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DOE OSTI2015

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1994

Building complex simulations rapidly using MATRIX(x): The Space Station redesign

MSFC's quick response to the Space Station redesign effort last year required the development of a computer simulation to model the attitude and station-keeping dynamics of a complex body with rotating solar arrays in orbit around the Earth. The simulation was written using a rapid-prototyping graphical simulation and design tool called MATRIX(x) and provided the capability to quickly remodel complex configuration changes by icon manipulation using a mouse. The simulation determines time-dependent inertia properties, and models forces and torques from gravity-gradient, solar radiation, and aerodynamic disturbances. Surface models are easily built from a selection of beams, plates, tetrahedrons, and cylinders. An optimization scheme was written to determine the torque equilibrium attitudes that balance gravity-gradient and aerodynamic torques over an orbit, and propellant-usage estimates were determined. The simulation has been adapted to model the attitude dynamics for small spacecraft.

Carrington, C. K.↗

DOE OSTI2017

Spanning the Core Design Space with Binary Perturbations - A Mathematical Investigation

A reactor core design engineer, even one with many years of experience or one using advanced fuel pattern optimization software, will likely fine tune the pattern before finalizing the design. Fine tuning can further minimize local enthalpy peaks, optimize reactivity to extend burnup, and add additional margin to limits on reactivity coefficients or heat flux. For reactors that have reached an equilibrium fuel cycle, the number of feeds each cycle is typically the similar to previous cycles as is their placement in the core. It is then the engineer's responsibly to efficiently select the placement of burned assemblies to ensure optimal fuel utilization, satisfy safety limits, and meet cycle energy requirements. One of the engineer's most commonly used tools in this fine tuning investigation is to swap the positions of two assemblies, most likely two previously irradiated ('burned') assemblies since their reactivity is lower than fresh fuel. Such an operation is referred to in this work as a binary perturbation or a 'swap'. If quarter core symmetry is maintained, the perturbation translates to the other three quadrants. Likewise if eighth core symmetry is maintained, the perturbation translates to other seven octants. The question is then, how much of the core design space can binary perturbations possibly span? This work seeks to quantitatively define the space spanned by m number of binary perturbations as a function of variable size through combinatorial principles and computer simulation. The results of this study are useful in understanding the in-core fuel management problem faced by both professionals who employ hand manipulations and those who attempt stochastic solutions of the problem.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

NASA NTRS2008

On-Orbit Multi-Field Wavefront Control with a Kalman Filter

A document describes a multi-field wavefront control (WFC) procedure for the James Webb Space Telescope (JWST) on-orbit optical telescope element (OTE) fine-phasing using wavefront measurements at the NIRCam pupil. The control is applied to JWST primary mirror (PM) segments and secondary mirror (SM) simultaneously with a carefully selected ordering. Through computer simulations, the multi-field WFC procedure shows that it can reduce the initial system wavefront error (WFE), as caused by random initial system misalignments within the JWST fine-phasing error budget, from a few dozen micrometers to below 50 nm across the entire NIRCam Field of View, and the WFC procedure is also computationally stable as the Monte-Carlo simulations indicate. With the incorporation of a Kalman Filter (KF) as an optical state estimator into the WFC process, the robustness of the JWST OTE alignment process can be further improved. In the presence of some large optical misalignments, the Kalman state estimator can provide a reasonable estimate of the optical state, especially for those degrees of freedom that have a significant impact on the system WFE. The state estimate allows for a few corrections to the optical state to push the system towards its nominal state, and the result is that a large part of the WFE can be eliminated in this step. When the multi-field WFC procedure is applied after Kalman state estimate and correction, the stability of fine-phasing control is much more certain. Kalman Filter has been successfully applied to diverse applications as a robust and optimal state estimator. In the context of space-based optical system alignment based on wavefront measurements, a KF state estimator can combine all available wavefront measurements, past and present, as well as measurement and actuation error statistics to generate a Maximum-Likelihood optimal state estimator. The strength and flexibility of the KF algorithm make it attractive for use in real-time optical system alignment when WFC alone cannot effectively align the system.

