Search NASA⌕ Search

SEARCH · Search NASA

Results for “Enhanced 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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗
DOE OSTI2026

Ab Initio Bulk Free Energy Surface of Proper Ferroelectrics

We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core of our approach is the metadynamics algorithm that extracts the polarization dependence of the FES from all-atom molecular dynamics simulations without an a priori ansatz. The rest of the FES is derived from the metadynamics trajectories that span the relevant phase space. We demonstrate our approach in the case of lead titanate. The errors across the phase transition, due to DFT numerics, all-atom molecular dynamics, and free energy evaluation by enhanced sampling, can be systematically controlled and are of the order of 1 meV/atom. The accuracy of the resulting ab initio FES is only limited by the adopted functional approximation of DFT.

Xie, Pinchen [Lawrence Berkeley National Laborator↗
DOE OSTI2026

From diamond to BC8 to simple cubic and back: Kinetic pathways to post-diamond carbon phases from metadynamics

Understanding the kinetic pathways connecting carbon polymorphs at multimegabar pressures remains a major unsolved problem in high-pressure physics. Here, we provide insights into the long-standing question of BC8 formation and stability by combining a state-of-the-art SNAP machine-learning interatomic potential with enhanced sampling via metadynamics, enabling direct access to transition mechanisms far beyond the reach of standard molecular dynamics. Our simulations show that carbon phase transformations are intrinsically complex, proceeding through multiple intermediate disordered and crystalline states governed by nontrivial kinetic ordering. We determine the upper pressure limit for BC8 formation and reveal that hexagonal diamond transforms to BC8 faster than cubic diamond—an unexpected and experimentally testable prediction. We also identify a 𝑃⁢222 carbon phase that becomes competitive with diamond and simple cubic above 1.8 TPa, and we demonstrate that BC8 may be quenched to ambient conditions at moderate temperatures. Altogether, these results establish a general and transferable framework for resolving kinetic pathways in solid-solid phase transitions and provide physical insights into carbon's complex high-pressure landscape.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Systematic modification of functionality in disordered elastic networks through free energy surface tailoring

A combined machine learning–physics–based approach is explored for molecular and materials engineering. Specifically, collective variables, akin to those used in enhanced sampled simulations, are constructed using a machine learning model trained on data gathered from a single system. Through the constructed collective variables, it becomes possible to identify critical molecular interactions in the considered system, the modulation of which enables a systematic tailoring of the system’s free energy landscape. To explore the efficacy of the proposed approach, we use it to engineer allosteric regulation and uniaxial strain fluctuations in a complex disordered elastic network. Its successful application in these two cases provides insights regarding how functionality is governed in systems characterized by extensive connectivity and points to its potential for design of complex molecular systems.

42 ENGINEERING↗
DOE OSTI2024

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

AL-ASMR: Active Learning of Atomistic Surrogate Models for Rare Events

Atomistic simulation with artificial intelligence (AI) is an emerging tool for understanding materials' properties and behaviors and predicting novel materials with optimized/targeted properties. Neural network potentials (NNPs) are outstanding in this field as they have shown a comparable accuracy to ab initio electronic structure calculations for reproducing potential energy surfaces while being several orders of magnitude faster. However, such NNPs can perform poorly outside of their training domain and typically fail catastrophically in the prediction of rare events in molecular dynamics (MD) simulations. For effective AL loops to distinguish the informative data from enhanced sampled configurations, we developed a decision engine by configurational similarity and uncertainty quantification (UQ) with data augmentation.

