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At least 343 records · Page 19

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DOE OSTI2021

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2

The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single–amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single– and multiple–amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Software Quality Assurance Plan ANSYS LSDYNA Version 2023R1

ANSYS Inc. develops and markets engineering simulation software and services used in the aerospace, automotive, manufacturing, electronics, biomedical, energy, defense, and many other industries. ANSYS is dedicated to engineering simulation and is the world’s leading software provider. ANSYS was founded in 1970 and is headquartered in Canonsburg, Pennsylvania. ANSYS provides an engineering analysis tool combining structural, thermal, computational fluid dynamics, acoustic and electromagnetic simulation capabilities. ANSYS LS-DYNA is the most used explicit simulation program capable of simulating the response of materials to short periods of severe loading. Its many elements, contact formulations, material models, and other controls can be used to simulate complex models with control over all the details of the problem. ANSYS LS-DYNA has a vast array of capabilities to simulate extreme deformation problems using its explicit solver. Engineers can tackle simulations involving material failure and look at how the failure progresses through a part or through a system. Models with large amounts of parts or surfaces interacting with each other are also easily handled, and the interactions and load passing between complex behaviors are modeled accurately. Using computers with higher numbers of CPU cores can drastically reduce solution times. In addition, many consulting firms and hundreds of universities use ANSYS for analysis, research, and educational purposes. ANSYS is recognized worldwide as one of the most widely used and capable programs of its type. ANSYS has successfully passed over 100 customer quality system audits against American Society of Mechanical Engineers (ASME) NQA-1 and 10 CFR Part 50, Appendix B, since the company was founded, over 60 of which have been since 1997. ANSYS has successfully passed over 100 International Organization for Standardization (ISO) 9001 assessments. ANSYS design analysis software is the first created within a quality system with ISO 9001 certification, which is the internationally accepted quality standard. Product development, testing, maintenance, and support processes also meet the US Nuclear Regulatory Commission’s (NRC’s) quality requirements, as they have for nearly four decades. ANSYS staff perform more than 60,000 software verification tests before releasing each new product. ASME NQA-1-2012 (Subpart 2.7 is specific to software) is the industry- and NRC-accepted approach (consensus standard) for meeting 10 CFR Part 50, Appendix B, requirements.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern↗

DOE OSTI2025

Wettability of Two-Dimensional Carbon Allotropes from Molecular Simulations

Force-field Monte Carlo and Molecular Dynamics simulations are used to compare wetting behaviors of model carbon sheets mimicking neat graphene, its saturated derivative, graphane, and related planar allotropes penta-graphene, γ-graphyne, and ψ-graphene in contact with aqueous droplets or an aqueous film confined between parallel carbon sheets. Atomistic and area-integrated surface/water potentials are found to be essentially equivalent in capturing moderate differences between the wetting free energies of tested substrates. Despite notable differences in mechanical and electric properties of distinct allotropes, the predicted allotrope/water contact angles span a narrow window of weakly hydrophilic values. Contact angles in the range of 80 ± 10° indicate modest hydration repulsion incapable of competing with van der Waals attraction between carbon particles. Poor dispersibility in neat water is hence a common feature of studied materials.

Biochemistry & Molecular Biology↗

DOE OSTI2021

Coupling dynamic in situ X-ray micro-imaging and indentation: A novel approach to evaluate micromechanics applied to oil shale

Oil and gas shales are a system where understanding the mechanical properties at the microscale is of paramount importance, e.g. to better understand the behavior of proppant-shale contacts and their role in the evolution of propped fractures in unconventional reservoirs. Here we show for the first time an experiment coupling indentation testing with in situ X-ray imaging in a Green River shale sample. A full compliance curve has been measured with the sample in water, allowing to visualize the indentation of the sample in function of axial load, in a purpose-built system for combined in situ indentation and X-ray imaging. A series of 3D datasets were used for a digital volume correlation study to obtain local strain fields. This analysis has been complemented with the analysis of cracks. Finally, geomechanical modeling has been carried out to replicate and generalize the observed behavior in the shale. This study validated this experimental approach, providing a breakthrough in understanding micro-mechanics in shales, and demonstrates how this class of experiments can be important for studies involving the prediction of the evolution of propped fractures in shale reservoirs, with possible applications in a much larger number of application fields (geothermal, materials science, etc.)

