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Mesoscale Modeling of Hydrogels Under Frictional Shear Stress

Hydrogels are three-dimensional networks of hydrophilic polymers often used as a simplified model of hydrated biological materials, from cartilaginous joints to the ocular tear film. However, the lubrication mechanisms of hydrogels remain poorly understood, partly due to their complex polymeric structure, which creates blurred interfaces during sliding that are challenging to study experimentally. In this study, we employ dissipative particle dynamics (DPD) to investigate the frictional behavior of a polymeric hydrogel network sliding against a solid wall in an explicit viscous solvent. This computational approach enables us to model hydrodynamic interactions and mesoscale polymer dynamics, capturing key aspects of hydrogel friction. Our simulations reveal that hydrogel friction is governed by the interplay between polymer relaxation and viscous shear, characterized by the Weissenberg number (Wi). At low Wi, friction coefficient remain nearly constant, dominated by polymer relaxation. However, at higher Wi, friction is dominated by viscous drag within a near-wall solvent layer, leading to a linear increase in friction coefficient with Wi. Furthermore, our results demonstrate an inverse relationship between the friction coefficient and the applied normal load, consistent with experimental observations. This work provides new insights into the fundamental tribological properties of hydrogels, shedding light on the micromechanics of hydrogel friction. Improving our understanding of hydrogel structure and dynamics under friction advances our knowledge of the mechanisms regulating biological lubrication in health and disease.

36 MATERIALS SCIENCE↗

SAM Theory Manual

The System Analysis Module (SAM) is an advanced and modern system analysis tool under development at Argonne National Laboratory for advanced non-LWR reactor safety analysis. It aims to provide fast-running, modest-fidelity, whole-plant transient analyses capabilities, which are essential for fast turnaround design scoping and engineering analyses of advanced reactor concepts. While SAM is being developed as a system-level modeling and simulation tool, advanced modeling techniques being implemented include a reduced-order three-dimensional module, pseudo 3-D conjugate heat transfer modeling in reactor core, flexible and multi-scale modeling of heat transfer between fluid and structures, in addition to the advances in software environments and design, and numerical methods. SAM aims to be a generic system-level safety analysis tool for advanced non-LWRs, including Liquid-Metal-cooled fast Reactors (LMR), Molten Salt Reactors (MSR), Fluoride-salt-cooled High-temperature Reactors (FHR), and High-Temperature Gas-cooled Reactors (HTGR). SAM takes advantage of advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability. It utilizes an object-oriented computational framework (MOOSE), and its underlying meshing and finite-element library and linear and non-linear solvers, to leverage the modern advanced software environments and numerical methods. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As new code capabilities and features are added, the SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Validation of the ERO2.0 code using W7-X and JET experiments and predictions for ITER operation

Abstract The paper provides an overview of recent modelling of global material erosion and deposition in the fusion devices Wendelstein 7-X (W7-X), JET and ITER using the Monte-Carlo code ERO2.0. For validating the modelling tool in a three-dimensional environment, W7-X simulations are performed to describe carbon erosion from the graphite test divertor units, which were equipped in operational phase OP 1.2 and analysed post-mortem. Synthetic spectroscopy of carbon line emission is compared with experimental results from the divertor spectrometer measurement system, showing a good agreement in the e-folding lengths in the radial intensity profiles of carbon. In the case of metallic wall materials, earlier modelling of the Be/W environment in JET and ITER is revisited and extended with an updated set of sputtering and reflection data, as well as including the mixing model for describing the Be/W dynamics in the divertor. Motivated by recent H/D/T isotope experiments in JET, limited and diverted configuration pulses are modelled, showing the expected trend of both Be and W erosion increasing with isotope mass. For the JET diverted configuration pulses, it is shown that Be migrates predominantly to the upper part of the inner divertor where it initially leads to strong W erosion. With longer exposure time, the growth of a Be deposited layer leads to a reduction of W erosion in that region. A similar trend is observed in simulations of the ITER baseline Q = 10 scenario, however with a more symmetric Be migration pattern leading to deposition also on the outer divertor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Study of impacts of two types of cellular aging on the yeast bud morphogenesis

Understanding the mechanisms of the cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short cell cycle, and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. By analyzing experimental data, this study shows that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional multiscale chemical-mechanical model was developed and used to suggest and test hypothesized impacts of aging on bud morphogenesis. Experimentally calibrated model simulations showed that during the early stage of budding, tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip, a process guided by the polarized Cdc42 signal. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage as observed in experiments in this work. The model simulation results suggest that the localization of new cell surface material insertion, regulated by chemical signal polarization, could be weakened due to cellular aging in yeast and other cell types, leading to the change and stabilization of the bud aspect ratio.

