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DOE OSTI2025

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗

DOE OSTI2025

Attractive Noncovalent Interactions versus Steric Confinement in Asymmetric Supramolecular Catalysis

The remarkable catalytic performance of enzymes stems from their ability to engage in precise noncovalent interactions (NCIs) within a sterically confined space. Supramolecular catalysis seeks to emulate and understand these strategies through the rational design of simple and controlled catalyst microenvironments. While both steric confinement and attractive interactions have been invoked as key to host activity, their relative contribution to rate enhancement and selectivity, as well as potential trade-offs, remains an outstanding question. Here, we address this question by systematically comparing two metal–organic supramolecular catalysts, which differ in the strength of their attractive noncovalent interactions and in their cavity volume. Our findings reveal that the catalyst with the larger cavity, and with stronger available NCIs, exhibits both significant rate acceleration (100-fold) and enhanced enantioselectivity (84% vs 14% ee) in a model ketone reduction compared to its smaller analogue. Mechanistic analysis, binding competition experiments, and computational modeling indicate that these differences predominantly stem from stabilizing noncovalent interactions in the larger catalyst, a result that challenges existing steric-based models of supramolecular stereoinduction. Understanding the governing factors of asymmetric induction and rate acceleration in supramolecular hosts will undoubtedly inform future catalyst design.

Catalysts↗

DOE OSTI2025

Quantifying the Resolution Sensitivity of the Kain–Fritsch Scheme Across the Gray Zone by Isolating Interactions: A TWP‐ICE Case Study

The resolution sensitivity of the Kain–Fritsch (KF) convection scheme and the role of interactions between the physics and dynamics within the gray zone (<10 km) were investigated using the Separate Physics and Dynamics Experiment (SPADE) framework. Two groups of experiments were conducted using the Weather Research and Forecasting (WRF) model via traditional (Tradition) runs and SPADE runs with resolutions of 1, 2, 4, and 8 km during the wet period of the Tropical Warm Pool–International Cloud Experiment (TWP‐ICE). Results show that the KF scheme simulates the weakened convective processes well as the resolution increases in both groups, and the changes in the convective variables with resolution in SPADE are smaller than in the Tradition group. This indicates the important effects of interactions between model components on convection parameterizations as the resolution changes. Additionally, the microphysics variables remain nearly unchanged with resolution in SPADE and weaken slightly in Tradition as the resolution decreases, suggesting the relatively weaker influences of model interactions for the resolved‐cloud parameterization. Therefore, the scale‐aware behavior of KF scheme is further strengthened in Tradition runs, primarily through inhibiting the strength of stratiform processes through physics–dynamics interactions and physical components.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Mitigation of ICRF—edge plasma interaction in Alcator C-Mod

The parasitic interaction between ion cyclotron range of frequencies (ICRF) waves and the edge plasma has long limited high-power ICRF utilization in magnetically confined fusion plasmas. In this paper, we report on the successful mitigation of this interaction by power tapering a four-strap field-aligned (FA) antenna in the Alcator C-Mod tokamak. With the antenna operated in dipole phasing ($0\pi0\pi$), the ratio of the power coupled by the central two straps ($P_\mathrm {cent}$) to the power coupled by the outer two straps was varied at fixed total coupled ICRF power ($P_\mathrm {tot}$). With $P_\mathrm {cent}$/$P_\mathrm {tot} \approx 0.8-0.9$, no enhancement of the plasma potential was measured despite 1 MW of coupled ICRF power. When the antenna is powered, energy deposition increases on its four corners and on neighboring limiter tiles magnetically connected to some of those corners. The energy deposited on the antenna and limiter is minimized together with near-field plasma potentials. Additionally, we show that deviation from $P_\mathrm {cent}$/$P_\mathrm {tot} \approx 0.8$ enhances wave-plasma interactions in places not magnetically connected to the antenna. These far-field effects are correlated with changes in the antenna spectrum. Hence, on C-Mod, near-field and far-field interactions were minimized for about the same range of $P_\mathrm {cent}$/$P_\mathrm {tot}$. Optimal power tapering was also found to improve ICRF heating efficiency and facilitate H-mode access. Finally, we show that the heat flux pattern on the toroidally aligned antennas reverses with the direction of the RF-induced E×B flow in front of the antenna, a correlation not observed for the FA antenna. We argue that the RF-induced E×B flow, which carries high-density plasma from the near-SOL, is aligned with the FA antenna and does not intercept its corners, where the plasma potential is large. This could explain the previously reported smaller impurity generation by the FA antenna (Wukitch et al 2013 Phys. Plasmas 20 056117).

