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DOE OSTI2025

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.

Biochemistry & Molecular Biology↗

DOE OSTI2025

Microturbulence Suppression by Alfvén Eigenmodes in the DIII-D Tokamak

Mitigation and suppression of low-𝑘 turbulence are observed during the nonlinear evolution of toroidicity-induced Alfvén eigenmodes (TAEs) in DIII-D experiments. Turbulence mitigation begins when the dominant TAE starts to depart from the typical shear Alfvén wave polarization. TAE activity then evolves into a new state, characterized by more discrete coherent modes, increased total amplitude, and more localized radial structures. During this transition, a narrow shear flow layer forms, driven by an enhanced Reynolds stress force, with a shearing rate that exceeds the local turbulence decorrelation rate, leading to a full turbulence suppression. Furthermore, these observations indicate the imbalance between Reynolds and Maxwell stress forces during the nonlinear evolution of the TAE and their important roles in shear flow generation and turbulence reduction.

Alfvén waves↗

DOE OSTI2024

Excitation protocols for nonlinear phononics in bismuth and antimony

Here, we study the optical generation and control of coherent phonons in elemental bismuth (Bi) and antimony (Sb) using a classical equation of motion informed by first-principles calculations of the potential energy surface and the frequency-dependent macroscopic dielectric function along the zone-centered optical phonon coordinates. Using this approach, we demonstrate that phonons with the largest optomechanical couplings also have the strongest degree of anharmonicity among the zone-centered modes, a result of the broken-symmetry structural ground state of Bi and Sb. We show how this anharmonicity, explaining the light-induced phonon softening observed in experiments, prevents the application of standard phonon-amplification and annihilation protocols. We introduce a simple linearization protocol that extends the use of such protocols to the case of anharmonic phonons in broken-symmetry materials, and demonstrate its efficiency at high displacement amplitudes. Our formalism and results provide a path for improving optical control in nonlinear phononics.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Single-molecule infrared spectroscopy with scanning tunneling microscopy

Probing vibrations at the single-molecule level is essential for achieving bond-specific chemical control in realistic heterogeneous environments. Here, we introduce a new measurement scheme that integrates frequency-tunable infrared excitation with scanning tunneling microscopy to characterize vibration-mediated nuclear motions of single molecules. We first validated the technique by monitoring the infrared-induced rotation of the ethynyl radical and then applied it to mapping pyrrolidine’s conformational dynamics. The resulting broadband spectra captured fundamental vibrational modes together with rich overtone and combination bands inaccessible by conventional methods, which we confirmed with isotopic substitutions. Density functional theory calculations showed that delocalized modes coupled with pyrrolidine ring puckering drive the structural transition, revealing altered selection rules compared with traditional infrared spectroscopy. Here, this new experimental platform enables molecular vibrations and transformations to be probed with atomic precision.

Liang, Kangkai [University of California, San Dieg↗

DOE OSTI2021

Integrability and Symmetries of Classical Geometries

This research project had two major objectives: advancement in constructing quantum theory of gravity and analytical understanding of strongly--coupled systems. The project contributed to advancing quantum theory of gravity by studying dynamics of black holes. A comprehensive analysis of excitations of rotating black holes in arbitrary dimensions has been performed, all solutions of Maxwell's equations as well as their generalizations to arbitrary p-forms in such backgrounds have been constructed, and a significant progress towards extension of these results to gravitational waves has been made. The project also advanced theoretical understanding of strongly-coupled theories by analyzing properties of exactly-solvable (integrable) models. A new method for solving dynamical equations for various fields in a large class of backgrounds without isometries has been developed, and this technique was used to extract spectra of supergravity modes in several integrable string theories. The analytical structure of large classes of integrable string theories has also been analyzed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Electron-scale Magnetic Holes Generation Driven by Whistler-to-Bernstein Mode Conversion in Fully Kinetic Plasma Turbulence

