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At least 19 records

Direct measurement of 5f delocalization with U XES

Delocalization of the 5f states in the early actinides in general and U metal in particular is significantly important and yet poorly understood. Here, extant spectroscopic techniques have failed to resolve the situation. Here it will be shown that X-Ray Emission Spectroscopy (XES) of the M 4,5 levels can provide the needed information, with a distinct difference between the delocalized U metal and localized uranium dioxide and uranium tetrafluoride cases. A Peak Ratio (PR) model, built upon electric dipole selection rules, has been developed and utilized, with quantitative agreement between experiment and theory. Possible expansion to other types of 5f mixing systems will be discussed.

36 MATERIALS SCIENCE↗

ROI-Finder : machine learning to guide region-of-interest scanning for X-ray fluorescence microscopy

The microscopy research at the Bionanoprobe (currently at beamline 9-ID and later 2-ID after APS-U) of Argonne National Laboratory focuses on applying synchrotron X-ray fluorescence (XRF) techniques to obtain trace elemental mappings of cryogenic biological samples to gain insights about their role in critical biological activities. The elemental mappings and the morphological aspects of the biological samples, in this instance, the bacterium Escherichia coli ( E. Coli ), also serve as label-free biological fingerprints to identify E. coli cells that have been treated differently. The key limitations of achieving good identification performance are the extraction of cells from raw XRF measurements via binary conversion, definition of features, noise floor and proportion of cells treated differently in the measurement. Automating cell extraction from raw XRF measurements across different types of chemical treatment and the implementation of machine-learning models to distinguish cells from the background and their differing treatments are described. Principal components are calculated from domain knowledge specific features and clustered to distinguish healthy and poisoned cells from the background without manual annotation. The cells are ranked via fuzzy clustering to recommend regions of interest for automated experimentation. The effects of dwell time and the amount of data required on the usability of the software are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Tools for uranium characterization in carbonate samples: case studies of natural U–Pb geochronology reference materials

Laser ablation U–Pb analyses of carbonate (LAcarb) samples has greatly expanded the potential for U–Pb dating to a variety of carbonate-producing settings. Carbonates that were previously considered impossible to date using isotope dilution methods may preserve radiogenic domains that can be dated using spatially resolved laser ablation geochronology techniques. Work is ongoing to identify reference materials and to consider best practices for LAcarb. In this study we apply standard and emerging characterization tool sets on three natural samples with the dual goal of enhancing the study of carbonates and establishing a new set of well-characterized natural reference materials for LAcarb studies. We start with the existing carbonate reference material WC-1 from the Permian Reef Complex of Texas, building on the published description to offer a deeper look at U and associated trace elements. We consider a tufa sample from the Miocene Barstow Formation of the Mojave Block, California, as a possible secondary calcite reference material due to its well-behaved U–Pb systematics. There are currently no natural dolomite standards. We present an unusual dolomite sample with very well-behaved U–Pb systematics from the Miocene of the Turkana Basin of Kenya as a possible dolomite reference material for LAcarb dating. In addition to using X-ray fluorescence (XRF) mapping and spectroscopy to better understand U in these natural samples, we have analyzed multiple aliquots of each of them for 87 Sr/ 86 Sr by thermal ionization mass spectrometry (TIMS). The Sr isotope compositions are analytically homogeneous within petrographically homogeneous regions of all three samples, and thus these materials could be used as Sr isotope standards as well. While not part of the current contribution, this combination could streamline simultaneous LA analyses of 87 Sr/ 86 Sr and U–Pb geochronology.