Alcator C-Mod↗

DOE OSTI2024

Topological edge conduction induced by strong anisotropic exchange interactions

Here, we predict that an interplay between isotropic and anisotropic exchange interactions in a honeycomb lattice structure can lead to topological edge conduction when the anisotropic interaction is at least twice the strength of the isotropic interaction. For materials like Na 2 ⁢IrO 3 , such a strong anisotropic exchange interaction simultaneously induces a zigzag type of antiferromagnetic order that breaks the time-reversal symmetry of the topological edge conductor. We show that the electronic transport in such topological conductors will exhibit a quantized Hall conductance without any external magnetic field when the Fermi energy lies within a particular energy range.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Theoretical description of proton-deuteron interactions using exact two-body dynamics of the femtoscopic correlation method

Modeling proton-deuteron interactions is particularly challenging. Due the deuteron's large size, the interaction can extend over several femtometers. The degree to which it can be modeled as a two-body problem might also be questioned. One way to study these interactions is through femtoscopic correlation measurements of particle pairs, extracting information using available theoretical models. In this work, we examine two approaches for describing proton-deuteron correlations: the Lednický-Lyuboshits formalism and full numerical solutions of the Schrödinger equation. Here, our results show that the differences between these methods are significant. Furthermore, we demonstrate that incorporating higher-order partial waves—particularly the p wave—is essential for accurately capturing the dynamics of proton–deuteron interactions and the full potential of the strong force.

Nucleon induced nuclear reactions↗

DOE OSTI2024

African Swine Fever Virus Protein–Protein Interaction Prediction

The African swine fever virus (ASFV) is an often deadly disease in swine and poses a threat to swine livestock and swine producers. With its complex genome containing more than 150 coding regions, developing effective vaccines for this virus remains a challenge due to a lack of basic knowledge about viral protein function and protein–protein interactions between viral proteins and between viral and host proteins. In this work, we identified ASFV-ASFV protein–protein interactions (PPIs) using artificial intelligence-powered protein structure prediction tools. We benchmarked our PPI identification workflow on the Vaccinia virus, a widely studied nucleocytoplasmic large DNA virus, and found that it could identify gold-standard PPIs that have been validated in vitro in a genome-wide computational screening. We applied this workflow to more than 18,000 pairwise combinations of ASFV proteins and were able to identify seventeen novel PPIs, many of which have corroborating experimental or bioinformatic evidence for their protein–protein interactions, further validating their relevance. Two protein–protein interactions, I267L and I8L, I267L__I8L, and B175L and DP79L, B175L__DP79L, are novel PPIs involving viral proteins known to modulate host immune response.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2015

Plume and Shock Interaction Effects on Sonic Boom in the 1-foot by 1-foot Supersonic Wind Tunnel

