Search NASA⌕ Search

SEARCH · Search NASA

Results for “dynamic sampling”

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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Dynamic Leaching Method for Intact Salt-stone Samples - 18495

At the Savannah River Site (SRS) low activity salt solution is stabilized via encapsulation within a grout termed salt-stone. Salt-stone is emplaced into large (multi-million liter) concrete storage containers referred to as Salt-stone Disposal Units (SDUs). Technetium-99 (Tc-99) and iodine-129 (I-129) are long-lived radionuclides contained in the low activity salt waste and subsequently incorporated into the grout waste form: both radionuclides are contributors to the potential long-term radiation exposure of the public and environment surrounding the SDUs. With respect to Tc-99, in the reducing, high pH environment within the grout, Tc-99 is expected to be relatively immobile since it exists in a reduced Tc(IV) oxidation state in the form of sparingly soluble hydrated oxides (TcO{sub 2}.xH{sub 2}O) or sulfides (TcS{sub x}). However, in the presence of O{sub 2} (associated with the future infiltration of air or oxygenated ground waters into the salt-stone monolith) it is possible for redox-sensitive Tc(IV) to transition into highly soluble (and mobile) Tc(VII) species, such as pertechnetate (TcO{sub 4}{sup -}), which are more readily transported to the surrounding environment. In contrast, I-129 is highly soluble and its leaching behavior is not anticipated to be significantly impacted by potential changes in redox environment or pH within salt-stone. Traditional approaches to quantifying the leaching behavior of Tc-99 and I-29 from cementitious matrices have involved partitioning experiments using size-reduced (crushed/ground) samples, and determination of the radionuclide fraction immobilized by the cementitious solids. Such experiments create artificially high solid-liquid contact areas that likely result in higher Tc-99 and I-129 leachate concentrations than would be expected for intact, monolithic samples. In the current study a new technique, termed the Dynamic Leaching Method (DLM), is being used to initially investigate the Tc-99 leaching behavior from monolithic salt-stone samples; the system will be used at a later date to evaluate the leaching characteristics of I-129. The data derived using this technique is intended to inform the SRS Salt-stone Disposal Facility (SDF) Performance Assessment (PA) which models the long-term transport of radionuclides from the SDUs to the environment. The DLM utilizes a flexible-wall permeameter to achieve saturated leaching under an elevated hydraulic gradient to simulate and accelerate the future transport of groundwater through salt-stone. Leachates are regularly analyzed with respect to radionuclide concentrations, key constituent concentrations (e.g., Al, Ca, Mg, Na, Si, CO{sub 3}{sup 2-}, NO{sub 2}{sup -}, NO{sub 3}{sup -}, SO{sub 4}{sup 2-}), pH, and reduction potential (E{sub h}) in order to develop an understanding of how chemical changes associated with the pore solution influence grout weathering and radionuclide leaching behavior. This paper provides a brief update with respect to data derived from preliminary Tc-99 leaching evaluations as the DLM was being developed, but the paper is predominantly focused on new sample data in which the DLM technique, pre- and post-DLM salt-stone sample characterization, and leachate analysis protocols have been optimized. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors

Optimization of binding affinities for ligands to their target protein is a primary objective in rational drug discovery. Herein, we report on a collaborative study that evaluates various compounds designed to bind to the SET and MYND domain-containing protein 3 (SMYD3). SMYD3 is a histone methyltransferase and plays an important role in transcriptional regulation in cell proliferation, cell cycle, and human carcinogenesis. Experimental measurements using the scintillation proximity assay show that the distributions of binding free energies from a large number of independent measurements exhibit non-normal properties. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to predict the binding free energies and to provide a detailed chemical insight into the nature of ligand-protein binding. Our results show that the 1-trajectory ESMACS protocol works well for the set of ligands studied here. Although one unexplained outlier exists, we obtain excellent statistical ranking across the set of compounds from the ESMACS protocol and good agreement between calculations and experiments for the relative binding free energies from the TIES protocol. ESMACS and TIES are again found to be powerful protocols for the accurate comparison of the binding free energies.

