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DOE OSTI2023

Regional and Teleconnected Impacts of Solar Radiation‐Topography Interaction Over the Tibetan Plateau

Abstract Solar radiation‐topography interaction plays an important role in surface energy balance over the Tibetan Plateau (TP). However, the impacts of such interaction over the TP on climate locally and in the Asian regions remain unclear. This study uses the Energy Exascale Earth System Model (E3SM) to evaluate the regional and teleconnected impacts of solar radiation‐topography interaction over the TP. Land‐atmosphere coupled experiments show that topography regulates the surface energy balance, snow processes, and surface climate over the TP across seasons. Accounting for solar radiation‐topography interaction improves E3SM simulation of surface climate. The winter cold bias in air temperature decreases from −4.57 to −3.79 K, and the wet bias in summer precipitation is mitigated in southern TP. The TP's solar radiation‐topography interaction further reduces the South and East Asian summer precipitation biases. Our results demonstrate the topographic roles in regional climate over the TP and highlight its teleconnected climate impacts.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Representing Soil Microbial Dynamics and Organo‐Mineral Interactions in the E3SM Land Model (ELM‐ReSOM)

Explicit representation of soil microbial processes and interactions with biotic and abiotic processes in Earth System Models (ESMs) remains limited, despite their importance in biogeochemical cycles. To address this gap, which hinders prediction of global biogeochemial cycling and responses to atmospheric conditions, we integrated a microbe- and mineral-surface-explicit model, the Reaction-network-based model of soil organic matter and Microbes (ReSOM), into the Energy Exascale ESM (E3SM) land model (ELM). Here, we describe ELM-ReSOM and show a case study at a conifer forest in California. ELM-ReSOM accurately simulated surface CO 2 fluxes and SOM stocks, demonstrating improved representations of microbial and mineral interactions compared to the default ELM. We examined ELM-ReSOM sensitivity to microbial traits, enzyme properties, and organo-mineral interactions. Microbial traits such as the maximum mortality rate, transporter-density scaling factor, and maximum monomer assimilation rate were strong controllers of heterotrophic respiration, while these microbial traits and enzyme-related properties collectively influenced SOM stocks. Mineral surfaces primarily affected SOM stocks by adsorbing enzymes, thereby limiting depolymerization. Synergies among processes led to stronger impacts of parameters when evaluated together versus separately (i.e., most parameters had greater indirect than direct effects). For example, due to interactions of microbial necromass with mineral surface adsorption, the indirect effect of the maximum microbial mortality rate was 33% larger than its direct effect on SOM stock. Thus, microbial and enzyme dynamics and their interactions with mineral surfaces play critical roles in SOM cycling. Tackling the challenges of microbe-explicit models will advance understanding and modeling of SOM dynamics.

Tao, Jing [Lawrence Berkeley National Laboratory (↗

DOE OSTI2026

NLML: A Deep Neural Network Emulator for the Exact Nonlinear Interactions in a Wind Wave Model

Nonlinear wave interactions describe the resonant energy transfer between wave components, playing a fundamental role in the evolution of ocean wave spectra. Nonlinear wave interactions significantly influence wave growth and development, making them essential for accurate wave modeling. However, resolving the full six-dimensional Boltzmann integral of the exact nonlinear wave interactions (Webb-Resio-Tracy method, WRT) is computationally expensive, limiting its application in real-time operational wave forecasting and for research purposes. Current approximations, such as the Discrete Interaction Approximation (DIA), prioritize computational speed over accuracy, resulting in significant errors in wave mean parameters. Here, we introduce NLML, a machine learning (ML) emulator designed to approximate the exact nonlinear wave interactions within WAVEWATCH III (WW3), with the goal of achieving the accuracy of WRT while maintaining the stability and computational speed of DIA. By leveraging GPU capabilities such as half precision inference, we achieved substantial speedups, up to 136x mathematical equation faster than the WRT and only a modest 1.04x mathematical equation slowdown relative to DIA, while achieving 2x mathematical equation the accuracy of DIA in global wave spectral energy and mean wave parameters, with up to 7x mathematical equation higher accuracy in some regions. Unlike previous ML approaches, NLML maintained inherent stability throughout model integration in a standalone, year-long WW3 simulation, without requiring additional constraints. Our new ML parameterization bridges the gap between accuracy and efficiency, offering a promising alternative for improving wave modeling in operational settings and research purposes.

