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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A block-spectral adaptive H-/$p$-refinement strategy for shock-dominated problems

An adaptive H-/p-refinement strategy using a novel sensor is devised and tested in a block-spectral compressible Euler code equipped with adaptive-mesh refinement (AMR) and high-order flux-reconstruction numerics. At each Gauss quadrature point (or solution point) within each spectral block (or mesh element) the discrete velocity jump ΔU = ∂U/∂y 1 Δy 1 + ∂V/∂y 2 Δy 2 + ∂W/∂y 3 Δy 3 is calculated and normalized by the local speed of sound, a. Here, the grid spacing, Δx i , is calculated in each direction as the distance between auxiliary Gauss-Lobatto points, staggered relative to the solution points. The polynomial order is increased from p = 0 to p = p max in regions of weak compression, (ΔU/a) crit < ΔU/a < 0 and kept at p = p max in regions of flow expansion ΔU/a ≥ 0, while staying at the H = 0 base mesh level. Regions experiencing strong compressions, i.e. ΔU/a < (ΔU/a) crit , are H-refined up to H = H max where H max is applied at the location of maximum compression, ΔU/a = min(ΔU/a) in the domain, while keeping p = 0 to guarantee robustness and monotonicity of the solution in the H refined region. The critical value of (ΔU/a) crit = -0.06 is found to effectively separate smooth and non-smooth solution regions, supported by a 1D detonation initiation test case in ideal gas and a shock-to-detonation transition in high explosives. Using this value, the Sod shock tube, Shu-Osher problem, double Mach reflection and a 2D detonation in a high-explosive are simulated with the proposed adaptive H-/p-refinement. In the Sod shock tube case, p-refinement resolves the (weak) contact discontinuity while H-refinement enhances the grid resolution in the shock exploiting the monotonicity of the p = 0 reconstruction. For the Shu-Osher problem, p-refinement captures the small-scale oscillations trailing the shock that would be otherwise attenuated, while H-refinement triggered by the ΔU-sensor appropriately tracks the shock. In the double Mach reflection problem, H-refinement confines the numerical diffusion around the reflected shock while p-refinement recaptures many physical features trailing the shock. Finally, in the 2D high-explosive detonation case, H-refinement follows the leading shock and resolves the curvature of the detonation wave, while p-refinement adds resolution to the trailing reaction zone. Finally, the proposed methodology is tested in a detonation-wave propagation test case in high-explosives with numerical predictions comparing favorably against experiments.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1999

Adaptive Mesh Refinement for Microelectronic Device Design

Finite element and finite volume methods are used in a variety of design simulations when it is necessary to compute fields throughout regions that contain varying materials or geometry. Convergence of the simulation can be assessed by uniformly increasing the mesh density until an observable quantity stabilizes. Depending on the electrical size of the problem, uniform refinement of the mesh may be computationally infeasible due to memory limitations. Similarly, depending on the geometric complexity of the object being modeled, uniform refinement can be inefficient since regions that do not need refinement add to the computational expense. In either case, convergence to the correct (measured) solution is not guaranteed. Adaptive mesh refinement methods attempt to selectively refine the region of the mesh that is estimated to contain proportionally higher solution errors. The refinement may be obtained by decreasing the element size (h-refinement), by increasing the order of the element (p-refinement) or by a combination of the two (h-p refinement). A successful adaptive strategy refines the mesh to produce an accurate solution measured against the correct fields without undue computational expense. This is accomplished by the use of a) reliable a posteriori error estimates, b) hierarchal elements, and c) automatic adaptive mesh generation. Adaptive methods are also useful when problems with multi-scale field variations are encountered. These occur in active electronic devices that have thin doped layers and also when mixed physics is used in the calculation. The mesh needs to be fine at and near the thin layer to capture rapid field or charge variations, but can coarsen away from these layers where field variations smoothen and charge densities are uniform. This poster will present an adaptive mesh refinement package that runs on parallel computers and is applied to specific microelectronic device simulations. Passive sensors that operate in the infrared portion of the spectrum as well as active device simulations that model charge transport and Maxwell's equations will be presented.

