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At least 721 records · Page 40

Prediction of vacancy defect diffusion paths in high entropy alloys via machine learning on molecular dynamics data

Identifying the diffusion path of point defects is a critical step in understanding their evolution and the mechanisms of related phenomena. Defect diffusion occurs at small length and time scales, with impacts on material properties that may continue to evolve over ns to μs, ms, and the continuum scale (s, min, etc., and cm, m, etc.). The time scale accessible to molecular dynamics (MD) simulations is limited by small step sizes, typically in the fs range. Thus, surrogate models of MD simulations through machine learning (ML)-based algorithms are of great interest, especially for complex systems such as high entropy alloys (HEAs). In this work, dynamics governing vacancy migration in HEA were approximated with graph convolutional network (GCN) models as ansatzes for kinetic Monte Carlo (KMC) rate catalogs. Network design considered that diffusion in crystalline solids generally depends on interactions between defects and their immediate neighbor atoms. Graphs represented the vacancy surroundings, MD-generated trajectories provided training and comparison datasets, and unsupervised GCN models approximated interatomic dynamics governing vacancy migration in HEAs as ansatzes for KMC. A proof-of-concept model trained on MD data for the Fe, Ni, Cr, Co, and Cu HEA environment was used with two different neighbor interactions to assess the feasibility of training a GCN to predict vacancy defect transition rates in the HEA environment. The resulting setup rapidly generated MD-formatted synthetic trajectories based on dynamics learned from the MD training set, with a time acceleration of roughly two orders of magnitude and a similar diffusion coefficient to MD observations. Additionally, Nudged Elastic Band (NEB) calculations were performed on randomly generated FeNiCrCoCu HEA structures to determine vacancy migration barriers across nearest-neighbor sites. Transition probabilities for each jump, categorized by atomic type, were extracted from these calculations. NEB-based and GCN-based approaches led to similar outcomes.

Reimer, C↗

Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses

The 1918 influenza A virus (IAV) caused the most severe flu pandemic in recorded human history. Nonstructural protein 1 (NS1) is an important virulence factor of the 1918 IAV. NS1 antagonizes host defense mechanisms through interactions with multiple host factors. One pathway by which NS1 increases virulence is through the activation of phosphoinositide 3-kinase (PI3K) by binding to its p85β subunit. Here we present the mechanism underlying the molecular recognition of the p85β subunit by 1918 NS1. Using X-ray crystallography, we determine the structure of 1918 NS1 complexed with p85β of human PI3K. We find that the 1918 NS1 effector domain (1918 NS1 ED ) undergoes a conformational change to bind p85β. Using NMR relaxation dispersion and molecular dynamics simulation, we identify that free 1918 NS1 ED exists in a dynamic equilibrium between p85β-binding–competent and –incompetent conformations in the submillisecond timescale. Moreover, we discover that NS1 ED proteins of 1918 (H1N1) and Udorn (H3N2) strains exhibit drastically different conformational dynamics and binding kinetics to p85β. These results provide evidence of strain-dependent conformational dynamics of NS1. Using kinetic modeling based on the experimental data, we demonstrate that 1918 NS1 ED can result in the faster hijacking of p85β compared to Ud NS1 ED , although the former has a lower affinity to p85β than the latter. Our results suggest that the difference in binding kinetics may impact the competition with cellular antiviral responses for the activation of PI3K. We anticipate that our findings will increase the understanding of the strain-dependent behaviors of influenza NS1 proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens

The synthesis of quinolinic acid from tryptophan is a critical step in the de novo biosynthesis of nicotinamide adenine dinucleotide (NAD + ) in mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4-dioxygenase responsible for quinolinic acid production was studied by performing time-resolved in crystallo reactions monitored by UV-vis microspectroscopy, electron paramagnetic resonance (EPR) spectroscopy, and X-ray crystallography. Seven catalytic intermediates were kinetically and structurally resolved in the crystalline state, and each accompanies protein conformational changes at the active site. Among them, a monooxygenated, seven-membered lactone intermediate as a monodentate ligand of the iron center at 1.59-Å resolution was captured, which presumably corresponds to a substrate-based radical species observed by EPR using a slurry of small-sized single crystals. Other structural snapshots determined at around 2.0-Å resolution include monodentate and subsequently bidentate coordinated substrate, superoxo, alkylperoxo, and two metal-bound enol tautomers of the unstable dioxygenase product. These results reveal a detailed stepwise O-atom transfer dioxygenase mechanism along with potential isomerization activity that fine-tunes product profiling and affects the production of quinolinic acid at a junction of the metabolic pathway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography

The genome of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronavirus has a capping modification at the 5'-untranslated region (UTR) to prevent its degradation by host nucleases. These modifications are performed by the Nsp10/14 and Nsp10/16 heterodimers using S-adenosylmethionine as the methyl donor. Nsp10/16 heterodimer is responsible for the methylation at the ribose 2'-O position of the first nucleotide. To investigate the conformational changes of the complex during 2'-O methyltransferase activity, we used a fixed-target serial synchrotron crystallography method at room temperature. We determined crystal structures of Nsp10/16 with substrates and products that revealed the states before and after methylation, occurring within the crystals during the experiments. Here we report the crystal structure of Nsp10/16 in complex with Cap-1 analog ( m7 GpppA m2'-O ). Inhibition of Nsp16 activity may reduce viral proliferation, making this protein an attractive drug target.

59 BASIC BIOLOGICAL SCIENCES↗

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.

60 APPLIED LIFE SCIENCES↗

Electron doping of a double-perovskite flat-band system

Electronic structure calculations indicate that the Sr 2 FeSbO 6 double perovskite has a flat-band set just above the Fermi level that includes contributions from ordinary subbands with weak kinetic electron hopping plus a flat subband that can be attributed to the lattice geometry and orbital interference. To place the Fermi energy in that flat band, electron-doped samples with formulas Sr 2- x La x FeSbO 6 (0 ≤ x ≤ 0.3) were synthesized, and their magnetism and ambient temperature crystal structures were determined by high-resolution synchrotron X-ray powder diffraction. All materials appear to display an antiferromagnetic-like maximum in the magnetic susceptibility, but the dominant spin coupling evolves from antiferromagnetic to ferromagnetic on electron doping. Which of the three subbands or combinations is responsible for the behavior has not been determined.

Science & Technology - Other Topics↗

CryoTransformer: a transformer model for picking protein particles from Cryo-EM micrographs

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of large protein complexes. Picking single protein particles from cryo-EM micrographs (images) is a crucial step in reconstructing protein structures from them. However, the widely used template-based particle picking process requires some manual particle picking and is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) can potentially automate particle picking, the current AI methods pick particles with low precision or low recall. The erroneously picked particles can severely reduce the quality of reconstructed protein structures, especially for the micrographs with low signal-to-noise-ratio (SNR).

59 BASIC BIOLOGICAL SCIENCES↗

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↗

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

Cosmic ray transport in mixed magnetic fields and their role on the observed anisotropies

ABSTRACT There is a growing set of observational data demonstrating that cosmic rays exhibit small-scale anisotropies (5°–30°) with amplitude deviations lying between 0.01–0.1 per cent that of the average cosmic ray flux. A broad range of models have been proposed to explain these anisotropies ranging from finite-scale magnetic field structures to dark matter annihilation. The standard diffusion transport methods used in cosmic ray propagation do not capture the transport physics in a medium with finite-scale or coherent magnetic field structures. Here, we present a Monte Carlo transport method, applying it to a series of finite-scale magnetic field structures to determine the requirements of such fields in explaining the observed cosmic ray, small-scale anisotropies.

79 ASTRONOMY AND ASTROPHYSICS↗

Spin excitations in the frustrated triangular lattice antiferromagnet NaYbO 2

In this work, we present a neutron scattering-based study of magnetic excitations and magnetic order in NaYbO 2 under the application of an external magnetic field. The crystal electric field-split J = 7=2 multiplet structure is determined, revealing a mixed |m z $\rangle$ ground state doublet and is consistent with a recent report Ding et al. Our measurements further suggest signatures of exchange effects in the crystal field spectrum, manifested by a small splitting in energy of the transition into the first excited doublet. The field-dependence of the low-energy magnetic excitations across the transition from the quantum disordered ground state into the fluctuation driven ordered regime is analyzed. Signs of a first-order phase transition into a noncollinear ordered state are revealed at the upper-field phase boundary of the ordered regime, and higher order magnon scattering, suggestive of strong magnon-magnon interactions, is resolved within the previously reported up-up-down phase. Our results reveal a complex phase diagram of field-induced order and spin excitations within NaYbO 2 and demonstrate the dominant role of quantum fluctuations cross a broad range of fields within its interlayer frustrated triangular lattice.