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2020

Fractal Model for Drag Reduction on Multiscale Nonwetting Rough Surfaces

Rough surfaces in contact with a flow of fluid exhibit alternating no-slip and free shear boundary conditions at the solid–liquid and air–liquid interfaces, respectively, thereby potentially offering drag reduction benefits. The balance between the dynamic pressure in the flow and the restoring capillary pressure in the interasperity spaces determines the stability of the Cassie state of wettability and is a function of the relative extent of no-slip and free shear regions per unit surface area. In the present study, using a fractal representation of rough surface topography, an analytical model is developed to quantify the stability of the Cassie state of wettability as well as drag reduction and the friction factor for laminar flow in a rectangular channel between nonwetting multiscale rough surfaces. A systematic study is conducted to quantify the effects of fractal parameters of the surfaces and the flow Reynolds number on drag reduction and the friction factor. The studies are used to develop friction factor curves extending the classical Moody diagram to hydrophobic and superhydrophobic surfaces. On the basis of the studies, regime maps are derived for estimating the extent of drag reduction offered by hydrophobic and superhydrophobic surfaces, revealing that superhydrophobic surfaces do not always offer the best drag reduction performance. The application of the fractal model to practical topographies of nonwetting surfaces of copper, aluminum, and zinc oxide fabricated via electrodeposition and etching is also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Integrated machine learning-molecular dynamics framework for electrolyte property prediction

Electrochemical stability windows determine the operating range of battery electrolytes, yet accurate prediction remains challenging because stability emerges from statistical ensembles of local solvation environments rather than single ground-state molecular structures. Traditional density functional theory calculations on energy-minimized clusters cannot capture the thermal variations in local coordination environments and geometries that govern decomposition, while SMILES-based machine learning methods lack explicit representation of three-dimensional solvation structure and ion pairing. Here, we introduce a structure-aware machine learning framework that predicts frontier orbital energies (HOMO and LUMO) directly from molecular dynamics-sampled solvation configurations, achieving sub-0.6 eV accuracy at computational costs 3–4 orders of magnitude lower than first-principles methods. Across twelve representative battery electrolytes, we demonstrate that solvent-separated and contact ion pairs exhibit strong size- and local chemistry dependent electronic stability, with variations in coordination shifts of HOMO or LUMO level by 2–3 eV, and that extended solvation structure and partially desolvated environment further modulate stability by up to 3 eV. By encoding the statistical nature of electrochemical failure through ensemble sampling of explicit solvation geometries, our approach enables high-throughput screening and rational design of next-generation battery electrolytes with mechanistic understanding of structure–property relationships.

Energy - Storage↗

DOE OSTI2024

Role of Dynamic Polarization Interactions in the Electrical Double Layer at Calcite (104) Interfaces with Aqueous Solutions

Reactions at mineral interfaces with aqueous solutions control many geochemical and biogeochemical processes in the Earth’s critical zone. At the molecular level, insights into important properties such as the structure of the electrical double layer (EDL) at specific mineral interfaces continue to improve due to the increasing fidelity of laboratory instrumentation and computational approaches. However, molecular simulation approaches suffer from limited reach into relevant scales of time, length, and system complexity. To span this gap, a novel hybrid approach that couples first principle plane-wave density functional theory (DFT) with classical DFT (cDFT) is demonstrated and applied to calcite (104) interfaces with various electrolytes. In this approach, a region of interest described using DFT interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. Benchmarking against experimental observations and entirely first principle DFT simulations demonstrates that this hybrid model efficiently encompasses the key short-range and collective interactions in the EDL. Simulations of calcite (104)/solution interfaces reveal the key static and dynamic polarization interactions that give rise to structuring of ions and water. Ion hydration interactions have the strongest effect on the depth of the first minimum in the density distribution of counterions at the surface, and the position and width of the first density peak is largely determined by the strength of ion-correlation forces. Finer details of ion distributions are controlled by mutual polarization of the calcite surface and interfacial electrolyte. Finally, this new ability to efficiently and rigorously predict EDL structure at mineral surfaces in contact with complex solutions paves the way to accurately modeling sorption, nucleation, dissolution, and growth in realistic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply

Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Influence of solutes on the core structures of $\langle$ α $\rangle$-type screw dislocations in $α$-Ti

The $\langle$ α $\rangle$-type screw dislocations are known to be significant mediators of plasticity in hexagonal-close-packed (HCP) metals. These dislocations have polymorphic core structures, and subtle changes in the relative energies of these core structures are known to have a large impact on the dynamics of the dislocations. Here, this work identifies a previously neglected long-range elastic interstitial-solute/dislocation interaction that influences the core structures. Essentially, interstitial solutes induce a change in the dislocation core structure to minimize the energy of interaction between the solutes and the dislocation. Molecular dynamics simulations, continuum linear elasticity, and statistical analysis show that this long-range interaction can locally alter the dislocation cores so that many different polymorphs appear along a single dislocation not only because of direct contact between interstitials and the dislocation core but also because of this long-range elastic interaction.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Deployment of salt sample extraction system at an engineering-scale electrorefiner

The goal of the salt sampling program at Argonne is to develop and deploy automated molten salt sampling approaches for interfacing relevant unit operations with salt analysis to improve the timeliness of sampling-based accountancy measurements. Two technologies under development in support of this goal are a vacuum sampling loop module and a high-throughput pneumatic sample generator module. Compared to traditional point sampling approaches (i.e., dip probes), the vacuum sampling loop facilitates the collection of a larger cross-section of the bulk salt in order to collect more representative samples. The vacuum sampling approach also eliminates the risk of dross contamination of samples and avoids the use of moving parts in the salt. The pneumatic sample generator module is used to facilitate high-throughput sample analysis to improve the measurement precision of any given analytical technique by averaging out random sampling and measurement errors. In FY21, two methods for integrating these two modules were tested including direct fluidic coupling and coupling using a solid salt transfer mechanism. Solid salt transfer was ultimately selected over fluidic coupling, primarily to enable the transport of samples over longer distances to support automated at-line integration with high-precision techniques (such as microcalorimetry) that cannot withstand the conditions near an electrorefining process. To facilitate rapid solid salt coupling, new mechanisms were developed for rapidly charging and discharging salt sample tubes at the vacuum sampling loop and pneumatic sample generator modules, respectively. While the charging mechanism will be deployed in FY22, the discharge mechanism was tested in FY21 and is described here. The solid salt tube transfer method was deployed at one of Argonne’s engineering-scale electrorefiners to implement at-line high-throughput pneumatic micro-sample generation capabilities. The approach was used to generate precise uranium- and lanthanide-bearing electrorefiner micro-samples with the specific dimensions requested by researchers at Los Alamos National Laboratory for use in testing their novel microcalorimeter x-ray techniques. The solid salt transfer mechanism proved not only to be an effective means of integrating the precision sample generator with vacuum sampling, but also improved the performance of the sampler generator. To discharge salt from the sample tubes at the sampler generator, tube segments were inserted directly into the sample generator’s Helmholtz chamber and pressure pulse actuations were used to generate precision molten salt samples directly from the tube segments. The direct insertion of sample tubes into the sample generator enabled rapid loading of the salt and prevented salt from contacting most of the interior surfaces of the sample generator, which eliminated cross-contamination between runs. The vacuum sampling-loop tube charging mechanism will support high-throughput tube sampling operations by employing a dynamic vacuum filling process to fill short charge tubes that are configured to be rapidly connected and disconnected from the loop. The dynamic vacuum sampling operation will be automated, and sample tube handling can be executed with simple overhead actuation. Because the modular sampling approach described here eliminates the need for new high-radiation sample handling capabilities, salt-wetted seals, salt-wetted moving parts, and heated transfer lines outside the electrorefiner, it will address most of the remaining technical challenges for the at-line deployment of high-precision analytical techniques which will enable significant reductions in the time delay for sampling-based high-precision accountancy measurements.