Cwik, Tom↗
DOE OSTI2019

Formation of Plastic Inclusions in U71Mnk High-Speed Heavy-Rail Steel Refined by CaO-SiO{sub 2}-Al{sub 2}O{sub 3}-MgO Slag

To precisely control the characteristics of nonmetallic inclusions with high plasticity in U71Mnk high-speed heavy-rail steel deoxidized by Si and Mn, the chemical composition of CaO-SiO{sub 2}-Al{sub 2}O{sub 3}-MgO slag in the ladle furnace (LF) refining process was optimized by thermodynamic calculations. Relationships among the refining slag, nonmetallic inclusions, and elemental concentrations in the steels were analyzed to obtain the conditions for determining the optimal composition of refining slag. The optimal compositions and the component activities of CaO-SiO{sub 2}-Al{sub 2}O{sub 3}-MgO refining slag were determined and discussed according to calculations using FactSage 7.0. Finally, ten industrial experiments were performed. Variations in the compositions of LF refining slag, inclusions, and steel, as well as the sizes of the inclusions, and metallographic classification assessment of the U71Mnk steel product, were investigated and discussed to verify the feasibility and effectiveness of the optimized LF refining slag. Kinetics of steel–slag and steel-inclusion reactions during LF refining was studied and compared. The results show that to obtain low [O], [Al], and [S] contents and inclusions with high plasticity in molten steel, the optimal composition of the LF refining slag should be CaO: 44.2 to 51.7 wt pct, SiO{sub 2}: 41.4 to 47.0 wt pct, Al{sub 2}O{sub 3}: 0 to 4.7 wt pct and MgO 5.0 to 7.0 wt pct, where the basicity R is above 1.00 and the C/A ratio is above 9.00. After the LF refining process, the contents of total oxygen (T.O.), [Al], and [S] gradually stabilized in the range of 0.0008 to 0.0012 wt pct, 0.002 to 0.0028 wt pct and 0.0026 to 0.0037 wt pct, respectively. The densities of the three kinds of typical inclusions (CaO-SiO{sub 2}-Al{sub 2}O{sub 3}-MgO, MnS, and CaO-SiO{sub 2}-Al{sub 2}O{sub 3}-MgO-MnS) also decreased and reached approximately 0.25/mm{sup 2}, and no inclusion larger than 6.0 μm was found. The composition of the inclusions gradually changed into the optimal range in the CaO-SiO{sub 2}-Al{sub 2}O{sub 3}-MgO slag system during the LF refining process.

36 MATERIALS SCIENCE↗
DOE OSTI2018

The grain refinement mechanisms of various phases in shot-peened Nickel-Aluminum bronze (NAB) alloy

Highlights: • There exist two grain refinement mechanisms at the same time in the α phase. • The refinement of β' phase is attributed to the formation of dense and ordered nano twins. • The brittle strip-shape κ{sub iii} phases are fragmented after large deformation. • The κ{sub iv} and κ{sub ii} phases exhibit the twinning and dislocation deformation modes, separately. • The microhardness increases significantly owing to work hardening effect and grain refinement. - Abstract: In this study, coarse-grained Nickel-Aluminum bronze (NAB) alloy is subjected to shot-peening (SP) treatment, and the grain refinement mechanisms of various phases in shot-peened NAB alloy are investigated separately. The results show that severe deformation layers are produced on the surface. Meanwhile, refined grains with the average size below 100 nm are induced through SP treatment indicated by the results of X-ray diffraction (XRD) patterns. Various phases in NAB alloy including α, β' and three intermetallic phases (κ{sub ii}, κ{sub iii} and κ{sub iv}) display different grain refinement mechanisms. The grain refinement in the α phase involves dislocation segmentation in the precipitation-free zone and the twinning intersection in the precipitation zone. The formation of nanotwins by emitting partial dislocations at the grain boundary is found to be responsible for the grain refinement in the β' phase. As for the κ phases, the strip-shaped κ{sub iii} phases are fragmented after severe deformation, and the κ{sub iv} and κ{sub ii} phases exhibit the twinning and dislocation deformation modes, respectively. Also, the microhardness is significantly enhanced after SP treatment, which is mainly attributed to the work hardening effect and grain refinement.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX – AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX – AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein–ligand PDB structures are presented. Refinements using PHENIX – AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented, PHENIX – AFITT refinements result in more chemically accurate models for small-molecule ligands.