36 MATERIALS SCIENCE↗

Micro- to nano-scale areal heterogeneity in pore structure and mineral compositions of a sub-decimeter-sized Eagle Ford Shale

Mineral and organic matter compositions & pore structures of fine-grained shale influence reservoir properties. To improve the understanding of spatial heterogeneity in core-sized samples, methods of microscale X-ray fluorescence (μXRF) mapping, (ultra-) small-angle x-ray scattering [(U)SAXS] and wide-angle X-ray scattering (WAXS) have been used to determine elemental, pore-structure variations at scales up to ~10 cm on two samples prepared at circular and rectangular orientations from a piece of Eagle Ford Shale outcrop in South Texas, USA. In addition, thin section petrography and field emission-scanning electron microscopy observations, X-ray diffraction (XRD), total organic carbon, and pyrolysis were utilized to investigate the potential spatial heterogeneity of pore types, mineral and organic matter compositions for cm-sized samples at both orientations. Overall, the siliceous-carbonate mineral contents in these two samples (8 cm×8 cm×0.08 cm and 5 cm × 8 cm × 0.08 cm, in terms of width×length×thickness) of carbonate-rich Eagle Ford Shale vary between laminations at mm scales. For the circular sample, porosity and specific surface area (SSA) variations range from 0.82 to 3.04% and 1.51 to 14.1 m 2 /g, respectively. For the rectangular sample, values for porosity and SSA vary from 0.93 to 2.50% and 3.95 to 10.8 m 2 /g. By analyzing six selected sub-samples on each of two samples with (U)SAXS and XRD techniques, nm-sized pores are mainly interparticle ones in the higher calcite regions, where the porosity is also relatively lower, while the lower calcite regions consist of both interparticle and intraparticle pore types with higher porosity. Lastly, the μXRF and (U)SAXS mappings are combined to generate porosity distribution maps to provide more insights about sample heterogeneity related to the laminations and fractures at our observational scales.

58 GEOSCIENCES↗

The impact of feedstock size and composition on the hydrothermal growth of (U,Th)O 2

Bulk crystal growth of refractory oxides requires unique approaches, and the U x Th 1-x O 2 solid solution is no exception. Hydrothermal transport reactions of U 0.1 Th 0.9 O 2 onto ThO 2 seeds with feedstocks comprised of U 0.1 Th 0.9 O 2 or mixtures of UO 2 and ThO 2 with a nominal composition of U 0.1 Th 0.9 O 2 are investigated with µ-Raman spectroscopy and X-ray fluorescence. In each case, the trends in stoichiometry as a function of distance from the seed are analyzed and the deviations from the nominal stoichiometry discussed. When the feedstock is composed of mixed oxides, the particle surface area’s influence on the feedstock dissolution rate is the dominant factor and can produce U-rich stoichiometries as high as U 0.75 Th 0.25 O 2 . When composed solely of U 0.1 Th 0.9 O 2 , the total growth amount depends on the particle size, but the obtained stoichiometry is the product of differing solubilities. Although the U0.1Th0.9O 2 feedstock produces the most homogeneous growth, the ending growth of the smallest particle UO 2 /ThO 2 mixture yields the stoichiometry closest to U 0.1 Th 0.9 O 2 . How to obtain desired stoichiometries from mixtures by matching the particle size and solubilities is briefly discussed.

36 MATERIALS SCIENCE↗

Direct observation of Mn distribution/speciation within and surrounding a basidiomycete fungus in the production of Mn-oxides important in toxic element containment

