Search NASA⌕ Search

SEARCH · Search NASA

Results for “Bounded domains”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Dynamical Signatures of Thermotoga maritima Maltose-Binding Proteins Affected by Ligand Binding

Functional segregation among protein isoforms depends on the interplay of their overall structures and the molecular dynamics of these structures. Thermotoga maritima maltose-binding protein (tmMBP) isoforms show size-dependent differential binding of maltose and malto-oligomers while maintaining remarkable fold conservation. This differential behavior needs detailed characterization in native-like aqueous conditions to understand the effects of protein dynamics on ligand binding and recognition. Small-angle neutron scattering (SANS), neutron spin echo (NSE) spectroscopy, and dynamic light scattering (DLS) were used in conjunction with previously published computational molecular dynamics (MD) simulations to understand the dynamic behavior of tmMBPs experimentally. SANS provided information on the overall structure of the molecules, while NSE was used to determine the dynamics in the nanosecond time scale. Both tmMBP2 and tmMBP3 have a bidomain architecture linked with a flexible hinge, with the binding pocket sitting in the cleft between the two domains. tmMBP2 and tmMBP3 showed different solution dynamics, with the translational and rotational components dominating the dynamics of both systems, resulting in a clear differentiation of their diffusion pattern. A faster dynamics component was also observed and was attributed to segmental dynamics. Differences observed between the ligand-free (apo) and ligand-bound (holo) states of the two proteins are attributed to conformational entropy. Our results highlight the intricacies of how structure and dynamics can together shape binding to a repertoire of substrates in structurally similar proteins.

Diffusion↗
DOE OSTI2021

Structural insights into photoactivation of plant Cryptochrome-2

Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Enhanced Planar Antenna Efficiency Through Magnetic Thin-Films

This work proposes to use magnetic material as the substrate of planar antennas to overcome the platform effect caused by the conducting ground plane. The upper bound of the radiation efficiency of an electric-current-driven low-profile antenna is theoretically derived, which is inversely proportional to the Gilbert damping factor of the magnetic material. Meanwhile, the improvement of radiation due to the use of magnetic material is demonstrated by a three-dimensional (3D) multiphysics and multiscale time-domain model. The simulation results match the theoretical derivation, showing 25% radiation efficiency from a planar antenna backed by a FeGaB thin film with 2.56 m thickness. Furthermore, for conductive ferromagnetic materials, it is shown that the eddy current loss can be well suppressed by laminating the thin film into multiple layers. Here, the radiation efficiency of the modeled antenna with a conductive ferromagnetic substrate is improved from 2.2% to 11.8% by dividing the substrate into 10 layers, with a ferromagnetic material fill factor of 93%.

42 ENGINEERING↗
DOE OSTI2025

Fully Homomorphic Encryption

This code implements a Fully Homomorphic Encryption (FHE) system, enabling secure computation on encrypted data without requiring decryption. It supports encryption, decryption, and homomorphic operations like matrix multiplication and addition. This code is adaptable for integrating FHE into linear-time invariant (LTI) systems, including digital control and filtering. With proper configuration from subject matter expertise, encrypted system parameters and signals can be manipulated to perform tasks like state updates, output calculations, and convolution in the encrypted domain. By preserving the structure of LTI systems while ensuring privacy, the framework facilitates secure applications in areas such as autonomous systems, signal processing, and industrial automation. The code initializes the encryption system using parameters provided in the env dictionary. These parameters include the ciphertext modulus, key dimension, plaintext fixed-point scaling factor, and noise bound. During initialization, a secret key is generated, which is essential for encrypting and decrypting data securely. The modular design allows users to tailor these parameters to specific use cases or security requirements. The code implements multiple cryptographic schemes. The learning with errors (LWE) encryption method encodes cleartext message to their plaintext fixed-point representation then encrypted into ciphertext space with additive noise. This noise ensures the security of the scheme, relying on the computational hardness of the LWE problem. The code also includes the Gentry-Sahai-Waters (GSW) scheme based off the LWE problem. Homomorphic matrix multiplication is performed between the LWE and GSW to encrypted data. This is achieved using a decomposition function on the LWE ciphertext during the multiplication operation. For higher-dimensional data, the code includes a method to encrypt entire matrices (GSWMat) using GSW encryption. These encrypted matrices can then be used for homomorphic matrix multiplications (MatMult). The decryption function uses the secret key to recover the original plaintext, removing the added noise and scaling that was originally applied during encryption.