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

Toward an understanding of the increase in enzymatic hydrolysis by mechanical refining

Mechanical refining is a low-capital and well-established technology used in pulp and paper industry to improve fiber bonding for product strength. Refining can also be applied in a biorefinery context to overcome the recalcitrance of pretreated biomass by opening up the biomass structure and modifying substrate properties (e.g., morphology, particle size, porosity, crystallinity), which increases enzyme accessibility to substrate and improves carbohydrate conversion. Although several characterization methods have been used to identify the changes in substrate properties, there is no systematic approach to evaluate the extent of fiber cell wall disruption and what physical properties can explain the improvement in enzymatic digestibility when pretreated lignocellulosic biomass is mechanically refined. This is because the fiber cell wall is complex across multiple scales, including the molecular scale, nano- and meso-scale (microfibril), and microscale (tissue level). A combination of advanced characterization tools is used in this study to better understand the effect of mechanical refining on the meso-scale microfibril assembly and the relationship between those meso-scale modifications and enzymatic hydrolysis. Enzymatic conversion of autohydrolysis sugarcane bagasse was improved from 69.6 to 77.2% (11% relative increase) after applying mechanical refining and an increase in enzymatic digestibility is observed with an increase in refining intensity. Based on a combination of advanced characterizations employed in this study, it was found that the refining action caused fiber size reduction, internal delamination, and increase in pores and swellability. A higher level of delamination and higher increase in porosity, analyzed by TEM and DSC, were clearly demonstrated, which explain the faster digestibility rate during the first 72 h of enzymatic hydrolysis for disc-refined samples when compared to the PFI-refined samples. Additionally, an increased inter-fibrillar distance between cellulose microfibrils at the nano-meso-scale was also revealed by SFG analysis, while no evidence was found for a change in crystalline structure by XRD and solid-state NMR analysis.

09 BIOMASS FUELS↗
DOE OSTI2018

Improving signal strength in serial crystallography with DIALS geometry refinement

The DIALS diffraction-modeling software package has been applied to serial crystallography data. Diffraction modeling is an exercise in determining the experimental parameters, such as incident beam wavelength, crystal unit cell and orientation, and detector geometry, that are most consistent with the observed positions of Bragg spots. These parameters can be refined by nonlinear least-squares fitting. In previous work, it has been challenging to refine both the positions of the sensors (metrology) on multipanel imaging detectors such as the CSPAD and the orientations of all of the crystals studied. Since the optimal models for metrology and crystal orientation are interdependent, alternate cycles of panel refinement and crystal refinement have been required. To simplify the process, a sparse linear algebra technique for solving the normal equations was implemented, allowing the detector panels to be refined simultaneously against the diffraction from thousands of crystals with excellent computational performance. Separately, it is shown how to refine the metrology of a second CSPAD detector, positioned at a distance of 2.5 m from the crystal, used for recording low-angle reflections. With the ability to jointly refine the detector position against the ensemble of all crystals used for structure determination, it is shown that ensemble refinement greatly reduces the apparent nonisomorphism that is often observed in the unit-cell distributions from still-shot serial crystallography. In addition, it is shown that batching the images by timestamp and re-refining the detector position can realistically model small, time-dependent variations in detector position relative to the sample, and thereby improve the integrated structure-factor intensity signal and heavy-atom anomalous peak heights.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Multi-Objective Adaptive Mesh Refinement Using Reinforcement Learning

Finite element methods approximate the solution to a partial differential equation (PDE) on a mesh consisting of many elements. In general, using more, smaller elements results in a lower error in the approximation. However, it is often possible to lower the error substantially by only refining, or decreasing the size of, the few elements in the mesh that have the highest error. Adaptive mesh refinement (AMR) is a process that selectively refines regions of a mesh with high error to achieve a desired accuracy in as few degrees of freedom (DOFs) as possible. AMR is favorable compared to uniform refinement, which refines all elements of the mesh equally, because it can often achieve the same accuracy without wasting extra computation time on refinement of elements that already have low error. However, it is difficult to know which elements to refine. In this report we explore ways to choose which elements to refine such that we minimize both the resulting error and the cumulative DOFs used in computation. In particular, we introduce a Pareto-front learning algorithm that trains a policy to give the optimal refinement actions to minimize the cumulative DOFs used to achieve a given target error. Such a policy is useful because it can be deployed on many different problem types where different accuracy levels are desired. Furthermore, training a single policy for a range of target errors allows us to use transfer learning to reduce the required training time.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

A template-based approach for parallel hexahedral two-refinement

Here, we provide a template-based approach for generating locally refined all-hex meshes. We focus specifically on refinement of initially structured grids utilizing a 2-refinement approach where uniformly refined hexes are subdivided into eight child elements. The refinement algorithm consists of identifying marked nodes that are used as the basis for a set of four simple refinement templates. The target application for 2-refinement is a parallel grid-based all-hex meshing tool for high performance computing in a distributed environment. The result is a parallel consistent locally refined mesh requiring minimal communication and where minimum mesh quality is greater than scaled Jacobian 0.3 prior to smoothing.

