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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Supercritical fluids behave as complex networks

Abstract Supercritical fluids play a key role in environmental, geological, and celestial processes, and are of great importance to many scientific and engineering applications. They exhibit strong variations in thermodynamic response functions, which has been hypothesized to stem from the microstructural behavior. However, a direct connection between thermodynamic conditions and the microstructural behavior, as described by molecular clusters, remains an outstanding issue. By utilizing a first-principles-based criterion and self-similarity analysis, we identify energetically localized molecular clusters whose size distribution and connectivity exhibit self-similarity in the extended supercritical phase space. We show that the structural response of these clusters follows a complex network behavior whose dynamics arises from the energetics of isotropic molecular interactions. Furthermore, we demonstrate that a hidden variable network model can accurately describe the structural and dynamical response of supercritical fluids. These results highlight the need for constitutive models and provide a basis to relate the fluid microstructure to thermodynamic response functions.

42 ENGINEERING↗
DOE OSTI2024

Influence of pump laser fluence on ultrafast myoglobin structural dynamics

High-intensity femtosecond pulses from an X-ray free-electron laser enable pump–probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern whether this experimental approach allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions. Here we describe ultrafast pump–probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe–CO bond distance (predicted by recent quantum wavepacket dynamics) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump–probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump–probe experiments such that mechanistically relevant insight emerges.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Unravelling the dynamics of the maturation protein in MS2 bacteriophage via molecular simulations

The MS2 bacteriophage capsid serves as a model system for studying viral structure and function. Mature MS2 virus consists of 178 capsid proteins and a single maturation protein (MP), which is essential for host receptor binding and infection initiation. Despite its critical role, the dynamic behavior of the capsid with the MP remains poorly understood. To address this, we conducted 0.5 µs all-atom molecular dynamics (MD) simulations of the MS2 capsid with and without the MP, revealing key insights into its structural dynamics. Our simulations showed that MP exhibits high flexibility, particularly in the “tip” and “side-loop” regions, which undergo significant motions that likely enhance its ability to engage with the F-pilus receptor. Detailed analysis of MP conformational states revealed that loop rearrangements around H357 enable transient switching between “semi-closed” and “open” conformations, suggesting a conformational selection mechanism for pilus binding. Additionally, ion interaction analyses revealed distinct sodium and chloride binding patterns, where sodium ions were mostly found at the outer capsid shell, while chloride ions interacted with the basic residues on the RNA-facing side. We also found that the presence of the MP enhances salt-bridge interactions, contributing to increased capsid stability, yet it does not significantly alter the pore sizes of pentameric and hexameric units. Together, these findings provide new insights into the functional role of the MP, highlighting its contribution to capsid stability and host receptor engagement. This study offers a foundation for understanding capsid dynamics relevant to viral infectivity and may guide future rational strategies aimed at disrupting host-virus interactions.

Capsid stability↗
DOE OSTI2018

Molecular model of J-aggregated pseudoisocyanine fibers

Aggregated cyanines form ordered supramolecular structures with the potential to transport energy efficiently over long distances, a hallmark of photosynthetic light-harvesting complexes. In concentrated aqueous solution, pseudoisocyanine (PIC) spontaneously forms fibers with a chiral J-band red-shifted 1600 cm -1 from the monomeric 0–0 transition. A cryogenic transmission electron microscopy analysis of these fibers show an average fiber width of 2.89 nm, although the molecular-level structure of the aggregate is currently unknown. To determine a molecular model for these PIC fibers, the calculated spectra and dynamics using a Frenkel exciton model are compared to experiment. A chiral aggregate model in which the PIC monomers are neither parallel nor orthogonal to the long axis of the fiber is shown to replicate the experimental spectra most closely. This model can be physically realized by the sequential binding of PIC dimers and monomers to the ends of the fiber. Furthermore, these insights into the molecular aggregation model for aqueous PIC can also be applied to other similar cyanine-based supramolecular complexes with the potential for long-range energy transport, a key building block for the rational design of novel excitonic systems

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Investigation and validation of the dynamic response of an acoustically levitated particle using the lattice Boltzmann method