Magnetic holes (MHs) are coherent structures characterized by a strong and localized magnetic field amplitude dip, commonly observed in the heliosphere. These structures come in different sizes, from magnetohydrodynamic to kinetic scales. Subion-scale MHs are usually sustained by an electron current vortex and exhibit a strong electron temperature anisotropy, with higher temperatures perpendicular to the background magnetic field. Magnetospheric multiscale observations (MMSs) have revealed electron-scale MHs to be ubiquitous in the turbulent Earth’s magnetosheath and the solar wind, potentially playing an important role in the energy cascade and dissipation. Despite abundant observations, the origin of electron-scale MHs is still unclear and debated. In this work, we use fully kinetic simulations to investigate the role of plasma turbulence in generating electron-scale MHs. We find that the turbulence spontaneously produces electron-scale MHs via the following mechanism: first, large-scale turbulent velocity shears produce regions with high electron temperature anisotropy; these localized regions become unstable, generating oblique electron-scale whistler waves; as they propagate over the inhomogeneous turbulent background, whistler fluctuations develop an electrostatic component, turning into Bernstein-like modes; the strong electrostatic fluctuations produce current filaments that merge into an electron-scale current vortex; the resulting electron vortex locally reduces the magnetic field amplitude, finally evolving into an electron-scale MH. We show that MHs generated by this mechanism have properties consistent with MMSs and nontrivial kinetic features with a “mushroom”-shaped electron velocity distribution function. Our results have potential implications for understanding the formation and occurrence of electron-scale MHs in astrophysical turbulent and space environments, such as the Earth’s magnetosheath and the solar wind.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Selective control of conductance modes in multi-terminal Josephson junctions

The Andreev bound state spectra of multi-terminal Josephson junctions form an artificial band structure, which is predicted to host tunable topological phases under certain conditions. However, the number of conductance modes between the terminals of a multi-terminal Josephson junction must be few in order for this spectrum to be experimentally accessible. In this work, we employ a quantum point contact geometry in three-terminal Josephson devices to demonstrate independent control of conductance modes between each pair of terminals and access to the single-mode regime coexistent with the presence of superconducting coupling. These results establish a full platform on which to realize tunable Andreev bound state spectra in multi-terminal Josephson junctions.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Mesoscopic two-point collective dynamics of glass-forming liquids

The collective density–density and hydrostatic pressure–pressure correlations of glass-forming liquids are spatiotemporally mapped out using molecular dynamics simulations. It is shown that the sharp rise of structural relaxation time below the Arrhenius temperature coincides with the emergence of slow, nonhydrodynamic collective dynamics on mesoscopic scales. The observed long-range, nonhydrodynamic mode is independent of wave numbers and closely coupled to the local structural dynamics. Below the Arrhenius temperature, it dominates the slow collective dynamics on length scales immediately beyond the first structural peak in contrast to the well-known behavior at high temperatures. Furthermore, these results highlight a key connection between the qualitative change in mesoscopic two-point collective dynamics and the dynamic crossover phenomenon.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

BioRT-Flux-PIHM v1.0: a biogeochemical reactive transport model at the watershed scale

Watersheds are the fundamental Earth surface functioning units that connect the land to aquatic systems. Many watershed-scale models represent hydrological processes but not biogeochemical reactive transport processes. This has limited our capability to understand and predict solute export, water chemistry and quality, and Earth system response to changing climate and anthropogenic conditions. Here we present a recently developed BioRT-Flux-PIHM (BioRT hereafter) v1.0, a watershed-scale biogeochemical reactive transport model. The model augments the previously developed RT-Flux-PIHM that integrates land-surface interactions, surface hydrology, and abiotic geochemical reactions. It enables the simulation of (1) shallow and deep-water partitioning to represent surface runoff, shallow soil water, and deeper groundwater and of (2) biotic processes including plant uptake, soil respiration, and nutrient transformation. The reactive transport part of the code has been verified against the widely used reactive transport code CrunchTope. BioRT-Flux-PIHM v1.0 has recently been applied in multiple watersheds under diverse climate, vegetation, and geological conditions. This paper briefly introduces the governing equations and model structure with a focus on new aspects of the model. It also showcases one hydrology example that simulates shallow and deep-water interactions and two biogeochemical examples relevant to nitrate and dissolved organic carbon (DOC). These examples are illustrated in two simulation modes of complexity. One is the spatially lumped mode (i.e., two land cells connected by one river segment) that focuses on processes and average behavior of a watershed. Another is the spatially distributed mode (i.e., hundreds of cells) that includes details of topography, land cover, and soil properties. Whereas the spatially lumped mode represents averaged properties and processes and temporal variations, the spatially distributed mode can be used to understand the impacts of spatial structure and identify hot spots of biogeochemical reactions. The model can be used to mechanistically understand coupled hydrological and biogeochemical processes under gradients of climate, vegetation, geology, and land use conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Strain fields in twisted bilayer graphene

