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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 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗
DOE OSTI2020

Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

Herein, we present a novel method to incorporate structural results from surface-sensitive scattering, such as X-ray or neutron reflectometry, into molecular dynamics simulations. While reflectometry techniques generally provide a means to determine the molecular-scale structures of organized interfacial films, they were recently shown to offer the capability to characterize the structures of protein-membrane complexes supported by a solid substrate. One-dimensional information inherent in the experimental results is used in the form of component volume occupancy (CVO) profiles, which describe the distribution of molecular components within an interfacial architecture, to construct real-space constraints in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown in the re-evaluation of an neutron-reflection-derived structure which was approximated by an independent molecular dynamics simulation in earlier work, and it also leads to faster equilibration of ensemble structures. We further show that time averaging the CVO profile that develops in the simulation while biasing with this approach permits fluctuations about the average that are necessary for conformational exploration of the system. This method is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and may take prohibitively long to equilibrate in simulations.

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

The Influence of African Easterly Waves on Atlantic Tropical Cyclone Tracks and Landfall in Large Ensembles

African easterly waves (AEWs) are an important precursor or “seed” for Atlantic tropical cyclones (TCs), with 60%–80% of major hurricanes observed to originate from AEWs. However, climate model simulations indicate that AEWs are not necessary to maintain annual Atlantic TC frequency. Furthermore, small ensembles suggest that AEWs may impact the spatial distribution and landfall of Atlantic TCs. Here, we investigated the influence of AEWs on the spatial distribution of Atlantic TC tracks and landfall using 50-member ensembles of TC-permitting regional model simulations for five hurricane seasons characterized by different levels of TC activity. The control simulations are seasonal hindcasts in which AEWs were prescribed through the eastern lateral boundary condition using reanalysis. In the experiments, we suppressed AEWs by applying a 2–10 day filter to the eastern lateral boundary condition. In response to AEW suppression, we discovered statistically significant increases in Atlantic TC frequency (10%–26%) and landfall (16%–44%), a westward shift in TC genesis location and tracks with increased landfall over the Caribbean Islands, southwestern Gulf Coast, and southeastern US coast, and increases in mid-tropospheric relative humidity in the main development region. In addition, we evaluated TC genesis mechanisms in the absence of AEWs and found evidence that the intertropical convergence zone (ITCZ) intensified and extended northward, resulting in ITCZ wave-breaking that shed vortices which served as TC seeds. By uncovering the connections between TC seed types and the likelihood of TC landfall, this research can provide Atlantic coastal and island communities with useful information to prepare for TC impacts.

African easterly waves↗
DOE OSTI2024

A method for examining ensemble averaging forms during the transition to turbulence in HED systems for application to RANS models

This paper discusses a strategy to initialize a two-dimensional (2D) Reynolds-averaged Navier–Stokes model [LANL's Besnard–Harlow–Rauenzahn (BHR) model] in order to describe an unsteady transitional Richtmyer–Meshkov (RM)-induced flow observed in on-going high-energy-density ensemble experiments performed on the OMEGA-EP facility. The experiments consist of a nominal single-mode perturbation (initial amplitude a 0 ≈ 10 and wavelength $λ$ = 100μm) with target-to-target variations in the surface roughness subjected to the RM instability with delayed Rayleigh–Taylor in a heavy-to-light configuration. Our strategy leverages high-resolution three-dimensional (3D) implicit large eddy simulations (ILES) simulations to initialize BHR-relevant parameters and subsequently validate the 2D BHR results against the 3D ILES simulations. A suite of five 3D ILES simulations corresponding to five experimental target profiles is undertaken to generate an ensemble dataset. Using ensemble averages from the 3D simulations to initialize the turbulent kinetic energy in the BHR model ( K 0 ) demonstrates the ability of the model to predict the time evolution of the interface as well as the density-specific-volume covariance, b . To quantify the sensitivity of the BHR results to the choice of K 0 and the initial turbulent length scale, S 0 , we execute a parameter sweep spanning four orders of magnitude for both S 0 and K 0 , generating a parameter space consisting of 26 simulations. The Pearson's correlation coefficient is used as a measure of discrepancy between the 2D BHR and 3D ILES simulations and reveals that the ranges 8≲S 0 ≲20 μm and 10 9 ≲K 0 ≲10 10 cm 2 /s 2 produce predictions that agree best with the 3D ILES results.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Quantifying the effects of mixing state on aerosol optical properties