Tsai, Kevin↗

Forest structural complexity and ignition pattern influence simulated prescribed fire effects

Background: Forest structural characteristics, the burning environment, and the choice of ignition pattern each influence prescribed fire behaviors and resulting fire effects; however, few studies examine the influences and interactions of these factors. Understanding how interactions among these drivers can influence prescribed fire behavior and effects is crucial for executing prescribed fires that can safely and effectively meet management objectives. To analyze the interactions between the fuels complex and ignition patterns, we used FIRETEC, a three-dimensional computational fluid dynamics fire behavior model, to simulate fire behavior and effects across a range of horizontal and vertical forest structural complexities. For each forest structure, we then simulated three different prescribed fires each with a unique ignition pattern: strip-head, dot, and alternating dot. Results: Forest structural complexity and ignition pattern affected the proportions of simulated crown scorch, consumption, and damage for prescribed fires in a dry, fire-prone ecosystem. Prescribed fires in forests with complex canopy structures resulted in increased crown consumption, scorch, and damage compared to less spatially complex forests. The choice of using a strip-head ignition pattern over either a dot or alternating-dot pattern increased the degree of crown foliage scorched and damaged, though did not affect the proportion of crown consumed. We found no evidence of an interaction between forest structural complexity and ignition pattern on canopy fuel consumption, scorch, or damage. Conclusions: We found that forest structure and ignition pattern, two powerful drivers of fire behavior that forest managers can readily account for or even manipulate, can be leveraged to influence fire behavior and the resultant fire effects of prescribed fire. These simulation findings have critical implications for how managers can plan and perform forest thinning and prescribed burn treatments to meet risk management or ecological objectives.

54 ENVIRONMENTAL SCIENCES↗

MURR LEU structural and thermal hydraulics analyses: Part I – Preliminary irradiation thermo-mechanical behavior

The University of Missouri Research Reactor (MURR) is expected to be converted from highly enriched uranium (HEU, ≥ 20 wt% U-235) U-Al x dispersion fuel to low-enriched uranium (LEU, < 20 wt% U-235) with U-10Mo monolithic fuel. This work introduces high-fidelity irradiation thermo–mechanical (T-M) analysis of the MURR LEU focusing on changes in coolant channel gap thickness. Three-dimensional (3D) finite element (FE) models were developed to simulate the irradiation T-M behavior of the MURR LEU element with all 23 curved fuel plates, the two side plates, and the combs. It was shown that channel gap thickness changes were influenced not only by plate thickness variations due to fuel swelling and creep but also by the radial displacement of consecutive MURR LEU plates. Modeling the fuel element assembly captured side plate displacements, which were shown to reduce radial fuel plate displacements towards the convex side. The maximum local radial displacement in the element was predicted at the end of life (EOL) as 23.7 mil (602.0 µm) on the lateral centerline of plate 23 towards the convex side. The maximum stripe-averaged reduction in channel gap thickness, particularly relevant for thermal hydraulics (TH) safety analysis, was calculated as 15.9 mil (403.9 µm) in single-side heated channel 24 (the outermost channel). These results account for the thermal resistance from the oxide build-up on cladding surfaces which was shown to be up to 0.82 mil (20.8 µm) thick. It was demonstrated that accounting for oxide layer thermal resistance led to a 10 °C higher peak fuel temperature and a 4.4 mil (111.8 µm) greater maximum local radial displacement. The impact of the calculated channel gap thickness changes on the MURR LEU TH safety analysis is evaluated in Part II.

Irradiation thermo-mechanical analysis↗

Galactic chemical evolution with the short-lived isotopes 53 Mn, 60 Fe, 182 Hf, and 244 Pu

We run a three-dimensional Galactic chemical evolution (GCE) model to follow the propagation of 53 Mn from supernovae of type Ia (SNIa), 60 Fe from core-collapse supernovae (CCSNe), 182 Hf from intermediate mass stars (IMSs), and 244 Pu from neutron star mergers (NSMs) in the Galaxy. We compare the GCE of these short-lived radioactive isotopes (SLRs) to recent detections on the deep-sea floor. We find that although these SLRs originate from different sites, they often arrive conjointly on Earth.