2-refinement↗
DOE OSTI2018

Research on Selective Oxidation of Carbon and Aluminum with Introduction of CO{sub 2} in RH Refining of Low-Carbon Steel Process

The injection of CO{sub 2} during the Rheinstahl–Heraeus (RH) refining process as a lifting gas is a new attempt for the steel industry, and can promote refining effect and realize the utilization of CO{sub 2} as a resource. In the present study, the thermodynamic equilibrium of the RH refining process through CO{sub 2} injection instead of Ar was calculated using FactSage software. A selective oxidation sequence of [C] and [Al] with CO{sub 2} was studied and analyzed under the RH refining temperature and vacuum degree. In addition, the oxidation zones of carbon and aluminum were both defined. Industrial trials were preliminarily conducted to verify the above theory. The results show that CO{sub 2} has the potential to be used to refine low-carbon steel in RH, but its refining effect is affected by the [Al] content in steel. By reducing the additive amount of aluminum alloy in the ladle furnace and replenishing the aluminum during the late stage of the RH refining process, CO{sub 2} injection can achieve a lower temperature drop of molten steel and a better refining effect than Ar during the RH degassing process.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Clarifying the formation of equiaxed grains and microstructural refinement in the additive manufacturing of Ti-Cu

Controlling microstructural evolution in metallic additive manufacturing (AM) is difficult, especially in producing refined as-built grains instead of coarse, directional grains. Traditional solutions involve adding inoculants to AM feedstocks, but titanium (Ti) alloys cannot employ this approach without producing detrimental secondary phases. Ti-Cu (Ti-copper) alloys offer a solution through constitutional supercooling and/or solid state thermal cycling under AM conditions. This work analyzes a compositionally graded directed energy deposition (DED) Ti-Cu build, single-melt laser tracks, and dilatometric heat treatments to evaluate if, when, and by what mechanism(s) microstructural refinement occurs. Refinement by inoculation of unmelted powder particles was also considered. Constitutional supercooling produced no net microstructural refinement as any equiaxed dendrites which form are remelted with new deposition. This finding agreed with solidification modeling of powder bed fusion-laser beam (PBF-LB) and DED builds. Solid state thermal cycling refined microstructures only during ex-situ dilatometric heat treatments, suggesting build parameter optimization is needed to achieve refinement in-situ. Accidental heterogeneous nucleation on unmelted Ti powder, originating from the different thermophysical properties of Ti and Cu, provided the most significant microstructural refinement. This work systematically assesses the microstructural refinement mechanisms of Ti-Cu in AM builds and offers insights into microstructural control in eutectoid alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Testing Different Methods for Estimating Uncertainties on Rietveld Refined Parameters Using SrRietveld

The advent of fast computing allows more computationally expensive, though possibly more accurate, approaches for estimating uncertainties on Rietveld refined parameters. Here we compare three such methods, using two different refinement programs, FullProf and GSAS. This is facilitated by the use of a new Rietveld refinement package, SrRietveld, that provides Python wrappers for FullProf and GSAS. The refined values on the parameters from two different refinement engines match each other very well. The uncertainty estimates determined using the different methods are also consistent, though FullProf and GSAS estimate the parameter uncertainties slightly differently from each other, which is discussed. More importantly, we find that the refined results are very sensitive to the statistical weights used in the least squares equation. Different weights, for example from uncertain or incorrectly propagated random errors on the data, lead to significantly different refined values. This means that uncertainty estimates on refined parameters should be increased when the random errors on the data are not well known, as for example in many cases where area detectors are used, and care should be taken to propagate errors correctly in any data preprocessing such as normalization by a smoothed spectrum. The computationally expensive bootstrap error estimation methods are facilitated by the use of SrRietveld, but are not required in most cases though may be useful in some cases, for example if the random errors on the data are not well known.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Evaluation of tropical channel refinement using MPAS‐A aquaplanet simulations

Abstract Climate models with variable‐resolution grids offer a computationally less expensive way to provide more detailed information and increased accuracy by resolving processes that cannot be adequately represented by a coarser grid. This study uses the Model for Prediction Across Scales‐Atmosphere (MPAS‐A), consisting of a nonhydrostatic dynamical core and a subset of Weather Research and Forecasting (WRF) model physics, to investigate the potential benefits of using tropical channel refinement. The simulations are performed with an idealized aquaplanet configuration using 30 and 240 km global grid spacing, and two variable‐resolution grids spanning the same grid spacing range; one with a narrow (20°S–20°N) and one with a wide (30°S–30°N) tropical channel refinement. Increasing resolution in the tropics impacts both the tropical and extratropical circulation. Compared to the 30 km global grid, both refined channel simulations exhibit slightly stronger updrafts inside the Hadley cell resulting in more resolved precipitation. Using a wider tropical refinement leads to a closer correspondence with the global high‐resolution grid. While different grid spacings produce similar cloud size distributions that are consistent with observations, the dependence of precipitation rate on cloud size varies among simulations. The refined channel simulations show improved tropical and extratropical precipitation relative to the global coarse simulation. All simulations show a single precipitation peak centered on the equator. Although the results show that tropical refinement is an effective method for avoiding artifacts due to grid resolution sensitivities seen in earlier studies that only refined a portion of the tropics, some biases remain well inside of the refinement region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Anomalies in the refinement of isoleucine