Lois, Roberts [Idaho National Laboratory (INL), Id↗
DOE OSTI2023

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A Review on the State of the Art of Machine Learning and Satellite Imaging: Detecting Scene Changes in Selected Nuclear Fuel Cycle Datasets

The timely detection of clandestine nuclear facilities is one of the greatest challenges faced by the International Atomic Energy Agency’s (IAEA). Idaho National Laboratory is currently applying machine learning (ML) to existing satellite imagery (SI) datasets to find facilities within the nuclear fuel life cycle, with primary focus placed on identifying critical predecessor (i.e., fuel fabrication and fuel enrichment) and successor (i.e., nuclear power plants) facilities. This could provide a satellite image methodology that the IAEA could leverage to discover clandestine facilities. The work presented in this paper describes the evolution of a workflow developed by this team for object detection related to critical infrastructure by expanding that workflow for the purpose of identifying nuclear fuel cycle components and automating dependency assessments. This will be done using two methods housed within a single pipeline. The first method involves implementing a DenseNet161 convolutional neural network to classify the images and explain the results using Local Interpretable Model-Agnostic Explanations (LIME). The second method implements You Only Look Once version 5 (YoloV5), to detect objects within images, provide a probability for the detection, and provide a bounding box that corresponds to the object of interest. The results of this work are anticipated to provide a clear picture of this portion of the nuclear fuel cycle and perform as a stand-alone tool for image assessment that can be expanded to additional fuel cycle components and implemented in international safeguards and national security domains. This capability addresses the IAEA’s need to detect undeclared nuclear materials and activities within a state while encompassing the entire nuclear fuel cycle.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Structural insights into RNA cleavage by a novel family of bacterial RNases

Abstract Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Thermodynamics of Light-Induced Nanoscale Polar Structures in Ferroelectric Superlattices

Here we study the thermodynamics of nanoscale polar structures in PbTiO 3 /SrTiO 3 ferroelectric superlattices induced by above-bandgap optical excitation using a phase-field model explicitly considering both structural and electronic processes. We demonstrate that the light-excited carriers provide the charge compensation of polarization bound charges and the lattice thermal energy, both of which are key to the thermodynamic stabilization of a previously observed supercrystal, a three dimensionally periodic nanostructure, within a window of substrate strains, while different mechanical and electrical boundary conditions can stabilize a number of other nanoscale polar structures by balancing the competing short-range exchange interactions responsible for the domain wall energy and longrange electrostatic and elastic interactions. The insights into the light-induced formation and richness of nanoscale structures from this work offer theoretical guidance for exploring and manipulating the thermodynamic stability of nanoscale polar structures employing a combination of thermal, mechanical, and electrical stimuli as well as light.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Recycling of Pretreated Polyolefin-Based Ocean-Bound Plastic Waste by Incorporating Clay and Rubber

Plastic waste found in oceans has become a major concern because of its impact on marine organisms and human health. There is significant global interest in recycling these materials, but their reclamation, sorting, cleaning, and reprocessing, along with the degradation that occurs in the natural environment, all make it difficult to achieve high quality recycled resins from ocean plastic waste. To mitigate these limitations, various additives including clay and rubber were explored. In this study, we compounded different types of ocean-bound (o-HDPE and o-PP) and virgin polymers (v-LDPE and v-PS) with various additives including a functionalized clay, styrene-multi-block-copolymer (SMB), and ethylene-propylene-based rubber (EPR). Physical observation showed that all blends containing PS were brittle due to the weak interfaces between the polyolefin regions and the PS domains within the polymer blend matrix. Blends containing clay showed rough surfaces and brittleness because of the non-uniform distribution of clay particles in the polymer matrix. To evaluate the properties and compatibility of the blends, characterizations using differential scanning calorimetry (DSC), scanning electron microscopy (SEM), and small-amplitude oscillatory shear (SAOS) rheology were carried out. The polymer blend (v-LDPE, o-HDPE, o-PP) containing EPR showed improved elasticity. Incorporating additives such as rubber could improve the mechanical properties of polymer blends for recycling purposes.

