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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 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

No Galaxy Left Behind: Measuring the Transfer Function of the Dark Energy Survey with Balrog

In this dissertation, we describe a calibration and diagnostic framework called Balrog which was used to directly sample the selection and photometric biases of the Dark Energy Survey (DES) Year 3 (Y3) dataset. We systematically inject onto the single-epoch images of a random 20% subset of the DES footprint an ensemble of nearly 30 million realistic galaxy models derived from DES Deep Field observations. These augmented images are analyzed in parallel with the original data to automatically inherit measurement systematics that are often too difficult to capture with traditional generative models. The resulting object catalog is a Monte Carlo sampling of the DES transfer function and is used as a powerful diagnostic and calibration tool for a variety of DES Y3 science, particularly for the calibration of the photometric redshifts of distant "source" galaxies and magnification biases of nearer "lens" galaxies. The recovered Balrog injections are shown to closely match the photometric property distributions of the fiducial Y3 GOLD catalog, particularly in color, and capture the number density fluctuations from observing conditions of the real data within 1% for a typical galaxy sample. We find that Y3 colors are extremely well calibrated, typically within ~1-8 millimagnitudes, but for a small subset of objects we detect significant magnitude biases correlated with large overestimates of the injected object size due to proximity effects and blending. Finally, we discuss approaches to extend the current methodology to capture more aspects of the transfer function for future analyses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

High-Efficiency Modular SiC-based Power-Converter for Flexible-CHP Systems with Stability-Enhanced Grid-Support Functions

This project seeks to develop a modular, scalable MV power converter featuring stability-enhanced grid-support functions for future grid-interface applications in flexible combined heat and power (F-CHP) cogeneration plants, being fully compliant with the IEEE Standard 1547, category B—for operation in local areas with high aggregated distributed energy resource (DER) penetration, and also with the IEEE standard for the specification of microgrid controllers, namely IEEE Std 2030.7, with the goal to enable F-CHP systems for both microgrid and standalone applications. Further, the proposed converter will use a modular circuit topology, the MMC, which is scalable both in voltage and current by interconnecting power-cell building blocks, thus flexibly suiting the needs of F-CHP systems in the 1–20 MWe range. Furthermore, the use of 10 kV SiC MOSFET devices will minimize the number of power-cells needed to operate in 2–13.8 kV MV distribution systems, but more importantly, they will render feasible a power conversion efficiency > 98 %, and a power density > 10 kW/l. This is highly relevant given that these are two key performance metrics that will further increase the value of F-CHP systems by shortening the time required to recover their investment costs.

14 SOLAR ENERGY↗
DOE OSTI2025

The phase diagram of quantum chromodynamics in one dimension on a quantum computer

The quantum chromodynamics (QCD) phase diagram, which reveals the state of strongly interacting matter at different temperatures and densities, is key to answering open questions in physics, ranging from the behaviour of particles in neutron stars to the conditions of the early universe. However, classical simulations of QCD face significant computational barriers, such as the sign problem at finite matter densities. Quantum computing offers a promising solution to overcome these challenges. Here, we take an important step toward exploring the QCD phase diagram with quantum devices by preparing thermal states in one-dimensional non-Abelian gauge theories. We experimentally simulate the thermal states of SU(2) and SU(3) gauge theories at finite densities on a trapped-ion quantum computer using a variational method. This is achieved by introducing two features: Firstly, we add motional ancillae to the existing qubit register to efficiently prepare thermal probability distributions. Secondly, we introduce charge-singlet measurements to enforce colour-neutrality constraints. This work pioneers the quantum simulation of QCD at finite density and temperature for two and three colours, laying the foundation to explore QCD phenomena on quantum platforms.

