Search NASA⌕ Search

SEARCH · Search NASA

Results for “interaction”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform

Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, these studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2018

Nozzle Plume/Shock Interaction Experimental and Computational Sonic Boom Analyses from the NASA Ames 9- by 7-Foot Supersonic Wind Tunnel

A wind tunnel test and a computational study were conducted to investigate the complex interactions between a supersonic nozzle plume and shock waves of differing strengths generated from various aft surfaces typical of supersonic aircraft. These analytically-defined aft surfaces were representative of horizontal tails of various sizes, and an aft deck. CFD simulations of many proposed model configurations allowed for assessments of the detailed flow interactions of components in close proximity to the nozzle, as well as assessments of the nozzle jet flow itself. The evaluation of the computational results for many candidate configurations guided the design of model components. The interactions of the waveforms from these surfaces with the jet exhaust plume can have significant adverse effects on the loudness of the sonic boom if the surfaces are not carefully integrated into an aircraft design. The greatest discrepancy in estimating sonic boom loudness for low-boom flight vehicles is currently in predicting the signatures from the aft part of an aircraft, including the interactions with the plume flow. The objectives of this test were to gain a better understanding of these interactions, and to provide a detailed experimental database from multiple sources for use as validation cases for CFD tool development. The subject test was run in the NASA Ames 9- by 7-Ft Supersonic Wind Tunnel in February 2016 at Mach numbers of 1.6 and 2.0, and was funded by the NASA Commercial Supersonics Technology (CST) Project. The nozzle flow was provided by high-pressure air (HPA) pumped through the model, and pressure signature data were acquired with the NASA 14-inch sonic boom pressure rail. The rail measured the locations of the shocks and expansions at various distances and off-track angles from the model. This enabled the impact of the nozzle plume/shock interactions on the near- and mid-field sonic boom pressure waveforms to be quantified. Schlieren images of the flow field around and behind the model were obtained with an RBOS (Retroreflective Background-Oriented Schlieren) technique to determine the origins of the shock and expansion waves, to identify the shape and boundaries of the plume, and to determine the changes in incoming and exiting waveforms within the plume. A total pressure rake was positioned closely behind the model nozzle in order to measure the total pressure profiles of the flow above, within, and below the nozzle exhaust. Model angles and positions in the tunnel were measured by photogrammetry using two cameras since the lack of a model force balance prevented the measurement of model deflections under load.Navier-Stokes computations using two different CFD codes were compared to the experimental sonic boom pressure signature data, and the rake total pressure data in the plume. A computational schlieren technique was used to compare the computed flow field with the RBOS images. The computational results were also used to complement the test data with flow field quantities that could not be measured, such as Mach number and pressure distributions to distinguish shock waves and expansion waves.

sonic boom↗
NASA NTRS2022

Quantifying Earth System Interactions for Sustainable Food Production Via Expert Elicitation

Several safe boundaries of critical Earth system processes have already been crossed due to human perturbations; not accounting for their interactions may further narrow the safe operating space for humanity. Using expert knowledge elicitation, we explored interactions among seven variables representing Earth system processes relevant to food production, identifying many interactions little explored in Earth system literature. We found that green water and land system change affect other Earth system processes strongly, while land, freshwater and ocean components of biosphere integrity are the most impacted by other Earth system processes, most notably blue water and biogeochemical flows. We also mapped a complex network of mechanisms mediating these interactions and created a future research prioritization scheme based on interaction strengths and existing knowledge gaps. Our study improves the understanding of Earth system interactions, with sustainability implications including improved Earth system modelling and more explicit biophysical limits for future food production.

Expert knowledge elicitation↗
DOE OSTI2025

First Measurement of Missing Energy due to Nuclear Effects in Monoenergetic Neutrino Charged-Current Interactions