42 ENGINEERING↗
DOE OSTI2024

Nanoscale Ion Transport Enhances Conductivity in Solid Polymer-Ceramic Lithium Electrolytes

The predictive design of flexible and solvent-free polymer electrolytes for solid-state batteries requires an understanding of the fundamental principles governing the ion transport. In this work, we establish a correlation among the composite structures, polymer segmental dynamics, and lithium ion (Li + ) transport in a ceramic-polymer composite. Elucidating this structure–property relationship will allow tailoring of the Li + conductivity by optimizing the macroscopic electrochemical stability of the electrolyte. The ion dissociation from the slow polymer segmental dynamics was found to be enhanced by controlling the morphology and functionality of the polymer/ceramic interface. The chemical structure of the Li + salt in the composite electrolyte was correlated with the size of the ionic cluster domains, the conductivity mechanism, and the electrochemical stability of the electrolyte. Polyethylene oxide (PEO) filled with lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) or lithium bis(fluorosulfonyl) imide (LiFSI) salts was used as a matrix. A garnet electrolyte, aluminum substituted lithium lanthanum zirconium oxide (Al-LLZO) with a planar geometry, was used for the ceramic nanoparticle moieties. Further, the dynamics of the strongly bound and highly mobile Li + were investigated using dielectric relaxation spectroscopy. The incorporation of the Al-LLZO platelets increased the number density of more mobile Li + . The structure of the nanoscale ion-agglomeration was investigated by small-angle X-ray scattering, while molecular dynamics (MD) simulation studies were conducted to obtain the fundamental mechanism of the decorrelation of the Li + in the LiTFSI and LiFSI salts from the long PEO chain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Efficient quantum algorithm for dissipative nonlinear differential equations

Significance Nonlinear differential equations appear in many domains and are notoriously difficult to solve. Whereas previous quantum algorithms for general nonlinear differential equations have complexity exponential in the evolution time, we give the first quantum algorithm for dissipative nonlinear differential equations that is efficient provided the dissipation is sufficiently strong relative to nonlinear and forcing terms and the solution does not decay too rapidly. We also establish a lower bound showing that differential equations with sufficiently weak dissipation have worst-case complexity exponential in time, giving an almost tight classification of the quantum complexity of simulating nonlinear dynamics. Furthermore, numerical results for the Burgers equation suggest that our algorithm may potentially address complex nonlinear phenomena even in regimes with weaker dissipation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes

Complex mechanisms regulate the cellular distribution of cholesterol, a critical component of eukaryote membranes involved in regulation of membrane protein functions directly and through the physiochemical properties of membranes. StarD4, a member of the steroidogenic acute regulator-related lipid-transfer (StART) domain (StARD)-containing protein family, is a highly efficient sterol-specific transfer protein involved in cholesterol homeostasis. Its mechanism of cargo loading and release remains unknown despite recent insights into the key role of phosphatidylinositol phosphates in modulating its interactions with target membranes. We have used large-scale atomistic Molecular dynamics (MD) simulations to study how the dynamics of cholesterol bound to the StarD4 protein can affect interaction with target membranes, and cargo delivery. We identify the two major cholesterol (CHL) binding modes in the hydrophobic pocket of StarD4, one near S136&S147 (the Ser-mode), and another closer to the putative release gate located near W171, R92&Y117 (the Trp-mode). We show that conformational changes of StarD4 associated directly with the transition between these binding modes facilitate the opening of the gate. To understand the dynamics of this connection we apply a machine-learning algorithm for the detection of rare events in MD trajectories (RED), which reveals the structural motifs involved in the opening of a front gate and a back corridor in the StarD4 structure occurring together with the spontaneous transition of CHL from the Ser-mode of binding to the Trp-mode. Further analysis of MD trajectory data with the information-theory based NbIT method reveals the allosteric network connecting the CHL binding site to the functionally important structural components of the gate and corridor. Mutations of residues in the allosteric network are shown to affect the performance of the allosteric connection. These findings outline an allosteric mechanism which prepares the CHL-bound StarD4 to release and deliver the cargo when it is bound to the target membrane.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Identification of Exported Plasmodium falciparum Proteins That Bind to the Erythrocyte Cytoskeleton