Quantum information↗
DOE OSTI2024

Excited states in warm and hot dense matter

Accurate modeling of warm and hot dense matter is challenging in part due to the multitude of excited states that must be considered. Here, we present a variational framework that models these excited states. In this framework an excited state is defined by a set of effective one-electron occupation factors, and the corresponding energy is defined by the effective one-body energy with an exchange and correlation term. Here, the variational framework is applied to an atom-in-plasma model (a generalization of the so-called average atom model). Comparisons with a density functional theory based average atom model generally reveal good agreement in the calculated pressure, but our model also gives access to the excitation energies and charge state distributions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2026

Real-space imaging of the electron-pair density hole in molecular Auger–Meitner decay

Electrons in matter can rearrange extremely quickly under external perturbations, underpinning subsequent structural and chemical transformations. Coulomb interactions between neighbouring electrons often shape this response, giving rise to correlated motion and strongly affecting the distribution of electrons in the system. Here we show that non-resonant hard X-ray scattering can directly access changes in the radial electron-pair density during the rapid rearrangement of core and valence electrons. We do this by studying sulfur hexafluoride molecules undergoing Auger–Meitner decay. We exploit a second-order interaction between the X-ray photons and the molecules to trigger and probe the decay dynamics with a single pulse, capturing the electron loss and redistribution before the molecules dissociate. The experiment shows that changes in electron-pair densities can be isolated and measured on ultrafast timescales, providing insight into the real-space evolution of highly excited and short-lived electronic states.

Simmermacher, Mats [University of Oxford (United K↗
DOE OSTI2024

Computing the QRPA level density with the finite amplitude method

Here, we describe a new algorithm to calculate the vibrational nuclear level density of an atomic nucleus. Fictitious perturbation operators that probe the response of the system are generated by drawing their matrix elements from some probability distribution function. We use the Finite Amplitude Method to explicitly compute the response for each such sample. With the help of the Kernel Polynomial Method, we build an estimator of the vibrational level density and provide the upper bound of the relative error in the limit of infinitely many random samples. The new algorithm can give accurate estimates of the vibrational level density. Since it is based on drawing multiple samples of perturbation operators, its computational implementation is naturally parallel and scales like the number of available processing units.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Laser Powder Bed Fusion Manufactured Alloys 625 and 282 and Properties Relevant to Advanced Nuclear Components

Under the Advanced Materials and Manufacturing Technologies program, two Ni-based alloys fabricated by laser powder bed fusion (LPBF) have been evaluated: γ′-strengthened Haynes 282 and solution-strengthened Inconel 625. Large printing defects were observed in the LPBF 282 alloy fabricated using a Renishaw AM250 machine, likely due to particle spattering during printing. Annealing at 1,180°C for 1 h followed by 4 h at 800°C in a high density of 50 nm γ′-strengthening precipitates as well as partial recrystallization resulted in a bimodal grain distribution. Creep testing performed at 750°C revealed lower creep life and ductility for the LPBF 282 compared with wrought 282. X-ray computed tomography combined with optical and scanning electron microscopy microstructural characterization revealed crack formation during creep testing, initiated either from printing defects or from creep cavitation at grain boundaries. Printing defects were the likely reason for the lower creep performance of LPBF 282 and could be suppressed by optimizing the build configuration. Printing 625 on an EOS M290 machine using the recommended EOS parameters resulted in a very low defect density. Superior creep strength at 725°C was observed for the as-printed LPBF 625 along the build direction when compared with wrought 625. No defect larger than ~50 µm could be detected by X-ray computed tomography in the as-printed conditions and after creep testing for 1,000 h at 725°C and 150 MPa. Small, needle-like δ-phase precipitates were observed after creep testing for 100 h at 725°C and 200 MPa. The rapid formation of the γ phase is directly related to the initial Nb and Mo segregation in the LPBF 625 cell walls, and its effect on the alloy’s high-temperature performance will be evaluated. Solution annealing was carried out at 1,150°C for 1 h and led to full recrystallization of the alloy. A decrease in strength and increase in ductility were observed after solution annealing, and the alloy recrystallization resulted in isotropic tensile properties at room temperature, contrary to what was observed for the as-printed LPBF 625.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Velocity-dependent J-factors for annihilation radiation from cosmological simulations