Van der Waals heteroepitaxy allows deterministic control over lattice mismatch or azimuthal orientation between atomic layers to produce long-wavelength superlattices. The resulting electronic phases depend critically on the superlattice periodicity and localized structural deformations that introduce disorder and strain. In this study we used Bragg interferometry to capture atomic displacement fields in twisted bilayer graphene with twist angles < 2°. Nanoscale spatial fluctuations in twist angle and uniaxial heterostrain were statistically evaluated, revealing the prevalence of short-range disorder in moiré heterostructures. By quantitatively mapping strain tensor fields, we uncovered two regimes of structural relaxation and disentangled the electronic contributions of constituent rotation modes. Further, we found that applied heterostrain accumulates anisotropically in saddle-point regions, generating distinctive striped strain phases. Our results establish the reconstruction mechanics underpinning the twist-angle-dependent electronic behaviour of twisted bilayer graphene and provide a framework for directly visualizing structural relaxation, disorder and strain in moiré materials.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Novel intrinsic helical cores and MHD dynamo flux pumping evidence in DIII-D

Evidence of a MHD dynamo brought about by intrinsic helical core structures in negative triangularity (NT) and ITER baseline scenario (IBS) plasmas demonstrates paths to operating tokamaks without seeds for deleterious global MHD modes. A stationary sawtooth- and edge localized mode-free state maintains high performance for long durations in a strong NT shape in the DIII-D tokamak. Disparity between minimum safety factor values predicted by magnetic flux diffusion theory and derived from experiment suggests anomalous flux diffusion by an MHD dynamo, driven by flows associated with quasi-interchange modes. Stability calculations with the GATO code find NT and IBS experimental equilibria unstable to quasi-interchange modes, in agreement with observed saturated activity. IBS discharges with similar magnetic winding structure occupy robust helical core states following a transition from sawtooth instabilities. These states agree with prior modeling of helical core bifurcation thresholds with the VMEC equilibrium code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Origin of light-induced metastability in ZrTe 5

Here we study the nonequilibrium electronic structure of a model Dirac semimetal ZrTe 5 by using time-and-angle resolved photoemission spectroscopy and density functional theory–based electron and phonon calculations. By measuring the electronic dispersion near the Γ point at time delays up to 10 picoseconds, we discovered that the band spectral weight does not recover during the measured temporal window, revealing the existence of a light-induced metastable state in the electronic structure of this material. Our calculations find that the photoexcited A 1⁢g phonon mode leads to a band renormalization that both supports our experimental observations at the zone center and predicts changes to the band structure outside of our experimental window, ultimately showing the evolution from a direct to an indirect gap semimetal; such band renormalization dramatically reduces the electron-hole recombination rate giving rise to the metastability in this system.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

First principles free energy model with dynamic magnetism for δ -plutonium

We present an ab initio free energy model derived from a fully relativistic density functional theory (DFT) electronic structure with dynamic magnetism for δ -plutonium (face-centered cubic, fcc). The DFT model is extended with orbital-orbital interaction in a parameter free orbital polarization (OP) mechanism consistent with previous modeling of plutonium. Gibbs free energy is built from components associated with the temperature dependence of the electronic structure and the corresponding electronic entropy, lattice vibrations within an anharmonic lattice dynamics model, and dynamical fluctuations of the magnetization density, i.e. magnetic fluctuations. The fluctuation model consists of transverse and longitudinal modes driven by temperature induced excitations of the DFT + OP electronic structure. The ab initio model thus incorporates fluctuating states beyond the electronic ground state. Thanks to the dynamic magnetism, the theory predicts excellent thermodynamic properties and a Gibbs free energy in accord with CALPHAD and semi-empirical modeling developed from the thermodynamic observables. The magnetic fluctuations further explain anomalous behaviors of the thermal expansion in plutonium. Specifically, a thermal expansion for the δ -plutonium system turning from positive to negative at temperatures above room temperature, a tendency for gallium to reduce and remove the negative thermal expansion depending on composition, and a positive thermal expansion for the high temperature ϵ phase.

