Search NASA⌕ Search

SEARCH · Search NASA

Results for “density”

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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A representation-independent electronic charge density database for crystalline materials

Abstract In addition to being the core quantity in density-functional theory, the charge density can be used in many tertiary analyses in materials sciences from bonding to assigning charge to specific atoms. The charge density is data-rich since it contains information about all the electrons in the system. With the increasing prevalence of machine-learning tools in materials sciences, a data-rich object like the charge density can be utilized in a wide range of applications. The database presented here provides a modern and user-friendly interface for a large and continuously updated collection of charge densities as part of the Materials Project. In addition to the charge density data, we provide the theory and code for changing the representation of the charge density which should enable more advanced machine-learning studies for the broader community.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Computational studies on scattering of radio frequency waves by density filaments in fusion plasmas

In modern magnetic fusion devices, such as tokamaks and stellarators, radio frequency (RF) waves are commonly used for plasma heating and current profile control, as well as for certain diagnostics. The frequencies of the RF waves range from ion cyclotron frequency to the electron cyclotron frequency. The RF waves are launched from structures, like waveguides and current straps, placed near the wall in a very low density, tenuous plasma region of a fusion device. The RF electromagnetic fields have to propagate through this scrape-off layer before coupling power to the core of the plasma. The scrape-off layer is characterized by turbulent plasmas fluctuations and by blobs and filaments. The variations in the edge density due to these fluctuations and filaments can affect the propagation characteristics of the RF waves—changes in density leading to regions with differing plasma permittivity. Analytical full-wave theories have shown that scattering by blobs and filaments can alter the RF power flow into the core of the plasma in a variety of ways, such as through reflection, refraction, diffraction, and shadowing [see, for example, Ram and Hizanidis, Phys. Plasmas 23, 022504 (2016), and references therein]. There are changes in the wave vectors and the distribution of power–scattering leading to coupling of the incident RF wave to other plasma waves, side-scattering, surface waves, and fragmentation of the Poynting flux in the direction towards the core. However, these theoretical models are somewhat idealized. In particular, it is assumed that there is step-function discontinuity in the density between the plasma inside the filament and the background plasma. In this paper, results from numerical simulations of RF scattering by filaments using a commercial full-wave code are described. The filaments are taken to be cylindrical with the axis of the cylinder aligned along the direction of the ambient magnetic field. The plasma inside and outside the filament is assumed to be cold. There are three primary objectives of these studies. The first objective is to validate the numerical simulations by comparing with the analytical results for the same plasma description—a step-function discontinuity in density. A detailed comparison of the Poynting flux shows that numerical simulations lead to the same results as those from the theoretical model. The second objective is to extend the simulations to take into account a smooth transition in density from the background plasma to the interior of the filament. The ensuing comparison shows that the deviations from the results of the theoretical model are quite small. The third objective is to consider the scattering process for situations well beyond a reasonable theoretical analysis. This includes scattering off multiple filaments with different densities and sizes. In conclusion, simulations for these complex arrangements of filaments show that, in spite of the obvious limitations, the essential physics of RF scattering is captured by the analytical theory for a single filament

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Mitigating laser-imprint effects in direct-drive inertial confinement fusion implosions with an above-critical-density foam layer

Low-density foams of low-/mid-Z materials have been previously proposed to mitigate laser imprint for direct-drive inertial confinement fusion (ICF). For foam densities above the critical density of the drive laser, the mechanism of laser-imprint mitigation relies on the reduced growth rate of Rayleigh–Taylor instability because of the increased ablation velocity and density scale length at the ablation surface. Experimental demonstration of this concept has been limited so far to planar-target geometry. The impact of foams on spherical implosions has not yet been explored in experiments. To examine the viability of using an above-critical-density foam layer to mitigate laser-imprint effects in direct-drive ICF implosions on OMEGA, we have performed a series of 2-D DRACO simulations with state-of-the-art physics models, including nonlocal thermal transport, cross-beam energy transfer, and first-principles equation-of-state tables. The simulation results indicate that a 40-μm-thick CH or SiO 2 foam layer with a density of p = 40 mg/cm 3 added to a D2-filled polystyrene (CH) capsule can significantly improve the moderate-adiabat (α ≈ 3) implosion performance. In comparison with the standard CH target implosion, an increase of neutron yield by a factor of 4 to 8 and the recovery of 1-D compression pR are predicted by DRACO simulations for a foam-target surface roughness of σ rms ≤ 0.5 μm. These encouraging results could readily facilitate experimental demonstrations of laser-imprint mitigation with an above-critical-density foam layer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Overlapped embedded fragment stochastic density functional theory for covalently-bonded materials