The desire to reduce or eliminate the operational restrictions of supersonic aircraft over populated areas has led to extensive research at NASA. Restrictions are due to the disturbance of the sonic boom, caused by the coalescence of shock waves formed by the aircraft. A study has been performed focused on reducing the magnitude of the sonic boom N-wave generated by airplane components with a focus on shock waves caused by the exhaust nozzle plume. Testing was completed in the 1-foot by 1-foot supersonic wind tunnel to study the effects of an exhaust nozzle plume and shock wave interaction. The plume and shock interaction study was developed to collect data for computational fluid dynamics (CFD) validation of a nozzle plume passing through the shock generated from the wing or tail of a supersonic vehicle. The wing or tail was simulated with a wedgeshaped shock generator. This test entry was the first of two phases to collect schlieren images and off-body static pressure profiles. Three wedge configurations were tested consisting of strut-mounted wedges of 2.5- degrees and 5-degrees. Three propulsion configurations were tested simulating the propulsion pod and aft deck from a low boom vehicle concept, which also provided a trailing edge shock and plume interaction. Findings include how the interaction of the jet plume caused a thickening of the shock generated by the wedge (or aft deck) and demonstrate how the shock location moved with increasing nozzle pressure ratio.

Shock wave interaction↗

NASA NTRS2015

Cart3D Analysis of Plume and Shock Interaction Effects on Sonic Boom

A plume and shock interaction study was developed to collect data and perform CFD on a configuration where a nozzle plume passed through the shock generated from the wing or tail of a supersonic vehicle. The wing or tail was simulated with a wedge-shaped shock generator. Three configurations were analyzed consisting of two strut mounted wedges and one propulsion pod with an aft deck from a low boom vehicle concept. Research efforts at NASA were intended to enable future supersonic flight over land in the United States. Two of these efforts provided data for regulatory change and enabled design of low boom aircraft. Research has determined that sonic boom is a function of aircraft lift and volume distribution. Through careful tailoring of these variables, the sonic boom of concept vehicles has been reduced. One aspect of vehicle tailoring involved how the aircraft engine exhaust interacted with aft surfaces on a supersonic aircraft, such as the tail and wing trailing edges. In this work, results from Euler CFD simulations are compared to experimental data collected on sub-scale components in a wind tunnel. Three configurations are studied to simulate the nozzle plume interaction with representative wing and tail surfaces. Results demonstrate how the plume and tail shock structure moves with increasing nozzle pressure ratio. The CFD captures the main features of the plume and shock interaction. Differences are observed in the plume and deck shock structure that warrant further research and investigation.

supersonic wind tunnels↗

NASA NTRS2022

Calculating Factors of Safety and Margins of Safety from Interaction Equations for Preloaded Bolts

This report presents the derivation of the factored interaction equations for preloaded bolts in two- or three-dimensional space. This is an extension of the previous work of the first author which covered factored interaction equations consisting of load or stress-ratios which were either solely constant or solely varying quantities. The factored interaction equations for preloaded bolts consist of an axial load-ratio that is a combination of a constant quantity, preload and thermal load at preload, and a varying quantity, tensile and bending loads, and was not covered under the previous work. Two forms of the factored interaction equations for preloaded bolts, arising from two perspectives, are presented and compared. Closed form solutions for the tensile, shear, and bending loads as functions of the other concurrent loads that produces zero margin of safety are presented.

interaction equations↗

NASA NTRS2022

Regolith Simulant Preparation and Geotechnical Characterization for Plume Surface Interaction Testing

Descent engine plumes interact with the lunar surface and accelerate regolith particles to potentially high velocities. These ejecta create risks to surface assets that have yet to be fully assessed. To better understand these risks, plume surface interactions can be simulated on the ground by firing a test engine plume into a bin of lunar regolith simulant under vacuum conditions. The dynamics of the resultant ejecta can then be recorded. In this technical memorandum we discuss the processes used in preparing a 150 kg bin of lunar regolith simulant for plume surface interaction ground tests under vacuum conditions for the NASA STMD Plume Surface Interaction project. We present our approach to mitigating regolith simulant eruptions during pump-down, the methods used to fill and reset the regolith simulant bin for each test, and the techniques used to characterize the consistency of regolith simulant geotechnical properties before each new firing. The challenges of preparing a regolith simulant test bin below an ambient pressure of one atmosphere, particularly on the large scale, could largely be overcome with a system that could fill the test bin with simulant inside the chamber and under vacuum conditions.