Jung, Gang Seob↗
DOE OSTI2025

Reticular Materials and AI-Driven Computer Simulations for Seawater Mining of Valuable Metals (Final Technical Report)

This Final Technical Report describes our exploratory efforts that combine reticular materials synthesis (hydrolytically robust metal–organic frameworks, MOFs) with AI‑enabled molecular simulations to develop mechanistic, quantitative design rules for recovering lithium and other alkali-metal ions from highly dilute, competitive aqueous resources (e.g., seawater). The central outcome is a joint experimental–computational study of ion uptake in MOF‑808 (Chemical Science, 2025) that quantifies both thermodynamics and kinetics of Li + , Na + , and K + uptake and identifies how pore size, pore hydration state, dehydration penalties, and pore-window transport barriers govern selectivity. Guided by these insights, we synthesized and tested functionalized MOF‑808 and multivariate MOFs incorporating ion-recognition motifs (including carboxylates and crown-ether linkers) and evaluated uptake in synthetic seawater, highlighting framework topology and pore chemistry as levers for improved Li + /Na + discrimination. We also developed transferable simulation models, enhanced-sampling protocols, and automated workflows that enable systematic screening of porous sorbents.

42 ENGINEERING↗
DOE OSTI2021

Pathways and Mechanism of Caffeine Binding to Human Adenosine A 2A Receptor

Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the pathways and mechanism of CFF binding to the target receptors remain unclear. In this study, we have performed all-atom-enhanced sampling simulations using a robust Gaussian-accelerated molecular dynamics (GaMD) method to elucidate the binding mechanism of CFF to human adenosine A 2A receptor (A 2A AR). Multiple 500–1,000 ns GaMD simulations captured both binding and dissociation of CFF in the A 2A AR. The GaMD-predicted binding poses of CFF were highly consistent with the x-ray crystal conformations with a characteristic hydrogen bond formed between CFF and residue N6.55 in the receptor. In addition, a low-energy intermediate binding conformation was revealed for CFF at the receptor extracellular mouth between ECL2 and TM1. While the ligand-binding pathways of the A 2A AR were found similar to those of other class A GPCRs identified from previous studies, the ECL2 with high sequence divergence serves as an attractive target site for designing allosteric modulators as selective drugs of the A 2A AR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Quiescent Galaxy Size, Velocity Dispersion, and Dynamical Mass Evolution

Abstract We use surveys covering the redshift range 0.05 < z < 3.8 to explore quiescent galaxy scaling relations and the redshift evolution of the velocity dispersion, size, and dynamical mass at fixed stellar mass. For redshift z < 0.6, we derive mass-limited samples and demonstrate that these large samples enhance constraints on the evolution of the quiescent population. The constraints include 2985 new velocity dispersions from the SHELS F2 survey. In contrast with the known substantial evolution of size with redshift, evolution in the velocity dispersion is negligible. The dynamical-to-stellar-mass ratio increases significantly as the universe ages, in agreement with recent results that combine high-redshift data with the Sloan Digital Sky Survey. Like other investigators, we interpret this result as an indication that the dark matter fraction within the effective radius increases as a result of the impact of the minor mergers that are responsible for size growth. We emphasize that dense redshift surveys covering the range 0.07 < z < 1 along with strong and weak lensing measurements could remove many ambiguities in evolutionary studies of the quiescent population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases are not available. L1, a class B3 enzyme expressed by Stenotrophomonas maltophilia , is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics simulations were performed, Markov State Models were built, and convolutional variational autoencoder-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, and R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changes of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Combined Machine Learning and High-Energy X-ray Diffraction Approach to Understanding Liquid and Amorphous Metal Oxides

Determining the structure-property relations of liquid and amorphous metal oxides is challenging, due to their variable short-range order and polyhedral connectivity. To predict chemically realistic structures, we have developed a Machine Learned, Gaussian Approximation Potential (GAP) for HfO 2 , with a focus on enhanced sampling of the training database and accurate density functional theory calculations. By using training datasets for the GAP model at the level of Density Functional Theory-Strongly Constrained and Appropriately Normed (DFT-SCAN) level of theory, our results show that the topology of both the low viscosity liquid and the amorphous form are dominated by edge-shared chains and small corner-shared rings of polyhedra. This topology is shown to be consistent with the structure of other liquid and amorphous transition metal oxides of variable ion size, such as TiO 2 and ZrO 2 . Current limitations of the ML-GAP modeling method for obtaining glass structures and future perspectives are also discussed.