We present the first measurement of the missing energy due to nuclear effects in monoenergetic, muon neutrino charged-current interactions on carbon, originating from 𝐾 + → 𝜇 + ⁢𝜈 𝜇 decay at rest (𝐸 𝜈 𝜇 = 235.5 MeV), performed with the J-PARC Sterile Neutrino Search at the J-PARC Spallation Neutron Source liquid scintillator based experiment. Toward characterizing the neutrino interaction, ostensibly 𝜈 𝜇 ⁢𝑛 → 𝜇 − ⁢𝑝 or 𝜈 𝜇 ⁢ 12 C → 𝜇 − ⁢ 12 N, we define the missing energy as the energy transferred to the nucleus (𝜔) minus the kinetic energy of the outgoing proton(s), 𝐸 𝑚 ≡ 𝜔−∑ 𝑇 𝑝 , and relate this to visible energy in the detector, 𝐸 𝑚 = 𝐸 𝜈 𝜇 ⁡(235.5 MeV) − 𝑚 𝜇⁡ (105.7 MeV) + [𝑚 𝑛 − 𝑚 𝑝⁡ (1.3 MeV)] − 𝐸 vis . The missing energy, which is naively expected to be zero in the absence of nuclear effects (e.g., nucleon separation energy, Fermi momenta, and final-state interactions), is uniquely sensitive to many aspects of the interaction, and has previously been inaccessible with neutrinos. The shape-only, differential cross section measurement reported, based on a (77 ± 3)% pure double-coincidence kaon decay-at-rest signal (621 total events), provides detailed insight into neutrino-nucleus interactions, allowing even the nuclear orbital shell of the struck nucleon to be inferred. The measurement provides an important benchmark for models and event generators at hundreds of MeV neutrino energies, characterized by the difficult-to-model transition region between neutrino-nucleus and neutrino-nucleon scattering, and relevant for applications in nuclear physics, neutrino oscillation measurements, and Type-II supernova studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Quantum dynamics of cosmological particle production: interacting quantum field theories with matrix product states

Understanding real-time dynamics of interacting quantum fields in curved space-time remains a major theoretical challenge. We employ tensor network methods to study such dynamics using interacting scalar and gauge theories in 1+1 spacetime dimensions, subject to a quench modeling a homogeneously expanding gravitational background. The models considered are the scalar λϕ 4 theory and the Schwinger model, i.e. a Dirac fermion coupled to a U(1) gauge field which is equivalent via bosonization to a scalar field with a cosine self-interaction. In the free scalar limit, both theories reproduce known analytical results, providing a nontrivial numerical validation of bosonization in curved spacetime for the Schwinger model. Our central finding is that self-interactions lead to a suppression of gravitational particle production compared to the free-field case, as evidenced by two-point functions and the spectra of produced particles. We further examine the behavior of entanglement generation and find that interactions suppress entanglement growth in the λϕ 4 theory, while in the Schwinger model, the interplay between suppressed particle production and enhanced inter-particle correlations leads to more complex entanglement behavior. Our results pave the way for further explorations of nonperturbative quantum real-time dynamics of interacting scalar and gauge theories in arbitrary gravitational backgrounds.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic–inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. Here, to understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31–calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ∼2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31–calcite interactions. While this work provides the first experimental confirmation that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31–calcite interface has advanced our fundamental understanding of the atomic interactions at the organic–inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Close, Emily G. S. [Pacific Northwest National Lab↗
DOE OSTI2024

Probing shocks interacting with radiation waves with the Radishock experiment

Both radiation flows and shocks have been extensively studied in the laboratory in the past few decades due to their critical roles in many astrophysical and high-energy density physics processes. In the Radishock experiment, a halfraum-powered radiation wave is driven into a low-density foam and interacts with an ablatively driven, counter-propagating shock. The interacting waves produce a spike in energy density with a temperature greater than the local temperature of the individual waves. As in the successful predecessor experiment, COAX, the primary diagnostic uses absorption spectroscopy at many locations down the cylindrical target, enabling a spatial temperature inference of the radiation wave and its interactions with the shock. Combined with a radiography diagnostic that is capable of imaging the shock and interaction features, we are able to study and inform model predictions of the interaction spike phenomenon. We describe the underlying physics behind the shock interactions with the radiation front and the implications of this experimental study for a broad range of astrophysical phenomena.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Spatially structured bacterial interactions alter algal carbon flow to bacteria

Phytoplankton account for nearly half of global photosynthetic carbon fixation, and the fate of that carbon is regulated in large part by microbial food web processing. We currently lack a mechanistic understanding of how interactions among heterotrophic bacteria impact the fate of photosynthetically fixed carbon. Here, we used a set of bacterial isolates capable of growing on exudates from the diatom Phaeodactylum tricornutum to investigate how bacteria-bacteria interactions affect the balance between exudate remineralization and incorporation into biomass. With exometabolomics and genome-scale metabolic modeling, we estimated the degree of resource competition between bacterial pairs. In a sequential spent media experiment, we found that pairwise interactions were more beneficial than predicted based on resource competition alone, and 30% exhibited facilitative interactions. To link this to carbon fate, we used single-cell isotope tracing in a custom cultivation system to compare the impact of different "primary" bacterial strains in close proximity to live P. tricornutum on a distal "secondary" strain. We found that a primary strain with a high degree of competition decreased secondary strain carbon drawdown by 51% at the single-cell level, providing a quantitative metric for the "cost" of competition on algal carbon fate. Additionally, a primary strain classified as facilitative based on sequential interactions increased total algal-derived carbon assimilation by 7.6 times, integrated over all members, compared to the competitive primary strain. Our findings suggest that the degree of interaction between bacteria along a spectrum from competitive to facilitative is directly linked to algal carbon drawdown.