Abstract. Calculations of the aerosol direct effect on climate rely on simulated aerosol fields. The model representation of aerosol mixing state potentially introduces large uncertainties into these calculations, since the simulated aerosol optical properties are sensitive to mixing state. In this study, we systematically quantified the impact of aerosol mixing state on aerosol optical properties using an ensemble of 1800 aerosol populations from particle-resolved simulations as a basis for Mie calculations for optical properties. Assuming the aerosol to be internally mixed within prescribed size bins caused overestimations of aerosol absorptivity and underestimations of aerosol scattering. Together, these led to errors in the populations' single scattering albedo of up to −22.3 % with a median of −0.9 %. The mixing state metric χ proved useful in relating errors in the volume absorption coefficient, the volume scattering coefficient and the single scattering albedo to the degree of internally mixing of the aerosol, with larger errors being associated with more external mixtures. At the same time, a range of errors existed for any given value of χ. We attributed this range to the extent to which the internal mixture assumption distorted the particles' black carbon content and the refractive index of the particle coatings. Both can vary for populations with the same value of χ. These results are further evidence of the important yet complicated role of mixing state in calculating aerosol optical properties.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Polariton creation in coupled cavity arrays with spectrally disordered emitters

Abstract Integrated photonics has been a promising platform for analog quantum simulation of condensed matter phenomena in strongly correlated systems. To that end, we explore the implementation of all-photonic quantum simulators in coupled cavity arrays with integrated ensembles of spectrally disordered emitters. Our model is reflective of color center ensembles integrated into photonic crystal cavity arrays. Using the Quantum Master equation and the Effective Hamiltonian approaches, we study energy band formation and wavefunction properties in the open quantum Tavis–Cummings–Hubbard framework. We find conditions for polariton creation and (de)localization under experimentally relevant values of disorder in emitter frequencies, cavity resonance frequencies, and emitter-cavity coupling rates. To quantify these properties, we introduce two metrics, the polaritonic and nodal participation ratios, that characterize the light-matter hybridization and the node delocalization of the wavefunction, respectively. These new metrics combined with the Effective Hamiltonian approach prove to be a powerful toolbox for cavity quantum electrodynamical engineering of solid-state systems.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

A framework for ensemble modelling of climate change impacts on lakes worldwide: the ISIMIP Lake Sector

Abstract. Empirical evidence demonstrates that lakes and reservoirs are warming across the globe. Consequently, there is an increased need to project future changes in lake thermal structure and resulting changes in lake biogeochemistry in order to plan for the likely impacts. Previous studies of the impacts of climate change on lakes have often relied on a single model forced with limited scenario-driven projections of future climate for a relatively small number of lakes. As a result, our understanding of the effects of climate change on lakes is fragmentary, based on scattered studies using different data sources and modelling protocols, and mainly focused on individual lakes or lake regions. This has precluded identification of the main impacts of climate change on lakes at global and regional scales and has likely contributed to the lack of lake water quality considerations in policy-relevant documents, such as the Assessment Reports of the Intergovernmental Panel on Climate Change (IPCC). Here, we describe a simulation protocol developed by the Lake Sector of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) for simulating climate change impacts on lakes using an ensemble of lake models and climate change scenarios for ISIMIP phases 2 and 3. The protocol prescribes lake simulations driven by climate forcing from gridded observations and different Earth system models under various representative greenhouse gas concentration pathways (RCPs), all consistently bias-corrected on a 0.5∘ × 0.5∘ global grid. In ISIMIP phase 2, 11 lake models were forced with these data to project the thermal structure of 62 well-studied lakes where data were available for calibration under historical conditions, and using uncalibrated models for 17 500 lakes defined for all global grid cells containing lakes. In ISIMIP phase 3, this approach was expanded to consider more lakes, more models, and more processes. The ISIMIP Lake Sector is the largest international effort to project future water temperature, thermal structure, and ice phenology of lakes at local and global scales and paves the way for future simulations of the impacts of climate change on water quality and biogeochemistry in lakes.