Abstract We determine the dark matter pair-wise relative velocity distribution in a set of Milky Way-like halos in the Auriga and APOSTLE simulations. Focusing on the smooth halo component, the relative velocity distribution is well-described by a Maxwell-Boltzmann distribution over nearly all radii in the halo. We explore the implications for velocity-dependent dark matter annihilation, focusing on four models which scale as different powers of the relative velocity: Sommerfeld, s-wave, p-wave, and d-wave models. We show that the J-factors scale as the moments of the relative velocity distribution, and that the halo-to-halo scatter is largest for d-wave, and smallest for Sommerfeld models. The J-factor is strongly correlated with the dark matter density in the halo, and is very weakly correlated with the velocity dispersion. This implies that if the dark matter density in the Milky Way can be robustly determined, one can accurately predict the dark matter annihilation signal, without the need to identify the dark matter velocity distribution in the Galaxy.

Astronomy & Astrophysics↗
DOE OSTI2023

Distribution of Copper States, Phases, and Defects across the Depth of a Cu-Doped CdTe Solar Cell

Copper has been used as a p-type dopant in cadmium telluride (CdTe) for decades. However, the density of Cu atoms in the finished device is much higher than that of holes, which means that most Cu atoms are not activated as acceptors during incorporation. Furthermore, studies have demonstrated that the distribution of copper (Cu) atoms across the device is highly inhomogeneous, with reports citing Cu substitution on Cd sites and segregation to grain boundaries. Fast diffusion along these boundaries and Cu accumulation at the CdTe/CdS interface have also been observed and validated computationally. These levels of inhomogeneity make it difficult to accurately characterize and correlate the performance with the nature of the Cu atomic species present. To address this challenge, we utilize X-ray microscopy and, specifically, nanoscale fluorescence-mode X-ray absorption near-edge structure to resolve the atomic Cu environment throughout the depth of the CdTe layer. Our results suggest that the majority of Cu atoms are in the form of Cu x Te phases (or similar local environments) near the ZnTe|CdTe interface, Cu x O phases in the CdTe absorber, and present in various oxidation states, including Cu 1+ and Cu 2+ , near the CdS/CdTe junction. Here this work also provides experimental evidence for the first time of the presence of CuS around the ZnTe|CdTe interface and the hypothesized Cu Cd -Cl i complex in the CdTe absorber.

14 SOLAR ENERGY↗
DOE OSTI2022

High Performance SOFCs with a Superior Stability for Reliable and Durable Power Systems

Next generation of fuel cells, electrolyzers, and batteries requires higher power, faster kinetics, and larger energy density, which necessitate the use of compositionally complex oxides to achieve multifunctionalities and activity. These compositionally complex oxides may change their phases and structures during an electrochemical process – a so-called “electrochemically driven phase transformation”. The origin for such a phase change has remained obscure. More importantly, there is a need to develop high performance solid oxide fuel cells with an enhanced stability. In this work, the La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3 (LSCF) cathode surface is modified by infiltration of Pr 6 O 11 and the power density at 0.8V and 750 °C is improved by 21%. In addition, by replacing the traditional barrier layer Gd 0.2 Ce 0.8 O 1.9 with mixed conducting Pr 0.1 Gd 0.1 Ce 0.8 O 1.9 , the power density increases by 38%. The different mechanism of promotions was investigated by electrochemical impedance spectroscopy. The ohmic resistance is dramatically reduced by applying the PGCO interlayer, and the distribution of relaxation time was used to analyze the mechanism for which the polarization resistance was decreased attributing to the mixed conduction nature in PrO x . An increase of power density at 0.8 V of 0.358 W/cm 2 (71%) is achieved with the implementation of both surface modification and buffer layer engineering. An experimental study and a theoretical analysis were then carried out on phase evolution in praseodymium nickelates. Nickelate-based electrodes show up to 60× greater phase transformation during operation when compared to thermally annealed ones. Theoretical analysis suggests that the presence of a reduced oxygen partial pressure at the interface between the oxygen electrode and the electrolyte is the origin for the phase change in an oxygen electrode. Guided by the theory, an addition of the electronic conduction in the interface layer leads to the significant suppression of phase change, while improving cell performance and performance stability. When an oxygen electrode is under polarization, the oxygen partial pressure at the interface between the oxygen electrode and the electrolyte is lower than that of incoming oxidant. Under a high polarization, the environment at the aforementioned interface may lead to phase transformation of the oxygen electrode. The local oxygen partial pressure is determined by the transport properties at the interfaces. An addition of the electronic conduction in the interface layer, for instance using (Pr,Gd)-doped ceria to replace Gd-doped ceria, results in improved cell performance and performance stability, while the phase transformation is significantly suppressed. This work provides a fundamental understanding of the origin for phase transformation in oxygen electrodes during operation and use this knowledge to develop a high-performance electrode that exhibits improved performance stability.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

