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DOE OSTI2020

Emergence of self-organized multivortex states in flocks of active rollers

Active matter, both synthetic and biological, demonstrates complex spatiotemporal self-organization and the emergence of collective behavior. A coherent rotational motion, the vortex phase, is of great interest because of its ability to orchestrate well-organized motion of self-propelled particles over large distances. However, its generation without geometrical confinement has been a challenge. Here, we show by experiments and computational modeling that concentrated magnetic rollers self-organize into multivortex states in an unconfined environment. We find that the neighboring vortices more likely occur with the opposite sense of rotation. Our studies provide insights into the mechanism for the emergence of coherent collective motion on the macroscale from the coupling between microscale rotation and translation of individual active elements. These results may stimulate design strategies for self-assembled dynamic materials and microrobotics.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Visualization of the HIV-1 Env glycan shield across scales

The dense array of N-linked glycans on the HIV-1 envelope glycoprotein (Env), known as the “glycan shield,” is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure–function analysis. Here, we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of interglycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same cell line used for vaccine production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner, we found that highly connected glycan clusters are resistant to digestion and help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials

The rigid constraints of chemistry-dictated by quantum mechanics and the discrete nature of the atom-limit the set of observable atomic crystal structures. What structures are possible in the absence of these constraints? Here, we systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. Sixteen of the structures have natural analogs spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. The discovered crystal structures constitute targets for self-assembly and expand our understanding of what a crystal structure can look like.

crystal structures↗

DOE OSTI2023

Structural OFF/ON transitions of myosin in relaxed porcine myocardium predict calcium-activated force

Contraction in striated muscle is initiated by calcium binding to troponin complexes, but it is now understood that dynamic transition of myosin between resting, ordered OFF states on thick filaments and active, disordered ON states that can bind to thin filaments is critical in regulating muscle contractility. These structural OFF to ON transitions of myosin are widely assumed to correspond to transitions from the biochemically defined, energy-sparing, super-relaxed (SRX) state to the higher ATPase disordered-relaxed (DRX) state. Here, in this study, we examined the effect of 2’-deoxy-ATP (dATP), a naturally occurring energy substrate for myosin, on the structural OFF to ON transitions of myosin motors in porcine cardiac muscle thick filaments. Small-angle X-ray diffraction revealed that titrating dATP in relaxation solutions progressively moves the myosin heads from ordered OFF states on the thick filament backbone to disordered ON states closer to thin filaments. Importantly, we found that the structural OFF to ON transitions are not equivalent to the biochemically defined SRX to DRX transitions and that the dATP-induced structural OFF to ON transitions of myosin motors in relaxed muscle are strongly correlated with submaximal force augmentation by dATP. These results indicate that structural OFF to ON transitions of myosin in relaxed muscle can predict the level of force attained in calcium-activated cardiac muscle. Computational modeling and stiffness measurements suggest a final step in the OFF to ON transition may involve a subset of DRX myosins that form weakly bound cross-bridges prior to becoming active force-producing cross-bridges.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Small molecules disaggregate alpha-synuclein and prevent seeding from patient brain-derived fibrils

The amyloid aggregation of alpha-synuclein within the brain is associated with the pathogenesis of Parkinson’s disease (PD) and other related synucleinopathies, including multiple system atrophy (MSA). Alpha-synuclein aggregates are a major therapeutic target for treatment of these diseases. We identify two small molecules capable of disassembling preformed alpha-synuclein fibrils. The compounds, termed CNS-11 and CNS-11g, disaggregate recombinant alpha-synuclein fibrils in vitro, prevent the intracellular seeded aggregation of alpha-synuclein fibrils, and mitigate alpha-synuclein fibril cytotoxicity in neuronal cells. Furthermore, we demonstrate that both compounds disassemble fibrils extracted from MSA patient brains and prevent their intracellular seeding. They also reduce in vivo alpha-synuclein aggregates in C. elegans . Both compounds also penetrate brain tissue in mice. A molecular dynamics–based computational model suggests the compounds may exert their disaggregating effects on the N terminus of the fibril core. These compounds appear to be promising therapeutic leads for targeting alpha-synuclein for the treatment of synucleinopathies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Tertiary folds of the SL5 RNA from the 5 ' proximal region of SARS-CoV-2 and related coronaviruses

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T’s “arms.” Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Interpreting dynamic-compression experiments to uncover the time dependence of freezing: Application to gallium