The stochastic density functional theory (DFT) is a valuable linear-scaling approach to Kohn-Sham DFT that does not rely on the sparsity of the density matrix. Linear (and often sub-linear) scaling is achieved by introducing a controlled statistical error in the density, energy, and forces. The statistical error (noise) is proportional to the inverse square root of the number of stochastic orbitals and thus decreases slowly; however, by dividing the system into fragments that are embedded stochastically, the statistical error can be reduced significantly. This has been shown to provide remarkable results for non-covalently-bonded systems; however, the application to covalently bonded systems had limited success, particularly for delocalized electrons. Here, we show that the statistical error in the density correlates with both the density and the density matrix of the system and propose a new fragmentation scheme that elegantly interpolates between overlapped fragments. In conclusion, we assess the performance of the approach for bulk silicon of varying supercell sizes (up to N e = 16 384 electrons) and show that overlapped fragments reduce significantly the statistical noise even for systems with a delocalized density matrix.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Carbon ablator areal density at fusion burn: Observations and trends at the National Ignition Facility

For inertial confinement fusion experiments, the pusher is composed of a high-density deuterium tritium cyrogenic fuel layer and an ablator, often made of carbon. In an ideal, no-mix implosion, increasing the areal density of the pusher transfers more pressure to the hot spot and increases the hot spot confinement time. There has been a lack of knowledge about the final compressed state of the ablator for implosions at the National Ignition Facility. 14 MeV fusion neutrons inelastically scattering on the remaining carbon ablator excites a nuclear metastable state that emits a prompt 4.4 MeV gamma ray. The gamma reaction history diagnostic data, when reduced by a new data analysis technique, can isolate and measure the carbon gamma rays, which are proportional to the areal density of the ablator during fusion burn. The trends over many National Ignition Facility campaigns show that the ablator areal density is weakly sensitive to the maximum shell velocity, the cold fuel radius, the ablator mass remaining, or the laser picket intensity. Controlled parameter scans reveal that, for specific campaigns, ablator compression has a strong dependence on laser coast time, high Z dopants, and the laser drive foot duration. Using a model of the compressed ablator density profile reveals that the greatest variation of the ablator areal density comes from its thickness, with highly compressed, thin layers having high areal density values. The compression and thickness of the ablator are other metrics that designers should understand to differentiate the types of capsule degradation and maximize the inertial confinement fusion performance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Forward and backward stimulated Raman scattering in multi-speckled beams: Density dependence and effects on cross-beam energy transfer

Particle-in-cell simulations of cross-beam energy transfer (CBET) between multi-speckled beams reveal a potentially prominent energy loss from forward stimulated Raman scattering (FSRS) in the amplified seed beam [Yin et al., Phys. Plasmas 26, 082708 (2019)]. In this work, an intensity scan is used to examine this energy loss in the CBET-amplified seed beam at intensities of a few times 1014 W/cm2. Electron tracers demonstrate both the trapping in the electron plasma waves that is sustained over multiple speckles and the subsequent acceleration to velocities well beyond the phase velocity. Motivated by expanding our understanding of this energy loss mechanism, we isolate the FSRS density dependence by using a 2×1014 W/cm2 pulse to scan densities between 0.06 ncr and 0.12 ncr; a spectral analysis characterizes the energy losses from scattering with the changing densities. At saturation, both greater beam attenuation is measured at the laser frequency and larger scattering FSRS angles are observed as density increases, along with a rapid transition to primarily backscatter SRS between 0.10 ncr and 0.12 ncr, earlier than predicted by linear theory. Density gradients are shown to effectively mitigate oblique FSRS and beam energy losses in the two lower density cases, whereas 0° forward scattering is primarily suppressed in the higher density cases. Finally returning to the two-beam CBET system of interest, the interplay and mitigation of the secondary instabilities at larger domain and beam spatial scales are discussed, here also examining backward stimulated Brillouin scattering.