Biogenic manganese (Mn) oxides occur ubiquitously in the environment including the uranium (U) mill tailings at the Ningyo-toge U mine in Okayama, Japan, being important in the sequestration of radioactive radium (Ra). To understand the nanoscale processes in Mn oxides formation at the U mill tailings site, Mn 2+ absorption by a basidiomycete fungus, Coprinopsis urticicola, isolated from Ningyo-toge mine water samples, was investigated in the laboratory under controlled conditions utilizing electron microscopy, synchrotron-based X-ray analysis, and fluorescence microscopy with molecular pH probe. The fungus’ growth was first investigated in an agar-solidified medium supplemented with 1.0 mmol/L of Mn 2+ , ± Cu 2+ (50 – 200 µM), ± Zn 2+ (50 – 200 µM), or ± diphenyleneiodonium chloride (DPI) (50 – 100 µM) at 25 °C. The results revealed that Zn 2+ has no significant effects on the Mn oxides formation, whereas Cu 2+ and DPI significantly inhibit both fungal growth and Mn oxidation, indicating superoxide-mediated Mn oxidation. During the interaction of Mn 2+ with the fungi in solution medium at the initial pH of 5.67, a small fraction of Mn 2+ infiltrated into the fungal hyphae within 8 h, forming a few tens nm-sized concentrates of soluble Mn2+ in the intracellular pH of ~6.5, which can be released back to solution within a day as shown in a subsequent releasing experiment. After 1 day of incubation, Mn oxides began to precipitate on the hyphae, which were characterized to be fibrous nanocrystals with a hexagonal birnessite-structure, these forming spherical aggregates with a diameter of ~1.5 µm. When the fungi were reacted using the Ningyo-toge mine water, the Mn concentration decreased at a rate of 1.0 mmol·day-1 per unit dry weight. The nanoscale processes associated with the fungi derived from the Ningyo-toge mine area provides additional insights into the existing mechanisms of Mn oxidation by filamentous fungi at other U mill tailings sites under circumneutral pH conditions. Such processes add to the class of reactions important to the sequestration of toxic elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geobacter sulfurreducens Immobilized Boron-Doped Diamond Electrodes for Uranium(VI) in Water Electrochemical Bioremediation

The proliferation of nuclear science and technology has resulted in an increase in nuclear waste containing uranium, posing significant risks to both human and environmental health. This study proposes the use of Geobacter sulfurreducens (G. sulfurreducens) modified boron-doped diamond electrodes to facilitate the reduction and removal of uranium(VI) from aqueous media. The bioremediation process involves electrochemically immobilizing the bacteria on a boron-doped diamond electrode (BDD). The immobilization process requires applying reduction potentials ranging from −0.40 to −0.70 V (vs Ag/AgCl (3 M NaCl)), with −0.60 V identified as the optimal potential for effective bacterial modification. The uranium source is provided by a 2.0 mM uranyl acetate solution in G. sulfurreducens growth medium. Scanning electron microscopy (SEM) reveals a highly uniform layer of uranium on the electrode surface. Energy-dispersive X-ray fluorescence spectroscopy (EDS) and cyclic voltammetry (CV) studies confirm the presence of uranium in the system. Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) successfully elucidate the reduction process of U(VI) to predominantly U(IV) using a bacteria-electrode coupled system. Additionally, a comparison is made with the electrochemical removal of uranyl ions using the electrodeposition method on unmodified BDD. Results demonstrate the presence of three uranium oxide species (UO 2 , UO 3 , and U 3 O 8 ) on the BDD electrode after experimentation, in contrast to the G. sulfurreducens/BDD assembly, which achieves the predominant reduction of UO 2 2+ to UO 2 with a small quantity of UO 3 as the final species. This study highlights the efficient electrochemical removal of uranyl ions from aqueous media at the G. sulfurreducens/BDD interface through chronoamperometry, presenting a promising approach for remediating sites contaminated with radioactive materials. The findings contribute to the exploration of sustainable alternatives for managing nuclear waste, emphasizing the potential of this electrochemical bioremediation strategy.

Bacteria↗

Chemical state mapping of simulant Chernobyl lava-like fuel containing material using micro-focused synchrotron X-ray spectroscopy