Crustal Strain Rates in the Western United States and Their Relationship with Earthquake Rates

Abstract We present a suite of strain rate models for the western United States based on geologic and geodetic data. The geologic data consist of Quaternary fault-slip rates and the geodetic data consists of a new compilation of Global Positioning System (GPS) velocities derived from continuous, semicontinuous, and campaign measurements. We remove postseismic deformation from the GPS time series in order for our geodetic strain rate model to best capture the interseismic strain accumulation rate. We present models based on either geologic or geodetic data, but also create a hybrid model. Although there are some differences between the models, the large-scale features are the same, with the noticeable exception for the Pacific Northwest where interseismic strain is naturally more distributed than the long-term strain release. We also present a map of earthquake rate densities based on mainshocks, and the result has similar spatial features similar to the strain rate models (at least in the southwestern United States). We perform a general correlation analysis between strain rate and seismicity rate (south of Cascadia) and find a change in linearity between seismicity and strain rates from slow to faster deforming areas with seismicity rates relatively lower for the latter. The extent of that change depends a bit on assumptions made on the declustering and completeness of the catalog, but the finding of a change in slope is robust across the different strain rate models. Linearity for all areas is only expected when Gutenberg–Richter parameters and parameters involved in the conversion from strain to moment rate are uniform across the study area. We discuss these qualifications, but find no single satisfactory explanation for our observation. Moreover, when considering a rather short time and space, theoretical considerations of sampling from a power-law distribution actually predict there to be a power law instead of a linear relationship, generally consistent with our observation.

Geochemistry & Geophysics↗
DOE OSTI2024

Solvent-mediated carboxylic acid diammonium spacer for synthesizing FA-based 2D Dion–Jacobson perovskites toward efficient solar cells

Two-dimensional (2D) perovskites are promising for photovoltaic applications due to their outstanding optical properties and better environmental stability compared to three-dimensional (3D) perovskites. Unlike 2D Ruddlesden–Popper (RP) perovskites, which use monovalent ammonium spacers, Dion–Jacobson (DJ) perovskites employ divalent organic spacers that enhance structural stability by mitigating weak van der Waals interactions. However, the random phase distribution and disorder crystal orientation in 2D DJ perovskites create deep quantum wells, hindering charge transfer and reducing short-circuit current density (J SC ) and overall photovoltaic performance. This study introduces an organic diammonium, 1,4-butanediamine diacetate (BDAAc 2 ), to replace the traditional halide spacer 1,4-butanediamine iodide (BDADI 2 ). This substitution regulates perovskites crystallization dynamics, reducing compositional disorder and random phase distribution, thus improving the quality of the perovskite films. The robust coordination interactions between BDAAc 2 and the perovskite inorganic framework lead to an ordered [PbX 6 ] 4− arrangement, suppressing the formation of complex intermediate phases and significantly enhancing δ phase crystallinity in the intermediate film. This results in a high yield of high-quality α phase. Consequently, the resulting 2D DJ perovskite solar cells based on BDAFA 3 Pb 4 (I 0.9 Br 0.1 ) 13 achieve a higher power conversion efficiency of 16.41% and an elevated J SC of 20.46 mA cm −2 .