16 TIDAL AND WAVE POWER↗

DOE OSTI2021

KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation

The first step of RAF activation involves binding to active RAS, resulting in the recruitment of RAF to the plasma membrane. To understand the molecular details of RAS-RAF interaction, we present crystal structures of wild-type and oncogenic mutants of KRAS complexed with the RAS-binding domain (RBD) and the membrane-interacting cysteine-rich domain (CRD) from the N-terminal regulatory region of RAF1. Our structures reveal that RBD and CRD interact with each other to form one structural entity in which both RBD and CRD interact extensively with KRAS. Mutations at the KRAS-CRD interface result in a significant reduction in RAF1 activation despite only a modest decrease in binding affinity. Combining our structures and published data, we provide a model of RAS-RAF complexation at the membrane, and molecular insights into RAS-RAF interaction during the process of RAS-mediated RAF activation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Resolving the structure of phage–bacteria interactions in the context of natural diversity

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse—with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Light-induced Kondo-like exciton-spin interaction in neodymium(II) doped hybrid perovskite

Abstract Tuning the properties of a pair of entangled electron and hole in a light-induced exciton is a fundamentally intriguing inquiry for quantum science. Here, using semiconducting hybrid perovskite as an exploratory platform, we discover that Nd 2+ -doped CH 3 NH 3 PbI 3 (MAPbI 3 ) perovskite exhibits a Kondo-like exciton-spin interaction under cryogenic and photoexcitation conditions. The feedback to such interaction between excitons in perovskite and the localized spins in Nd 2+ is observed as notably prolonged carrier lifetimes measured by time-resolved photoluminescence, ~10 times to that of pristine MAPbI 3 without Nd 2+ dopant. From a mechanistic standpoint, such extended charge separation states are the consequence of the trap state enabled by the antiferromagnetic exchange interaction between the light-induced exciton and the localized 4 f spins of the Nd 2+ in the proximity. Importantly, this Kondo-like exciton-spin interaction can be modulated by either increasing Nd 2+ doping concentration that enhances the coupling between the exciton and Nd 2+ 4 f spins as evidenced by elongated carrier lifetime, or by using an external magnetic field that can nullify the spin-dependent exchange interaction therein due to the unified orientations of Nd 2+ spin angular momentum, thereby leading to exciton recombination at the dynamics comparable to pristine MAPbI 3 .

36 MATERIALS SCIENCE↗

DOE OSTI2025

Molecular basis for human respiratory syncytial virus transcriptional regulator NS1 interactions with MED25

The Mediator complex facilitates interactions between transcription factors and RNA polymerase II, a process that is required for host gene transcription, including in response to viral infections. Among the many subunits in the Mediator complex, the MED25 subunit has been shown to be a target for viral activators during infection. Here we provide the molecular basis for the interaction between human respiratory syncytial virus (hRSV) nonstructural 1 protein (NS1) and the activator interaction domain (ACID) of MED25. The X-ray crystal structure of the complex revealed that NS1 straddles and binds two faces of MED25 ACID. This interaction is distinct from previously known viral activators. Importantly, our data support the conformational flexibility of viral transcriptional regulators. Furthermore, ChIP-seq and RNA-seq analysis identified the ATF3 transcription factor and a role for NS1/Mediator/ATF3 interaction in host gene regulation in hRSV infections. Our findings provide a molecular basis for hRSV NS1-based regulation of host gene transcription and reveal how viruses exploit the conformational heterogeneity at fuzzy transcription activator interfaces.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Extending quantum-mechanical benchmark accuracy to biological ligand-pocket interactions