genome-scale metabolic model↗
DOE OSTI2024

Electron– K -phonon interaction in twisted bilayer graphene

We develop an analytic theory to describe the interaction between electrons and K phonons and study its influence on superconductivity in the bare bands of twisted bilayer graphene (TBG). We find that, due to symmetry and the two-center approximation, only one optical K phonon (160meV) of graphene is responsible for the intervalley electron-phonon interaction. Here, this phonon has recently been found in angular-resolved photoemission spectroscopy to be responsible for replicas of the TBG flat bands. By projecting the interaction to the TBG flat bands, we perform the full symmetry analysis of the phonon-mediated attractive interaction and pairing channels in the Chern basis, and show that several channels are guaranteed to have gapless order parameters. From the linearized gap equations, we find that the highest T c pairing induced by this phonon is a singlet gapped s-wave inter-Chern-band order parameter, followed closely by a gapless nematic d-wave intra-Chern-band order parameter. We justify these results analytically, using the topological heavy-fermion mapping of TBG which has allowed us to obtain an analytic form of a phonon-mediated attractive interaction and to analytically solve the linearized and T = 0 gap equations. For the intra-Chern-band channel, the nematic state with nodes is shown to be stabilized in the chiral flat-band limit. While the flat-band Coulomb interaction can be screened sufficiently enough—around the Van Hove singularities—to allow for electron-phonon based superconductivity, it is unlikely that this effect can be maintained in the lower density of states excitation bands around the correlated insulator states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Influence of extended interactions on spin dynamics in one-dimensional cuprates

Quasi-one-dimensional (1D) materials provide a unique platform for understanding the importance and influence of extended interactions on the physics of strongly correlated systems due to their relative structural simplicity and the existence of powerful theoretical tools well-adapted to one spatial dimension. Recently, this was highlighted by anomalous observations in the single-particle spectral function A(q, ω) of 1D cuprate chain compounds, measured by angle-resolved photoemission spectroscopy (ARPES), which were explained by the presence of a long-range attractive interaction. Such an extended interaction should leave its fingerprints on other observables, notably the dynamical spin structure factor S(q, ω), measured by neutron scattering or resonant inelastic x-ray scattering (RIXS). Starting from a simple Hubbard Hamiltonian in 1D and using time-dependent density matrix renormalization group (tDMRG) methods, we show that the presence of long-range attractive coupling, directly through an instantaneous Coulomb interaction V or retarded electron phonon (el-ph) coupling, can introduce significant spectral weight redistribution in S(q, ω) across a wide range of doping. Here, this underscores the significant impact that extended interactions can have on dynamical correlations among particles, and the importance of properly incorporating this influence in modeling. Our results demonstrate that S(q, ω) can provide a sensitive experimental constraint, which complements ARPES measurements, in identifying key interactions in 1D cuprates, beyond the standard Hubbard model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Tagging efficiency study of incoherent diffractive vector meson production at the second interaction region at the Electron-Ion Collider

The Electron-Ion Collider (EIC) is an upcoming accelerator facility aimed at exploring the properties of quarks and gluons in nucleons and nuclei, shedding light on their structure and dynamics. The inaugural experimental apparatus, ePIC (electron-Proton and Ion Collider), is designed as a general-purpose detector to address the National Academy of Sciences and the Nuclear Science Advisory Committee physics program at the EIC. The wider EIC community is strongly supporting a second interaction region and an associated second detector to enhance the full science program. In this study, we evaluate how this second interaction region and detector can be complementary to ePIC. The layout of an interaction region for the second detector offers a secondary focus that provides better forward detector acceptance at scattering angles near θ ~ 0 mrad, which can specifically enhance the exclusive, tagging, and diffractive physics program. Here, this article presents an analysis of a tagging program using the second interaction region layout with incoherent diffractive vector meson production. The current design of the second EIC interaction region is evaluated for its vetoing capabilities of incoherent events required for the study of coherent diffractive measurements. We find an increased vetoing performance compared to the ePIC interaction region, thus improving measurements which are important for the spatial imaging of nucleons and nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Interacting dark sector within ETHOS: Cosmological constraints from SPT cluster abundance with DES and HST weak lensing data