The stable levitation of an analyte sample in an acoustic levitator is a primary requirement for accurate x-ray characterization of its scientific structure. A rigid particle oscillates in an under-damped manner when introduced into the node of established standing acoustic waves. This investigation has employed the lattice Boltzmann method (LBM), a computational fluid dynamics technique, for the analysis of such rigid particle dynamics in acoustic levitation. The simulation uses the two dimensional and nine velocity (D2Q9) Bhatnagar-Gross-Krook formulation to levitate a rigid 1.6 mm diameter nylon ($\rho$ = 1150 kg/m 3 ) particle in the air at standard pressure and temperature conditions. The presented work is the first reported simulation of realistic acoustic levitator boundary conditions using the LBM. The simulation can capture the particle-fluid interactions that produce dynamic levitation at less than one-period timescale in the ultrasonic frequency regime. An experiment was conducted by levitating a 1.6mm-diameter nylon sphere to estimate the oscillations, and the oscillating frequency was found to be 50 Hz. The dynamic simulation results are consistent with experimental results for particle oscillations within the same order of magnitude, indicating that LBM formulation can be successfully used to study acoustic levitation to understand and mitigate particle jitter. The distortion of the acoustic field due to a levitating particle's presence was also analyzed to demonstrate how the presence of the particle can disrupt adjacent levitating nodes.

42 ENGINEERING↗
DOE OSTI2018

A molecular model for LINC complex regulation: activation of SUN2 for KASH binding

Linkers of the nucleoskeleton and cytoskeleton are key molecular complexes that span the nuclear envelope (NE) and provide a direct linkage between the nucleoskeleton and cytoskeleton. Two major components of these complexes are members of the SUN and KASH protein families that interact in the perinuclear space to allow the transmission of mechanochemical signals across the NE. Structural details of the mammalian SUN domain protein SUN2 have established that SUN2 must form a trimer to bind to KASH, and that this trimerization is mediated through two predicted coiled-coil regions of the protein, CC1 and CC2, which precede the SUN domain. Recent crystallographic data suggest that CC2-SUN formed an unexpected autoinhibited monomer unable to bind to KASH. These structural insights raise the question of how full-length SUN2 transitions from a monomer to a trimer inside the NE. In this study we used a computational approach to model a fragment of SUN2 containing CC1, CC2, and the SUN domain. We observed the dynamics of these modeled structures using ~1 μs molecular dynamics simulations and showed that the interplay between CC1 and CC2 may be sufficient for the release of CC2-SUN2 from its autoinhibited state. Additionally, using our models and gel filtration analysis, we show the involvement of an E452 residue on CC1 in the monomer–­trimer transition of SUN2. Intriguingly, mutations in this residue have been seen in muscular dystrophy–associated SUN2 variants. Finally, we propose a Ca 2+ -dependent monomer–trimer transition of SUN2.

Cell Biology↗
DOE OSTI2018

Structural and chemical orders in N i 64.5 Z r 35.5 metallic glass by molecular dynamics simulation

The atomic structure of Ni 64.5 Zr 35.5 metallic glass has been investigated by molecular dynamics (MD) simulations. The calculated structure factors from the MD glassy sample at room temperature agree well with the X-ray diffraction (XRD) and neutron diffraction (ND) experimental data. Using the pairwise cluster alignment and clique analysis methods, we show that there are three types dominant short-range order (SRO) motifs around Ni atoms in the glass sample of Ni 64.5 Zr 35.5 , i.e., Mixed- Icosahedron(ICO)-Cube, Twined-Cube and icosahedron-like clusters. Furthermore, chemical order and medium-range order (MRO) analysis show that the Mixed-ICOCube and Twined-Cube clusters exhibit the characteristics of the crystalline B2 phase. In conclusion, our simulation results suggest that the weak glass-forming ability (GFA) of Ni 64.5 Zr 35.5 can be attributed to the competition between the glass forming ICO SRO and the crystalline Mixed-ICO-Cube and Twined-Cube motifs.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Instability analysis of a cylindrical stellar object in Brans–Dicke gravity

This paper investigates instability ranges of a cylindrically symmetric collapsing cosmic filamentary structure in the Brans–Dicke theory of gravity. For this purpose, we use a perturbating approach to the modified field equations as well as dynamic equations and construct a collapse equation. The collapse equation with an adiabatic index (Γ) is used to explore the instability ranges of both isotropic and anisotropic fluid in Newtonian and post-Newtonian approximations. It turns out that the instability ranges depend on the dynamic variables of collapsing filaments. We conclude that the system always remains unstable for 0 < Γ < 1, while Γ > 1 provides instability only in a special case.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Scour Estimation for Tsunami at Bridges

The potential hazard to bridges from a tsunami event may include inundation hazard to the traffic, force effect on the structure, erosion of the foundation caused by hydraulic load on soils or rocks, and erosion of the approach. This study uses a laboratory-validated hybrid numerical scheme that combines Computational Fluid Dynamics (CFD) with sediment transport analysis to provide a practical evaluation method for scour depth at bridge foundations

