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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure and intermolecular organization. Synthetic rings are hybrid objects with conformations that display both ideal random walk and compact globular features, which can serve as models of genomic DNA. To date, emphasis has been placed on the effect of ring molecular weight on their unusual behaviors. Here, we combine simulations and a microscopic force-level theory to build a unified understanding for how key aspects of ring dynamics depend on different tunable molecular properties including backbone rigidity, monomer concentration, degree of traditional entanglement, and molecular weight. Our large-scale molecular dynamics simulations of ring melts with very different backbone stiffnesses reveal unanticipated behaviors which agree well with our generalized theory. This includes a universal master curve for center-of-mass diffusion constants as a function of molecular weight scaled by a chemistry and thermodynamic state-dependent critical molecular weight that generalizes the concept of an entanglement cross-over for linear chains. The key physics is how backbone rigidity and monomer concentration induced changes of the entanglement length, interring packing, degree of interpenetration, and liquid compressibility slow down space-time dynamic-force correlations on macromolecular scales. A power law decay of the center-of-mass diffusion constant with inverse molecular weight squared is the first consequence, followed by an ultraslow activated hopping transport regime. Our results set the stage to address slow dynamics and kinetic arrest in different families of compact synthetic and biological polymeric systems.

Science & Technology - Other Topics↗
DOE OSTI2023

Polarized Resonant X-ray Scattering to Measure Molecular Orientation and Conformation in Organic Nanostructures

The ordering of organic (carbon-based) molecules into nanostructures drives useful materials properties for applications such as organic light emitting diodes, flexible batteries, and polymer nanocarriers. However, there is a current lack of techniques to measure this ordering. X-ray scattering techniques involving molecular resonances have shown promise in identifying molecular types, locations, and orientation. However, resonant soft X-ray scattering (RSoXS) techniques have not been developed even lacking basic optical models. The objectives achieved by this research were the development of methods, models, and analysis techniques that harness these resonant phenomena in X-ray scattering measurements to quantitatively probe ordering of organic molecules within devices and nanostructures. This award resulted in 11 peer reviewed publications with two others soon to be submitted. New physical models for X-ray scattering that accurately describe these complex molecular resonances enable measurements of how molecules assemble, orient and conform at the nanometer scale. These new techniques were applied to both organic electronic devices and aqueous nanoparticles being developed for hydrocarbon sequestration. This new measurement capability will enable characterization of structure-property relationships that lead to disruptive technologies of printable, stretchable, and biocompatible devices based on organic materials.

14 SOLAR ENERGY↗
DOE OSTI2024

Direct numerical simulations of three-component Rayleigh–Taylor mixing and an improved model for multicomponent reacting mixtures

We present direct numerical simulations of a three-layer Rayleigh–Taylor instability (RTI) problem with a configuration based on the experiments of Suchandra & Ranjan ( J. Fluid Mech. , vol. 974, 2023, A35) and Jacobs & Dalziel ( J. Fluid Mech. , vol. 542, 2005, pp. 251–279). The problem consists of a layer of light fluid between two layers of heavy fluid with an Atwood number of 0.3. These simulations are first validated through comparison with available experimental data. The validated simulations are then utilized to analyse statistics in this three-component flow. First, length scales are examined utilizing spectra and two-point spatial correlations of velocity and species concentration fluctuations. Next, joint probability density functions (p.d.f.s) of species concentration are compared against several model p.d.f.s representing generalizations of the bivariate beta distribution. Notably, the joint p.d.f.s do not appear to be accurately described by a Dirichlet distribution, indicating the marginal distributions do not conform to a beta distribution. Finally, similarity of the present configuration to three-component mixing found in inertial confinement fusion (ICF) applications is exploited to develop and validate an improved model for the impact of multicomponent mixing on thermonuclear (TN) reaction rates. A single time instant from the present simulations is chosen for a TN burn calculation under the hypothetical assumption of ICF materials and temperatures. Total TN output from this second calculation is then compared against the prediction of the improved model. The new model is found to accurately predict TN reaction rates in both premixed and non-premixed configurations.