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

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Gas-Dynamic Research Technique of Indirectly Irradiated Targets in Porous Materials at Iskra-5 Fasility

In this paper, studies of gas-dynamic flows in samples of various materials loaded with an X-ray flux in “Illuminator”-type targets on Iskra-5 laser facility of the ILFI VNIIEF are presented. The obtained results on the velocity of shock waves in the sample under the study are compared with model calculations to match the gas-dynamic parameters to their calculated estimates.

42 ENGINEERING↗
DOE OSTI2026

ML-AMD/exa-pd

Exa-pd is a highly parallelizable workflow for constructing multi-element phase diagrams (PDs). It uses standard sampling techniques—molecular dynamics (MD) and Monte Carlo (MC)—as implemented in the LAMMPS package, to simultaneously sample multiple phases on a fine temperature–composition mesh for free-energy calculations. The workflow uses Parsl as a global controller to manage the MD/MC jobs to achieve massive parallelization with almost ideal scalability. The resulting free energies of both liquid and solid phases (including solid solutions) are then fed to CALPHAD modeling using the PYCALPHAD package for the construction of a multi-element PD.

Zhang, Feng [Ames Laboratory (AMES), Ames, IA (Uni↗
DOE OSTI2019

Dynamical mean field theory simulations with the adaptive sampling configuration interaction method

In the pursuit of accurate descriptions of strongly correlated quantum many-body systems, dynamical mean field theory (DMFT) has been an invaluable tool for elucidating the spectral properties and quantum phases of both phenomenological models and ab initio descriptions of real materials. Key to the DMFT process is the self-consistent map of the original system into an Anderson impurity model, the ground state of which is computed using an impurity solver. The power of the method is thus limited by the complexity of the impurity model the solver can handle. Simulating realistic systems generally requires many correlated sites. By adapting the recently proposed adaptive sampling configuration interaction (ASCI) method as an impurity solver, we enable much more efficient zero-temperature DMFT simulations. The key feature of the ASCI method is that it selects only the most relevant Hilbert space degrees of freedom to describe the ground state. This reduces the numerical complexity of the calculation, which will allow us to pursue future DMFT simulations with more correlated impurity sites than in previous works. Here, we present the ASCI-DMFT method and example calculations on the one- and two-dimensional Hubbard models that exemplify its efficient convergence and timing properties. We show that the ASCI approach is several orders of magnitude faster than the current best published ground-state DMFT simulations, which allows us to study the bath discretization error in simulations with small clusters, as well as to address cluster sizes beyond the current state of the art. Finally, our approach can also be adapted for other embedding methods such as density matrix embedding theory and self-energy embedding theory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Nanoscale transient gratings excited and probed by extreme ultraviolet femtosecond pulses

Advances in developing ultrafast coherent sources operating at extreme ultraviolet (EUV) and x-ray wavelengths allow the extension of nonlinear optical techniques to shorter wavelengths. Here, we describe EUV transient grating spectroscopy, in which two crossed femtosecond EUV pulses produce spatially periodic nanoscale excitations in the sample and their dynamics is probed via diffraction of a third time-delayed EUV pulse. The use of radiation with wavelengths down to 13.3 nm allowed us to produce transient gratings with periods as short as 28 nm and observe thermal and coherent phonon dynamics in crystalline silicon and amorphous silicon nitride. This approach allows measurements of thermal transport on the ~10-nm scale, where the two samples show different heat transport regimes, and can be applied to study other phenomena showing nontrivial behaviors at the nanoscale, such as structural relaxations in complex liquids and ultrafast magnetic dynamics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. Furthermore, this study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Reagent-Triggered Isomerization of Fluxional Cluster Catalyst via Dynamic Coupling

