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DOE OSTI2025

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗

DOE OSTI2023

Flavor-changing light bosons with accidental longevity

We consider a model with a complex scalar field that couples to (e, μ) or (μ, τ) within the “longevity” window: [|m l 1 – m l 2 |, m l 1 + m l 2 ] in which l 1 and l 2 are the two different charged leptons. Within such a mass window, even a relatively large coupling (e.g. of the size commensurate with the current accuracy/discrepancy in the muon g – 2 experiment) leads to long lifetimes and macroscopic propagation distance between production and decay points. We propose to exploit several existing neutrino experiments and one future experiment to probe the parameter space of this model. For the μ – e sector, we exploit the muonium decay branching ratio and the production and decay sequence at the LSND experiment, excluding the parametric region suggested by g μ – 2 anomaly. For the τ – μ sector, we analyze three main production mechanisms of scalars at beam dump experiments: the Drell-Yan process, the heavy meson decay, and the muon scattering. We explore the constraints from the past CHARM and NuTeV experiments, and evaluate sensitivity for the proposed beam dump experiment, SHiP. The latter can thoroughly probe the parameter space relevant for the g μ – 2 anomaly.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Zero-truncated Poisson regression for sparse multiway count data corrupted by false zeros

Abstract We propose a novel statistical inference methodology for multiway count data that is corrupted by false zeros that are indistinguishable from true zero counts. Our approach consists of zero-truncating the Poisson distribution to neglect all zero values. This simple truncated approach dispenses with the need to distinguish between true and false zero counts and reduces the amount of data to be processed. Inference is accomplished via tensor completion that imposes low-rank tensor structure on the Poisson parameter space. Our main result shows that an $N$-way rank-$R$ parametric tensor $\boldsymbol{\mathscr{M}}\in (0,\infty )^{I\times \cdots \times I}$ generating Poisson observations can be accurately estimated by zero-truncated Poisson regression from approximately $IR^2\log _2^2(I)$ non-zero counts under the nonnegative canonical polyadic decomposition. Our result also quantifies the error made by zero-truncating the Poisson distribution when the parameter is uniformly bounded from below. Therefore, under a low-rank multiparameter model, we propose an implementable approach guaranteed to achieve accurate regression in under-determined scenarios with substantial corruption by false zeros. Several numerical experiments are presented to explore the theoretical results.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Crosslink V.0.11.x User Manual

CrossLink is a novel two-dimensional and three-dimensional geometry and mesh generation software package developed by the Simulation Tools team at Los Alamos National Laboratory. This software represents the third generation of topology-based mesh generation technology developed by the Department of Defense and the Department of Energy with a special focus on complex multi-material hydrodynamic applications, mesh scalability, and high-order element mesh generation. The topology-based meshing approach offered by CrossLink enables users to quickly and easily mesh complex geometries in a repeatable and robust manner. CrossLink’s topology-based meshing approach is well-suited for parametric design studies, parametric design optimization, damage scenario assessment, and iterative design modification (i.e. feature addition and/or removal). CrossLink’s python API allows workflow scripting of the geometry creation and mesh generation process for traceability, repeatability, data provenance, and version control. CrossLink consists of three main components: a graphical user interface (GUI), a geometry creation and mesh generation engine, and a python API that provides a workflow scripting interface to the geometry and meshing functions.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1986

Development of a water recovery subsystem based on Vapor Phase Catalytic Ammonia Removal (VPCAR)

An integrated engineering breadboard subsystem for the recovery of potable water from untreated urine was designed, fabricated and tested. It was fabricated from commercially available components without emphasis on weight, volume and power requirement optimization. Optimizing these parameters would make this process competitive with other spacecraft water recovery systems. Unlike other phase change systems, this process is based on the catalytic oxidation at elevated temperatures of ammonia and volatile hydrocarbons to innocuous products; therefore, no urine pretreatment is required. The testing program consisted of parametric tests, one month of daily tests, and a continuous run of 165 hours. The recovered water is low in ammonia, hydrocarbons and conductivity and requires only adjustment of its pH to meet drinking water standards.