Uranium speciation and redox behaviour is of critical importance in the nuclear fuel cycle. X-ray absorption near-edge spectroscopy (XANES) is commonly used to probe the oxidation state and speciation of uranium, and other elements, at the macroscopic and microscopic scale, within nuclear materials. Two-dimensional (2D) speciation maps, derived from microfocus X-ray fluorescence and XANES data, provide essential information on the spatial variation and gradients of the oxidation state of redox active elements such as uranium. In the present work, we elaborate and evaluate approaches to the construction of 2D speciation maps, in an effort to maximize sensitivity to the U oxidation state at the U L 3 -edge, applied to a suite of synthetic Chernobyl lava specimens. Our analysis shows that calibration of speciation maps can be improved by determination of the normalized X-ray absorption at excitation energies selected to maximize oxidation state contrast. The maps are calibrated to the normalized absorption of U L 3 XANES spectra of relevant reference compounds, modelled using a combination of arctangent and pseudo-Voigt functions (to represent the photoelectric absorption and multiple-scattering contributions). We validate this approach by microfocus X-ray diffraction and XANES analysis of points of interest, which afford average U oxidation states in excellent agreement with those estimated from the chemical state maps. This simple and easy-to-implement approach is general and transferrable, and will assist in the future analysis of real lava-like fuel-containing materials to understand their environmental degradation, which is a source of radioactive dust production within the Chernobyl shelter.

36 MATERIALS SCIENCE↗

Safely probing the chemistry of Chernobyl nuclear fuel using micro-focus X-ray analysis

Detailed chemical analysis of the solidified molten fuel still residing in the stricken Chernobyl reactor unit 4 are inferred using multi-modal micro-focus X-ray analysis of a low-radioactivity proxy. A fascinating mixture of molten UO 2 , nuclear fuel cladding, concrete, stainless steel and other nuclear reactor components, these materials behaved like lava, solidifying to form a complex, highly radioactive glass-ceramic. Using element-specific chemical probes (micro-X-ray fluorescence and X-ray absorption spectroscopy), coupled with micro-diffraction analysis, the crystalline phase assemblage of simulants of these heterogeneous materials was established, which included “chernobylite” and a range of compositions in the (U 1-x Zr x )O 2 solid solution. Novel insight to nuclear accident fuel chemistry was obtained by establishing the oxidation state and local coordination of uranium not only in these crystalline phases, but uniquely in the amorphous fraction of the material, which varied depending on the history of the nuclear lava as it flowed through the reactor. This study demonstrates that micro-focus X-ray analysis of very small fractions of material can yield rich chemical information, which can be applied to nuclear-melt down materials to aid decommissioning and nuclear fuel management at nuclear accident sites.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Extraction of branching ratios from HERFD data

A quantitative analysis method has been developed that allows the cross calibration of separate Uranium M 4 and M 5 X-ray absorption spectra (XAS), in particular those collected with the new High Energy Resolution Fluorescence Detection (HERFD) method. With this method, it is now possible to generate experimental Branching Ratio (BR) values from the U M 4,5 XAS HERFD data.

36 MATERIALS SCIENCE↗

XRF-ROI Finder: Machine Learning to Guide Region-of-Interest Scanning for X-ray Fluorescence Microscopy

The ROI-finder software is being developed for use by several Microscopy Group beamlines at Argonne National Laboratory, including 2-ID microprobes and 9-ID-B Bionanoprobe which use multi-scale scanning fluorescence microscopy to acquire elemental maps (multi-modal image data). Microscopy experiments require scan of samples at a coarse resolution followed by ROI identification using feature detection based on domain expertise. Finer resolution scans are then conducted based on identified ROI. The decision-making process based on domain expertise will be difficult to perform for faster data rates and much larger sampling volumes anticipated after APS-U necessitating the need for the ROI-finder software. The ROI- finder detects regions of interest through a continuous learning process, starting with a unsupervised representation learning and improving its recommendations through supervised learning and an interactive tool for user annotation. The scope of ongoing development efforts includes the integration of image registration module to correlate optical and X-ray images, extraction of feature morphology as well as elemental signatures in the image space and incorporation of beamtime streaming data by the scanning probe via EPICS.