Predicting the binding affinity of ligands to protein pockets is key in the drug design pipeline. The flexibility of ligand-pocket motifs arises from a range of attractive and repulsive electronic interactions during binding. Accurately accounting for all interactions requires robust quantum-mechanical (QM) benchmarks, which are scarce for ligand-pocket systems. Additionally, disagreement between “gold standard” Coupled Cluster (CC) and Quantum Monte Carlo (QMC) methods casts doubt on many benchmarks for larger non-covalent systems. We introduce the “QUantum Interacting Dimer” (QUID) benchmark framework containing 170 non-covalent (non-)equilibrium systems modeling chemically and structurally diverse ligand-pocket motifs. Symmetry-adapted perturbation theory shows that QUID broadly covers non-covalent binding motifs and energetic contributions. Robust binding energies are obtained using complementary CC and QMC methods, achieving agreement of 0.5 kcal/mol. The benchmark data analysis reveals that several dispersion-inclusive density functional approximations provide accurate energy predictions, though their atomic van der Waals forces differ in magnitude and orientation. Contrarily, semiempirical methods and empirical force fields require improvements in capturing non-covalent interactions (NCIs) for out-of-equilibrium geometries. The wide span of NCIs, highly accurate interaction energies, and analysis of molecular properties take QUID beyond the “gold standard” for QM benchmarks of ligand-protein systems.

Puleva, Mirela [University of Luxembourg, Luxembou↗

DOE OSTI2023

Interaction-driven spontaneous ferromagnetic insulating states with odd Chern numbers

Motivated by recent experimental work on moiré systems in a strong magnetic field, we compute the compressibility as well as the spin correlations and Hofstadter spectrum of spinful electrons on a honeycomb lattice with Hubbard interactions using the determinantal quantum Monte Carlo method. While the interactions in general preserve quantum and anomalous Hall states, emergent features arise corresponding to an antiferromagnetic insulator at half-filling and other incompressible states following the Chern sequence ± (2N + 1). These odd integer Chern states exhibit strong ferromagnetic correlations and arise spontaneously without any external mechanism for breaking the spin-rotation symmetry. Analogs of these magnetic states should be observable in general interacting quantum Hall systems. In addition, the interacting Hofstadter spectrum is qualitatively similar to the experimental data at intermediate values of the on-site interaction.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Programmable Heisenberg interactions between Floquet qubits

Abstract The trade-off between robustness and tunability is a central challenge in the pursuit of quantum simulation and fault-tolerant quantum computation. In particular, quantum architectures are often designed to achieve high coherence at the expense of tunability. Many current qubit designs have fixed energy levels and consequently limited types of controllable interactions. Here by adiabatically transforming fixed-frequency superconducting circuits into modifiable Floquet qubits, we demonstrate an XXZ Heisenberg interaction with fully adjustable anisotropy. This interaction model can act as the primitive for an expressive set of quantum operations, but is also the basis for quantum simulations of spin systems. To illustrate the robustness and versatility of our Floquet protocol, we tailor the Heisenberg Hamiltonian and implement two-qubit iSWAP, CZ and SWAP gates with good estimated fidelities. In addition, we implement a Heisenberg interaction between higher energy levels and employ it to construct a three-qubit CCZ gate, also with a competitive fidelity. Our protocol applies to multiple fixed-frequency high-coherence platforms, providing a collection of interactions for high-performance quantum information processing. It also establishes the potential of the Floquet framework as a tool for exploring quantum electrodynamics and optimal control.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Probing the core of the strong nuclear interaction

The strong nuclear interaction between nucleons (protons and neutrons) is the effective force that holds the atomic nucleus together. This force stems from fundamental interactions between quarks and gluons (the constituents of nucleons) that are described by the equations of quantum chromodynamics. However, as these equations cannot be solved directly, nuclear interactions are described using simplified models, which are well constrained at typical inter-nucleon distances but not at shorter distances. This limits our ability to describe high-density nuclear matter such as that in the cores of neutron stars. Here we use high-energy electron scattering measurements that isolate nucleon pairs in short-distance, high-momentum configurations, accessing a kinematical regime that has not been previously explored by experiments, corresponding to relative momenta between the pair above 400 mega electron volts per c (c, speed of light in vacuum). As the relative momentum between two nucleons increases and their separation thereby decreases, we observe a transition from a spin-dependent tensor force to a predominantly spin-independent scalar force. These results demonstrate the usefulness of using such measurements to study the nuclear interaction at short distances and also support the use of point-like nucleon models with two- and three-body effective interactions to describe nuclear systems up to densities several times higher than the central density of the nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