dynamic↗

DOE OSTI2023

Electrochemical Li intercalation in b-As y P 1–y alloys: In-situ Raman spectroscopy study

Structural evolution of b-As y P 1-y alloys with varying As concentration, y was studied during Li-intercalation using in-situ Raman spectroscopy. A monotonic redshift of all the vibrational modes corresponding to P-P bonds (A 1 g , A 2 g , B 2g ), As-As bonds (A 1 g , A 2 g , B 2g ), and As-P bonds of all the samples was observed during the initial stages of the intercalation process due to the softening of each mode caused by the intercalation driven donor-type charge-transfer from Li to b-As y P 1-y . The emergence of a new peak identified as the E g mode of gray As, above an intercalation threshold, is indicative of the presence of an intercalation-driven structural phase segregation process. Further, the A 1g mode of gray As emerging after this intercalation threshold lies in close proximity of the A 2 g Raman mode of b-As y P 1-y . All the peaks beyond the intercalation threshold show an upshift due to the co-existence of gray As with b-As y P 1-y alloys causing strain and thus hardening of the phonon modes. In the sample with the highest As concentration phase segregation takes place during the synthesis process. Computational modeling reveals the co-existence of gray As in the b-As y P 1-y alloys with high As concentrations. It also confirms the existence of a local structural segregation taking place at a critical Li concentration during the intercalation process. Furthermore, this work shows the significance of intercalation on structural changes in the search for new phases of b-As y P 1-y alloys.

2D Materials↗

DOE OSTI2023

Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV)

We analyzed the spike protein S1/S2 cleavage of selected strains of a prototype coronavirus, mouse hepatitis virus (MHV) by the cellular protease furin, in order to understand the structural requirements underlying the sequence selectivity of the scissile segment. The probability of cleavage of selected MHV strains was first evaluated from furin cleavage scores predicted by the ProP computer software, and then cleavage was measured experimentally with a fluorogenic peptide cleavage assay consisting of S1/S2 peptide mimics and purified furin. We found that in vitro cleavability varied across MHV strains in line with predicted results—but with the notable exception of MHV-A59, which was not cleaved despite a high score predicted for its sequence. Using the known X-Ray structure of furin in complex with a substrate-like inhibitor as an initial structural reference, we carried out molecular dynamics (MD) simulations to learn the modes of binding of the peptides in the furin active site, and the suitability of the complex for initiation of the enzymatic cleavage. We identified the 3D structural requirements of the furin active site configuration that enable bound peptides to undergo cleavage, and the way in which the various strains tested experimentally are fulfilling these requirements. We find that despite some flexibility in the organization of the peptide bound to the active site of the enzyme, the presence of a histidine at P2 of MHV-A59 fails to properly orient the sidechain of His194 of the furin catalytic triad and therefore produces a distortion that renders the peptide/complex structural configuration in the active site incompatible with requirements for cleavage initiation. The Ser/Thr in P1 of MHV-2 and MHV-S has a similar effect of distorting the conformation of the furin active site residues produced by the elimination of the canonical salt-bridge formed by arginine in P1 position. This work informs a study of coronavirus infection and pathogenesis with respect to the function of the viral spike protein, and suggests an important process of viral adaptation and evolution within the spike S1/S2 structural loop.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Coherent Transfer of Lattice Entropy via Extreme Nonlinear Phononics in Metal Halide Perovskites