Stark, D. J. (ORCID:0000000203642733)↗
DOE OSTI2022

Quantitative spatiotemporal density evolution of aluminum heated purely by monochromatic electrons

A spatially resolved air-wedge shearing interferometer and shadowgraph diagnostic provides measurements of electron density with a resolution of ∼40 μm. A ∼100-ns-long, monoenergetic electron bunch at 19.8 MeV and a current of 1.4 kA (8.5×1014 e−) heats 100-μm-thick aluminum (Al) foils in a 1-mm-spot to Te∼1 eV. A 5-ns-long, ∼60 mJ, frequency doubled Nd:YAG laser probes the dense Al plasma. Electron densities up to 1020cm−3 are resolved; the maximum resolvable density is limited by opacity, transmission, and spatial fringe density achievable with the detector. This diagnostic provides measurements of the total phase shift, transmission, and electron density. Several measurements at different time slices provide the ability to determine the velocity of the leading edge of the shadowgraph and compare it to the motion of different density shells. These measurements are also compared to radiation hydrodynamics simulations. A rough quantitative agreement is shown between the hydro simulations and the measurements; there are differences in the exact density distributions.

Coleman, J. E. (ORCID:0000000308873757)↗
DOE OSTI2022

Impact of pedestal density gradient and collisionality on ELM dynamics

BOUT++ turbulence simulations are conducted to capture the underlying physics of small ELM characteristics achieved by increasing separatrix density via controlling strike points from vertical to horizontal divertor plates for three EAST discharges. BOUT++ linear simulations show that the most unstable modes change from high-n ideal ballooning modes to intermediate-n peeling–ballooning modes and eventually to peeling–ballooning stable plasmas in the pedestal. Nonlinear simulations show that the fluctuation is saturated at a high level for the lowest separatrix density. The ELM size decreases with increasing separatrix density, until the fraction of this energy lost during the ELM crash becomes less than 1% of the pedestal stored energy, leading to small ELMs. Simulations indicate that small ELMs can be triggered either by the marginally peeling–ballooning instability near the peak pressure gradient position inside the pedestal or by a local instability in the pedestal foot with a larger separatrix density gradient. The pedestal collisionality scan for type-I ELMs with steep pedestal density gradient shows that both linear growth rate and ELM size decrease with increasing collisionality. On the contrary, the pedestal collisionality and pedestal density width scan with a weak pedestal density gradient indicate small ELMs can either be triggered by a high-n ballooning mode or by a low-n peeling mode in a low collisionality region 0.04–0.1. We report the simulations indicate the weaker the linear unstable modes near marginal stability with small linear growth rate, the lower nonlinearly saturated fluctuation intensity and the smaller turbulence spreading from the linear unstable zone to stable zone in the nonlinear saturation phase, leading to small ELMs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Al–W gradient density materials—Processing and dynamic ramp compression

Materials with high-density gradients are desired for controlling loading paths in dynamic compression, important for studying material properties in extreme conditions and inertial confinement fusion. The large density difference between Al and W makes them ideal choices for producing gradient density materials, but their extremely different melting temperatures make them challenging to fabricate simultaneously. We report a method for producing Al–W porosity-free materials with a fourfold increase in density (2.7–11 g/cm 3 ) across the composition range, from Al-rich to W-rich, without intermetallic phase formation. This was achieved by understanding the aluminum-dominated densification behavior and examining the influence of pressure and temperature on the densification of Al–W composites. Dynamic compression experiments conducted with the Al–W gradient density material produced shock ramp compressions as expected based on the designed composition, and the performed hydrodynamics simulations showed excellent agreement with experimental results. The results demonstrate that current activated pressure-assisted densification allows for the easy and rapid fabrication of gradient density materials with significant density gradients and tailored compositions, facilitating precise control of the loading paths. These materials have the potential to create customized pressure drives for advancing the fields of material science in extreme environments and dynamic compression.