36 MATERIALS SCIENCE↗
NASA NTRS1990

Drop evaporation in a single-axis acoustic levitator

A 20 kHz single-axis acoustic positioner is used to levitate aqueous-solution drops (volumes less than or approximately equal to 100 micro-liters). Drop evaporation rates are measured under ambient, isothermal conditions for different relative humidities. Acoustic convection around the levitated sample enhances the mass loss over that due to natural convection and diffusion. A theoretical treatment of the mass flow is developed in analogy to previous studies of the heat transfer from a sphere in an acoustic field. Predictions of the enhanced mass loss, in the form of Nusselt (Sherwood) numbers, are compared with observed rages of drop shrinking. The work is part of an ESA crystal growth from levitated solution drops.

Lierke, E. G.↗
NASA NTRS1998

Evaluation of the 29-km Eta Model: Objective Verification at Three Selected Stations - Part 1

This paper describes an objective verification of the National Centers for Environmental Prediction (NCEP) 29-km eta model from May 1996 through January 1998. The evaluation was designed to assess the model's surface and upper-air point forecast accuracy at three selected locations during separate warm (May - August) and cool (October - January) season periods. In order to enhance sample sizes available for statistical calculations, the objective verification includes two consecutive warm and cool season periods. Systematic model deficiencies comprise the larger portion of the total error in most of the surface forecast variables that were evaluated. The error characteristics for both surface and upper-air forecasts vary widely by parameter, season, and station location. At upper levels, a few characteristic biases are identified. Overall however, the upper-level errors are more nonsystematic in nature and could be explained partly by observational measurement uncertainty. With a few exceptions, the upper-air results also indicate that 24-h model error growth is not statistically significant. In February and August 1997, NCEP implemented upgrades to the eta model's physical parameterizations that were designed to change some of the model's error characteristics near the surface. The results shown in this paper indicate that these upgrades led to identifiable and statistically significant changes in forecast accuracy for selected surface parameters. While some of the changes were expected, others were not consistent with the intent of the model updates and further emphasize the need for ongoing sensitivity studies and localized statistical verification efforts. Objective verification of point forecasts is a stringent measure of model performance, but when used alone, is not enough to quantify the overall value that model guidance may add to the forecast process. Therefore, results from a subjective verification of the meso-eta model over the Florida peninsula are discussed in the companion paper by Manobianco and Nutter. Overall verification results presented here and in part two should establish a reasonable benchmark from which model users and developers may pursue the ongoing eta model verification strategies in the future.

Nutter, Paul A.↗
NASA NTRS2019

Emissions Relationships in Western Forest Fire Plumes: I. Reducing the Effect of Mixing Errors on Emission Factors

Studies of emission factors from biomass burning using aircraft data complement the results of lab studies and extend them to conditions of immense hot conflagrations. We illustrate and discuss emission relationships for 422 individual samples from many forest-fire plumes in the Western US. The samples are from two NASA investigations: ARCTAS (Arctic Research of the Composition of the Troposphere from Aircraft and Satellites) and SEAC4RS (Studies of Emissions and Atmospheric Composition, Clouds, and Climate Coupling by Regional Surveys). This work provides sample-by-sample enhancement ratios (EnRs) for 23 gases and particulate properties. Many EnRs provide candidates for emission ratios (ERs, corresponding to the EnR at the source) when the origin and degree of transformation is understood and appropriate. From these, emission factors (EFs) can be estimated when the fuel dry mass consumed is known or can be estimated using the carbon mass budget approach. This analysis requires understanding the interplay of mixing of the plume with surrounding air. Some initial examples emphasize that measured C(tot) = CO2 + CO in a fire plume does not necessarily describe the emissions of the total carbon liberated in the flames, C(burn). Rather, it represents C(tot) = C(burn) + C(bkgd), which includes possibly varying background concentrations for entrained air. Consequently, we present a simple theoretical description for plume entrainment for multiple tracers from flame to hundreds of kilometers downwind and illustrate some intrinsic linear behaviors. The analysis suggests a Mixed Effects Regression Emission Technique (MERET), which can eliminate occasional strong biases associated with the commonly used normalized excess mixing ratio (NEMR) method. MERET splits C(tot) to reveal C(burn) by exploiting the fact that C(burn) and all tracers respond linearly to dilution, while each tracer has consistent EnR behavior (slope of tracer concentration with respect to C(burn)). The two effects are separable. Two or three or preferably more emission indicators are required as a minimum; here we used ten. Limited variations in the EnRs for each tracer can be incorporated and the variations and co-variations analyzed. The percentage CO yield (or the modified combustion efficiency) plays some role. Other co-relationships involving nitrogen and organic classes are more prominent; these have strong relationships to the C(burn) to O3 emission relationship. In summary, MERET allows fine spatial resolution (EnRs for individual observations) and comparison of similar plumes distant in time and space. Alkene ratios provide us with an approximate photochemical timescale. This allows discrimination and definition, by fire situation, of ERs, allowing us to estimate emission factors.