A detailed map of Higgs boson interactions by the ATLAS experiment ten years after the discovery

The standard model of particle physics describes the known fundamental particles and forces that make up our Universe, with the exception of gravity. One of the central features of the standard model is a field that permeates all of space and interacts with fundamental particles. The quantum excitation of this field, known as the Higgs field, manifests itself as the Higgs boson, the only fundamental particle with no spin. In 2012, a particle with properties consistent with the Higgs boson of the standard model was observed by the ATLAS and CMS experiments at the Large Hadron Collider at CERN. Since then, more than 30 times as many Higgs bosons have been recorded by the ATLAS experiment, enabling much more precise measurements and new tests of the theory. Here, on the basis of this larger dataset, we combine an unprecedented number of production and decay processes of the Higgs boson to scrutinize its interactions with elementary particles. Interactions with gluons, photons, and W and Z bosons—the carriers of the strong, electromagnetic and weak forces—are studied in detail. Interactions with three third-generation matter particles (bottom (b) and top (t) quarks, and tau leptons (τ)) are well measured and indications of interactions with a second-generation particle (muons, μ) are emerging. These tests reveal that the Higgs boson discovered ten years ago is remarkably consistent with the predictions of the theory and provide stringent constraints on many models of new phenomena beyond the standard model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs

Tuberculosis (TB) is the deadliest infectious disease worldwide. The design of new treatments for TB is hindered by the large number of candidate drugs, drug combinations, dosing choices, and complex pharmaco-kinetics/dynamics (PK/PD). Here we study the interplay of these factors in designing combination therapies by linking a machine-learning model, INDIGO-MTB, which predicts in vitro drug interactions using drug transcriptomics, with a multi-scale model of drug PK/PD and pathogen-immune interactions called GranSim. We calculate an in vivo drug interaction score (iDIS) from dynamics of drug diffusion, spatial distribution, and activity within lesions against various pathogen sub-populations. The iDIS of drug regimens evaluated against non-replicating bacteria significantly correlates with efficacy metrics from clinical trials. Our approach identifies mechanisms that can amplify synergistic or mitigate antagonistic drug interactions in vivo by modulating the relative distribution of drugs. Our mechanistic framework enables efficient evaluation of in vivo drug interactions and optimization of combination therapies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Intense laser interaction with micro-bars

Intense laser fields interact very differently with micrometric rough surfaces than with flat objects. The interaction features high laser energy absorption and increased emission of MeV electrons, ions, and of hard x-rays. In this work, we irradiated isolated, translationally-symmetric objects in the form of micrometric Au bars. The interaction resulted in the emission of two forward-directed electron jets having a small opening angle, a narrow energy spread in the MeV range, and a positive angle to energy correlation. Our numerical simulations show that following ionization, those electrons that are pulled into vacuum near the object’s edge, remain in-phase with the laser pulse for long enough so that the Lorentz force they experience drive them around the object’s edge. After these electrons pass the object, they form attosecond duration bunches and interact with the laser field over large distances in vacuum in confined volumes that trap and accelerate them within a narrow range of momentum. The selectivity in energy of the interaction, its directionality, and the preservation of the attosecond duration of the electron bunches over large distances, offer new means for designing future laser-based light sources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Electronic excitations and spin interactions in chromium trihalides from embedded many-body wavefunctions