CHOWDHURY, M. ARSHAD ZAHANGIR↗

Structural transition and uranium valence change in UTe 2 at high pressure revealed by x-ray diffraction and spectroscopy

High-pressure x-ray diffraction up to 30 GPa, in conjunction with resonant emission x-ray spectroscopy and partial fluorescence yield x-ray absorption spectroscopy up to 52 GPa, were used to study how the structural and electronic properties of UTe2 evolve with pressure at room temperature. An orthorhombic-to-tetragonal phase transition was observed to occur between 5 and 7 GPa, with a large volume collapse of nearly 10% and a nearest U-U distance increase by about 4%. This lower-to-higher symmetry transition suggests less 5⁢f electron participation in bonding when the weakly correlated superconducting phase in the tetragonal structure of UTe 2 appears. Beyond 7 GPa, no new structural transitions were found up to 30 GPa. The resonant x-ray emission spectra clearly demonstrate an intermediate valence of U, nearly +3.74 at 1.8 GPa and room temperature, and reveal that the U valence shifts towards 4+, passes through a peak at 2.8 GPa, then decreases towards 3+ and settles down to a nearly constant value above 15 GPa. These experiments reveal that some fundamental structural and valence changes occur in UTe 2 at relatively low pressures, which could be responsible for the interplay between unconventional superconductivity, magnetic ordering, and weakly correlated superconductivity that is manifested in the temperature-pressure phase diagram of UTe 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nondestructive geochemical characterization of fossil hominin taphonomy and burial history

To date, only three Homo habilis specimens have been discovered that have associated craniodental and postcranial elements, providing a limited fossil record of the ontogeny and morphology of early members of the genus Homo. Recently, a nearly complete dentition, likely attributable to H. habilis, was discovered and excavated from early Pleistocene-age fluvial-lacustrine sediments of the upper Burgi Member of the Koobi Fora Formation at site F25787 in Area 13, near Ileret, Kenya. On the surface less than 15 m away, at site F25966, postcranial elements were found, which, if from the same individual as the nearby dentition, would represent the fourth associated craniodental and postcranial assemblage of this species. We developed a geochemical taphonomic history of these ca. 2 Ma hominin fossils using nondestructive X-ray based microanalytical tools (synchrotron and benchtop X-ray fluorescence chemical imaging and micro- and nano-computed tomography volumetric reconstruction), bulk analyses of sediments and paleosols at the excavation sites, and sedimentologic and stratigraphic observations. We integrate the chemical and physical taphonomic histories to test whether teeth (excavated in situ) and postcranial bones (eroded onto the outcrop surface) derive from a single individual. Minor differences in taphonomic history are attributable to the different biomineral properties of the dental and osseous components and to differences in physical damage during early post-mortem scavenging, dispersal, and burial in adjacent depositional settings. Microscale geochemical mapping enabled the temporal ordination of chemical and physical events in the specimens’ chemical taphonomic histories. Specifically, authigenic Fe- and K-bearing clays and Y, U, and Sr uptake occurred in post-burial fractures in bones and were also incorporated pervasively throughout dentin in teeth. Barite mineralization occurred along the latest fractures in both materials, and as a coating on tooth roots. The stratigraphic, taphonomic, and geochemical evidence supports the interpretation that the hominin fossils represent a single individual. Finally, successful application of these nondestructive sample characterization methods demonstrates capabilities for thorough interrogation of the taphonomic histories of other potential hominin fossil associations, enabling more robust and accurate palaeontologic constraints using those relationships.

36 MATERIALS SCIENCE↗

Mechanical Design Progress of the In Situ Nanoprobe Instrument for APS-U

The In Situ Nanoprobe (ISN, 19-ID) beamline will be a new best-in-class long beamline to be constructed as part of the Advanced Photon Source Upgrade (APS-U) project [1, 2]. To achieve long working distance at high spatial resolution, the ISN instrument will be positioned 210 m downstream of the x-ray source, in a dedicated satellite building, currently under construction [3]. The ISN instrument will use a nano-focusing Kirkpatrick-Baez (K-B) mirror system, which will focus hard x-rays to a focal spot as small as 20 nm, with a large working distance of 61 mm. The large working distance provides space for various in situ sample cells for x-ray fluorescence tomography and ptychographic 3D imaging, allows the use of a separate, independent vacuum chambers for the optics and sample, and provides the flexibility to run experiments in vacuum or at ambient pressure. A consequence of the small spot size and large working distance are stringent requirements for high angular stability of the K-B mirrors (5 nrad V-mirror and 16 nrad H-mirror) and high relative stability be-tween focus spot and sample (4 nmRMS). Additional features include fly-scanning up to 2 kg mass, sample plus in situ cell, at 1 mm/s in vertical and/or horizontal directions over an area of 10 mm x 10 mm. Environmental capabili-ties will include heating and cooling, flow of fluids and applied fields, as required for electrochemistry and flow of gases at high temperature for catalysis. To achieve these capabilities and precise requirements we have used precision engineering fundamentals to guide the design process.