58 GEOSCIENCES↗
DOE OSTI2014

N2A: a computational tool for modeling from neurons to algorithms

The exponential increase in available neural data has combined with the exponential growth in computing (“Moore’s law”) to create new opportunities to understand neural systems at large scale and high detail. The ability to produce large and sophisticated simulations has introduced unique challenges to neuroscientists. Computational models in neuroscience are increasingly broad efforts, often involving the collaboration of experts in different domains. Furthermore, the size and detail of models have grown to levels for which understanding the implications of variability and assumptions is no longer trivial. Here, we introduce the model design platform N2A which aims to facilitate the design and validation of biologically realistic models. N2A uses a hierarchical representation of neural information to enable the integration of models from different users. N2A streamlines computational validation of a model by natively implementing standard tools in sensitivity analysis and uncertainty quantification. The part-relationship representation allows both network-level analysis and dynamical simulations. We will demonstrate how N2A can be used in a range of examples, including a simple Hodgkin-Huxley cable model, basic parameter sensitivity of an 80/20 network, and the expression of the structural plasticity of a growing dendrite and stem cell proliferation and differentiation.

biologically realistic modeling↗
DOE OSTI2022

High-Temperature Latent Heat Storage System using Transportable Heat Pipes for Versatile Integration with Emerging Microreactors

With the growing interest in the development of micro nuclear reactors and their application to microgrid, high-temperature thermal energy storage (TES) has also been receiving great attention as a technology to reinforce the energy utilization and profitability of this class of reactors. Given the importance and research needs of the TES technology, a research project is underway at Idaho National Laboratory (INL) to develop high-temperature TES that can be easily interfaced with emerging micro nuclear reactors. Currently under development is the Heat pipe-Integrated Thermal Battery (HITB), a novel latent heat storage design that enables flexible and robust integration with any design of currently considered micro nuclear reactors. The development of detailed design based on the proposed TES concept, HITB, requires not only development and validation of modeling and simulation capabilities, but also research that spans thermal performance analysis, component- and system-scale design optimization, and experimental demonstrations including high-temperature feasibility testing. The current research efforts (and plans) are divided into the following four areas: (i) Thermal and structural modeling and analysis at both system- and component-scales for evaluating performance and conducting design optimization, (ii) Small-scale experimental demonstrations for the key components of the proposed HITB design, (iii) Modelica-based dynamic model development for developing a control strategy under dynamic operation within integrated energy systems configuration, (iv) Integrated experimental testing and demonstration. This paper introduces the overall research efforts that have been and are being conducted to develop and demonstrate the novel design of the high-temperature latent heat storage device, HITB. The key design features, ongoing research efforts including the development of modeling and simulation capabilities, small-scale demonstrations of the HITB’s key functionalities prior to scaled-up experimental demonstration, are discussed. Then, this paper concludes with a remark on the future research plans for this project.

25 ENERGY STORAGE↗
DOE OSTI2024

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Safe Physics-Informed Machine Learning for Dynamics and Control

This tutorial paper focuses on safe physics-informed machine learning in the context of dynamics and control, providing a comprehensive overview of how to integrate physical models and safety guarantees. As machine learning techniques enhance the modeling and control of complex dynamical systems, ensuring safety and stability remains a critical challenge, especially in safety-critical applications like autonomous vehicles, robotics, medical decision-making, and energy systems. We explore various approaches for embedding and ensuring safety constraints, including structural priors, Lyapunov and Control Barrier Functions, predictive control, projections, and robust optimization techniques. Additionally, we delve into methods for uncertainty quantification and safety verification, including reachability analysis and neural network verification tools, which help validate that control policies remain within safe operating bounds even in uncertain environments. The paper includes illustrative examples demonstrating the implementation aspects of safe learning frameworks that combine the strengths of data-driven approaches with the rigor of physical principles, offering a path toward the safe control of complex dynamical systems.