Chatfield, Robert B.↗
DOE OSTI2022

Dispersion-enhanced sequential batch sampling for adaptive contour estimation

In computer simulation and optimal design, sequential batch sampling offers an appealing way to iteratively stipulate optimal sampling points based upon existing selections and efficiently construct surrogate modeling. Nonetheless, the issue of near duplicates poses tremendous quandary for sequential learning. It refers to the situation that selected critical points cluster together in each sampling batch, which are individually but not collectively informative towards the optimal design. Near duplicates severely diminish the computational efficiency as they barely contribute extra information towards update of the surrogate. To address this issue, we impose a dispersion criterion on concurrent selection of sampling points, which essentially forces a sparse distribution of critical points in each batch, and demonstrate the effectiveness of this approach in adaptive contour estimation. Specifically, we adopt Gaussian process surrogate to emulate the simulator, acquire variance reduction of the critical region from new sampling points as a dispersion criterion, and combine it with the modified expected improvement (EI) function for critical batch selection. The critical region here is the proximity of the contour of interest. This proposed approach is vindicated in numerical examples of a two-dimensional four-branch function, a four-dimensional function with a disjoint contour of interest and a time-delay dynamic system.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1988

Observation of enhanced properties in samples of silver oxide doped YBa2Cu3O(x)

Samples of YBa2Cu3O(x) doped with silver oxide (Tc is about 93 K) have exhibited attractive forces in gradient magnetic fields, both normal and tangential to the surfaces, which are more than twice the sample weight. This allows sample suspension below a rare earth magnet. Critical current density was increased by about 100 at 77 K. Persistent fields, flux pinning, magnetization, and modeling are described.

Peters, P. N.↗
NASA NTRS2013

The Intercalibration of Geostationary Visible Imagers Using Operational Hyperspectral SCIAMACHY Radiances

Spectral band differences between sensors can complicate the process of intercalibration of a visible sensor against a reference sensor. This can be best addressed by using a hyperspectral reference sensor whenever possible because they can be used to accurately mitigate the band differences. This paper demonstrates the feasibility of using operational Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY) large-footprint hyperspectral radiances to calibrate geostationary Earth-observing (GEO) sensors. Near simultaneous nadir overpass measurements were used to compare the temporal calibration of SCIAMACHY with Aqua Moderate Resolution Imaging Spectroradiometer band radiances, which were found to be consistent to within 0.44% over seven years. An operational SCIAMACHY/GEO ray-matching technique was presented, along with enhancements to improve radiance pair sampling. These enhancements did not bias the underlying intercalibration and provided enough sampling to allow up to monthly monitoring of the GEO sensor degradation. The results of the SCIAMACHY/GEO intercalibration were compared with other operational four-year Meteosat-9 0.65-μm calibration coefficients and were found to be within 1% of the gain, and more importantly, it had one of the lowest temporal standard errors of all the methods. This is more than likely that the GEO spectral response function could be directly applied to the SCIAMACHY radiances, whereas the other operational methods inferred a spectral correction factor. This method allows the validation of the spectral corrections required by other methods.

Doelling, David R.↗