42 ENGINEERING↗

DOE OSTI2022

Investigation of Cutter–Woodchip Contact Pressure in a New Biomass Comminution System

A Crumbler ® rotary shear system was recently developed to process fuel-grade woodchips into feedstocks having more uniform particle sizes for improved flowability and higher thermochemical output yield than a traditional hammer mill. It represents a significant innovation in the state of the art of biomass comminution equipment. However, the milling unit has experienced significant abrasive wear of the feeding teeth and cutters when processing hard and dusty feedstocks, such as logging residue and corn stover. Here, we present initial simulation results from a finite-element stress analysis of the rotary shear, which is used to investigate the dynamics of interaction between the cutters and woodchips. This is the first step for optimizing the cutter design to improve the system lifetime and processing efficiency, thus reducing downtime and improving overall productivity.

42 ENGINEERING↗

DOE OSTI2025

Multiscale Physics of Atomic Nuclei from First Principles

Atomic nuclei exhibit multiple energy scales ranging from hundreds of MeV in binding energies to fractions of an MeV for low-lying collective excitations. As the limits of nuclear binding are approached near the neutron and proton drip lines, traditional shell structure starts to melt with an onset of deformation and an emergence of coexisting shapes. It is a long-standing challenge to describe this multiscale physics starting from nuclear forces with roots in quantum chromodynamics. Here, we achieve this within a unified and nonperturbative quantum many-body framework that captures both short- and long-range correlations starting from modern nucleon-nucleon and three-nucleon forces from chiral effective field theory. The short-range (dynamic) correlations which account for the bulk of the binding energy are included within a symmetry-breaking framework, while long-range (static) correlations (and fine details about the collective structure) are included by employing symmetry projection techniques. Our calculations accurately reproduce—within theoretical error bars—available experimental data for low-lying collective states and the electromagnetic quadrupole transitions in 20−30 Ne. In addition, we reveal coexisting spherical and deformed shapes in 30 Ne, which indicates the breakdown of the magic neutron number 𝑁 = 20 as the key nucleus 28 O is approached, and we predict that the drip line nuclei 32,34 Ne are strongly deformed and collective. By developing reduced-order models for symmetry-projected states, we perform a global sensitivity analysis and find that the subleading singlet 𝑆-wave contact and a pion-nucleon coupling strongly impact nuclear deformation in chiral effective field theory. The techniques developed in this work clarify how microscopic nuclear forces generate the multiscale physics of nuclei spanning collective phenomena as well as short-range correlations and allow one to capture emergent and dynamical phenomena in finite fermion systems such as atom clusters, molecules, and atomic nuclei.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Design of intrinsically disordered protein variants with diverse structural properties

Intrinsically disordered proteins (IDPs) perform a broad range of functions in biology, suggesting that the ability to design IDPs could help expand the repertoire of proteins with novel functions. Computational design of IDPs with specific conformational properties has, however, been difficult because of their substantial dynamics and structural complexity. We describe a general algorithm for designing IDPs with specific structural properties. We demonstrate the power of the algorithm by generating variants of naturally occurring IDPs that differ in compaction, long-range contacts, and propensity to phase separate. We experimentally tested and validated our designs and analyzed the sequence features that determine conformations. We show how our results are captured by a machine learning model, enabling us to speed up the algorithm. Our work expands the toolbox for computational protein design and will facilitate the design of proteins whose functions exploit the many properties afforded by protein disorder.