We use galaxy cluster abundance measurements from the South Pole Telescope enhanced by multicomponent matched filter confirmation and complemented with mass information obtained using weak-lensing data from Dark Energy Survey Year 3 (DES Y3) and targeted Hubble Space Telescope observations for probing deviations from the cold dark matter paradigm. Concretely, we consider a class of dark sector models featuring interactions between dark matter (DM) and a dark radiation (DR) component within the framework of the effective theory of structure formation (ETHOS). We focus on scenarios that lead to power suppression over a wide range of scales, and thus can be tested with data sensitive to large scales, as realized, for example, for DM–DR interactions following from an unbroken non-Abelian 𝑆⁢𝑈⁡(𝑁) gauge theory (interaction rate with power-law index 𝑛 = 0 within the ETHOS parametrization). Cluster abundance measurements are mostly sensitive to the amount of DR interacting with DM, parametrized by the ratio of DR temperature to the cosmic microwave background (CMB) temperature, 𝜉 DR = 𝑇 DR /𝑇 CMB . We find an upper limit 𝜉 DR < 17% at 95% credibility. When the cluster data are combined with Planck 2018 CMB data along with baryon acoustic oscillation (BAO) measurements we find 𝜉 DR < 10%, corresponding to a limit on the abundance of interacting DR that is around 3 times tighter than that from CMB + BAO data alone. We also discuss the complementarity of weak lensing informed cluster abundance studies with probes sensitive to smaller scales, explore the impact on our analysis of massive neutrinos, and comment on a slight preference for the presence of a nonzero interacting DR abundance, which enables a physical solution to the 𝑆 8 tension.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

WELLS Interactive Application

The Wellbore Exploration and Location Logistic System (WELLS) Interactive Application is an interactive tool to enable easy exploration and visualization of the living national wellbore database (WELLS Database (https://edx.netl.doe.gov/dataset/wells_database)). The tool and underlying database were created and are maintained by the National Energy Technology Laboratory (NETL), providing visualization of the more than six million public wellbore records from more than 65 authoritative state, federal, and tribal resources. The WELLS Interactive Application serves up wellbore data from oil, gas, underground injection, research, geothermal, geotechnical, groundwater, and other types of wells in a single, standardized, unified system. In addition to the surface location of these wells, the underlying database combines select key attributes for features such as well age, depth, and operating status. The system also provides users with references back to the original sources used in this unified platform. The underlying data can be accessed through the WELLS Database: https://edx.netl.doe.gov/dataset/wells_database Additional Information: The WELLS Interactive Application (formerly titled CO2-Locate) enables visualization and access to the public wellbore records through an intuitive web-based mapping tool. The WELLS Interactive Application was designed to help users visualize, query, analyze, and download wellbore records. Public wellbore points are included as a layer in the Map page, called Public Wells. Additionally, a multivariate hexagon grid summarizing well density from proprietary well data, called Well Density, is included to identify data gaps between the public and proprietary well data. Filtering functionalities in the tool allow these two layers to be spatially filtered by state, county, or basin as well as by status, type, true vertical depth, and spud year. The WELLS Interactive Application also contains a Near Me tool can be used to search and explore wellbore data within a user-defined distance of a specified location on the map, which can also be downloaded. The Query tool allows users to query the selected or filtered wells in the Public Wells layer and export the data. For additional information on these tool functionalities, see the help documentation on the About page of the tool. Notes for Consideration: The Well Density layer provided in this application is derived from proprietary wellbore data, the records of which do not always contain values for key features (status, type, true vertical depth, or spud year). Therefore, data might not be available when layers are queried for all filter combinations. Additionally, visualizing layers and applying filters may take additional time to load (i.e., draw on the map) due to the large size of the data.

ccs↗
DOE OSTI2024

Measuring Muon Antineutrino Charged-Current Interactions Without Mesons in the Final State, in the NOvA Near Detector

NOvA is a long-baseline neutrino experiment based at Fermilab in the US, with the primary aim of measuring neutrino and antineutrino oscillations. This will enhance our understanding of electroweak interactions by measuring the neutrino mixing angles, CP-violating phase and neutrino mass ordering. To measure these oscillations, we first need to have a deep understanding of how neutrinos and antineutrinos interact with matter. Antineutrino interaction cross sections are, at present, particularly poorly constrained, and processes such as meson exchange currents are not well understood in the antineutrino sector. This analysis will develop a cross-section measurement of muon antineutrino interactions without mesons (e.g. pions or kaons) in the final state, in the NOvA near detector. A high-statistics, high-purity sample is obtained through a cut-based selection process implementing machine learning techniques. The sample is dominated by quasi-elastic and meson exchange current interactions which are sensitive to nuclear effects such as Final-State Interactions. The cross section will be extracted as a function of the incoming neutrino energy and the kinematics of the outgoing particles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Continuing Analysis of Charge Current Interactions in ANNIE