Lou, John↗

NASA NTRS1994

Computational Investigation of an F-18 Aircraft in the High-Alpha Regime

One of the goals of NASA's High Alpha Technology Program is to provide flight-validated design methods for the high-angle-of-attack regime. This is an integrated effort utilizing computational simulations, wind tunnel experiments, and flight tests using the F-18 High Alpha Research Vehicle (HARV). The dominant physics of the aircraft flows in the high alpha regime changes as the angle of attack is increased. At moderate angle of attack the flow is characterized by boundary layer separation and the formation of tight vortices. As the angle of attack is increased, these vortices break down producing unsteady wakes. With further increase in angle of attack, the, vortex breakdown moves progressively upstream until the entire flowfield becomes dominated by the unsteady wake. Previous computational work has demonstrated the ability to simulate flows about the F-18 HARV in the medium-to-high angle of attack range, where the flowfield is characterized by the vortex formation and subsequent breakdown. This paper extends the previous computations to include conditions of 45 degree angle of attack where the flowfield becomes dominated by the unsteady wake shed from the Leading Edge Extension (LEX), and regions of laminar and transitional flow appear on the fuselage forebody. A more complete surface geometry is utilized, which includes the features of the engine nacelle, inlet diffuser, and the boundary layer diverter duct. A volume grid sensitivity study was also performed to extend the accuracy of the results, most notably in the prediction of the LEX vortex breakdown position. This paper includes comparisons of computational results with both in-flight surface pressure measurements, and flow visualizations of the surface and off-surface particle trajectories.

Murman, Scott M.↗

NASA NTRS1991

Neural network architecture for crossbar switch control

A Hopfield neural network architecture for the real-time control of a crossbar switch for switching packets at maximum throughput is proposed. The network performance and processing time are derived from a numerical simulation of the transitions of the neural network. A method is proposed to optimize electronic component parameters and synaptic connections, and it is fully illustrated by the computer simulation of a VLSI implementation of 4 x 4 neural net controller. The extension to larger size crossbars is demonstrated through the simulation of an 8 x 8 crossbar switch controller, where the performance of the neural computation is discussed in relation to electronic noise and inhomogeneities of network components.

Troudet, Terry P.↗

DOE OSTI2019

Classical trajectory Monte Carlo simulation of plasma fueling using magnetic plasma expulsion

The possibility of fueling a magnetically confined plasma using particle sources located inside of the plasma is studied by computer simulation. Magnetic plasma expulsion [R. E. Phillips and C. A. Ordonez, Phys. Plasmas 25, 012508 (2018)] would serve to keep the magnetically confined plasma away from the particle sources without adversely affecting plasma confinement. The simulations show how charged particles can be injected into a plasma by using particle sources located directly between two current-carrying wires that create a magnetic expulsion field. Plasma fueling with the average energy of injected particles greater than the average energy of plasma particles may serve for heating the plasma. Also, plasma fueling with positive and negative particles injected at different rates may serve for changing the neutrality of the plasma. Conditions for plasma fueling are investigated using a classical trajectory Monte Carlo simulation. Two types of particle sources are considered, and the fraction of emitted particles that reach (and fuel) the magnetically confined plasma is evaluated for each.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

The ENDF/B Nuclear Data Library and Its Impact on Reactor Simulations

The ENDF/B library, which is developed, maintained, and distributed by the Cross Section Evaluation Working Group, is the main source of nuclear data for analyses and computational simulations in nuclear applications, like different nuclear reactors concepts, radiation shielding, medical applications, astrophysics, etc. The library is constantly being improved and updated, with each release bringing an optimal representation of nuclear interactions as they are understood in their time. The most recent release, ENDF/B-VIII.1, represents a significant improvement in terms of the performance and consistency of the measured differential data relative to previous versions, as it combines the most recent experimental differential data and advanced theoretical nuclear models. As one of the many highlights, ENDF/B-VIII.1 restores a high-burnup depletion performance, comparable to ENDF/B-VII.1, that had been degraded in ENDF/B-VIII.0, while further improving the performance in criticality benchmarks, such as those in the Mosteller’s suite. Additionally noteworthy is the improved performance of ENDF/B-VIII.1 in radiation shielding and thick-target leakage spectrum integral experiments, which are also important for fusion and reactor applications. In this work we present in a very summarized way the main updates implemented in the ENDF/B-VIII.1 release and its main impacts, and also begin to delineate the path forward as to what to expect in the future for the next ENDF/B release, which, based on the timeline of the past few releases, is estimated to happen around 5 years from now. We emphasize that the ENDF/B-VIII.1 release was the product of an enormous collaborative effort among many authors and that for a complete detailed picture, the reader is strongly encouraged to refer to the article accompanying the release, which is currently in the publication process, but available as preprint [G. P. A. Nobre et al. arXiv Preprint arXiv: 2511.03564 (2025)].