Budininkas, P.↗

NASA NTRS1989

The secondary flow and its stability for natural convection in a tall vertical enclosure

The multicellular flow between two vertical parallel plates is numerically simulated using a time-splitting pseudospectral method. The steady flow of air and the time-periodic flow of oil are investigated, and descriptions of these flows using both physical and spectral approaches are presented. The time dependence of the flow and temperature fields of oil are shown, and the dynamics of the process is discussed. The spectral transfer of energy among the axial modes comprising the flow is explored. The three-dimensional linear stabiltiy of the multicellular air flow is parametrically studied. The domain of stable two-dimensional cellular motion is found to be constrained by the Eckhaus instability and by two types of monotone instability. The two-dimensional multicellular flow is unstable above a Grashof number of about 8550.

Chait, Arnon↗

NASA NTRS1992

STME Hydrogen Mixer Study

The hydrogen mixer for the Space Transportation Main Engine is used to mix cold hydrogen bypass flow with warm hydrogen coolant chamber gas, which is then fed to the injectors. It is very important to have a uniform fuel temperature at the injectors in order to minimize mixture ratio problems due to the fuel density variations. In addition, the fuel at the injector has certain total pressure requirements. In order to achieve these objectives, the hydrogen mixer must provide a thoroughly mixed fluid with a minimum pressure loss. The AEROVISC computational fluid dynamics (CFD) code was used to analyze the STME hydrogen mixer, and proved to be an effective tool in optimizing the mixer design. AEROVISC, which solves the Reynolds Stress-Averaged Navier-Stokes equations in primitive variable form, was used to assess the effectiveness of different mixer designs. Through a parametric study of mixer design variables, an optimal design was selected which minimized mixed fuel temperature variation and fuel mixer pressure loss. The use of CFD in the design process of the STME hydrogen mixer was effective in achieving an optimal mixer design while reducing the amount of hardware testing.

Blumenthal, Rob↗

NASA NTRS1993

A study of the effects of macrosegregation and buoyancy-driven flow in binary mixture solidification

A generalized anisotropic porous medium approach is developed for modelling the flow, heat and mass transport processes during binary mixture solidification. Transient predictions are obtained using FEM, coupled with an implicit time-marching scheme, for solidification inside a two-dimensional rectangular enclosure. A parametric study focusing attention on the effects of solutal buoyancy and thermal buoyancy is presented. It is observed that three parameters, namely the thermal Rayleigh number, the solutal Rayleigh number, and the relative density change parameter, significantly alter the flow fields in the liquid and the mushy regions. Depending upon the nature of these flow fields, the solute enrichment caused by macrosegregation may occur in the top or the bottom region of the enclosure.

Sinha, S. K.↗

NASA NTRS1994

Aerodynamic shape optimization of a HSCT type configuration with improved surface definition

Two distinct parametrization procedures of generating free-form surfaces to represent aerospace vehicles are presented. The first procedure is the representation using spline functions such as nonuniform rational b-splines (NURBS) and the second is a novel (geometrical) parametrization using solutions to a suitably chosen partial differential equation. The main idea is to develop a surface which is more versatile and can be used in an optimization process. Unstructured volume grid is generated by an advancing front algorithm and solutions obtained using an Euler solver. Grid sensitivity with respect to surface design parameters and aerodynamic sensitivity coefficients based on potential flow is obtained using an automatic differentiator precompiler software tool. Aerodynamic shape optimization of a complete aircraft with twenty four design variables is performed. High speed civil transport aircraft (HSCT) configurations are targeted to demonstrate the process.