79 ASTRONOMY AND ASTROPHYSICS↗

Increasing Rubisco as a simple means to enhance photosynthesis and productivity now without lowering nitrogen use efficiency

Summary Global demand for food may rise by 60% mid‐century. A central challenge is to meet this need using less land in a changing climate. Nearly all crop carbon is assimilated through Rubisco, which is catalytically slow, reactive with oxygen, and a major component of leaf nitrogen. Developing more efficient forms of Rubisco, or engineering CO 2 concentrating mechanisms into C 3 crops to competitively repress oxygenation, are major endeavors, which could hugely increase photosynthetic productivity (≥ 60%). New technologies are bringing this closer, but improvements remain in the discovery phase and have not been reduced to practice. A simpler shorter‐term strategy that could fill this time gap, but with smaller productivity increases (c. 10%) is to increase leaf Rubisco content. This has been demonstrated in initial field trials, improving the productivity of C 3 and C 4 crops. Combining three‐dimensional leaf canopies with metabolic models infers that a 20% increase in Rubisco increases canopy photosynthesis by 14% in sugarcane (C 4 ) and 9% in soybean (C 3 ). This is consistent with observed productivity increases in rice, maize, sorghum and sugarcane. Upregulation of Rubisco is calculated not to require more nitrogen per unit yield and although achieved transgenically to date, might be achieved using gene editing to produce transgene‐free gain of function mutations or using breeding.

Plant Sciences↗

Wear of Wave Energy Converters Mooring Lines Belts

Using a belt as a replacement for a rope on a rotary power take-offs (PTOs) system has become more common for wave energy converters, improving cyclic bend over sheave performance with a smaller bending thickness for belts. However, the service life predictions of PTOs are a major concern in design, because belt performance under harsh underwater environments is largely less studied. Here, in this work, the effect of fleet and twist angles on wear life is being investigated both experimentally and numerically. Two three-dimensional equivalent static finite element models are constructed to evaluate the complex stress state of polyurethane-steel belts around steel drums. The first is to capture the response of the experimental investigation performed on the wear life, and the second to predict the wear life of an existing functional PTO. The results show a significant effect for fleet and twist angles on stress concentrations and estimated service life.

16 TIDAL AND WAVE POWER↗

Understanding and Predicting the Spatially Resolved Adsorption Properties of Nanoporous Materials

Using knowledge from statistical thermodynamics and crystallography, we develop an image–image translation model, called SorbIIT, that uses three-dimensional grids of adsorbate–adsorbent interaction energies as input to predict the spatially resolved loading surface of nanoporous materials over a broad range of temperatures and pressures. SorbIIT consists of a closed-form differential model for loading-surface prediction and a U-Net to generate spatial differential distributions from the energy grids. SorbIIT is trained using the energy grids and adsorbate distributions (obtained from high-throughput simulations) of 50 synthesized and 70 hypothetical zeolites and applied for predicting the adsorption of carbon dioxide, hydrogen sulfide, n-butane, 2-methylpropane, krypton, and xenon in other zeolites from 256 to 400 K. In conclusion, employing a quadratic isotherm model for the local differentiation, SorbIIT yields mean R 2 values of 0.998 for total adsorption and 0.6904 for local adsorption with a resolution of 0.2 Å, and a value of 0.721 for the structural similarity of the local loading distribution.

Sun, Yangzesheng [Univ. of Minnesota, Minneapolis,↗

River–aquifer interactions enhancing evapotranspiration in a semiarid riparian zone: A modelling study