Plasmodium proteins are exported to the erythrocyte cytoplasm to create an environment that supports parasite replication. Although hundreds of proteins are predicted to be exported through Plasmodium export element (PEXEL)-dependent and -independent mechanisms, the functions of exported proteins are largely uncharacterized. In this study, we used a biochemical screening approach to identify putative exported P. falciparum proteins that bound to inside-out vesicles prepared from erythrocytes. Out of 69 P. falciparum PEXEL-motif proteins tested, 18 bound to inside-out vesicles (IOVs) in two or more independent assays. Using co-affinity purifications followed by mass spectrometry, pairwise co-purification experiments, and the split-luciferase assay, we identified 31 putative protein–protein interactions between erythrocyte cytoskeletal proteins and predicted exported P. falciparum proteins. We further showed that PF3D7_1401600 binds to the spectrin-binding domain of erythrocyte ankyrin via its MESA erythrocyte cytoskeleton binding (MEC) motif and to the N-terminal domains of ankyrin and 4.1R through a fragment that required an intact Plasmodium helical interspersed sub-telomeric (PHIST) domain. Introduction of PF3D7_1401600 into erythrocyte ghosts increased retention in the microsphiltration assay, consistent with previous data that reported a reduction of rigidity in red blood cells infected with PF3D7_1401600-deficient parasites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Stochastic finite volume method for uncertainty quantification of transient flow in gas pipeline networks

We develop a weakly intrusive framework to simulate the propagation of uncertainty in solutions of generic hyperbolic partial differential equation systems on graph-connected domains with nodal coupling and boundary conditions. The method is based on the Stochastic Finite Volume (SFV) approach and can be applied for uncertainty quantification (UQ) of the dynamical state of fluid flow over actuated transport networks. The numerical scheme has specific advantages for modeling intertemporal uncertainty in time-varying boundary parameters, which cannot be characterized by strict upper and lower (interval) bounds. We describe the scheme for a single pipe, and then formulate the controlled junction Riemann problem (JRP) that enables the extension to general network structures. In conclusion, we demonstrate the method's capabilities and performance characteristics using a standard benchmark test network.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called “lag time”). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5–10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Multi-Objective design of interlocking metasurfaces using conditional diffusion models

Unit cell design remains a major challenge for interlocking metasurfaces, a promising joining technology for dissimilar materials, due to the complex, competing, multivariate design space and the need for rapid adaptation to varying performance requirements. This study explores Conditional Diffusion Models as a design optimization tool for interlocking metasurfaces. Given the complex, competing, multivariate design space for interlocking metasurfaces, unit cell design remains a major challenge for this joining technology. We trained a conditional diffusion model on 25,000 finite element analysis-simulated interlocking metasurface unit cells to generate designs with tailored thermo-mechanical properties (tensile strength, shear strength, and thermal conductivity) based on specified performance criteria. The model demonstrated a success rate of approximately 72 % in producing designs that met specified property bounds. The conditional diffusion model generated both thermally resistive and conductive designs, revealing clear trends in design characteristics: taller, dendritic structures were advantageous for tensile loads, while shorter, robust designs excelled in shear applications. Our findings indicate that the model's performance is more influenced by the breadth of the design space than by the quantity of training data, highlighting the importance of expansive design domains for generating innovative solutions. This work establishes conditional diffusion models as a highly efficient and adaptable tool for rapid interlocking metasurface unit cell design, paving the way for advancements in multi-material joining technologies, as well as highlighting the justification to leverage conditional diffusion models as design tools across complex design domains.

Conditional diffusion models↗
DOE OSTI2020

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface

The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of “undruggability” for an intracellular target. Structural studies reveal extensive protein–WDB002 and protein–protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise “undruggable” targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.

59 BASIC BIOLOGICAL SCIENCES↗