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1981

Simulation of charge exchange plasma propagation near an ion thruster propelled spacecraft

A model describing the charge exchange plasma and its propagation is discussed, along with a computer code based on the model. The geometry of an idealized spacecraft having an ion thruster is outlined, with attention given to the assumptions used in modeling the ion beam. Also presented is the distribution function describing charge exchange production. The barometric equation is used in relating the variation in plasma potential to the variation in plasma density. The numerical methods and approximations employed in the calculations are discussed, and comparisons are made between the computer simulation and experimental data. An analytical solution of a simple configuration is also used in verifying the model.

Robinson, R. S.↗

NASA NTRS1993

Simulations of particle acceleration in parallel shocks: Direct comparison between Monte Carlo and one-dimensional hybrid codes

We have made a direct comparison between two different computer simulations of a plane, parallel, collisionless shock including particle acceleration to energies typical of those of diffuse ions observed at the earth bow shock. Despite the fact that the one-dimensional hybrid and Monte Carlo techniques employ entirely different algorithms, they give surprisingly close agreement in the overall shapes of the complete distribution functions for protons as well as heavier ions. Both methods show that energetic ions emerge smoothly from the background thermal plasma with approximately the same relative injection rate and that the fraction of the incoming plasma's energy flux that is converted into downstream enthalpy flux of the accelerated population (i.e., the acceleration efficiency) is similar in the two cases. The fraction of the downstream proton distribution made up of superthermal particles is quite large, with at least 10% of the energy flux going into protons with energies above 10 keV. In addition, an upstream precursor, produced by backstreaming energetic particles, is present in both shocks, although the Monte Carlo precursor is considerably longer than that produced in the hybrid shock. These results offer convincing evidence that, at least in these ways, the two simulations are consistent in their description of parallel shock structure and particle acceleration, and they lay the groundwork for development of shock models employing a combination of both methods.

Ellison, Donald C.↗

DOE OSTI2017

System dynamic simulation: A new method in social impact assessment (SIA)

Many complex social questions are difficult to address adequately with conventional methods and techniques, due to the complicated dynamics, and hard to quantify social processes. Despite these difficulties researchers and practitioners have attempted to use conventional methods not only in evaluative modes but also in predictive modes to inform decision making. The effectiveness of SIAs would be increased if they were used to support the project design processes. This requires deliberate use of lessons from retrospective assessments to inform predictive assessments. Social simulations may be a useful tool for developing a predictive SIA method. There have been limited attempts to develop computer simulations that allow social impacts to be explored and understood before implementing development projects. In light of this argument, this paper aims to introduce system dynamic (SD) simulation as a new predictive SIA method in large development projects. We propose the potential value of the SD approach to simulate social impacts of development projects. We use data from the SIA of Gareh-Bygone floodwater spreading project to illustrate the potential of SD simulation in SIA. It was concluded that in comparison to traditional SIA methods SD simulation can integrate quantitative and qualitative inputs from different sources and methods and provides a more effective and dynamic assessment of social impacts for development projects. We recommend future research to investigate the full potential of SD in SIA in comparing different situations and scenarios.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Hybrid Quantum Mechanical, Molecular Mechanical, and Machine Learning Potential for Computing Aqueous-Phase Adsorption Free Energies on Metal Surfaces

Performing reliable computer simulations of elementary processes occurring at metal–water interfaces is pivotal for novel catalyst design in sustainable energy applications. Computational catalyst design hinges on the ability to reliably and efficiently compute the potential energy surface (PES) of the system. Here, due to the large system sizes needed for studying processes at liquid water–metal interfaces, these systems can currently not be described using density functional theory (DFT). In this work, we used a hybrid quantum mechanical, molecular mechanical, and machine learning potential for studying the adsorption behavior of phenol, atomic hydrogen, 2-butanol, and 2-butanone on the (0001) facet of Ru under reducing conditions when Ru is not oxidized. Specifically, we describe the adsorbate and the surrounding metal atoms at the DFT level of theory. Here, we also considered the electrostatic field effect of the water molecules on adsorbate–metal interactions. Next, for the water–water and water–adsorbate interactions, we used established classical force fields. Finally, for the water–Ru surface interaction, for which no reliable force fields have been published, we used Behler–Parrinello high-dimensional neural network potentials (HDNNPs). Employing this setup, we used our explicit solvation for metal surface (eSMS) approach to compute the aqueous-phase effect on the low-coverage adsorption of selected molecules and atoms on the (0001) facet of Ru. In agreement with previous experimental and computational studies of oxygenated molecules over transition metal facets, we found that liquid water destabilizes the tested adsorbates on Ru(0001). Interestingly, our findings indicate that adsorbates on Ru are less affected by the presence of an aqueous phase than on other transition metals (e.g., Pt), highlighting the necessity of experimental investigations of Ru-based catalytic systems in liquid water.