42 ENGINEERING↗
DOE OSTI2020

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

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

Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding

The heterogeneous fast side-chain dynamics of proteins plays crucial roles in molecular recognition and binding. Site-specific NMR experiments quantify these motions by measuring the model-free order parameter (O axis 2 ) on a scale of 0 (most flexible) to 1 (least flexible) for each methyl-containing residue of proteins. In this work, we have examined ligand-induced variations in the fast side-chain dynamics and conformational entropy of calmodulin (CaM) using five different CaM–peptide complexes. O axis 2 of CaM in the ligand-free (O axis,U 2 ) and ligand-bound (O axis,B 2 ) states are calculated from molecular dynamics trajectories and conformational energy surfaces obtained using the adaptive biasing force (ABF) method. ΔO axis 2 = O axis,B 2 – O axis,U 2 follows a Gaussian-like unimodal distribution whose second moment is a potential indicator of the binding affinity of these complexes. The probability for the binding-induced O axis,U 2 → O axis,B 2 transition decreases with increasing magnitude of ΔO axis 2 , indicating that large flexibility changes are improbable for side chains of CaM after ligand binding. A linear correlation established between ΔOaxis2 and the conformational entropy change of the protein makes possible the determination of the conformational entropy of binding of protein–ligand complexes. The results not only underscore the functional importance of fast side-chain fluctuations but also highlight key motional and thermodynamic correlates of protein–ligand binding.

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

Oil Recovery Prediction for Polymer Flood Field Test of Heavy Oil on Alaska North Slope Via Machine Assisted Reservoir Simulation

The first ever polymer flood field pilot to enhance the recovery of heavy oils on the Alaska North Slope is ongoing. This study constructs and calibrates a reservoir simulation model to predict the oil recovery performance of the pilot through machine-assisted reservoir simulation techniques. To replicate the early water breakthrough observed during waterflooding, transmissibility contrasts are introduced into the simulation model, forcing viscous fingering effects. In the ensuing polymer flood, these transmissibility contrasts are reduced to replicate the restoration of injection conformance during polymer flooding, as indicated by a significant decrease in water cut. Later, transmissibility contrasts are reinstated to replicate a water surge event observed in one of the producing wells during polymer flooding. This event may represent decreased injection conformance from fracture overextension; its anticipated occurrence in the other production well is included in the final forecast. The definition of polymer retention in the simulator incorporates the tailing effect reported in laboratory studies; this tailing effect is useful to the simultaneous history match of producing water cut and produced polymer concentration. The top 24 best-matched simulation models produced at each stage of the history matching process are used to forecast oil recovery. The final forecast clearly demonstrates that polymer flooding significantly increases the heavy oil production for this field pilot compared to waterflooding alone. This exercise displays that a simulation model is only valid for prediction if flow behavior in the reservoir remains consistent with that observed during the history matched period. Critically, this means that a simulation model calibrated for waterflooding may not fully capture the benefits of an enhanced oil recovery process such as polymer flooding. Therefore, caution is recommended in using basic waterflood simulation models to scope potential enhanced oil recovery projects.

Keith, Cody Douglas↗
DOE OSTI2022

The spread of technological innovations: effects of psychology, culture and policy interventions

Technological innovations drive the evolution of human societies. The success of innovations depends not only on their actual benefits but also on how potential adopters perceive them and how their beliefs are affected by their social and cultural environment. To deepen our understanding of socio-psychological processes affecting the new technology spread, we model the joint dynamics of three interlinked processes: individual learning and mastering the new technology, changes in individual attitudes towards it, and changes in individual adoption decisions. We assume that the new technology can potentially lead to a higher benefit but achieving it requires learning. We posit that individual decision-making process as well as their attitudes are affected by cognitive dissonance and conformity with peers and an external authority. Individuals vary in different psychological characteristics and in their attitudes. We investigate both transient dynamics and long-term equilibria observed in our model. We show that early adopters are usually individuals who are characterized by low cognitive dissonance and low conformity with peers but are sensitive to the effort of an external authority promoting the innovation. We examine the effectiveness of five different intervention strategies aiming to promote the diffusion of a new technology: training individuals, providing subsidies for early adopters, increasing the visibility of peer actions, simplifying the exchange of opinions between people, and increasing the effort of an external authority. We also discuss the effects of culture on the spread of innovations. Finally, we demonstrate that neglecting the cognitive forces and the dynamic nature of individual attitudes can lead to wrong conclusions about adoption of innovations. Our results can be useful in developing more efficient policies aiming to promote the spread of new technologies in different societies, cultures and countries.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking

A critical step in structure-based drug discovery is predicting whether and how a candidate molecule binds to a model of a therapeutic target. However, substantial protein side chain movements prevent current screening methods, such as docking, from accurately predicting the ligand conformations and require expensive refinements to produce viable candidates. Here, we present the development of a high-throughput and flexible ligand pose refinement workflow, called “tinyIFD”. The main features of the workflow include the use of specialized high-throughput, small-system MD simulation code mdgx.cuda and an actively learning model zoo approach. We show the application of this workflow on a large test set of diverse protein targets, achieving 66% and 76% success rates for finding a crystal-like pose within the top-2 and top-5 poses, respectively. We also applied this workflow to the SARS-CoV-2 main protease (M pro ) inhibitors, where we demonstrate the benefit of the active learning aspect in this workflow.

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

Integrable field theories and their CCFT duals

We compute the Mellin transforms of various two-dimensional integrable S-matrices, providing the first explicit, non-perturbative realizations of celestial CFT. In two dimensions, the Mellin transform is simply the Fourier transform in rapidity space, and the “celestial correlator” has no position dependence. The simplified setting allows us to study the analytic properties of CCFT correlators exactly as a function of the conformal dimensions. We find that the correlators exist as real distributions of the conformal weights, with asymptotics controlled by the mass spectrum and three-point couplings of the model. Coupling these models to a flat space limit of JT gravity preserves integrability and dresses the amplitudes by a rapidly varying gravitational phase. We find that the coupling to gravity smooths out certain singular aspects of the Mellin-transformed correlators.

2D Gravity↗
DOE OSTI2022

Quantifying Equiaxed vs Epitaxial Solidification in Laser Melting of CMSX-4 Single Crystal Superalloy

The competition between epitaxial vs. equiaxed solidification has been investigated in CMSX-4 single crystal superalloy during laser melting as practiced in additive manufacturing. Single-track laser scans were performed on a powder-free surface of directionally solidified CMSX-4 alloy with several combinations of laser power and scanning velocity. Electron backscattered diffraction (EBSD) mapping facilitated identification of new orientations, i.e., “stray grains” that nucleated within the fusion zone along with their area fraction and spatial distribution. Using high-fidelity computational fluid dynamics simulations, both the temperature and fluid velocity fields within the melt pool were estimated. This information was combined with a nucleation model to determine locations where nucleation has the highest probability to occur in melt pools. In conformance with general experience in metals additive manufacturing, the as-solidified microstructure of the laser-melted tracks is dominated by epitaxial grain growth; nevertheless, stray grains were evident in elongated melt pools. It was found that, though a higher laser scanning velocity and lower power are generally helpful in the reduction of stray grains, the combination of a stable keyhole and minimal fluid velocity further mitigates stray grains in laser single tracks.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Distinct Mechanisms and Hydricities of Cp*Ir-Based CO 2 Hydrogenation Catalysts in Basic Water