Kearney, Steven P.↗

Resonant x-ray emission across the L 3 edge of uranium compounds

A narrow bandwidth x-ray beamline and a multi-crystal von Hamos spectrometer were used to record x-ray absorption and x-ray emission (XES) across the uranium L 3 edge of UO 2 , UO 3 , Cs 2 UO 2 Cl 4 , and Cs 2 UCl 6 . Measurements were made over 17150–17250 eV with an instrumental resolution of ∼2 eV. This resolution allowed the use of Lorentzian peak fits to the L 3 N 4 and L 3 N 5 characteristic x-ray fluorescence lines that have ∼12–13 eV lifetime widths. The fluorescence yields of the four compounds display strong white lines near threshold and multiple scattering features at higher energies. The XES spectra were fit with three Lorentzians, two for the L 3 N 4 and L 3 N 5 lines and one for inelastic scattering by 2p–6d excitations and 4d–6d final states. The intensities of the white lines were largely due to the inelastic scattering component. To support the measurements, relativistic equation-of-motion coupled-cluster and restricted active space configuration interaction calculations were performed for uranium core-excitation energies in Cs 2 UO 2 Cl 4 and Cs 2 UCl 6 . These calculations with rigorous treatments of relativistic effects are shown to provide accurate uranium L 3 -edge binding energies, L 3 N 5 emission energies, as well as the energy losses in the inelastic scattering process. The measured and calculated results show variations between compounds with U(IV) oxidation states that contain 6d 0 5f 2 electrons in their ground configurations (UO 2 and Cs 2 UCl 6 ) compared with U(VI) compounds (UO 3 and Cs 2 UO 2 Cl 4 ) with empty 5f and 6d configurations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Optical control of ultrafast structural dynamics in a fluorescent protein

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump–probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic optical spectroscopy and pyrometry of static targets under optical and x-ray laser heating at the European XFEL

Experiments accessing extreme conditions at x-ray free electron lasers (XFELs) involve rapidly evolving conditions of temperature. Here, we report time-resolved, direct measurements of temperature using spectral streaked optical pyrometry of x-ray and optical laser-heated states at the High Energy Density instrument of the European XFEL. This collection of typical experiments, coupled with numerical models, outlines the reliability, precision, and meaning of time dependent temperature measurements using optical emission at XFEL sources. Dynamic temperatures above 1500 K are measured continuously from spectrally- and temporally-resolved thermal emission at 450–850 nm, with time resolution down to 10–100 ns for 1–200 μs streak camera windows, using single shot and integrated modes. Targets include zero-pressure foils free-standing in air and in vacuo, and high-pressure samples compressed in diamond anvil cell multi-layer targets. Radiation sources used are 20-fs hard x-ray laser pulses at 17.8 keV, in single pulses or 2.26 MHz pulse trains of up to 30 pulses, and 250-ns infrared laser single pulses. A range of further possibilities for optical measurements of visible light in x-ray laser experiments using streak optical spectroscopy are also explored, including for the study of x-ray induced optical fluorescence, which often appears as background in thermal radiation measurements. We establish several scenarios where combined emissions from multiple sources are observed and discuss their interpretation. Challenges posed by using x-ray lasers as non-invasive probes of the sample state are addressed.

47 OTHER INSTRUMENTATION↗

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