58 GEOSCIENCES↗
DOE OSTI2023

Bayesian merging of numerical modeling and remote sensing for saltwater intrusion quantification in the Vietnamese Mekong Delta

Saltwater intrusion has become one of the most concerning issues in the Vietnamese Mekong Delta (VMD) due to its increasing impacts on agriculture and food security of Vietnam. Reliable estimation of salinity plays a crucial role to mitigate the impacts of saltwater intrusion. Here, this study developed a hybrid technique that merges satellite imagery with numerical simulations to improve the estimation of salinity in the VMD. The salinity derived from Landsat images and by numerical simulations was fused using the Bayesian inference technique. The results indicate that our technique significantly reduces the uncertainties and improves the accuracy of salinity estimates. The Nash–Sutcliffe coefficient is 0.74, which is much higher than that of numerical simulation (0.63) and Landsat estimation (0.6). The correlation coefficient between the ensemble and measured salinity is relatively high (0.88). The variance of the ensemble salinity errors (5.0 ppt 2 ) is lower than that of Landsat estimation (10.4 ppt 2 ) and numerical simulations (9.6 ppt 2 ). The proposed approach shows a great potential to combine multiple data sources of a variable of interest to improve its accuracy and reliability wherever these data are available.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Scaling Ensembles of Data-Intensive Quantum Chemical Calculations for Millions of Molecules

Deep learning models are efficient computational tools that can accelerate the inverse design of molecules with desired functional properties by generating predictions at a fraction of the time required by traditional quantum chemical approaches. To ensure that a model maintains accuracy and transferability across broad regions of the chemical space explored during the inverse design, it must be trained on massively large volumes of simulation data. This requires running large-scale ensemble quantum chemical calculations on high-performance computing (HPC) systems for data collection. However, the efficient execution of such large ensemble calculations and the management of large volumes of output data require tools that can judiciously utilize computational resources and manage metadata overhead on the file system. Therefore, we present a high-performance, scalable, ensemble management framework for performing data-intensive quantum chemical electronic structure calculations for organic molecules. This framework provides abstractions to plug different ab initio, first principles, and first principles-based semi-empirical methods and executes them efficiently at large scale on HPC systems. It dynamically distributes tasks to resources and uses tiered storage for managing large collections of files. We employed this framework to process over ten million organic molecules and generate open-source datasets that provide UV-vis absorption spectra by running time-dependent density-functional tight-binding calculations. It is the largest database containing molecular optical spectra that were simulated with quantum chemical methods in a consistent manner.

Mehta, Kshitij↗
DOE OSTI2021

Evaluating Variable‐Resolution CESM Over China and Western United States for Use in Water‐Energy Nexus and Impacts Modeling

Abstract Climate models are critical tools to study earth system processes and are often further downscaled to provide refined‐resolution data sets for regional water‐energy impact analyses. In this study, the Variable‐Resolution Community Earth System Model (VR‐CESM), a new dynamical downscaling method, is employed to generate 1/8° simulations for China and the western United States over 1970–2006. Precipitation, temperature, snowpack, radiation, and wind speed are compared with two 1° global climate models, regional climate model ensemble, and reference data sets to evaluate their fidelity. Simulated precipitation skill is dependent upon the reference data sets used, a slight (<+10%) and spatially consistent wet bias in China during summer and the western United States during winter. Precipitation bias in VR‐CESM is the smallest among models and demonstrates the added value provided by resolution refinement. However, temperature biases are generally greater than precipitation due to more complicated interactions among processes. VR‐CESM simulates +2°C warm bias in the low‐elevation regions in China but −2°C cold bias in mountains. However, DJF cold bias (−2.23°C to−3.37°C) and JJA warm bias (+1.13°C to +1.87°C) exist in the western United States. The modeling skills of precipitation and temperature at various topographies are similar in the two evaluated regions. The cold bias was likely affected by downward shortwave radiation deficit (−15%) and slow bias of surface wind speeds (−16% to −29%). Despite the wet and cold bias, snow water equivalent and snow cover are underestimated in mountains. We conclude that VR‐CESM outperforms other models evaluated and provides the best estimation of downscaled climate model data for water‐energy studies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

An uncertainty visualization framework for large-scale cardiovascular flow simulations: A case study on aortic stenosis