The side-chain torsion angles of isoleucines in X-ray protein structures are a function of resolution, secondary structure and refinement software. Detailing the standard torsion angles used in refinement software can improve protein structure refinement. A study of isoleucines in protein structures solved using X-ray crystallography revealed a series of systematic trends for the two side-chain torsion angles χ{sub 1} and χ{sub 2} dependent on the resolution, secondary structure and refinement software used. The average torsion angles for the nine rotamers were similar in high-resolution structures solved using either the REFMAC, CNS or PHENIX software. However, at low resolution these programs often refine towards somewhat different χ{sub 1} and χ{sub 2} values. Small systematic differences can be observed between refinement software that uses molecular dynamics-type energy terms (for example CNS) and software that does not use these terms (for example REFMAC). Detailing the standard torsion angles used in refinement software can improve the refinement of protein structures. The target values in the molecular dynamics-type energy functions can also be improved.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

A Refinement-by-Superposition -Method for (curl)- and (div)-Conforming Discretizations

Here, we present refinement-by-superposition (RBS) hp-refinement infrastructure for computational electromagnetics (CEMs), which permits exponential rates of convergence. In contrast to dominant approaches to hp-refinement for continuous Galerkin methods, which rely on explicit constraint equations, the multilevel strategy presented drastically reduces the implementation complexity. Through the RBS methodology, enforcement of continuity occurs by construction, enabling arbitrary levels of refinement with ease, and without the practical (but not theoretical) limitations of constrained-node refinement. We outline the construction of the RBS hp-method for refinement with H (curl)- and H (div)-conforming finite cells. Numerical simulations for the 2-D finite element method (FEM) solution of the Maxwell eigenvalue problem demonstrate the effectiveness of RBS hp-refinement. As an additional goal of this work, we aim to promote the use of mixed-order (low- and high-order) elements in practical CEM applications.

42 ENGINEERING↗
DOE OSTI2018

Novel Fabrication of a TiB{sub 2} Grain Refiner and its Effect on Reducing Hot Tearing in AZ91D Magnesium Alloy

Despite the increased use of magnesium (Mg) alloys in diverse engineering applications in recent years, further incorporation of complex Mg alloy castings remains challenging due to the alloy’s relatively high susceptibility to hot tearing. A significant reduction in hot tearing via grain refinement was achieved in aluminum and ferrous alloys; however, an effective, long-lasting and inexpensive grain refiner for aluminum-containing Mg alloys remains elusive. In this work, a TiB{sub 2} grain refiner was fabricated via a novel spark plasma sintering (SPS) powder metallurgy process. Then, its effectiveness in grain refining an AZ91D magnesium alloy was compared to that of a commercially available TiB{sub 2} grain refiner produced by hot extrusion. Due to the homogeneous distribution of the TiAl{sub 3} and TiB{sub 2} particles in the grain refiner, as well as their effect on the alloy’s microstructure evolution and solidification behavior, the SPS-TiB{sub 2} grain refiner was observed to achieve a significant reduction in the grain size and hot tearing of the Al-containing AZ91D magnesium alloy.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

The refinement of biomolecular crystallographic models relies on geometric restraints to help address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here we present an integration of the full all-atom Amber molecular dynamics force field into Phenix crystallographic refinement, which enables a more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of non-bonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over twenty-two thousand protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better; clash scores and MolProbity scores are significantly improved; and the modelling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined with traditional geometry restraints. We find in general that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum mechanical representation of active sites and improved geometric restraints for simulated annealing. This document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr Word tools (available from http://journals.iucr.org/services/docxtemplate/ ) are installed when editing this document. The full Amber force field has been integrated into Phenix as an alternative refinement target. With a slight loss in speed, it achieves improved stereochemistry, fewer steric clashes and better hydrogen bonds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Real-space refinement in PHENIX for cryo-EM and crystallography

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.

59 BASIC BIOLOGICAL SCIENCES↗