Transition metal-catalyzed reversible hydrogenation of CO 2 to formate in aqueous solutions under ambient conditions is an attractive environmentally friendly strategy for the storage and transportation of H 2 in a liquid chemical form. Here, mechanistic details for the CO 2 hydrogenation by a series of pentamethylcyclopentadienyl iridium(III) (Cp*Ir) complexes with picolinamidate ligands are investigated through density functional theory and kinetic isotope effects (KIEs) calculations. Additionally, adopting a speciation approach at a pH of 8.2, CO 2 hydrogenation mechanisms of 37 distinct protonation states and conformers of Cp*Ir type complexes are investigated. This imposes a challenging test for the computational modeling in terms of providing a consistent correlation with experimental kinetics and KIE studies of multiple catalysts instead of a single complex. Overall, H 2 heterolysis to generate an iridium hydride intermediate was demonstrated to be the rate determining step, which proceeds via distinct pathways depending on the stereoelectronic properties of the ligand. A peculiar iridium dihydride route was also uncovered, which could be optimized to accelerate the H 2 heterolysis. We have further computed the thermodynamic and kinetic hydricities of 74 complexes with [Cp*Ir(L)(H)] q ( q = -1, 0, 1 depending on the ligand charge by deprotonation or protonation events) general formula. Hydricity values do not show any noticeable correlation with the thermodynamics (Δ G ) of [Cp*Ir(L)(HCO 2 – )] formation but exhibit linear correlation with the kinetics (Δ G ‡ ) of electrophilic CO 2 attack to iridium hydride species, especially when the charges and local structural effects of the metal hydrides are considered. Insights gained in this study on (i) the factors determining the preferred pathway for the rate-limiting H 2 heterolysis step, (ii) the correlation between thermodynamic hydricity and the kinetics of CO 2 insertion to iridium hydride species, and (iii) mechanistic analysis via combination of free energy profiles and KIE studies for a series of iridium catalysts will provide guidelines for the design of next-generation catalysts for the reversible H 2 storage through CO 2 utilization.

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

Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase

Flaviviruses use a ~70 nucleotide stem-loop structure called stem-loop A (SLA) at the 5' end of the RNA genome as a promoter for RNA synthesis. Flaviviral polymerase NS5 specifically recognizes SLA to initiate RNA synthesis and methylate the 5' guanosine cap. We report the crystal structures of dengue (DENV) and Zika virus (ZIKV) SLAs. DENV and ZIKV SLAs differ in the relative orientations of their top stem-loop helices to bottom stems, but both form an intermolecular three-way junction with a neighboring SLA molecule. To understand how NS5 engages SLA, we determined the SLA-binding site on NS5 and modeled the NS5-SLA complex of DENV and ZIKV. Our results show that the gross conformational differences seen in DENV and ZIKV SLAs can be compensated by the differences in the domain arrangements in DENV and ZIKV NS5s. We describe two binding modes of SLA and NS5 and propose an SLA-mediated RNA synthesis mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Inverse design of cellular structures with the targeted nonlinear mechanical response

Advanced additive manufacturing capabilities have enabled a transformational ability to create sophisticated cellular structures using diverse materials. By altering the topology of the unit cell, the mechanical behavior, such as the stress-strain response during compression, can be modulated. Nevertheless, identifying a printable topology within an enormous design space that would precisely deliver the targeted nonlinear material response is challenging. We propose a data-driven generative framework based on a conditional variational autoencoder (cVAE) architecture that can inverse design the cellular structure based on the intended nonlinear stress-strain response. Trained on a dataset of structure-property pairs, the cVAE learns a compact and expressive latent space that enables efficient mapping from targets to feasible geometries. Two inference modes are explored: (1) decoder-only generation, which enables the exploration of diverse designs conditioned solely on the desired mechanical response, and (2) encoder-decoder generation, which further allows for the incorporation of desired topologies, ensuring the generated structure conforms to both mechanical properties and to desired-topology constraints. The results demonstrate that the model can generate structurally plausible and mechanically accurate designs, with the predicted stress-strain curves closely matching the targets. Even under joint conditioning, the model effectively balances geometric fidelity and functional performance.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Uncertainty-driven dynamics for active learning of interatomic potentials

Machine learning (ML) models, if trained to data sets of high-fidelity quantum simulations, produce accurate and efficient interatomic potentials. Active learning (AL) is a powerful tool to iteratively generate diverse data sets. In this approach, the ML model provides an uncertainty estimate along with its prediction for each new atomic configuration. If the uncertainty estimate passes a certain threshold, then the configuration is included in the data set. Here we develop a strategy to more rapidly discover configurations that meaningfully augment the training data set. The approach, uncertainty-driven dynamics for active learning (UDD-AL), modifies the potential energy surface used in molecular dynamics simulations to favor regions of configuration space for which there is large model uncertainty. The performance of UDD-AL is demonstrated for two AL tasks: sampling the conformational space of glycine and sampling the promotion of proton transfer in acetylacetone. The method is shown to efficiently explore the chemically relevant configuration space, which may be inaccessible using regular dynamical sampling at target temperature conditions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A mini-TGA protein modulates gene expression through heterogeneous association with transcription factors