lunar regolith↗

NASA NTRSDate not supplied

Summary of Shock Wave Turbulent Boundary Layer Interaction Experiments In a Circular Test Section

A series of experiments were performed at Mach 2.5 in a 17 cm diameter circular test section to characterize an impinging/reflected shock wave turbulent boundary layer interaction generated by a cone-cylinder centerbody. The cone-cylinder centerbody generates a conical shock wave that interacts with the naturally occurring boundary layer developing on the test section wall. Three different cone angles were used in the experiment to study unseparated, incipiently separated, and separated interactions. When the cone-cylinder centerbody is positioned on the centerline, a flowfield which is two-dimensional in the mean is generated. Three dimensional interactions were also created by offsetting the cone-cylinder centerbody from the test section centerline. The results are intended to provide benchmark quality datasets for computational fluid dynamics (CFD) validation without the pitfalls inherent in rectangular configurations where corner effects prohibit a truly two-dimensional flow in the mean. The experimental measurements included surface flow visualization, wall static pressure, flowfield Pitot tube pressure, constant-voltage anemometry (CVA) normal hot-wire, and particle image velocimetry (PIV) measurements. The hot-wire measurements were used to calculate mean mass flux and total temperature profiles, mass flux and total temperature turbulence intensities, and the mass flux-total temperature correlation. The PIV measurements provide three-dimensional mean velocity measurements. Agreement between the pressure, hot-wire, and PIV measurements is established in the undisturbed upstream flowfield.

Supersonic↗

NASA NTRSDate not supplied

Summary of Shock Wave Turbulent Boundary Layer Interaction Experiments in a Circular Test Section

compressible flow↗

NASA NTRSDate not supplied

Developing New Tools for Modeling Rocket Plume-Surface Interactions

With NASA’s goal to land the next human on the lunar surface in the next few years, it has become vitally important that we have a better understanding of how future landing spacecraft will interact with the unique properties of regolith¬¬––the layer of loose, unconsolidated dust and rock on the lunar surface¬¬––which can cause hazards like visual obstructions, particulate clouds, and cratering of the landing zone. Researchers from the Fluid Dynamics Branch at NASA’s Marshall Space Flight Center are performing plume-surface interaction (PSI) simulations between lander engine plumes and unprepared regolith surfaces, and have developed new tools to provide predictive PSI environments for various NASA projects and missions, including the Human Lander System (HLS), Commercial Lunar Payload Services (CLPS), and future Mars landers. These tools allow the researchers to determine how to best meet the simulation and time requirements for each project by varying model fidelity. The highest fidelity tool is the Gas Granular Flow Solver (Loci/GGFS) that models gas-particle multi-phase interactions to predict regolith cratering and ejection of particles into the immediate surroundings of the lander. At its highest fidelity, it can model microscopic regolith particle interactions with a particle size/shape distribution that statistically replicates actual regolith, however, to be most effective with today’s computing resources, it is currently run using only one to three equivalent particle sizes/shapes. The team also incorporated engineering models into their software suite to create production-ready hybrid tools with reduced fidelity. At the lowest fidelity, the computational fluid dynamics (CFD) code Loci/CHEM+DIGGEM can predict crater depth over time by relating local CFD-predicted surface shear stresses to a model of erosion mass flux.

plume surface interaction↗

NASA NTRSDate not supplied

Development Efforts and Status of Plume-Surface Interaction Capabilities for Propulsive Landing Systems

Rocket plume-surface interaction is a multi-phase problem characterized by plume flow physics, erosion physics, and ejecta dynamics. All propulsive landers will experience plume-surface interaction. The risks posed by such effects can vary greatly as a function of the local environment, lander concept of operations, configuration, and physical scale. Prior Lunar and Martian landers have overcome challenges posed by these environments, on the basis of scaled ground testing and subsequent flight experience, but the landing systems for present and future missions are planning to operate increasingly outside of NASA's current experience with plume-surface interaction. This presentation discusses the current efforts and status of activities within NASA to progress understanding of fundamental plume-surface interaction physics, the capability to predict resulting environments and effects, and the definition of implications for current and future Lunar and planetary landing systems.