Thomas, Almuttil M.↗

NASA NTRS2004

Bayesian Vision for Shape Recovery

We present a new Bayesian vision technique that aims at recovering a shape from two or more noisy observations taken under similar lighting conditions. The shape is parametrized by a piecewise linear height field, textured by a piecewise linear irradiance field, and we assume Gaussian Markovian priors for both shape vertices and irradiance variables. The observation process. also known as rendering, is modeled by a non-affine projection (e.g. perspective projection) followed by a convolution with a piecewise linear point spread function. and contamination by additive Gaussian noise. We assume that the observation parameters are calibrated beforehand. The major novelty of the proposed method consists of marginalizing out the irradiances considered as nuisance parameters, which is achieved by Laplace approximations. This reduces the inference to minimizing an energy that only depends on the shape vertices, and therefore allows an efficient Iterated Conditional Mode (ICM) optimization scheme to be implemented. A Gaussian approximation of the posterior shape density is computed, thus providing estimates both the geometry and its uncertainty. We illustrate the effectiveness of the new method by shape reconstruction results in a 2D case. A 3D version is currently under development and aims at recovering a surface from multiple images, reconstructing the topography by marginalizing out both albedo and shading.

Jalobeanu, Andre↗

NASA NTRS2012

Key Decision Record Creation and Approval Module

Retaining good key decision records is critical to ensuring the success of a project or operation. Having adequately documented decisions with supporting documents and rationale can greatly reduce the amount of rework or reinvention over a project's, vehicle's, or facility's lifecycle. Stennis Space Center developed and uses a software tool that automates the Key Decision Record (KDR) process for its engineering and test projects. It provides the ability for a user to log key decisions that are made during the course of a project. By customizing Parametric Technology Corporation's (PTC) Windchill product, the team was able to log all information about a decision, and electronically route that information for approval. Customizing the Windchill product allowed the team to directly connect these decisions to the engineering data that it might affect and notify data owners of the decision. The user interface was created in JSP and Javascript, within the OOTB (Out of the Box) Windchill product, allowing users to create KDRs. Not only does this interface allow users to create and track KDRs, but it also plugs directly into the OOTB ability to associate these decision records with other relevant engineering data such as drawings, designs, models, requirements, or specifications

Hebert, Barrt↗

DOE OSTI2022

On the hot surface ignition of a wall-stagnating spray flame

The ignition of fuel sprays due to interaction with hot surfaces is an important phenomenon in the safety analysis of many engineering systems. We perform a parametric study of the hot surface ignition (HSI) of a fuel spray approaching a heated surface caused by the accidental leakage of a fuel line. Here, to this end, we employ a one-dimensional Eulerian-Eulerian formulation with a non-equilibrium evaporation model and a realistic chemical mechanism to describe $n$-dodecane fuel chemistry. We first describe and analyze the phenomenology of the unsteady processes leading to ignition using non-dimensionalized quantities. Through consideration of the temporal development of the most reactive mixture, we demonstrate that ignition occurs at a fuel-lean composition in a premixed region near the hot surface. Using non-dimensional parameters identified from the governing equations, we perform a parametric study of the time, location and local mixture composition at ignition and determine the ignition limits. We then identify the most important parametric sensitivities for physical analysis using a data-driven classification method. Our analysis demonstrates a contraction of the ignition limits with increased Stokes number and a regime of parametric insensitivity of igniting mixture composition. We also show that at high Damköhler numbers, the ignition location conforms to the parametric behavior of the thermal boundary layer, whereas at low Damköhler numbers approaching the ignition limit it reaches a near-unity value of the quenching Peclet number. We then compare the demonstrated parametric dependencies to the results of the quasi-steady asymptotic ignition literature, showing that our results are consistent with those obtained analytically within the limitations imposed by the simplified formulation of the latter.

42 ENGINEERING↗

NASA NTRS2002

Parametric Powered-Lift Navier-Stokes Computations

The goal of this work is to enable the computation of large numbers of unsteady high-fidelity flow simulations for a YAV-8B Harrier aircraft in ground effect by improving the solution process and taking advantage of NASA parallel supercomputers. The YAV-8B Harrier aircraft can take off and land vertically, or utilize short runways by directing its four exhaust nozzles toward the ground. Transition to forward flight is achieved by rotating these nozzles into a horizontal position.