Entropy transfer in metal halide perovskites, characterized by significant lattice anharmonicity and low stiffness, underlies the remarkable properties observed in their optoelectronic applications, ranging from solar cells to lasers. The conventional view of this transfer involves stochastic processes occurring within a thermal bath of phonons, where the lattice arrangement and energy flow from higher- to lower-frequency modes. Here, we unveil a comprehensive chronological sequence detailing a conceptually distinct coherent transfer of entropy in a prototypical perovskite CH 3 NH 3 Pbl 3 . The terahertz periodic modulation imposes vibrational coherence into electronic states, leading to the emergence of mixed (vibronic) quantum beat between approximately 3 and 0.3 THz. We highlight a well-structured bidirectional time-frequency transfer of these diverse phonon modes, each developing at different times and transitioning from high to low frequencies from 3 to 0.3 THz, before reversing direction and ascending to around 0.8 THz. First-principles molecular dynamics simulations disentangle a complex web of coherent-phononic coupling pathways and identify the salient roles of the initial modes in shaping entropy evolution at later stages. Capitalizing on coherent entropy transfer and dynamic anharmonicity presents a compelling opportunity to exceed the fundamental thermodynamic (Shockley-Queisser) limit of photoconversion efficiency and to pioneer novel optoelectronic functionalities. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Epitaxial intergrowths and local oxide relaxations in natural bixbyite Fe 2– x Mn x O 3

The scattering pattern of a crystal obeys the symmetry of the crystal structure through the corresponding Laue group. This is usually also true for the diffuse scattering, containing information about disorder, but here a case is reported where the diffuse scattering is of lower symmetry than the parent crystal structure. The mineral bixbyite has been studied by X-ray and neutron scattering techniques since 1928 with some of the most recent studies characterizing the low-temperature transition to a magnetically disordered spin-glass state. However, bixbyite also exhibits structural disorder, and here single-crystal X-ray and neutron scattering is used to characterize the different modes of disorder present. One-dimensional rods of diffuse scattering are observed in the cubic mineral bixbyite, which break the expected symmetry of the scattering pattern. It is shown that this scattering arises from epitaxial intergrowths of the related mineral, braunite. The presence of this disorder mode is found to be directly observable as well-defined residuals in the average structure refined against the Bragg diffraction. An additional three-dimensional diffuse scattering component is observed in neutron scattering data, which is shown to originate from the substitutional disorder on the Fe/Mn sites. This occupational disorder gives rise to local relaxations of the oxide sublattice, and the pattern of oxide displacements can be rationalized based on crystal-field theory. The combined use of neutron and X-ray single-crystal scattering techniques highlights their great complementarity. In particular, the large sample requirements for neutron scattering experiments prove to be an obstacle in solving the intergrowth disorder due to several growth orientations, whereas for X-ray scattering the one-dimensional nature of the intergrowth disorder renders solving this a more tractable task. On the other hand, the oxide relaxations cannot be resolved using X-rays due to the low Mn/Fe contrast. By combining the two approaches both types of disorder have been characterized.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Optically induced changes in the band structure of the Weyl charge-density-wave compound (TaSe 4 ) 2 I

Collective modes are responsible for the emergence of novel quantum phases in topological materials. In the quasi-one dimensional (1D) Weyl semimetal (TaSe 4 ) 2 I , a charge density wave (CDW) opens band gaps at the Weyl points, thus turning the system into an axionic insulator. Melting the CDW would restore the Weyl phase, but 1D fluctuations extend the gapped regime far above the 3D transition temperature (T CDW = 263 K), thus preventing the investigation of this topological phase transition with conventional spectroscopic methods. Here we use a non-equilibrium approach: we perturb the CDW phase by photoexcitation, and we monitor the dynamical evolution of the band structure by time- and angle-resolved photoelectron spectroscopy. We find that, upon optical excitation, electrons populate the linearly dispersing states at the Fermi level (E F ), and fill the CDW gap. The dynamics of both the charge carrier population and the band gap renormalization (BGR) show a fast component with a characteristic time scale of a few hundreds femtoseconds. However, the BGR also exhibits a second slow component on the µs time scale. The combination of an ultrafast response and of persistent changes in the spectral weight at E$_\mathrm{F}$, and the resulting sensitivity of the linearly dispersing states to optical excitations, may explain the high performances of (TaSe 4 ) 2 I as a material for broadband infrared photodetectors.

36 MATERIALS SCIENCE↗