Landing↗

DOE OSTI2025

Long-Range Interaction between Molecules with Electronic Degeneracy: Beyond the Born–Oppenheimer Approximation

Long-range intermolecular interaction plays an essential role in (ultra)cold collisions. For monomers with degenerate electronic states, an accurate description of the long-range interaction can be challenging due to the potential breakdown of the Born–Oppenheimer approximation. In this work, we developed a general method to construct long-range interaction potential energy surfaces (IPESs) between arbitrary molecules using the degenerate perturbation theory of Schrödinger. To further simplify the application of this method, a group-theoretical method is introduced to identify nonzero components of electrostatic properties of monomers, especially for the nonlinear molecules. To demonstrate this approach, we report the long-range IPESs of the O( 3 P)–OH( 2 Π) and OH( 2 Π)–OH( 2 Π) systems. The excellent agreement with ab initio calculations in large separations, even near electronic degeneracies, confirms the accuracy of our approach. The method is expected to lay the groundwork for the accurate investigation of (ultra)cold collisional dynamics involving open-shell species.

ab initio calculations↗

DOE OSTI2025

New particle pusher with hadronic interactions for modeling multimessenger emission from compact objects

We propose novel numerical schemes based on the Boris method in curved spacetime, incorporating both hadronic and radiative interactions for the first time. Once the proton has lost significant energy due to radiative and hadronic losses, and its gyroradius has decreased below typical scales on which the electromagnetic field varies, we apply a guiding center approximation (GCA). We fundamentally simulate collision processes either with a Monte-Carlo method or, where applicable, as a continuous energy loss, contingent on the local optical depth. To test our algorithm for the first time combining the effects of electromagnetic, gravitational, and radiation fields including hadronic interactions, we simulate highly relativistic protons traveling through various electromagnetic fields and proton backgrounds. We provide unit tests in various spatially dependent electromagnetic and gravitational fields and background photon and proton distributions, comparing the trajectory against analytic results. We propose that our method can be used to analyze hadronic interactions in black hole accretion disks, jets, and coronae to study the neutrino abundance from active galactic nuclei.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Effect of Molecular Conformation on Intermolecular Interactions and Photovoltaic Performances of Giant Molecule Acceptors

The molecular conformation of giant molecule acceptors (GMAs) plays a significant role in regulating the intermolecular interactions and their photovoltaic performances in organic solar cells (OSCs). For the linear GMA GT‐l, the stronger homo‐molecular interaction causes its aggregation being weakly affected by the donor, thus forming an ordered molecular stacking and proper phase separation in its blend film. The star‐shaped GMA GT‐s‐based blend film shows a dominant hetero‐molecular interaction that suppresses the aggregation of the donor and acceptor, resulting in smaller phase separation and more uniform vertical phase distribution. While for another star‐shaped GMA GTs, the weakest hetero‐molecular interaction causes its blend film to form larger phase separation. Therefore, the GT‐l based OSC with PM6 as donor shows the highest charge mobilities, the fastest charge transfer (CT) process, reduced energy loss and less charge recombination, contributing to a higher power conversion efficiency (PCE) of 19.03%. Comparatively, the PCEs of the OSCs based on GTs and GT‐s are 18.05% and 17.58% respectively. Notably, all the three GMAs based OSCs show excellent thermal stability and long‐term storage stability. This study provides a facile strategy by tuning the linking unit and its connecting mode for designing highly efficient and stable organic photovoltaic materials.

Chemistry↗