Chaderjian, Neal M.↗

DOE OSTI2024

Generalized models for inflationary preheating: Oscillations and symmetries

The paradigm of the inflationary universe provides a possible explanation for several observed cosmological properties. In order for such solutions to be successful, the universe must convert the energy stored in the inflaton potential into standard model particles through a process known as reheating. In this paper, we reconsider the reheating process for the case where the inflaton potential respects an approximate (but spontaneously broken) conformal symmetry during the reheating epoch. After reviewing the Effective Field Theory of Reheating, we present solutions for the nonlinear oscillations of the inflaton field, derive the corresponding Hill’s equation for the coupled reheating field, and determine the stability diagram for parametric resonance. For this class of models —the simplest realization being a scalar field with a quartic term—the expansion of the universe drives the coupled field toward a more unstable part of parameter space, in contrast to the standard case. We also generalize this class of models to include quadratic breaking terms in the potential during the reheating epoch and address the process of stability in that universality class of models.

Barrowes, Leia [University of Michigan, Ann Arbor]↗

NASA NTRS1990

Interpreting the handling qualities of aircraft with stability and control augmentation

The general process of designing an aircraft for good flying qualities is first discussed. Lessons learned are pointed out, with piloted evaluation emerging as a crucial element. Two sources of rating variability in performing these evaluations are then discussed. First, the finite endpoints of the Cooper-Harper scale do not bias parametric statistical analyses unduly. Second, the wording of the scale does introduce some scatter. Phase lags generated by augmentation systems, as represented by equivalent time delays, often cause poor flying qualities. An analysis is introduced which allows a designer to relate any level of time delay to a probability of loss of aircraft control. This view of time delays should, it is hoped, allow better visibility of the time delays in the design process.

Hodgkinson, J.↗

NASA NTRSDate not supplied

System Modeling of a Lunar Molten Regolith Electrolysis Plant

Introduction: In-Situ Resource Utilization (ISRU) is the process of extracting local resources to produce commodities for propulsion, life support systems, and off-planet construction rather than transporting consumables from Earth. Molten Regolith Electrolysis (MRE) is a novel ISRU method of extracting oxygen gas and metal alloy from lunar regolith. The MRE process involves placing lunar regolith between two electrodes, through which current is passed, to melt the regolith and reduce the metal oxide constituents by direct electrolysis (e.g. FeO, SiO2, MgO, Al2O3) into oxygen gas and metal alloys. The oxygen is liquefied and used as propellant for landers, while the metals (e.g. Ferro-alloys) are further processed and used in structural building materials and parts manufacturing. A system model was developed that accounted for the major processes of an MRE plant (from excavation of raw materials to storage of products) to assess the feasibility of a lunar MRE plant. The System Engineering and Integration (SE&I) ISRU Modeling and Analysis (SIMA) team utilized its previously documented system sizing model, the Mission Analysis and Integration Tool (MAIT) [1] as framework of the system model. MAIT uses MATLAB/Simulink to integrate subsystem models into a complete system model of the MRE plant. Total mass, volume, and power requirements were computed for numerous iterations of a MRE plant. System Model: Figure 1: MRE Plant Block Diagram The regolith excavation model determines the mass and power needed to excavate sufficient regolith. The preheating auger initiates the regolith heating process before regolith enters the MRE re-actor to reduce the energy required to turn the solid into a molten liquid. The MRE reactor is modeled in COMSOL Multiphysics and based on the research by Dominguez, Sibille, and Schreiner [2, 3, 4]. This preliminary reactor model provides an accurate calculation of thermal equilibrium during electrochemical operation of the reactor system to assess the optimal mass and power required to process the inlet flow of regolith. The model also computes the outlet flowrates of oxygen and molten products. For this analysis, the primary components of the metal alloy considered were iron and silicon. The oxygen is then purified using an Yttrium Stabilized Zirconia (YSZ) electrode, followed by liquefaction using a 90K cryocooler to be stored as liquid oxygen in insulated cylindrical tanks. In future iterations of the system model, the molten metal tapped from the MRE reactor will undergo additional processing or refinement. However, downstream handling of metals is currently a technology gap that is missing a high TRL subsystem model. Therefore, for this analysis, the accumulated metal alloy stream terminates after leaving the MRE reactor. Study Goals: This analysis investigates multiple input variables to the system to determine the sensitivity of a (near) complete plant at full-scale. This preliminary investigation ran parametric sweeps on the MRE reactor geometry, electrical current supply, layers of multi-layer insulation (MLI) on the reactor, size of the electrodes in the oxygen purification model, and regolith composition (based on landing site location). Three production targets of oxygen (1,000, 10,000, and 50,000 kg/yr) were investigated for this analysis. The parametric sweeps conducted in this analysis provide valuable insight into the expected impact of the various model inputs on plant size. This information can be used to identify the most critical components of the plant and guide future decisions on allocating funding for research and development, providing subsystem developers with appropriate interfaces with downstream and upstream processes, and assessing the overall feasibility of MRE when compared to other ISRU plants. References: [1] Carlson, A. et al. (2024) ICES, ICES-2024-53. [2] Dominguez, D.A., and Sibille, L. (2011) AIAA, AIAA-2011-700. [3] Schreiner, S.S. (2015) MIT, Dissertation. [4] Schreiner, S.S. et al. (2016) ASR, 57(7), pp.1585-1603.