Metallic cluster catalysts have many thermodynamically accessible isomers with diverse active sites and low reaction barriers, and lately a strong hypothesis emerged that the many catalyst states collectively drive the catalysis. Furthermore, it remained a hypothesis that catalyst isomerization is actually kinetically feasible under the current reaction conditions. Using high-temperature dynamics simulations and sampling, a range of orientations, and vibrational energy distributions, we probe how thermal effects and molecular events affect cluster catalyst dynamics. We show that even such a delicate affair as the dissociation or scattering of a methane molecule on the heavy and thus slow Pt 13 cluster triggers substantial isomerization of the catalyst, far beyond thermal at 700 K. A kinetic coupling between the methane activity and cluster catalyst dynamics is observed. In return, the thermal dynamics of the cluster affects the methane reaction and scattering probabilities. Hence, molecular events at the surfaces of fluxional cluster catalysts should facilitate the population of an ensemble of catalyst states under the current reaction conditions, with implications for available active sites, reaction mechanisms, and apparent rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run microseconds or longer simulations using femtoseconds time steps. While there are several existing methods to overcome this timescale barrier and efficiently sample thermodynamic and/or kinetic properties, problems remain in regard to being able to sample un- known systems, deal with high-dimensional space of collective variables, and focus the computational effort on slow timescales. Hence, in this work, a new sampling method, called the “Concurrent Adaptive Sampling (CAS) algorithm,” has been developed to tackle these three issues and efficiently obtain conformations and pathways. The method is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective vari- ables and uses macrostates (a partition of the collective variable space) to enhance the sampling. The exploration is done by running a large number of short simula- tions, and a clustering technique is used to accelerate the sampling. In this paper, we introduce the new methodology and show results from two-dimensional models and bio-molecules, such as penta-alanine and triazine polymer

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Elucidating and contrasting the mechanisms for Mg and Ca sulfate ion-pair formation with multi-level embedded quantum mechanics/molecular dynamics simulations

Here, solutions and minerals containing sulfate (SO 4 2- ), and Ca 2+ and Mg 2+ cations, are ubiquitous throughout the lithosphere and are significant components of seawater, thus presenting a prototypical system for the study of strong electrolytes and crystal nucleation mechanisms. However, despite their relative abundance, key questions remain unanswered about the most fundamental atomic-level steps of their mineralization pathways and aqueous dynamics. Here, we carry out enhanced sampling multi-level molecular dynamics (MD) embedded correlated wavefunction theory simulations to elucidate ion-pairing mechanisms for Mg–SO 4 and Ca–SO 4 in concentrated aqueous solution, accurately capturing effects arising from both structural dynamics and electron exchange–correlation. We predict contact-ion-pair formation to be barrierless and highly exoergic for Ca–SO 4 , in agreement with its minimal solubility, whereas for Mg–SO 4 , solvent-shared and contact ion pairs have similar free energies, qualitatively consistent with its higher solubility. Finally, we demonstrate that brief high-temperature pre-equilibration may be utilized to accelerate convergence of free energies in blue-moon-ensemble enhanced-sampling MD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A Wearable Microfluidic Sensing Patch for Dynamic Sweat Secretion Analysis

Wearable sweat sensing is a rapidly rising research area driven by its promising potential in health, fitness, and diagnostic applications. Despite the growth in the field, major challenges in relation to sweat metrics remain to be addressed. These challenges include sweat rate monitoring for its complex relation with sweat compositions and sweat sampling for sweat dynamics studies. Here, we present a flexible microfluidic sweat sensing patch that enhances real-time electrochemical sensing and sweat rate analysis via sweat sampling. The device contains a spiral-patterned microfluidic component that is embedded with ion-selective sensors and an electrical impedance-based sweat rate sensor on a flexible plastic substrate. The patch is enabled to autonomously perform sweat analysis by interfacing the sensing component with a printed circuit board that is capable of on-site signal conditioning, analysis, and transmission. Progressive sweat flow in the microfluidic device, governed by the pressure induced by the secreted sweat, enhances sweat sampling and electrochemical detection via a defined sweat collection chamber and a directed sweat route. The characteristic of the sweat rate sensor is validated through a theoretical simulation, and the precision and accuracy of the flow rate is verified with a commercial syringe pump and a Macroduct sweat collector. On-body simultaneous monitoring of ion (H + , Na + , K + , Cl – ) concentration and sweat rate is also demonstrated for sensor functionality. This sweat sensing patch provides an integrated platform for a comprehensive sweat secretion analysis and facilitates physiological and clinical investigations by closely monitoring interrelated sweat parameters.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