Alloys↗
DOE OSTI2024

Medium-density amorphous ice unveils shear rate as a new dimension in water’s phase diagram

Recent experiments revealed a new amorphous ice phase, medium-density amorphous ice (MDA), formed by ball-milling ice I h at 77 K [Rosu-Finsen et al., Science 379, 474–478 (2023)]. MDA has density between that of low-density amorphous (LDA) and high-density amorphous (HDA) ices, adding to the complexity of water’s phase diagram, known for its glass polyamorphism and two-state thermodynamics. The nature of MDA and its relation to other amorphous ices and liquid water remain unsolved. Here, we use molecular simulations under controlled pressure and shear rate at 77 K to produce and investigate MDA. Here. we find that MDA formed at constant shear rate is a steady-state nonequilibrium shear-driven amorphous ice (SDA), that can be produced by shearing ice I h , LDA, or HDA. Our results suggest that MDA could be obtained by ball-milling water glasses without crystallization interference. Increasing the shear rate at ambient pressure produces SDAs with densities ranging from LDA to HDA, revealing shear rate as a new thermodynamic variable in the nonequilibrium phase diagram of water. Indeed, shearing provides access to amorphous states inaccessible by controlling pressure and temperature alone. SDAs produced with shearing rates as high as 10 6 s −1 sample the same region of the potential energy landscape than hyperquenched glasses with identical density, pressure, and temperature. Intriguingly, SDAs obtained by shearing at ~10 8 s −1 have density, enthalpy, and structure indistinguishable from those of water “instantaneously” quenched from room temperature to 77 K over 10 ps, making them good approximants for the “true glass” of ambient liquid water.

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

Analysis of the density field around a supersonic conical projectile using quantitative schlieren

Quantitative schlieren imaging is a flow measurement technique that is capable of measuring density fields throughout refractive flowfields. The technique was applied here to measure the density field surrounding supersonic conical projectiles in free flight. Shock waves attached to a supersonic conical projectile offer a simple geometry with the well-established Taylor–Maccoll analytical flow solution to which these experimental measurements were compared. The schlieren images recorded a projection of the index of refraction field surrounding the 10° half-angle cones which was converted to density first through an Abel inversion and then the Gladstone–Dale law. Three Abel inversion methods—two-point, three-point, and arbitrary ray axisymmetric projection (ARAP)—were applied to deconvolute the three-dimensional flow within the constrained axisymmetric flow field. The resulting reconstructed density profiles were compared to the Taylor–Maccoll solution, parameterized by cone geometry and Mach number. The experimental density fields demonstrated strong agreement with the theoretical profiles. Experimental consistency was confirmed across various projectile speeds, demonstrating quantitative schlieren’s capability to accurately reconstruct the density of the flow field, even within the resolution constraints imposed by high-speed imaging. In conclusion, an assessment of experimental uncertainties in the density reconstruction was performed.

Abel Inversion↗
DOE OSTI2025

High-field side scrape-off layer density profile measurements and implications for high-field side LHCD coupling in DIII-D

The high-field side (HFS) scrape-off layer (SOL) is an often under-diagnosed region of tokamak plasmas. Situated in a region with favorable curvature, the HFS SOL has minimal turbulence-induced radial transport compared to the low-field side. Using profile reflectometry, the HFS SOL density profile is measured with high temporal resolution for a wide range of DIII-D plasma discharges for the first time. The magnetic configuration, particularly the location of the secondary separatrix (SS) largely determines the HFS SOL density profile. Additionally, density perturbations induced by edge-localized modes (ELMs) are observed in the HFS SOL, and the impact of ELMs on the SOL density profile is characterized for a range of magnetic configurations. It is found that ELM-induced HFS SOL perturbations are generally localized to within the SS and ELM-induced changes to the HFS wall density are minimized in near double-null configurations. The characterization of the HFS SOL density profile on DIII-D is crucial for the effective coupling of the planned HFS lower hybrid current drive (LHCD) launcher. Experimental HFS SOL measurements are used as input to full-wave simulations of LHCD coupling. Furthermore, this work simulates the effect of the magnetic configuration on LHCD coupling. It also simulates LHCD coupling in ELMs and high q min discharges. During such discharges, the LHCD coupling is predicted to be resilient to ELM-induced SOL density perturbations.

high-field side↗
DOE OSTI2017

Modification of SOL profiles and fluctuations with line-average density and divertor flux expansion in TCV