Using pulsed-power magnetic field sources to compress gallium to gigapascal pressures on nanosecond timescales, we report here experiments on shockless dynamic compression of a liquid metal. Time-resolved velocimetry data reveal signatures of rapid freezing from a metastable liquid state, and we demonstrate that the kinetics of this nonequilibrium solidification can be accurately simulated with a computational modeling framework we have developed in previous studies, where classical nucleation theory is coupled with hydrodynamics. Notably, velocity traces in some of our experiments show evidence of a phase transition, while others do not, even though other types of evidence suggest that solidification may be occurring in all of them. We explain how predictions made by our models regarding the presence or absence of these phase-transition signatures motivated additional experiments that later confirmed the theoretical predictions. Our analysis shows that due to the rapid, quasi-isentropic nature of the loading path, our experiments were able to compress liquid gallium to metastable states that are undercooled below the equilibrium melt temperature by more than 300 K and exhibit pressures that approach five times the equilibrium melt pressure. The understanding gained in this study should form the basis for future dynamic-compression experiments aimed at interrogating melt curves at high pressures.

gallium↗

DOE OSTI2020

Kilopower Reactor Using Stirling TechnologY (KRUSTY) Component Critical Experiments

A series of critical experiments were conducted at the National Criticality Experiments Research Center (NCERC) in Nevada to evaluate the operational performance of a compact reactor that eventually will resemble the flight unit the National Aeronautics and Space Administration will use for deep space exploration. The results from the experiments are compared to preliminary results from computational models using MCNP and ENDF/B-7.1 neutron cross-section data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Design of a High-Assay Low-Enriched Uranium Tri-Structural Isotropic Critical Experiment for Advanced Reactor Validation

High-assay low-enriched uranium (HALEU) fuel is a key component of many small modular reactor designs. Critical experiments are an important way to understand the neutronic performance of systems by obtaining nuclear data validations through measurements. Data reduce uncertainty and risk by showing that systems respond as predicted to changes such as temperature, subsequently advancing the overall technology readiness level of the materials within. Numerous critical experiments have been performed at the National Criticality Experiments Research Center (NCERC) operated by Los Alamos National Laboratory at the Nevada National Security Site since it became operational in 2011. However, the first experiment with HALEU fuel did not occur until 2024. Through extensive engineering, the experiment described in this paper was successfully designed and executed for the Comet vertical lift assembly at NCERC to perform measurements with HALEU tri-structural isotropic fuel that will assist in validation of nuclear data and computational modeling of small modular reactors for years to come.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Serpent and MCNP Calculations of the Energy Deposition in the Transformational Challenge Reactor

This paper focuses on the calculation of the energy deposition in the Transformational Challenge Reactor by two major Monte Carlo codes: Serpent and MCNP. The first software computation relies on Kinetic Energy Released per unit Mass (KERMA) factors while the second one relies on Q-values. The results from these two independent computation methodologies are in very good agreement; however, Serpent runs much faster than MCNP (for the same computational model) and allows for a detailed energy deposition distribution from a 1-mm-side square mesh with a relative statistical error between 0.5% and 1%. This detailed energy deposition is suitable for multiphysics analyses aimed at design optimizations. In order to calculate the energy deposition, Serpent needs enhanced ACE files (distributed by the software developers). Unlike other Monte Carlo software that uses inputs based on Python or Java languages, the Serpent input syntax is very similar to that of MCNP; a Python script can convert a MCNP input to a Serpent input in seconds. For simulations not requiring the calculation of the energy deposition, Serpent can also read nuclear data from MCNP ACE files, which eventually improves the comparison of the results of the two codes.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

What Composition of High-Energy Physics Collaborations is Epistemically Optimal?

Computer simulations have recently come to the fore as a crucial tool for studying epistemic dynamics of scientific collectives. One pressing issue in big-ticket, long-term, and crowded particle physics research is the optimal organization of collaborations. This research developed a computation model of collaborations in high-energy physics and performed simulations to investigate the epistemic efficiency of groups and its dependence on the size of such groups and their composition: namely, percentages of pure, partially theoretically competent, and fully theoretically competent experimentalists. The present study reveals that in both small (100-member) and large (3000-member) groups, epistemic payoff as the measure of epistemic efficiency of collaborations is, generally, positively correlated with an increase in both the number of theoretically fully competent and pure (incompetent) experimentalists. Here, we are less certain of such conclusion in the case of the small collaborations. Although the subcommunity of experimentalists who are partially expert is not found to be immediately epistemically beneficial for collaborations, nevertheless they also crucially serve as a transitional community between the theorists and the experimentalists. Predicated on the toy model simulations, I suggest that institutions should provide measures to assist members of the latter subgroup in progressing toward developing a full theoretical expertise.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