Drgona, Jan↗
DOE OSTI2022

Thermal dynamics of P2-Na 0.67 Ni 0.33 Mn 0.67 O 2 cathode materials for sodium ion batteries studied by in situ analysis

Cobalt-free layered Na 0.67 Ni 0.33 Mn 0.67 O 2 is an attractive cathode material for sodium ion batteries. The thermal stability of cathode materials is crucial to their practical applications. In the current work, we investigate structural and morphological evolution in P2-type Na 0.67 Ni 0.33 Mn 0.67 O 2 cathode materials during annealing via in situ synchrotron X-ray diffraction and transmission electron microscopy. Insights are obtained from the two complementary in situ characterizations (at different length scales) in term of the thermal stability of P2-Na 0.67 Ni 0.33 Mn 0.67 O 2 cathode materials. Here, the results indicate that the hexagonal P2 phase remains unchanged during the heat treatment process, and thermally driven expansion/contraction of lattice parameters exhibit an anisotropic character in the a and c directions. In addition, interfaces/grain boundaries play an important role in the structural stability, which leads to the distinct morphological evolution between the polycrystalline and single-crystal particles.

25 ENERGY STORAGE↗
DOE OSTI2020

Machine learning Frenkel Hamiltonian parameters to accelerate simulations of exciton dynamics

In this manuscript, we develop multiple machine learning (ML) models to accelerate a scheme for parameterizing site-based models of exciton dynamics from all-atom configurations of condensed phase sexithiophene systems. This scheme encodes the details of a system’s specific molecular morphology in the correlated distributions of model parameters through the analysis of many single-molecule excited-state electronic-structure calculations. These calculations yield excitation energies for each molecule in the system and the network of pair-wise intermolecular electronic couplings. In this work, we demonstrate that the excitation energies can be accurately predicted using a kernel ridge regression (KRR) model with Coulomb matrix featurization. We present two ML models for predicting intermolecular couplings. The first one utilizes a deep neural network and bi-molecular featurization to predict the coupling directly, which we find to perform poorly. The second one utilizes a KRR model to predict unimolecular transition densities, which can subsequently be analyzed to compute the coupling. We find that the latter approach performs excellently, indicating that an effective, generalizable strategy for predicting simple bimolecular properties is through the indirect application of ML to predict higher-order unimolecular properties. Such an approach necessitates a much smaller feature space and can incorporate the insight of well-established molecular physics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions

Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of $T$ = 4 and $T$ = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3–2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1’, α1’–α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral $T$ = 4 and $T$ = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Identification of key parameters controlling demographically structured vegetation dynamics in a land surface model: CLM4.5(FATES)

Vegetation plays an important role in regulating global carbon cycles and is a key component of the Earth system models (ESMs) that aim to project Earth's future climate. In the last decade, the vegetation component within ESMs has witnessed great progress from simple “big-leaf” approaches to demographically structured approaches, which have a better representation of plant size, canopy structure, and disturbances. These demographically structured vegetation models typically have a large number of input parameters, and sensitivity analysis is needed to quantify the impact of each parameter on the model outputs for a better understanding of model behavior. In this study, we conducted a comprehensive sensitivity analysis to diagnose the Community Land Model coupled to the Functionally Assembled Terrestrial Simulator, or CLM4.5(FATES). Specifically, we quantified the first- and second-order sensitivities of the model parameters to outputs that represent simulated growth and mortality as well as carbon fluxes and stocks for a tropical site with an extent of 1 x 1°. While the photosynthetic capacity parameter (V c,max25 )is found to be important for simulated carbon stocks and fluxes, we also show the importance of carbon storage and allometry parameters, which determine survival and growth strategies within the model. The parameter sensitivity changes with different sizes of trees and climate conditions. The results of this study highlight the importance of understanding the dynamics of the next generation of demographically enabled vegetation models within ESMs to improve model parameterization and structure for better model fidelity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Composite entanglement topology and extensional rheology of symmetric ring-linear polymer blends

Extensive molecular simulations are applied to characterize the equilibrium dynamics, entanglement topology, and nonlinear extensional rheology of symmetric ring-linear polymer blends with systematically varied ring fraction ϕR. Chains with degree of entanglement Z≈14 are mixed to produce 10 well-entangled systems with ϕR varying from neat linear to neat ring melts. Z is large enough that except for very large ϕR, the rings are threaded by multiple linear chains in equilibrium. Primitive path analysis is used to visualize and quantify the structure of the composite ring-linear entanglement network. We measure the quantity of ring-linear threading and linear-linear entanglement as a function of ϕR and identify with simple arguments a ring fraction ϕR≈0.4 where the topological constraints of the composite entanglement network are maximized. These topological analyses are used to rationalize the ϕR-dependence of ring and linear chain dynamics, conformations, and rheology. Simulations of startup uniaxial elongation flows demonstrate the extensional stress overshoot observed in recent filament stretching experiments and characterize how it depends on the blend composition and entanglement topology. The overshoot is driven by an overstretching and recoil of ring polymers due to the convective unthreading of rings from linear chains.

O’Connor, Thomas C.↗