Abstract TGA (TGACG-binding) transcription factors, which bind their target DNA through a conserved basic region leucine zipper (bZIP) domain, are vital regulators of gene expression in salicylic acid (SA)-mediated plant immunity. Here, we investigated the role of StTGA2.1, a potato (Solanum tuberosum) TGA lacking the full bZIP, which we named a mini-TGA. Such truncated proteins have been widely assigned as loss-of-function mutants. We, however, confirmed that StTGA2.1 overexpression compensates for SA-deficiency, indicating a distinct mechanism of action compared with model plant species. To understand the underlying mechanisms, we showed that StTGA2.1 can physically interact with StTGA2.2 and StTGA2.3, while its interaction with DNA was not detected. We investigated the changes in transcriptional regulation due to StTGA2.1 overexpression, identifying direct and indirect target genes. Using in planta transactivation assays, we confirmed that StTGA2.1 interacts with StTGA2.3 to activate StPRX07, a member of class III peroxidases (StPRX), which are known to play role in immune response. Finally, via structural modeling and molecular dynamics simulations, we hypothesized that the compact molecular architecture of StTGA2.1 distorts DNA conformation upon heterodimer binding to enable transcriptional activation. This study demonstrates how protein truncation can lead to distinct functions and that such events should be studied carefully in other protein families.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Variational quantum simulation of the critical Ising model with symmetry averaging

Here we investigate the use of deep multiscale entanglement renormalization ansatz (DMERA) circuits as a variational ansatz. We use the exactly solvable one-dimensional critical transverse-field Ising model as a test bed. Numerically exact simulation of the quantum circuit ansatz can in this case be carried out to hundreds of qubits by exploiting efficient classical algorithms for simulating matchgate circuits. We find that, for this system, the DMERA strongly outperforms a standard quantum approximate optimization algorithm (QAOA)–style ansatz, and that a major source of systematic error in correlation functions approximated using the DMERA is the breaking of the translational and Kramers-Wannier symmetries of the transverse-field Ising model. We are able to reduce this error by up to four orders of magnitude by symmetry averaging, without incurring additional cost in qubits or circuit depth. Here, we propose that this technique for mitigating systematic error could be applied to noisy intermediate-scale quantum (NISQ) simulations of physical systems with other symmetries.

1-dimensional spin chains↗
DOE OSTI2023

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

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

Operation of helium sub-atmospheric multistage cryogenic centrifugal compressor trains: Part 2 – Transient modeling and pump-down path selection

Low-pressure conditions required for operation of helium cryogenic systems below the normal boiling point (i.e. 4.2 K) are established through a transient process, commonly referred to as ‘pump-down’. This process is defined as the transition from pressures above atmospheric conditions to the saturation pressure which corresponds to a specified operational temperature. The FRIB 2 K system consists of five cryogenic centrifugal compressors which are operated in series. Historically, the pump-down process path has been established through empirical methods and system operator experience. Investigation into the pump-down process at FRIB aimed to develop a pump-down methodology which relies on theoretical model predictions rather than empirically developed process paths. Ensuring stable operation during the pump-down process involved application of a centrifugal compressor performance prediction model, which is described in Part 1 of this paper. Compressor performance maps can be directly used to evaluate the stability of a selected pump-down path and anticipate the overall reliability of the selected path. In conjunction with the compressor performance maps, a system pressure model was developed to estimate the transient pressure response during the pump-down process. Lastly, an explicit equation was developed to establish a mass flow rate profile for the pump-down process. Implementation of the presented methodology (including the developed models) allows for the system operator to determine a continuous pump-down path which maintains compressor stability while conforming to overall system capabilities. Altogether, the methodology presented has resulted in simplification of transient pump-down operations and increased the reliability, stability and efficiency of the pump-down process.

Compressor train control↗