The “Missing” Bicarbonate in CO 2 Chemisorption Reactions on Solid Amine Sorbents

We have identified a hydrated bicarbonate formed by chemisorption of 13 CO 2 on both dimethylaminopropylsilane (DMAPS) and aminopropylsilane (APS) pendant molecules grafted on SBA-15 mesoporous silica. The most commonly used sequence in solid-state NMR, 13 C CPMAS, failed to detect bicarbonate in these solid amine sorbent samples; here, we have employed a Bloch decay (“pulse-acquire”) sequence (with 1 H decoupling) to detect such species. The water that is present contributes to the dynamic motion of the bicarbonate product, thwarting CPMAS but enabling direct 13 C detection by shortening the spin–lattice relaxation time. Since solid-state NMR plays a major role in characterizing chemisorption reactions, these new insights that allow for the routine detection of previously elusive bicarbonate species (which are also challenging to observe in IR spectroscopy) represent an important advance. We note that employing this straightforward NMR technique can reveal the presence of bicarbonate that has often otherwise been overlooked, as demonstrated in APS, that has been thought to only contain adsorbed CO 2 as carbamate and carbamic acid species. As in other systems (e.g., proteins), dynamic species that sample multiple environments tend to broaden as their motion is frozen out. In this paper, we show two distinct bicarbonate species upon freezing, and coupling to different protons is shown through preliminary 13 C– 1 H HETCOR measurements. This work demonstrates that bicarbonates have likely been formed in the presence of water but have gone unobserved by NMR due to the nature of the experiments most routinely employed, a perspective that will transform the way the sorption community will view CO 2 capture by amines.

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

Custom-trained Machine-learning Interatomic Potentials: ZnCl2 Aqueous Solution

This dataset was generated using an iterative active-learning strategy implemented in the ArcaNN software package (https://github.com/arcann-chem/arcann_training) to train machine-learning interatomic potentials for aqueous ZnCl2 solutions. Each active-learning cycle consisted of three stages: training, exploration, and labeling. The initial training set combined configurations generated in this work from enhanced-sampling ab initio molecular dynamics simulations with configurations from a previously reported neural-network-potential study of aqueous ZnCl2. The enhanced-sampling ab initio molecular dynamics simulations involved Zn–Cl separation and the chloride coordination number around Zn²? as collective variables. These configurations served as the seed dataset. Subsequent active-learning cycles expanded the training set by identifying and labeling configurations that were poorly represented by the current models, thereby improving coverage of ion-association states and changes in local coordination and charge-state environments relevant to the solution free-energy landscape. For all selected configurations, single-point calculations of the total energies and atomic forces were performed within density functional theory using the CP2K Quickstep module. Reference calculations employed the revPBE-D3 and r2SCAN exchange-correlation functionals. Motivated by recent work on aqueous Zn²?, the main revPBE calculations omitted D3 dispersion contributions involving Zn²?, while retaining the D3 correction for water and chloride. For comparison, fully dispersion-corrected revPBE-D3 reference calculations were also performed, with D3 applied to all species, including Zn²?. Valence electrons were treated explicitly, while core electrons were represented using norm-conserving Goedecker–Teter–Hutter pseudopotentials. The wave functions were expanded using the mixed Gaussian-and-plane-wave scheme with TZV2P-MOLOPT basis sets for all elements and a 600 Ry auxiliary plane-wave cutoff for the electron density. Self-consistent-field convergence was accelerated using the orbital-transformation and Direct Inversion in the Iterative Subspace algorithms, with a convergence threshold of 10?6. All single-point calculations were performed in periodic orthorhombic cells. The CELL_REF keyword in CP2K was used to define a fixed reference cell with a box length of 25 Å. This treatment ensured a consistent reference for configurations extracted from NpT trajectories with fluctuating cell dimensions. The resulting DFT energies and atomic forces constitute the ground-truth labels used to train the MLIPs. The resulting MLIP was trained for aqueous ZnCl2 solutions spanning concentrations from 0 to 30 molal and a broad pH range, from strongly acidic to strongly basic conditions. Representative examples of configurations included in the MLIP training dataset are provided below. These include 1) Representative configurations from the dataset labeled at the revPBE-D3 level, with D3 dispersion interactions involving Zn2+ excluded (revPBE-wo-D3). 2) Representative configurations from the dataset labeled at the fully dispersion-corrected revPBE-D3 level, with D3 interactions applied to all species, including Zn2+ (revPBE-D3). 3) Representative configurations from the dataset labeled at the r2SCAN level of theory (r2SCAN).