14 SOLAR ENERGY↗
DOE OSTI2021

Nuclear energy density functionals grounded in ab initio calculations

Here, we discuss the construction of a nuclear energy density functional (EDF) from ab initio computations and advocate the need for a methodical approach that is free from ad hoc assumptions. The equations of state (EoSs) of symmetric nuclear and pure neutron matter are computed using the chiral NNLO sat and the phenomenological AV4' + UIX c Hamiltonians as inputs to self-consistent Green's function (SCGF) and auxiliary field diffusion Monte Carlo (AFDMC) methods. We propose a convenient parametrization of the EoS as a function of the Fermi momentum and fit it on the SCGF and AFDMC calculations. We apply the ab initio based EDF to carry out an analysis of the binding energies and charge radii of different nuclei in the local density approximation. The NNLO sat -based EDF produces encouraging results, whereas the AV4' + UIX c -based one is farther from experiment. Possible explanations of these different behaviors are suggested, and the importance of gradient and spin-orbit terms is analyzed. Our paper paves the way for a practical and systematic way to merge ab initio nuclear theory and density functional theory, while shedding light on some critical aspects of this procedure.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Lattice quantum chromodynamics at large isospin density

We present an algorithm to compute correlation functions for systems with the quantum numbers of many identical mesons from lattice quantum chromodynamics (QCD). The algorithm is numerically stable and allows for the computation of n-pion correlation functions for n ϵ {1, … , N} using a single N × N matrix decomposition, improving on previous algorithms. We apply the algorithm to calculations of correlation functions with up to 6144 charged pions using two ensembles of gauge field configurations generated with quark masses corresponding to a pion mass m π = 170 MeV and spacetime volumes of (4.4 3 × 8.8) fm 4 and (5.8 3 × 11.6) fm 4 . We also discuss statistical techniques for the analysis of such systems, in which the correlation functions vary over many orders of magnitude. In particular, we observe that the many-pion correlation functions are well-approximated by log-normal distributions, allowing the extraction of the energies of these systems. Using these energies, the large-isospin-density, zero-baryon-density region of the QCD phase diagram is explored. A peak is observed in the energy density at an isospin chemical potential μ I ~ 1.5m π , signaling the transition into a Bose-Einstein condensed phase. The isentropic speed of sound, c s , in the medium is seen to exceed the ideal-gas (conformal) limit ($c^{2}_{s} ≤ 1/3)$ over a wide range of chemical potential before falling towards the asymptotic expectation at μ I ~ 15m π . These, and other thermodynamic observables, indicate that the isospin chemical potential must be large for the system to be well described by an ideal gas or perturbative QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

End-of-Winter Snow Depth, Temperature, Density and SWE Measurements at Teller Road Site, Seward Peninsula, Alaska, 2016-2018

Measurements of end-of-winter snow properties were collected at the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) for three consecutive years - 2016, 2017, and 2018. This dataset contains one *.pdf user guide and four *.csv data files spatially distributed values of snow depth, snow water equivalent (SWE), temperature at the snow surface and at the bottom of the snowpack, and snow density as a function of depth from top of snowpack. Data was collected toward the end of the winter season, typically in late March or early April, when the snowpack would be near its maximum. In 2016, snow depth measurements were taken using either a thaw probe or avalanche probe. In 2017 and 2018 a Snow-Hydro MagnaProbe http://www.snowhydro.com/products/column2.html was used to improve collection efficiency and enhance spatial coverage. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Thermal management of a high temperature sodium sulphur battery stack