Adsorption↗

DOE OSTI2016

Analyzing and sense making of human factors in the Malaysian radiation and nuclear emergency planning framework

The evolution of current Radiation and Nuclear Emergency Planning Framework (RANEPF) simulator emphasizes on the human factors to be analyzed and interpreted according to the stakeholder’s tacit and explicit knowledge. These human factor criteria are analyzed and interpreted according to the “sense making theory” and Disaster Emergency Response Management Information System (DERMIS) design premises. These criteria are corroborated by the statistical criteria. In recent findings, there were no differences of distributions among the stakeholders according to gender and organizational expertise. These criteria are incrementally accepted and agreed the research elements indicated in the respective emergency planning frameworks and simulator (i.e. 78.18 to 84.32, p-value <0.05). This paper suggested these human factors criteria in the associated analyses and theoretical perspectives to be further acomodated in the future simulator development. This development is in conjunction with the proposed hypothesis building of the process factors and responses diagram. We proposed that future work which implies the additional functionality of the simulator, as strategized, condensed and concise, comprehensive public disaster preparedness and intervention guidelines, to be a useful and efficient computer simulation.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2019

Scattering of Radio Frequency Waves by Density Fluctuations in Tokamak Plasmas

In tokamak fusion plasmas, coherent fluctuations in the form of blobs or filaments and incoherent fluctuations due to turbulence are routinely observed in the scrape-off layer. Radio frequency (RF) electromagnetic waves, excited by antenna structures placed near the wall of a tokamak, have to propagate through the scrape-off layer before reaching the core of the plasma. RF waves in the electron cyclotron and lower hybrid range of frequencies are commonly used to modify the current profile. In the International Thermonuclear Experimental Reactor (ITER), electron cyclotron waves are expected to stabilize the neoclassical tearing mode by providing current in the island region. While the effect of fluctuations on RF waves has not been quantified experimentally, there are telltale signs, arising from differences between results from simulations and from experiments, that fluctuations can modify the spectrum of RF waves. Consequently, pioneering theoretical studies and complementary computer simulations have been pursued to elucidate the impact of fluctuations on RF waves. These studies, using the full complement of Maxwell's equations for a cold, magnetized plasma, show that the Poynting flux in the wake of the filament develops spatial structure due to diffraction and shadowing. The uniformity of power flow into the plasma is affected by side-scattering, modifications to the wave spectrum, and coupling to plasma waves other than the incident RF wave. The Snell's law and the Fresnel equations have been reformulated within the context of magnetized plasmas. These are distinctly different from their counterparts in scalar dielectric media, and reveal new and important physical insight into the scattering of RF waves. All of these studies apply to the scattering of RF waves in any frequency range and for arbitrary variations in density.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1987

Cellular automaton supercomputing

Many of the models now used in science and engineering are over a century old. And most of them can be implemented on modern digital computers only with considerable difficulty. Some new basic models are discussed which are much more directly suitable for digital computer simulation. The fundamental principle is that the models considered herein are as suitable as possible for implementation on digital computers. It is then a matter of scientific analysis to determine whether such models can reproduce the behavior seen in physical and other systems. Such analysis was carried out in several cases, and the results are very encouraging.

Wolfram, Stephen↗

NASA NTRS2004

Computational Methods for Dynamic Stability and Control Derivatives

Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.

Green, Lawrence L.↗

NASA NTRS2003

Computational Methods for Dynamic Stability and Control Derivatives

Green, Lawrence L.↗

NASA NTRS1989

Tools for 3D scientific visualization in computational aerodynamics

The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording.

Bancroft, Gordon↗