Dinpajooh, Mohammadhasan [Pacific Northwest Nation↗
DOE OSTI2022

Iron corrosion in the “inert” supercritical CO 2 , ab initio dynamics insights: How impurities matter

Metal corrosion from exposure to supercritical fluids is a long-standing challenge lacking atomistic understanding for effective corrosion prevention in diverse important applications. Here, in this work, reactions relevant to corrosion in supercritical CO 2 (sCO 2 ), with H 2 O and NO 2 as impurities, are revealed using ab initio molecular dynamics and enhanced sampling methods. While little reactivity is observed in bulk sCO 2 , the iron surface is found to play a crucial almost-catalytic role in its own corrosion, activating the inert CO2 and hence facilitating $\ast$HCO 3 – and $\ast$CO 3 2– formation at the interface. Moreover, the hydrogen bond network of $\ast$H 2 O assists the H shuttling to the activated CO 2 and impurities, forming reactive species observed in experiments. Such atomistic insight elucidates the reaction mechanisms of metal corrosion in aqueous and supercritical fluids and can point to possible remedies.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Optimizing infrasound observations for sample return capsule re-entry: Insights from OSIRIS-REx and Hayabusa2

The atmospheric entry of meteoroids presents a rare and unpredictable phenomenon, posing challenges for systematic observation and detailed characterization. Such events are nonetheless critical for advancing understanding of acoustic wave propagation, atmospheric structure, and entry dynamics. In contrast, sample return capsules (SRCs) from space missions follow well constrained re-entry trajectories, enabling planned observations of shock wave generation and propagation under controlled conditions. This study compares two SRC atmospheric entries, Hayabusa2 in 2020 and OSIRIS-REx in 2023, to assess how different infrasound array configurations influence shock wave detection and trajectory validation. Hayabusa2’s re-entry was monitored using a distributed network of 28 portable infrasound sensors across seven arrays in Woomera, Australia, permitting three-dimensional reconstruction of the trajectory and analysis of wave characteristics. For OSIRIS-REx, a compact four-sensor array deployed near Eureka Airport provided trajectory confirmation through arrival-time differences and back-azimuth estimates. Spectral and waveform analyses revealed differences in signal properties associated with variations in entry angle and velocity. The results illustrate both the strengths and the limitations of the deployed array configurations. The dense and distributed arrays during Hayabusa2’s re-entry enabled detailed trajectory reconstruction, whereas the compact array at Eureka primarily provided confirmation of signal coherence and back-azimuth consistency. These case studies highlight that even relatively small arrays, if located close to the predicted ground track, can still capture useful information on arrival direction and timing. Such insights provide practical guidance for planning future observational campaigns of SRC returns and other controlled atmospheric entries, and may also inform approaches to opportunistic observations of meteoroid events and other atmospheric acoustic phenomena.

celestial mechanics: orbit determination↗