We present a generalizable uncertainty quantification (UQ) and visualization framework for lattice Boltzmann method simulations of high Reynolds number vascular flows, demonstrated on a patient-specific stenosed aorta. The framework combines EasyVVUQ for parameter sampling with large-eddy simulation turbulence modeling in HemeLB, and executes ensembles on the Frontier exascale supercomputer. Spatially resolved metrics, including entropy and isosurface-crossing probability, are used to map uncertainty in pressure and wall shear stress fields directly onto vascular geometries. Two sources of model variability are examined: inlet peak velocity and the Smagorinsky constant. Inlet velocity variation produces high uncertainty downstream of the stenosis where turbulence develops, while upstream regions remain stable. Smagorinsky constant variation has little effect on the large-scale pressure field but increases WSS uncertainty in localized high-shear regions. In both cases, the stenotic throat manifests low entropy, indicative of robust identification of elevated WSS. By linking quantitative UQ measures to three-dimensional anatomy, the framework improves interpretability over conventional 1D UQ plots and supports clinically relevant decision-making, with broad applicability to vascular flow problems requiring both accuracy and spatial insight.

Hemodynamics↗
DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Validating first-principles molecular dynamics calculations of oxide/water interfaces with x-ray reflectivity data

Metal oxide/water interfaces play a crucial role in many electrochemical and photocatalytic processes, such as photoelectrochemical water splitting, the creation of fuel from sunlight, and electrochemical CO 2 reduction. First-principles electronic structure calculations can reveal unique insights into these processes, such as the role of the alignment of the oxide electronic energy levels with those of liquid water. An essential prerequisite for the success of such calculations is the ability to predict accurate structural models of these interfaces, which in turn requires careful experimental validation. Here we report a general, quantitative validation protocol for first-principles molecular dynamics simulations of oxide/aqueous interfaces. The approach makes direct comparisons of interfacial x-ray reflectivity (XR) signals from experimental measurements and those obtained from ab initio simulations with semilocal and van der Waals functionals. The protocol is demonstrated here for the case of the Al 2 O 3 (001)/water interface, one of the simplest oxide/water interfaces. We discuss the technical requirements needed for validation, including the choice of the density functional, the simulation cell size, and the optimal choice of the thermodynamic ensemble. Our results establish a general paradigm for the validation of structural models and interactions at solid/water interfaces derived from first-principles simulations. Furthermore, while there is qualitative agreement between the simulated structures and the experimental best-fit structure, direct comparisons of simulated and measured XR intensities show quantitative discrepancies that derive from both bulk regions (i.e., alumina and water) as well as the interfacial region, highlighting the need for accurate density functionals to properly describe interfacial interactions. Our results show that XR data are sensitive not only to the atomic structure (i.e., the atom locations) but also to the electron-density distributions in both the substrate and at the interface.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Future projections and uncertainty assessment of precipitation extremes in the Korean peninsula from the CMIP5 ensemble

Abstract Projections of changes in extreme climate are sometimes predicted by multimodel ensemble methods that combine forecasts from individual simulation models using weighted averaging. One method to assign weight to each model is the Bayesian model averaging (BMA) in which posterior probability is used. For the cases of extreme climate, the generalized extreme value distribution (GEVD) is typically used. We applied the approach of GEV‐embedded BMA to a series of 35 years of the annual maximum daily precipitation data (both historical data and data gathered from simulation experiments for future periods) over the Korean peninsula as simulated by the models in the Coupled Model Intercomparison Project Phase 5 (CMIP5). Simulation data under two Representative Concentration Pathway (RCP) scenarios, namely RCP4.5 and RCP8.5, were used. Observed data and 17 CMIP5 models for 12 gird cells in Korea have been examined to predict future changes in precipitation extremes. A simple regional frequency analysis of pooling observations from three stations in each cell was employed to reduce the estimation variance and local fluctuations. A bias correction technique using the regression‐type transfer function was applied to these simulation data. Return levels spanning over 20 and 50 years, as well as the return periods relative to the reference years (1971–2005), were estimated for two future periods, namely Period 1 (2021–2050) and Period 2 (2066–2095). From these analyses, relative increase observed in the spatially averaged 20‐year (50‐year) return level was approximately 23% (16%) and 45% (36%) in the RCP4.5 and RCP8.5 experiments, respectively, by the end of the 21st century. We concluded that extreme rainfalls will likely occur two times and four times more frequently in the RCP4.5 and RCP8.5 scenarios, respectively, as compared to in the reference years by the end of the 21st century.