Although chromium trihalides are widely regarded as a promising class of two-dimensional magnets for next-generation devices, an accurate description of their electronic structure and magnetic interactions has proven challenging to achieve. Here, we quantify electronic excitations and spin interactions in CrX 3 (X = Cl, Br, I) using embedded many-body wavefunction calculations and fully generalized spin Hamiltonians. We find that the three trihalides feature comparable d-shell excitations, consisting of a high-spin 4 A 2 ($t^3_{2g}$$e^0_g$) ground state lying 1.5–1.7 eV below the first excited state 4 T 2 ($t^2_{2g}$$e^1_g$). CrCl 3 exhibits a single-ion anisotropy A sia = - 0.02 meV, while the Cr spin-3/2 moments are ferromagnetically coupled through bilinear and biquadratic exchange interactions of J 1 = - 0.97 meV and J 2 = - 0.05 meV, respectively. The corresponding values for CrBr 3 and CrI 3 increase to A sia = -0.08 meV and A sia = - 0.12 meV for the single-ion anisotropy, J 1 = -1.21 meV, J 2 = -0.05 meV and J 1 = -1.38 meV, J 2 = -0.06 meV for the exchange couplings, respectively. We find that the overall magnetic anisotropy is defined by the interplay between A sia and A dip due to magnetic dipole–dipole interaction that favors in-plane orientation of magnetic moments in ferromagnetic monolayers and bulk layered magnets. The competition between the two contributions sets CrCl 3 and CrI 3 as the easy-plane (A sia + A dip >0) and easy-axis (A sia + A dip <0) ferromagnets, respectively. The differences between the magnets trace back to the atomic radii of the halogen ligands and the magnitude of spin–orbit coupling. Our findings are in excellent agreement with recent experiments, thus providing reference values for the fundamental interactions in chromium trihalides.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Staphylococcus aureus vWF-binding protein triggers a strong interaction between clumping factor A and host vWF

The Staphylococcus aureus cell wall-anchored adhesin ClfA binds to the very large blood circulating protein, von Willebrand factor (vWF) via vWF-binding protein (vWbp), a secreted protein that does not bind the cell wall covalently. Here we perform force spectroscopy studies on living bacteria to unravel the molecular mechanism of this interaction. We discover that the presence of all three binding partners leads to very high binding forces (2000 pN), largely outperforming other known ternary complexes involving adhesins. Strikingly, our experiments indicate that a direct interaction involving features of the dock, lock and latch mechanism must occur between ClfA and vWF to sustain the extreme tensile strength of the ternary complex. Our results support a previously undescribed mechanism whereby vWbp activates a direct, ultra-strong interaction between ClfA and vWF. This intriguing interaction represents a potential target for therapeutic interventions, including synthetic peptides inhibiting the ultra-strong interactions between ClfA and its ligands.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Significance and challenges in dissecting cancer-bacteriome interactions

Cancer is the leading cause of death around the world. While some types of cancer have become manageable due to advancements in medicine, most cancers still lack available cures and treatments. Recent studies have shown that changes in the human microbiome, especially in the bacteriome, are associated with some cancers. Certain bacterial strains have been reported to promote the initiation and progression of cancer in humans. Other studies have used sequencing to observe changes in the bacteriome of healthy and cancer patients. However, studies that investigate the interactions between cancer cells and the complex bacteriome as a whole remain scarce. This is due to the absence of experimental methods to study the interactions between cancer cells and complex bacterial populations, which has delayed the progress in identifying cancer-causing and cancer-inhibiting bacteria, and in understanding the bacterial interactions and their influence on host cells. Here, we review approaches to studying cancer cell interactions with complex bacteriomes and suggest possible routes to overcome this problem, highlighting the need for interdisciplinary studies that may help advance this field. We speculate that a good understanding of cancer-bacteriome interactions may open the door to new lines of holistic bacteriotherapy for cancer that is otherwise unavailable.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Molecular interactions in diffusion-controlled aldol condensation with mesoporous silica nanoparticles

The aldol reaction of p-nitrobenzaldehyde in amino-catalyzed mesoporous silica nanoparticles (MSN) has revealed varying catalytic activity with the size of the pores of MSN. The pore size dependence related to the reactivity indicates that the diffusion process is important. A detailed molecular-level analysis for understanding diffusion requires assessment of the noncovalent interactions of the molecular species involved in the aldol reaction with each other, with the solvent, and with key functional groups on the pore surface. Such an analysis is presented here based upon the effective fragment potential (EFP). The EFP method can calculate the intermolecular interactions, decomposed into Coulomb, polarization, dispersion, exchange-repulsion, and charge-transfer interactions. In this study, the potential energy surfaces corresponding to each intermolecular interaction are analyzed for homo- and hetero-dimers with various configurations. The monomers that compose dimers are five molecules such as p-nitrobenzaldehyde, acetone, n-hexane, propylamine, and silanol. The results illustrate that the dispersion interaction is crucial in most dimers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