The sodium sulfur battery is an advanced secondary battery with high potential for grid-level storage due to their high energy density, low cost of the reactants, and high open-circuit voltage. However, as the operating temperature of the battery is high (about 300 °C), effective thermal management is required to prevent thermal runaway under high current density operation. Here, to develop efficient thermal management strategies, a detailed, thermo-electrochemical, non-isothermal, distributed dynamic model of a sodium-sulfur battery stack is developed. Models of three thermal management strategies are developed and analyzed in this work: active cooling, passive cooling, and hybrid cooling. The active cooling strategy uses air as the cooling medium whereas, the passive cooling strategy uses a phase change material. In the hybrid cooling strategy, both active and passive cooling strategies are used. Due to the high operating temperature of the sodium sulfur batteries, the rejected heat can be utilized effectively and consequently a high variability in the heat rejection rate may not be acceptable. Performance of these strategies is analyzed under high current density operation by evaluating the variability in the cell temperature during charge/discharge cycles, temperature difference between the cells based on their locations, and variability in the heat rejection rate. The phase change-based hybrid thermal management strategy with an embedded controller maintained the temperature variation within ±/- 2.8 °C. Considering the tradeoff between the capital cost for PCM, fan power requirement, and variability in the heat rejection rate, the optimal quantity of the PCM and the maximum air velocity for the maximum current density of 260 mA/cm 2 (0.55 C-rate) were found be 0.74 g/Wh and 3 m/s, respectively.

25 ENERGY STORAGE↗
DOE OSTI2021

Developing Accelerated Test Protocols and Tuning Microstructures of the Common Materials to Improve Robustness, Reliability, and Endurance of SOFC Cells

This work is built on our prior work where we found that phase transformation in praseodymium nickelates, e.g. Pr 2 NiO 4 (PNO) and (Pr 1-x Nd x ) 2 NiO 4 (PNNO), can be electrochemically driven, and is substantially faster when compared to thermal annealing studies. The first task aims at an attempt to further accelerate the phase transformation in the oxygen electrode by alternating the current input in the cells, which lead to the development of accelerated test protocols (ATPs). ATPs showed up to 60x faster phase transformation and up to 10x faster performance degradation in (Pr 0.50 Nd 0.50 ) 2 NiO 4 electrodes, when compared to long-term operation under constant current density. Furthermore, the phase stable Nd 2 NiO 4 and (La 0.6 Sr 0.4 )(Co 0.8 Fe 0.2 )O 3 (LSCF6482) electrodes were tested in full cells under ATPs, and showed up to 10x faster performance degradation within 1,100 hours in a comparison with long-term thermal annealing studies and electrochemical operation under constant current density. The second task aims at the quantification of the contributions of cell components to the total impedance of a solid oxide fuel cell (SOFC) using electrochemical impedance spectroscopy (EIS) and distribution of relaxation times (DRT). Specifically, the role of gas composition at both anode and cathode was systematically studied, aiming at deconvoluting, identifying and quantifying the contributions of different electrode processes. This was achieved by first tuning the partial pressure of H 2 at the anode and subsequently varying the partial pressure of O 2 at the cathode. The results suggest that, while DRT offers a viable way of deconvoluting different times distributions, additional attention is needed before assigning a peak to a specific electrode process due to the significant overlap of the contributions from the cathode and the anode. Density function theory studies show that both Pr-vacancies and O-defects play a key role on the activity and stability for nickelates towards oxygen reduction reaction. The resident O-interstitials and oxygen ions in the PrO layer form peroxide (O 2 2- ) nearby Pr vacancies. The O 2 2- limits oxygen-ion transport due to the required additional energy to break its O-O bond. We further calculated the formation and segregation energies for different Ln ions (La, Pr, Nd, Pm, Sm, Gd, Tb, Dy, and Ho) in PNO and CeO 2 (111) surfaces. In addition to Nd, Pm and La are suggested as potential dopants in PNO to enhance it stability without decomposition due to their more negative formation energies, lower diffusion energies, and positive separation energies.

01 COAL, LIGNITE, AND PEAT↗
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↗