A set of Ohmic density ramp experiments addressing the role of parallel connection length in modifying scrape off layer (SOL) properties has been performed on the TCV tokamak. The parallel connection length has been modified by varying the poloidal flux expansion f x . It will be shown that this modification does not influence neither the detachment density threshold, nor the development of a flat SOL density profile which instead depends strongly on the increase of the core line average density. The modification of the SOL upstream profile, with the appearance of what is generally called a density shoulder, has been related to the properties of filamentary blobs. Blob size increases with density, without any dependence on the parallel connection length both in the near and far SOL. The increase of the density decay length, corresponding to a profile flattening, has been related to the variation of the divertor normalized collisionality Λ div , showing that in TCV the increase of Λ div is not sufficient to guarantee the SOL upstream profile flattening.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Experimental investigation of PDI bifurcation of lower hybrid waves during electron density ramp-up in EAST

Abstract The effect of parametric decay instability (PDI) on the current drive efficiency of 4.6 GHz lower hybrid (LH) waves in EAST is investigated experimentally, showing the PDI channel bifurcation of LH waves for the first time in EAST. First, experiments with three platforms of LH power were performed, achieving the LH power required for the PDI occurrence. Second, PDI bifurcation experiments were further carried out by ramping up the plasma electron density. The loop voltage increases with an increase in density, implying a decrease in the current driven by the LH wave. PDI bifurcation during electron density ramp-up was studied by analyzing the parallel refractive index ( n ∥ ) and the frequency spectrum broadening, which is measured with a radio frequency magnetic probe array recently installed close to the LH antenna. It is observed for the first time that they both first increase with density, then there is not much variation and a clear sideband in the frequency spectrum is also observed when the density is up to 4 × 10 19 m − 3 , suggesting a change in the PDI channel. Calculation of the mode growth rate driven by PDI shows that when the edge electron density is up to 1.9 × 10 18 m − 3 , the growth rate of the ion cyclotron quasi-mode (ICQM) will exceed that of the ion sound quasi-mode (ISQM), quantitively explaining that with an increase in density, the PDI channel partly transits from the ISQM to the ICQM channel. Studies provide a possible way to reduce the power deposition in the edge region and improve drive capability by means of mitigating PDI behavior.

Physics↗
DOE OSTI2024

Impact of ionization and transport on pedestal density structure in DIII-D and Alcator C-Mod

Abstract This paper investigates the role of ionization on the pedestal structure using both measurements and modeling for H-mode plasmas on DIII-D and Alcator C-Mod to enhance our ability to predict pedestal behavior in future pilot plants. The impact of the neutral penetration depth on the pedestal density is investigated using dimensionally matching hydrogen and deuterium DIII-D H-mode discharges at low and high electron density. The DIII-D Lyman- α diagnostic measurements show that hydrogen neutrals penetrate deeper inside the plasma on both the high field and low field side, while the pedestal electron density structure is similar for both isotopes. However, as the opaqueness increases we observe that the pedestal density gradient becomes stiff, similar to prior observations on DIII-D and C-Mod (Mordijck 2020 Nuclear Fusion 60 082006). In addition, these results also confirm prior measured and modeled poloidal asymmetries in neutral densities, indicating that to make transport predictions, 2D neutral modeling is necessary. The first direct validation of SOLPS-ITER for the measured brightness, emissivity and neutral densities for three different confinement regimes on C-Mod is introduced. The SOLPS-ITER model shows good agreement, within the constrains of the model for all regimes. In addition, a comparison of SOLPS-ITER modeling for DIII-D and C-Mod shows that as opaqueness increases, the role of divertor fueling and thus poloidal asymmetries in the neutral density profiles decreases. Based on these experimental and modeling results we estimate the size of a potential particle pinch using typical values for the diffusion coefficient for both DIII-D and C-Mod H-mode discharges.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Non-linear dependence of ion heat flux on plasma density at the L–H transition of JET NBI-heated deuterium–tritium plasmas