Lee, Youngsaeng↗
DOE OSTI2022

Influence of African Easterly Wave Suppression on Atlantic Tropical Cyclone Activity in a Convection-Permitting Model

African easterly waves (AEWs) are strongly linked to Atlantic tropical cyclones (TCs) on the synoptic timescale by serving as seedling disturbances for TC genesis. However, it is unclear whether climatological TC frequency is limited by AEWs. We investigated the impact of suppressing AEWs using a 3-member ensemble of convection-permitting regional model simulations, in which AEWs were either retained or removed through the lateral boundary conditions. Suppressing AEWs did not substantially change seasonal TC number, but did influence TC intensity, genesis time and location. Suppressing AEWs produced stronger TCs, shifted peak TC genesis from September to August, and reduced (increased) TC genesis in the eastern Atlantic (Gulf of Mexico). Without AEWs, TCs generated under more favorable large-scale atmospheric conditions. Furthermore, these results indicate that AEWs may not be reliable predictors of basin-wide seasonal TC frequency. However, simulations provide evidence that AEWs could influence the large-scale environment that is important for TCs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

MISPR : an open-source package for high-throughput multiscale molecular simulations

Computational tools provide a unique opportunity to study and design optimal materials by enhancing our ability to comprehend the connections between their atomistic structure and functional properties. However, designing materials with tailored functionalities is complicated due to the necessity to integrate various computational-chemistry software (not necessarily compatible with one another), the heterogeneous nature of the generated data, and the need to explore vast chemical and parameter spaces. The latter is especially important to avoid bias in scattered data points-based models and derive statistical trends only accessible by systematic datasets. Here, we introduce a robust high-throughput multi-scale computational infrastructure coined MISPR (Materials Informatics for Structure–Property Relationships) that seamlessly integrates classical molecular dynamics (MD) simulations with density functional theory (DFT). By enabling high-performance data analytics and coupling between different methods and scales, MISPR addresses critical challenges arising from the needs of automated workflow management and data provenance recording. The major features of MISPR include automated DFT and MD simulations, error handling, derivation of molecular and ensemble properties, and creation of output databases that organize results from individual calculations to enable reproducibility and transparency. In this work, we describe fully automated DFT workflows implemented in MISPR to compute various properties such as nuclear magnetic resonance chemical shift, binding energy, bond dissociation energy, and redox potential with support for multiple methods such as electron transfer and proton-coupled electron transfer reactions. The infrastructure also enables the characterization of large-scale ensemble properties by providing MD workflows that calculate a wide range of structural and dynamical properties in liquid solutions. MISPR employs the methodologies of materials informatics to facilitate understanding and prediction of phenomenological structure–property relationships, which are crucial to designing novel optimal materials for numerous scientific applications and engineering technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Projected changes in cross-equatorial northerly surges and their hydrological impacts in the near future

Recent decades have witnessed unprecedented extreme precipitation and catastrophic flooding in some of the most populated regions in Southeast Asia during boreal winter. These extreme events are often influenced by the cross-equatorial northerly surge (CENS), characterized by a strengthening of northerly moist monsoon winds south of the equator in the western Maritime Continent. However, the potential future changes in CENS and its hydrological impacts remain underexplored. Here, using an ensemble of high-resolution climate model simulations (CMIP6 HighResMIP), we show that the regional impacts of CENS on the intensity and frequency of extreme precipitation events are projected to significantly increase in the near future (2030–2050), particularly over the adjacent coastal regions of southern Indonesia and northwestern Australia. More specifically, the risk of CENS-related extreme precipitation is projected to increase by up to 39 ± 1.2% relative to the seasonal probability, despite no apparent changes in the CENS characteristics in the near future. Such stronger impact is attributed to the enhanced moistening efficiency and moist static instability due to a more humid and warmer environment, which leads to more intense CENS convection. Our results suggest the need for effective monitoring and disaster managements to respond to the increasing severity of such events in the near future.

Climate sciences↗
DOE OSTI2020

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

59 BASIC BIOLOGICAL SCIENCES↗