The impact of optical measurement techniques on measured aerosol particle size distributions

Ambient aerosol particle size distributions measured by the Ultra-High Sensitivity Aerosol Spectrometer (UHSAS) at various sites around the world exhibit modes at optical diameters near 600 nm and 850 nm. These modes are not present in concurrent measurements with the Grimm 11-D Optical Particle Counter (OPC). Here, in this study, we argue that these modes result from the optical measurement technique itself, and we explain why they appear in measurements by the UHSAS but not in those by the Grimm OPC. We construct computer models of the UHSAS and Grimm (“digital UHSAS” and “digital Grimm”) and use these to investigate the size distribution that would result from measurements of artificial aerosol particle size distributions that do not contain modes. The appearance of modes for the structureless incoming size distributions sampled by the digital UHSAS is explained by the nonlinear behavior of partial scattering cross sections of uniform spherical particles as a function of their diameter. The absence of modes in the digital Grimm is explained by the coarser size resolution of that instrument. Detailed analysis of the relationship between optical and geometric diameters for uniform spherical particles reveals two important results. First, these diameters generally have different numerical values for the same particle, and second, the relationship is nonlinear; thus, widths of size bins in terms of optical diameter differ from those in geometric diameter. These results explain the modes observed in the ambient size distributions and highlight concerns with attempts to create a merged size distribution by combining measurements from different instruments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Simulating water adsorption in metal–organic frameworks with open metal sites using the 12-6-4 Lennard–Jones potential

Metal-organic frameworks (MOFs) with coordinatively unsaturated open metal sites (OMSs) are promising sorbent materials in atmospheric water harvesting (AWH) systems at low relative humidity (RH) due to their strong interactions with water molecules. However, accurate computational modelling of water adsorption in those materials are challenging, as standard force fields (FFs) based on the 12-6 Lennard-Jones (L-J) potential cannot properly describe the water-OMS interactions. In biomolecular simulations, the 12-6-4 L-J potential has been successfully used to model metal ion-water interactions in which the extra 1/r 4 -term is for charge-induced dipole electrostatics. In this work, we adopted this strategy and used the 12-6-4 L-J potential to model water-OMS interactions in MOFs for low RH AWH applications. Notably, without any modifications, the parameters used for aqueous metal ions were able to greatly improve the accuracy in predicting water adsorption isotherms in MOF-74, which highlights the simplicity and transferability of this method.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2024

Variable domain mutational analysis to probe the molecular mechanisms of high viscosity of an IgG 1 antibody

Subcutaneous injection is the preferred route of administration for many antibody therapeutics for reasons that include its speed and convenience. However, the small volume limit (typically ≤2 mL) for subcutaneous delivery often necessitates antibody formulations at high concentrations (commonly ≥100 mg/mL), which may lead to physicochemical problems. For example, antibodies with large hydrophobic or charged patches can be prone to self-interaction giving rise to high viscosity. Here, we combined X-ray crystallography with computational modeling to predict regions of an anti-glucagon receptor (GCGR) IgG 1 antibody prone to self-interaction. An extensive mutational analysis was undertaken of the complementarity-determining region residues residing in hydrophobic surface patches predicted by spatial aggregation propensity, in conjunction with residue-level solvent accessibility, averaged over conformational ensembles from molecular dynamics simulations. Dynamic light scattering (DLS) was used as a medium throughput screen for self-interaction of ~200 anti-GCGR IgG 1 variants. A negative correlation was found between the viscosity determined at high concentration (180 mg/mL) and the DLS interaction parameter measured at low concentration (2–10 mg/mL). Additionally, anti-GCGR variants were readily identified with reduced viscosity and antigen-binding affinity within a few fold of the parent antibody, with no identified impact on overall developability. The methods described here may be useful in the optimization of other antibodies to facilitate their therapeutic administration at high concentration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Bibliometric review and recent advances in total scattering pair distribution function analysis: 21 years in retrospect