The hydrologic flows across the river–aquifer interface play an important role in groundwater dynamics and biogeochemical reactions within the subsurface; however, little is known about the effects of river–aquifer interactions on land surface processes. In this study, we developed a fully coupled three-dimensional (3D) land surface and subsurface model at a high resolution (~1 km) that accounts for high-frequency hydrologic exchange flow conditions to investigate how river–aquifer interactions modulate surface water budgets in the Upper Columbia-Priest Rapids watershed, a typical semiarid watershed located in the northwestern United States where river stage fluctuates in response to reservoir releases changing. Our results show that the spatiotemporal dynamics of river–aquifer interactions are highly heterogeneous, driven mainly by river-stage fluctuations. Adding 6.64 × 10 6 m 3 year –1 of water over the watershed from the river to groundwater owing to the lateral flow, river–aquifer interactions led to an increase in soil evaporation and transpiration supplied by higher soil moisture content, particularly in deeper subsurface. In a hypothetic future scenarios where a 5-m rise in river stage was assumed, the hydrologic flow exchange rates were intensified, resulting in higher surface water over the entire watershed. Overall, lateral flow induced by river–aquifer exchanges leads to an increase in evapotranspiration of ~75% in the historical period and of ~83% in the hypothetical future scenario. Finally, our study demonstrates the potential of coupled model as an effective tool for understanding river–aquifer–land surface interactions, and indicates that river–aquifer interactions fundamentally alter the water balance of the riparian zone for the semiarid watershed and will likely become more frequent and intense in the future under the effects of climate change.

54 ENVIRONMENTAL SCIENCES↗

Mineralized sclerites in the gorgonian coral Leptogorgia chilensis as a natural jamming system

The soft corals (Cnidaria, Octocorallia), a diverse group of colonial marine invertebrates, can reversibly tune their body stiffness in response to external stimuli. This capability is attributed to their dynamic skeletal systems, which consist of thousands of mineralized skeletal elements, called sclerites, embedded within a gel-like matrix that swells/deswells and unjams/jams the sclerites, thus modulating skeletal stiffness. While sclerite morphology is widely used for species identification, its role in the mechanical performance of a soft coral’s skeletal system is largely unknown. Here, we investigated structure-jamming relationships in sclerite-based skeletal architectures using the red gorgonian octocoral Leptogorgia chilensis as a model system. The sclerites of L. chilensis exhibit a shaft-like geometry with two axial branches and two sets of triradiate side branches, which are aligned with the crystallographic symmetry of the constituent magnesium-containing calcite. By combining multiscale three-dimensional (3D) structural characterization, parametric geometrical modeling, 3D printing, mechanical testing, and discrete element simulations, we demonstrate how sclerite geometry achieves a balanced jamming performance in terms of stiffness, weight, strength, and fracture resistance in comparison to alternative geometries parametrically modified from the native sclerites (e.g., changes in the length and number of side branches). Here, we also found that these performance metrics are achieved through the effective interlocking among side and axial branches, which is further enhanced by the fractal-like microscopic spikes on the branch tips. The findings in this natural jamming system offer insights for designing synthetic mechanotunable material architectures for a wide range of applications, from soft robotics to mechanical dampeners.

36 MATERIALS SCIENCE↗

Chromatin structures from integrated AI and polymer physics model

The physical organization of the genome in three-dimensional space regulates many biological processes, including gene expression and cell differentiation. Three-dimensional characterization of genome structure is critical to understanding these biological processes. Direct experimental measurements of genome structure are challenging; computational models of chromatin structure are therefore necessary. We develop an approach that combines a particle-based chromatin polymer model, molecular simulation, and machine learning to efficiently and accurately estimate chromatin structure fromindirectmeasures of genome structure. More specifically, we introduce a new approach where the interaction parameters of the polymer model are extracted from experimental Hi-C data using a graph neural network (GNN). We train the GNN on simulated data from the underlying polymer model, avoiding the need for large quantities of experimental data. The resulting approach accurately estimates chromatin structures across all chromosomes and across several experimental cell lines despite being trained almost exclusively on simulated data. The proposed approach can be viewed as a general framework for combining physical modeling with machine learning, and it could be extended to integrate additional biological data modalities. Ultimately, we achieve accurate and high-throughput estimations of chromatin structure from Hi-C data, which will be necessary as experimental methodologies, such as single-cell Hi-C, improve.

