition analysis was used to identify the dynamics of the detonation wave and other secondary waves that exist in the system. These studies have helped the identification and investigation of injector and detonation dynamics arising from coupling, and how they affect RDE mixing, detonation structure, operability and performance. Performance of RDEs was investigated through thrust stand measurements, which was used to evaluate the effective pressure gain generated by the system through the concept of equivalent available pressure. Optical diagnostics were developed and implemented to investigate the distribution of heat release, across the detonation wave. Novel optical diagnostics of NIR imaging was also developed and applied to investigate the high temperature / high pressure distribution across the detonation wave. In order to complement the experiments, the computational tools were geared to simulate the full experimental setup. GPU-based acceleration of the models and computations were developed to enable rapid simulation of the full system. In addition, the use of adaptive mesh refinement, and unstructured grid formulation, enabled the investigation of realistic geometries studied in the laboratory. The simulations produced a wealth of detail on the structure of the detonation wave under different operating conditions. Emphasis was placed on quantifying mixture pre-burning and the impact on wave propagation and structure.

03 NATURAL GAS↗

DOE OSTI2025

Energy Conversion and Electron Acceleration and Transport in 3D Simulations of Solar Flares

Recent observations and simulations indicate that solar flares undergo extremely complex 3D evolution, making 3D particle transport models essential for understanding electron acceleration and interpreting flare emissions. In this study, we investigate this problem by solving Parker’s transport equation with 3D MHD simulations of solar flares. By examining energy conversion in the 3D system, we evaluate the roles of different acceleration mechanisms, including reconnection current sheet (CS), termination shock (TS), and supra-arcade downflows (SADs). We find that large-amplitude turbulent fluctuations are generated and sustained in the 3D system. The model results demonstrate that a significant number of electrons are accelerated to hundreds of keV and even a few MeV, forming power-law energy spectra. These energetic particles are widely distributed, with concentrations at the TS and in the flare looptop region, consistent with results derived from recent hard X-ray (HXR) and microwave (MW) observations. By selectively turning particle acceleration on or off in specific regions, we find that the CS and SADs effectively accelerate electrons to several hundred keV, while the TS enables further acceleration to MeV. However, no single mechanism can independently account for the significant number of energetic electrons observed. Instead, the mechanisms work synergistically to produce a large population of accelerated electrons. Our model provides spatially and temporally resolved electron distributions in the whole flare region and at the flare footpoints, enabling synthetic HXR and MW emission modeling for comparison with observations. These results offer important insights into electron acceleration and transport in 3D solar flare regions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Machine learning-enabled prediction of chemical durability of A 2 B 2 O 7 pyrochlore and fluorite

Pyrochlore-structure type and its derivative in a general formula A 2 B 2 O 7 (A = rare earth elements and actinides; B = Ti, Sn, Zr, Hf, Pb, Si, etc.) display excellent structural flexibility and rich crystal chemistry as promising nuclear waste form materials capable of immobilizing actinides and fission products. It is essential to understand these materials’ chemical durability and element release of radionuclides in order to evaluate their performance in near-field environment. However, it is a formidable grand technological challenge to experimentally perform durability testing across hundreds of thousands of possibilities resulting from their extreme compositional complexities due to cation substitutions at both A and B-sites. In this work, we demonstrate a machine learning approach to determine the key materials parameters and structural characteristics governing the leaching behaviors from a small set of selected compositions as model systems, enabling a science-based prediction of their chemical durability that can be extended to a wide range of chemical compositions. The combination of four key structural characteristics and materials parameters, including ionic radius size difference , ionic potential difference , electronegativity difference , and lattice parameter , creates features an optimized prediction of the chemical durability. Two machine learning models, linear regression and Kernel ridge regression models, are trained on the randomly-split training dataset derived from the experimentally-determined elemental release rates, and subsequently tested on the testing dataset. The predicted leaching rates from both machine learning models show an excellent agreement with the experimental data, demonstrating the feasibility of rapidly evaluating the material properties of new compositions. These results highlight the immense potential of synergizing informatics through machine learning-based models and well-controlled experiments of selected model systems to accelerate materials design and discovery with optimized compositions and performance of promising materials for effective nuclear waste management.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Benchmarking collective effects of electron interactions in a wiggler with OPAL-FEL

OPAL-FEL is a recently developed tool for the modeling of particle accelerators containing wigglers or undulators. It extends the well established 3D electrostatic particle-tracking code OPAL, by merging it with the finite-difference time-domain electromagnetic solver MITHRA. We present results of two benchmark cases where OPAL-FEL simulations are compared to experimental results. Both experiments concern electron beamlines where the longitudinal phase space is modulated with a short magnetic wiggler. Good agreement was found in both the space charge and radiation dominated regimes.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Profiling overstory survival trends following varying thinning and burning disturbance regimes in a mixed pine-hardwood forest in the US South

Prescribed burning as a silvicultural tool may be effective for achieving various management objectives, yet some practitioners have concerns about inadvertently increasing overstory tree mortality. Using extensive data from a long-term, ongoing study in northcentral Alabama, USA, that systematically applies a variety of thinning and prescribed burning disturbances on mixed pine-hardwood stands, we assess survival trends for different groups of trees. The primary research question is whether more frequent prescribed burns adversely affects overstory survival versus infrequent or no burns; secondary questions explore whether overstory survival trends differ based on thinning level, species group, or size class. Interest is in broad groups of trees, not individual tree survival or mortality; consequently, survival analysis methods are used, including nonparametric Kaplan-Meier (KM) techniques for examining single grouping factors, and parametric accelerated failure time models for analyzing simultaneous effects of multiple covariates. Leveraging relatively recent methodological advances, the statistical techniques are adjusted for interval censored data. KM survival curves showed that more frequent prescribed fires did not result in differing survival trends. Also, trees in unthinned stands had the lowest 14-year survival compared to thinned stands, oaks had the highest survival compared to pines and the others species group, and the smallest size class of overstory trees had the lowest survival. In conclusion, these results support managing transitional mixed pine-hardwoods using thinning and multiple prescribed fires to restore specific species composition and structure.

54 ENVIRONMENTAL SCIENCES↗