Global research activities have been driven by the quest to develop and characterize novel materials for technological advancements. The total scattering pair distribution function (TSPDF) is a powerful and versatile characterization technique for examining the structural details of diverse complex materials including liquid, amorphous, disordered crystalline, and nanostructured materials. Thus, it is critical to keep track of research progress, identify research gaps, and future research directions of the application of the TSPDF technique in materials development and discovery. In this work, a bibliometric analysis of literature regarding the TSPDF technique between 2000 and 2021 was conducted using datasets retrieved from the Web of Science database. The research trends based on publication outputs, research subject distribution, co-authorships among institutions, countries/regions, co-citation of referenced sources, and keyword co-occurrence are evaluated and discussed herein. The impact of the TSPDF technique is projected to increase due to its importance in probing emerging functional materials, and the advances in specialized facilities and instrumentation among the scientific communities engaged with it. Finally, current and emerging research hotspots related to TSPDF technique such as catalysis, computer modeling and simulation, pharmaceutics, machine learning, hydrogen storage, battery materials, and layered structured materials are also identified and discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2020

The 2020 plasma catalysis roadmap

Abstract Plasma catalysis is gaining increasing interest for various gas conversion applications, such as CO 2 conversion into value-added chemicals and fuels, CH 4 activation into hydrogen, higher hydrocarbons or oxygenates, and NH 3 synthesis. Other applications are already more established, such as for air pollution control, e.g. volatile organic compound remediation, particulate matter and NO x removal. In addition, plasma is also very promising for catalyst synthesis and treatment. Plasma catalysis clearly has benefits over ‘conventional’ catalysis, as outlined in the Introduction. However, a better insight into the underlying physical and chemical processes is crucial. This can be obtained by experiments applying diagnostics, studying both the chemical processes at the catalyst surface and the physicochemical mechanisms of plasma-catalyst interactions, as well as by computer modeling. The key challenge is to design cost-effective, highly active and stable catalysts tailored to the plasma environment. Therefore, insight from thermal catalysis as well as electro- and photocatalysis is crucial. All these aspects are covered in this Roadmap paper, written by specialists in their field, presenting the state-of-the-art, the current and future challenges, as well as the advances in science and technology needed to meet these challenges.

Bogaerts, Annemie (ORCID:0000000198756460)↗

DOE OSTI2021

From thermal catalysis to plasma catalysis: a review of surface processes and their characterizations

The use of atmospheric pressure plasma to enhance catalytic chemical reactions involves complex surface processes induced by the interactions of plasma-generated fluxes with catalyst surfaces. Industrial implementation of plasma catalysis necessitates optimizing the design and realization of plasma catalytic reactors that enable chemical reactions that are superior to conventional thermal catalysis approaches. This requires the fundamental understanding of essential plasma-surface interaction mechanisms of plasma catalysis from the aspect of experimental investigation and theoretical analysis or computational modeling. In addition, experimental results are essential to validate the relative theoretical models and hypotheses of plasma catalysis that was rarely understood so far, compared to conventional thermal catalysis. This overview focuses on two important application areas, nitrogen fixation and methane reforming, and presents a comparison of important aspects of the state of knowledge of these applications when performed using either plasma-catalysis or conventional thermal catalysis. We discuss the potential advantage of plasma catalysis over thermal catalysis from the aspects of plasma induced synergistic effect and in situ catalyst regeneration. In-situ/operando surface characterization of catalysts in plasma catalytic reactors is a significant challenge since the high pressure of realistic plasma catalysis systems preclude the application of many standard surface characterization techniques that operate in a low-pressure environment. Here, we present a review of the status of experimental approaches to probe gas-surface interaction mechanisms of plasma catalysis, including an appraisal of demonstrated approaches for integrating surface diagnostic tools into plasma catalytic reactors.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Atomic structure and Mott nature of the insulating charge density wave phase of 1T-TaS 2

Here, using x-ray pair distribution function (PDF) analysis and computer modeling, we explore structure models for the complex charge density wave (CDW) phases of layered 1T-TaS 2 that both well capture their atomic-level features and are amenable to electronic structure calculations. The models give the most probable position of constituent atoms in terms of 3D repetitive unit cells comprising a minimum number of Ta–S layers. Structure modeling results confirm the emergence of star-of-David (SD) like clusters of Ta atoms in the high-temperature incommensurate (IC) CDW phase and show that, contrary to the suggestions of recent studies, the low-temperature commensurate (C) CDW phase expands upon cooling thus reducing lattice strain. The C-CDW phase is also found to preserve the stacking sequence of Ta–S layers found in the room temperature, nearly commensurate (NC) CDW phase to a large extent. DFT based on the PDF refined model shows that bulk C-CDW 1T-TaS 2 also preserves the insulating state of individual layers of SD clusters, favoring the Mott physics description of the metal-to-insulator (NC-CDW to C-CDW) phase transition in 1T-TaS 2 . Our work highlights the importance of using precise crystal structure models in determining the nature of electronic phases in complex materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