36 MATERIALS SCIENCE↗

Dynamics of dust particles confined in imposed potential structures in strongly magnetized, low-temperature plasmas

A new phenomenon called imposed ordered structures has been of particular interest to the dusty plasma community within the past several years. These structures are a new type of pattern formation within a dusty plasma in which the dust particles become fixed to a background confining potential whose spatial structure is determined by some conducting element present in the plasma. In previous works, this element has typically been a conducting wire mesh. One of the unanswered questions is whether the dust particles become trapped beneath the conducting surface of the mesh or in the gaps (holes) between the wires. This work makes use of a new electrode whose shape is designed to mimic that of wire mesh, but with much larger dimensions to facilitate in situ diagnostic measurements. Observations of the dust show that particles become confined to the regions beneath the holes of this new electrode. Measurements of the dust particle velocities allow for a determination of the kinetic energy within the dust cloud which show that the particles are in an energetic steady state. Further, comparisons of spatial profiles of the particle velocities also show that the dust particles typically reside in areas of increased plasma glow, possibly being trapped by plasma filaments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Origin of liquid fragility

Liquid fragility characterizes how steeply the viscosity of a glass-forming liquid decreases with increasing temperature above the glass transition. It is one of the most fundamental properties of a liquid, with high importance for science and application. Yet, its origin is unclear. Here we show that it is directly related to the structural coherence of the medium-range order (MRO) in liquid defined by the decay of the pair-distribution function with distance. The MRO can also be evaluated from the first peak of the structure function determined by x-ray or neutron diffraction, and it is a measure of the cooperativity of atomic motion in a diffusive event in supercooled liquids. These findings shed light on the mechanism of atomic transport in supercooled liquids.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Confinement Controls the Bend Instability of Three-Dimensional Active Liquid Crystals

Spontaneous growth of long-wavelength deformations is a defining feature of active liquid crystals. We investigate the effect of confinement on the instability of 3D active liquid crystals in the isotropic phase composed of extensile microtubule bundles and kinesin molecular motors. When shear aligned, such fluids exhibit finite-wavelength self-amplifying bend deformations. By systematically changing the channel size we elucidate how the instability wavelength and its growth rate depend on the channel dimensions. Experimental findings are qualitatively consistent with a minimal hydrodynamic model, where the fastest growing deformation is set by a balance of active driving and elastic relaxation. Furthermore, our results demonstrate that confinement determines the structure and dynamics of active fluids on all experimentally accessible length scales.

59 BASIC BIOLOGICAL SCIENCES↗

Tunable magnetic excitations in the honeycomb antiferromagnet (Co,Ni)⁢TiO3

The solid solution of the honeycomb antiferromagnet (AFM) Co0.5⁢Ni0.5⁢TiO3 (CNTO) was synthesized by mixing a 1:1 molar ratio of CoTiO3 (CTO) and NiTiO3 (NTO). Powder neutron scattering was used to determine the structure and magnetic spectrum, where the nuclear and magnetic structures resemble those of the end members. The Néel temperature (T𝑁 = 27 ± 1 K), the ordered magnetic moment (M = 2.29 ± 0.03 𝜇𝐵 per magnetic ion), and lattice parameters are intermediate between those of the two. From inelastic neutron scattering, it is observed that the magnon density of states (MDOS) extends up to 13 meV, and the interaction can be described by an XXZ-type magnetic Hamiltonian. Above 15 meV, spin-orbit excitons (SOEs) are observed similarly to those in CTO, but with modified spin-orbit crystal-field splitting because of the substitution of Ni at Co sites, and the disorder induced by the Ni substitution modifies the spin-orbit crystal field. Thus, the magnetic dynamics of the CNTO cannot be described as a simple average of the two parent compounds.

Rathnayaka, Srimal [University of Virginia, Charlo↗

Co-flow injection for serial crystallography at X-ray free-electron lasers

Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macromolecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.

3D printing↗

Revisiting the structures and phase transitions of Ba 2 NaNb 5 O 15

The room-temperature and low-temperature structure(s) of Ba 2 NaNb 5 O 15 (BNN) have been debated since the structure was proposed in the 1960s. This work revisits the structures and phase transitions of BNN, combining high-resolution X-ray and neutron powder diffraction with density functional theory calculations. Temperature-dependent high-resolution X-ray powder diffraction patterns are collected from 4 to 918 K, and sequential batch Rietveld refinement using a symmetry mode approach to describe the structure is used to extract the main structural changes as a function of temperature. The data show that the average structure of BNN is best described by the Ama2 space group, and no other structural phase transitions were observed below the ferroelastic transition. The symmetry mode analysis, combining results from diffraction and density functional theory, shows significant octahedral tilting and corrugations of both the A1 and A2 sites along the c direction. A strong correlation between the spontaneous strain and the octahedral tilting was observed, and a potential connection with emerging microstructure at low temperatures is proposed, all enabled by the symmetry mode approach used in this work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