Science & Technology - Other Topics↗

DOE OSTI2024

The Tribomechadynamics Research Challenge: Confronting blind predictions for the linear and nonlinear dynamics of a thin-walled jointed structure with measurement results

The present article summarizes the submissions to the Tribomechadynamics Research Challenge announced in 2021. The task was a blind prediction of the vibration behavior of a system comprising a thin plate clamped on two sides via bolted joints. Both geometric and frictional contact nonlinearities are expected to be relevant. Provided were the CAD models and technical drawings of all parts as well as assembly instructions. The main objective was to predict the frequency and damping ratio of the lowest-frequency mode as function of the amplitude. Many different prediction approaches were pursued, ranging from well-known methods to very recently developed ones. After the submission deadline, the system has been fabricated and tested. The aim of this article is to evaluate the current state of the art in modeling and vibration prediction, and to provide directions for future methodological advancements.

42 ENGINEERING↗

DOE OSTI2023

Decomposition of liquid-liquid extraction organic phase structure into critical and pre-peak contributions

Solution nanostructure induced by amphiphile self-association plays an important role in various chemical and physical processes, including liquid-liquid extraction (LLE). Small angle scattering techniques are an essential means of probing this structure, but, due to non-uniqueness of scattering patterns, their interpretation is not trivial. Here, in this study, we decompose small angle x-ray scattering (SAXS) patterns for a range of binary LLE organic phases into two components: Ornstein-Zernike and pre-peak contributions resulting from, respectively, critical concentration fluctuations and packing of the amphiphilic extractant molecules in the nonpolar aliphatic diluent. While we previously applied Ornstein-Zernike scattering models to similar organic phases, including the pre-peak explicitly in the fit allows us to measure weak fluctuations at high extractant concentration and simultaneously obtain information on the position and intensity of the correlation peak related to amphiphile packing. Scattering patterns and partial structure factors calculated from molecular dynamics simulations support this interpretation. We demonstrate how this minimal scattering model describes nanostructuring for a large number of extractant types over their entire extractant/diluent composition ranges, suggesting simple and universal behavior. The straightforward assignment of these structural contributions facilitates the comparison of these features between different classes of extractant molecules and will enable further studies of organic phase aggregation. Applicability to more complex, process-relevant organic phases is illustrated with post-contact organic phases containing significant quantities of extracted lanthanide nitrate salt, which we find are readily described by this model.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

An interface-aware sub-scale dynamics multi-material cell model for solids with void closure and opening at all speeds

Here, we present a multi-material cell model (closure model) for demanding arbitrary Lagrangian-Eulerian (ALE) simulations of fluids and solids. It is based on the interface-aware sub-scale dynamics (IASSD) approach which utilizes the exact material interface geometry within the computational cell to calculate internal material interactions. Our formulation of the closure model also aims to improve the accuracy in low-speed impact events. Voids are used to represent ambient vacuum and internal free boundaries of the distinct materials. Void regions can close and open at contact surfaces, allowing a transition from contact physics to free motion in vacuum. The coupling of void closure and opening with a new formulation of the IASSD model for solids is tested on several one- and two-dimensional numerical examples, ranging from gas expansion in vacuum to planar and round object impacts at various speeds.

42 ENGINEERING↗

DOE OSTI2022

Ion-Pair Reorganization Regulates Reactivity in Photoredox Catalysts

Cyclometalated and polypyridyl complexes of d6 metals are promising photoredox catalysts, using light to drive reactions with high kinetic or thermodynamic barriers via the generation of reactive radical intermediates. However, while tuning of their redox potentials, absorption energy, excited-state lifetime and quantum yield are well-known criteria for modifying activity, other factors could be important. Here we show that dynamic ion-pair reorganization controls the reactivity of a photoredox catalyst, [Ir[dF(CF3)ppy]2(dtbpy)]X. Time-resolved dielectric-loss experiments show how counter-ion identity influences excited-state charge distribution, evincing large differences in both the ground- and excited-state dipole moment depending on whether X is a small associating anion (PF6-) that forms a contact-ion pair versus a large one that either dissociates or forms a solvent-separated pair (BArF4-). These differences correlate with the reactivity of the photocatalyst toward both reductive and oxidative electron transfer, amounting to a 4-fold change in selectivity toward oxidation versus reduction. These results suggest that ion pairing could be an underappreciated factor that modulates reactivity in ionic photoredox catalysts.

catalysis↗