Biochemistry & Molecular Biology↗

Three-dimensional analysis of microbunched electron cooling

Microbunched electron cooling (MBEC, Ratner, ), a special category of coherent electron cooling, has been under consideration as a candidate method for the strong hadron cooling component of the Electron Ion Collider (EIC) at BNL. Most of the theoretical treatments of this scheme so far have been based on simplified models for the key space charge effect in which electrons and/or hadrons are approximated by charged disks. Although such disk-based models provide a flexible tool that captures a good part of the underlying physics, they lack the fidelity and robustness of a rigorous analysis that explicitly treats the hadron and cooler electron beams as collections of point charges. In this paper, we present such a rigorous, three-dimensional (3D) model, both from a theory-based and a simulation perspective. Specifically, we calculate the generalized wakefield (or Green’s function) of the cooling system—a crucial quantity that determines the overall performance—paying special attention to the dependence of the wake on the hadron transverse positions. Additionally, our treatment takes into account previously neglected 3D effects that can cause damping of the plasma oscillations in the amplification section of the cooler, such as focusing and the angular spread of the electron beam. Published by the American Physical Society 2025

43 PARTICLE ACCELERATORS↗

S U ( 2 ) principal chiral model with tensor renormalization group on a cubic lattice

We study the continuous phase transition and thermodynamic observables in the three-dimensional Euclidean S U ( 2 ) principal chiral field model with the triad tensor renormalization group and the anisotropic tensor renormalization group methods. Using these methods, we find results that are consistent with previous Monte Carlo estimates and the predicted renormalization group scaling of the magnetization close to criticality. These results bring us one step closer to studying finite-density quantum chromodynamics in four dimensions using tensor network methods. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Modeling the evolution of slip localization: Realization of link to material strength

Slip localization formation is the chief mechanism underlying the deformation of almost all metals, from pure elements to high-performance superalloys. The intensity of individual slip localizations is often related to the ultimate strain level for failure but not to the strength of the metal. Here we show that across 15 distinct metals, the intensity of slip in individual slip localizations and slip localization spacings are strongly related to material yield strength. Using a three-dimensional crystal plasticity-based micromechanical model that explicitly simulates the growth of discrete slip localizations, we reveal that the stronger the metal, the faster and earlier slip localizations intensify. The relationship is attributed to the formation of a zone that surrounds the slip localization where the driving force for slip is absent. We find that the zone size is controlled by the strength of the neighboring crystal. Consequently, as strength increases, slip becomes increasingly preferred within the slip localization itself and formation of other slip localizations becomes more likely further away.

36 MATERIALS SCIENCE↗

Effects of Dissolution Regimes on Flow Channelization and Solute Transport in 3D Fracture Networks: Insights From Graph‐Based Reactive Transport Modeling

We investigate how mineral dissolution reshapes flow pathways and solute transport in three‐dimensional discrete fracture networks using a computationally efficient graph‐based reactive transport model. The DFNs are inspired by field‐site observations of fractured carbonate and represent realistic connectivity and structural heterogeneity. Flow is simulated with the Reynolds equation, and dissolution follows first‐order kinetics with diffusive limitations captured through an effective mass‐transfer coefficient. By systematically varying two key dimensionless parameters, the effective Damköhler number (Da), governing reaction versus advection rates, and a transport parameter (Da), analogous to the Thiele modulus, distinct flow channelization regimes emerge: mildly channelized at low G, highly channelized at intermediate Da, and extreme wormhole formation at high Da and low G. Eulerian and Lagrangian analyses, including breakthrough curves, particle tortuosity, dispersivity, and flow channeling indicators quantitatively characterize the progression of dissolution‐driven network restructuring. Across all regimes, initial fracture heterogeneity persists. The results underscore how the interplay between this initial structure, advection, reaction, and diffusion critically shapes subsurface flow pathways, with implications for applications ranging from groundwater remediation to enhanced geothermal systems.

54 ENVIRONMENTAL SCIENCES↗

A mixed formulation of the plane-stress problem to facilitate reuse of constitutive models in finite-element programs

Here, the plane-stress assumption can be challenging to support in a finite element program because it traditionally requires separate implementations of constitutive models than those intended for three-dimensional or two-dimensional plane-strain simulations. As a solution to this issue, this paper presents a method to solve the plane-stress problem using a mixed formulation. In this formulation, the out-of-plane strain is treated as a field variable that is solved for in addition to the standard in-plane displacement variables, in a manner that weakly enforces the condition that the out-of-plane stress is zero. The proposed formulation is non-intrusive, requiring no modifications to the constitutive models in contrast to the conventional plane-stress formulation. The proposed mixed formulation has been benchmarked against analytical solutions and numerical solutions, with good performance and accuracy.

97 MATHEMATICS AND COMPUTING↗