ISRU↗

DOE OSTI2025

Statistical model of the stimulated forward Brillouin scattering driven by a randomized laser beam in plasma

The modeling of a spatially incoherent laser beam remains a central problem of the parametric instabilities in the context of inertial confinement fusion. This letter gives a simplified and comprehensive overview of the recent analytical developments regarding the modeling of these laser beams and a comparison with a dedicated experiment. Our model accounts for the first time for the statistical standard deviation of the gain and accurately captures the entanglement between wave mixing processes and the speckle correlations thus resolving the longstanding contradictions between the random phase approximation and the model of independent speckles. It is successfully compared to a recent laser beam spray experiment and the associated paraxial simulations, demonstrating that backscattering predictions require accounting for the beam spray. Furthermore, our framework thus provides a way to evaluate and guide the analysis of parametric instabilities in high laser energy experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Ultra–high molecular weight polyethylene micro–ribbon fibers gel spun using orange terpenes

Toxic, hazardous petrochemical solvents are commonly used for industrial-scale ultra-high molecular weight polyethylene (UHMWPE) fiber production, but orange terpenes, a byproduct of orange fruit production, present a bio-derived, sustainable alternative. In this work, fine UHMWPE fibers were spun using orange terpenes as the spin solvent, hot-drawn at a draw ratio of 5:1, investigated for their morphology, microstructure, and thermal and mechanical properties. The resulting fibers exhibited a flat, micro-ribbon cross-section, which is highly desirable for achieving high fiber volume fractions in UHMWPE-fiber reinforced composites. After drawing, the fibers possessed 4× greater breaking tenacity than any previously published studies on UHMWPE fibers spun using orange terpenes with a tenacity of 8.6 cN/dtex and tensile modulus of 229.2 cN/dtex. Microstructural analysis via differential scanning calorimetry and X-ray diffraction revealed that the hot drawing process significantly increased molecular orientation, but crystallinity decreased due to crystallite melting during drawing. Therefore, the mechanical properties of these fibers may be significantly improved with optimization of the fiber drawing process. As a work, this work establishes the strong potential of orange terpenes as an environmentally-friendly alternative solvent for UHMWPE gel spinning and sets a foundation for future parametric optimization of the spinning and drawing of these fibers.

36 MATERIALS SCIENCE↗