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a gadolinium-loaded water Cherenkov detector on the Fermilab Booster Neutrino Beam (BNB).Using νμ in the energy range of 500 to 1000 MeV, ANNIE is designed to measure final-state neutrons.In this poster we will cover the ongoing analysis work exploring Charged-Current neutrino interactions. Charged-Current (CC) νμ interactions in this regime have uncertainties in the relative contributions of quasielastic and res- onance production. Together with intranuclear final-state interactions (FSI) and missing hadronic energy, these interactions drive important biases in neutrino energy reconstruction. ANNIE mit- igates these effects by combining muon kinematics from the downstream Muon Range Detector (MRD) with neutron identification via delayed gamma cascades from thermal captures on gadolin- ium. We characterize CC0π and Δ samples by measuring neutron multiplicity versus event topology and reconstructed kinematics, comparing neutron-tagged data to interaction-model predictions to probe resonance production and pion FSI/absorption

Fleming, Dylon [UC, Davis; Fermilab] (ORCID:000000↗
DOE OSTI2026

Measurement of charged-current quasi elastic-like and inclusive muon (anti-) neutrino interactions using NuMI beam the ICARUS detector

The ICARUS experiment, utilizing Liquid Argon Time Projection Chamber (LArTPC) technology, has been successfully taking physics data at Fermilab since June 2022. The experiment's primary objective is to function as the far detector of the Short Baseline Neutrino program (SBN), searching for hints of physics beyond three-flavour PMNS neutrino oscillations. ICARUS also offers other diverse physics capabilities, including searches beyond the standard model and measurements of cross-sections. In addition to being exposed to the Booster Neutrino (BNB) beamline of the SBN experiment, ICARUS sits 795 m downstream and 5.75 degrees off-axis from the NuMI beam line. Due to the off-axis angle between NuMI and ICARUS, coupled with contributions from both pion and kaon decays to neutrino fluxes, interactions of NuMI neutrinos within ICARUS can be detected over a range of several GeV in energy. Measurements of these interactions present unique opportunities to infer neutrino interaction cross sections on an argon nuclear target within an energy range that overlaps both the SBN oscillation search and a significant portion of the DUNE spectrum. This poster will summarize the current status of muon-neutrino and muon-antineutrino charged current inclusive cross section measurements in ICARUS using the FHC and RHC NuMI sample respectively. Such inclusive measurements provide robust benchmarks for the overall interaction rate and muon kinematics, with reduced dependence on hadronic final-state modeling. The measurement of the muon-antineutrino Argon charged current inclusive cross section is particularly exciting and highly relevant for DUNE, given the scarcity of antineutrino-Argon cross section measurements in the literature. In addition, this poster will highlight ICARUS's first measurement of muon-neutrino Argon charged current mesonless final states using both transverse kinematic imbalance (TKI) variables and muon-proton kinematic variables. These measurements provide sensitivity to nuclear effects, final-state interactions, and nucleon correlations in argon, offering important constraints for improving neutrino interaction modeling for upcoming DUNE.

Roy, Promita [Fermilab; Virginia Tech.]↗
DOE OSTI2024

Microscale Thermophoresis (MST) as a Tool to Study Binding Interactions of Oxygen-Sensitive Biohybrids

Microscale thermophoresis (MST) is a technique used to measure the strength of molecular interactions. MST is a thermophoretic-based technique that monitors the change in fluorescence associated with the movement of fluorescent-labeled molecules in response to a temperature gradient triggered by an IR LASER. MST has advantages over other approaches for examining molecular interactions, such as isothermal titration calorimetry, nuclear magnetic resonance, biolayer interferometry, and surface plasmon resonance, requiring a small sample size that does not need to be immobilized and a high-sensitivity fluorescence detection. In addition, since the approach involves the loading of samples into capillaries that can be easily sealed, it can be adapted to analyze oxygen-sensitive samples. In this Bio-protocol, we describe the troubleshooting and optimization we have done to enable the use of MST to examine protein–protein interactions, protein–ligand interactions, and protein–nanocrystal interactions. The salient elements in the developed procedures include 1) loading and sealing capabilities in an anaerobic chamber for analysis using a NanoTemper MST located on the benchtop in air, 2) identification of the optimal reducing agents compatible with data acquisition with effective protection against trace oxygen, and 3) the optimization of data acquisition and analysis procedures. The procedures lay the groundwork to define the determinants of molecular interactions in these technically demanding systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