Abstract Recent JET D–T campaigns opened the possibility of unique isotope studies to investigate the L–H transition physics in view of reactor plasmas and to study the origin of the observed power threshold minimum. In the present paper, we characterise L–H transitions in the low and high-density branches of JET NBI-heated D–T plasmas. As discussed in the paper, L–H transition has been hypothesised to be determined by the transport power losses of plasma ions, i.e. the so-called ion heat flux ( Q i ). We present the first power balance analysis of JET NBI-heated D–T plasmas to evaluate the ion heat flux at the transition. Due to the experimental setting being similar to previous JET D experiments, we also directly compare the results, discussing the isotope effect and similarities between datasets. First, we find an isotope effect between D and D–T Q i , with a lower Q i in D–T plasmas. We confirm that the ion heat flux deviates from density linearity compared to the linear trend observed in wave-heated D plasmas of other tokamaks. The deviation we observe in NBI-heated L–H transitions happens at an isotope-dependent density. Plasma edge rotation correlates with Q i deviation from density linearity in the low-density branch. However, further investigations would be required to assess the role of rotation on Q i and the power threshold minimum at JET. At low plasma density, NBI power dominates Q i , while increasing the density makes the equipartition power dominant. We finally compare our results with hypotheses proposed from evidence in other tokamaks to present a complete overview of ion heat flux analyses in D and D–T NBI-heated plasmas at JET.

Vincenzi, P. (ORCID:0000000251564354)↗
DOE OSTI2025

Exploring the transition from continuous turbulence fluctuations to bursting ELMs in high SOL density regimes

BOUT++ turbulence simulations of the DIII-D reveal that the density profile between the separatrix and pedestal plays a crucial role in the dynamics of edge localized modes (ELMs) and edge plasma turbulent transport. Nonlinear simulations demonstrate that small ELMs in the DIII-D hybrid scenario under high SOL density conditions are predominantly driven by local ballooning modes near the separatrix, stabilizing global instabilities while enhancing localized pressure fluctuations. A key control parameters for ELM dynamics is the separatrix-to-pedestal density ratio, n e,sep /n e,ped . A high ratio indicates a shallow gradient, favoring small ELMs, while a lower ratio signals a steep gradient, which increases the likelihood of large ELMs. Comprehensive parameter scans, including n e,sep /n e,ped , density gradient profiles near the separatrix, and resistivity, reveal the critical role of these parameters in shaping transitions between turbulence-driven transport and ELM bursting. The scans demonstrate that in high SOL density regimes, small ELMs can result from either global resistive MHD instabilities or local ballooning modes near the separatrix, depending on the steepness of the separatrix density gradient. These findings also highlight the transition from continuous turbulence to small ELMs. The post-crash peak in pressure fluctuations, δP rms serves as a critical metric for identifying transition from continuous turbulence fluctuations to ELM bursting. Larger δP rms values correlate with ELM bursts driven by local or global instabilities, whereas smaller values indicate turbulence-dominated transport. Drift-Alfvén and resistive ballooning turbulence enhance the entrainment of fluctuations from the pedestal to the SOL, contributing to the complex interplay of dynamics in this regime. These findings emphasize the importance of separatrix density shaping and pedestal gradient control for optimizing ELM behavior in ITER and future fusion devices.

Li, Nami [Lawrence Livermore National Laboratory (↗
DOE OSTI2025

CryoTEN: efficiently enhancing cryo-EM density maps using transformers

Abstract Motivation Cryogenic electron microscopy (cryo-EM) is a core experimental technique used to determine the structure of macromolecules such as proteins. However, the effectiveness of cryo-EM is often hindered by the noise and missing density values in cryo-EM density maps caused by experimental conditions such as low contrast and conformational heterogeneity. Although various global and local map-sharpening techniques are widely employed to improve cryo-EM density maps, it is still challenging to efficiently improve their quality for building better protein structures from them. Results In this study, we introduce CryoTEN—a 3D UNETR++ style transformer to improve cryo-EM maps effectively. CryoTEN is trained using a diverse set of 1295 cryo-EM maps as inputs and their corresponding simulated maps generated from known protein structures as targets. An independent test set containing 150 maps is used to evaluate CryoTEN, and the results demonstrate that it can robustly enhance the quality of cryo-EM density maps. In addition, automatic de novo protein structure modeling shows that protein structures built from the density maps processed by CryoTEN have substantially better quality than those built from the original maps. Compared to the existing state-of-the-art deep learning methods for enhancing cryo-EM density maps, CryoTEN ranks second in improving the quality of density maps, while running >10 times faster and requiring much less GPU memory than them. Availability and implementation The source code and data are freely available at https://github.com/jianlin-cheng/cryoten.

Biochemistry & Molecular Biology↗