Search NASA⌕ Search

SEARCH · Search NASA

Results for “interaction potential”

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 487 records · Page 27

Phylogeny, morphology, virulence, ecology, and host range of Ordospora pajunii (Ordosporidae), a microsporidian symbiont of Daphnia spp.

ABSTRACT The impacts of microsporidia on host individuals are frequently subtle and can be context dependent. A key example of the latter comes from a recently discovered microsporidian symbiont of Daphnia , the net impact of which was found to shift from negative to positive based on environmental context. Given this, we hypothesized low baseline virulence of the microsporidian; here, we investigated the impact of infection on hosts in controlled conditions and the absence of other stressors. We also investigated its phylogenetic position, ecology, and host range. The genetic data indicate that the symbiont is Ordospora pajunii , a newly described microsporidian parasite of Daphnia . We show that O. pajunii infection damages the gut, causing infected epithelial cells to lose microvilli and then rupture. The prevalence of this microsporidian could be high (up to 100% in the lab and 77% of adults in the field). Its overall virulence was low in most cases, but some genotypes suffered reduced survival and/or reproduction. Susceptibility and virulence were strongly host-genotype dependent. We found that North American O. pajunii were able to infect multiple Daphnia species, including the European species Daphnia longispina , as well as Ceriodaphnia spp. Given the low, often undetectable virulence of this microsporidian and potentially far-reaching consequences of infections for the host when interacting with other pathogens or food, this Daphnia–O. pajunii symbiosis emerges as a valuable system for studying the mechanisms of context-dependent shifts between mutualism and parasitism, as well as for understanding how symbionts might alter host interactions with resources. IMPORTANCE The net outcome of symbiosis depends on the costs and benefits to each partner. Those can be context dependent, driving the potential for an interaction to change between parasitism and mutualism. Understanding the baseline fitness impact in an interaction can help us understand those shifts; for an organism that is generally parasitic, it should be easier for it to become a mutualist if its baseline virulence is relatively low. Recently, a microsporidian was found to become beneficial to its Daphnia hosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidium Ordospora pajunii . Despite the parasitic nature of microsporidia, we found O. pajunii to be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establish O. pajunii is a valuable model for investigating shifts along the mutualism-parasitism continuum.

59 BASIC BIOLOGICAL SCIENCES↗

Transcription Factors Controlling the Rhizobium–Legume Symbiosis: Integrating Infection, Organogenesis and the Abiotic Environment

Abstract Legume roots engage in a symbiotic relationship with rhizobia, leading to the development of nitrogen-fixing nodules. Nodule development is a sophisticated process and is under the tight regulation of the plant. The symbiosis initiates with a signal exchange between the two partners, followed by the development of a new organ colonized by rhizobia. Over two decades of study have shed light on the transcriptional regulation of rhizobium–legume symbiosis. A large number of transcription factors (TFs) have been implicated in one or more stages of this symbiosis. Legumes must monitor nodule development amidst a dynamic physical environment. Some environmental factors are conducive to nodulation, whereas others are stressful. The modulation of rhizobium–legume symbiosis by the abiotic environment adds another layer of complexity and is also transcriptionally regulated. Several symbiotic TFs act as integrators between symbiosis and the response to the abiotic environment. In this review, we trace the role of various TFs involved in rhizobium–legume symbiosis along its developmental route and highlight the ones that also act as communicators between this symbiosis and the response to the abiotic environment. Finally, we discuss contemporary approaches to study TF-target interactions in plants and probe their potential utility in the field of rhizobium–legume symbiosis.

Cell Biology↗

Influence of non-adiabatic effects on linear absorption spectra in the condensed phase: Methylene blue

Modeling linear absorption spectra of solvated chromophores is highly challenging as contributions are present both from coupling of the electronic states to nuclear vibrations and from solute–solvent interactions. In systems where excited states intersect in the Condon region, significant non-adiabatic contributions to absorption line shapes can also be observed. Here, we introduce a robust approach to model linear absorption spectra accounting for both environmental and non-adiabatic effects from first principles. This model parameterizes a linear vibronic coupling (LVC) Hamiltonian directly from energy gap fluctuations calculated along molecular dynamics (MD) trajectories of the chromophore in solution, accounting for both anharmonicity in the potential and direct solute–solvent interactions. The resulting system dynamics described by the LVC Hamiltonian are solved exactly using the thermalized time-evolving density operator with orthogonal polynomials algorithm (T-TEDOPA). The approach is applied to the linear absorption spectrum of methylene blue in water. We show that the strong shoulder in the experimental spectrum is caused by vibrationally driven population transfer between the bright S1 and the dark S2 states. The treatment of the solvent environment is one of many factors that strongly influence the population transfer and line shape; accurate modeling can only be achieved through the use of explicit quantum mechanical solvation. The efficiency of T-TEDOPA, combined with LVC Hamiltonian parameterizations from MD, leads to an attractive method for describing a large variety of systems in complex environments from first principles.

Dunnett, Angus J. (ORCID:0000000285797826)↗

Local integrals of motion and the quasiperiodic many-body localization transition

We study the many-body localization (MBL) transition for interacting fermions subject to quasiperiodic potentials by constructing the local integrals of motion (LIOMs) in the MBL phase as time-averaged local operators. Here, we study numerically how these time-averaged operators evolve across the MBL transition. We find that the norm of such time-averaged operators drops discontinuously to zero across the transition; as we discuss, this implies that LIOMs abruptly become unstable at some critical localization length of order unity. We analyze the LIOMs using hydrodynamic projections and isolating the part of the operator that is associated with interactions. Equipped with these data we perform a finite-size scaling analysis of the quasiperiodic MBL transition. Our results suggest that the quasiperiodic MBL transition occurs at considerably stronger quasiperiodic modulations and has a larger correlation-length critical exponent than previous studies had found.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Affinity and Treatment of LDR Organics in Low Activity Waste by Cementitious Materials – 26109

The physiochemical interactions between organic contaminants, minerals, and polymer additives in grout/cementitious materials are being identified. This research supports a proposed Resource Conservation and Recovery Act (RCRA) treatment variance relevant to the Land Disposal Restriction (LDR) organics present in Hanford tank waste. It provides the technical basis to address the aspects documented by the Environmental Protection Agency in a draft memo necessary to establish that organics can be immobilized/stabilized in a cementitious matrix. The organic species may interact with cementitious minerals, including slag, fly ash, cement, and other components/dopants like activated carbon. A list of 132 reasonably expected LDR organics associated with Hanford tank waste (RPP-RPT-63493, Rev 1a) was screened by functional groups, octanol-water partitioning coefficients, and detection frequency in Hanford tank waste samples. A subset of 15 compounds spanning the identified properties was tested using sorption and leachate tests. These compounds were subjected to traditional batch sorption tests and leaching tests on/from Cast Stone cementitious material with and without activated carbon (a potential organic adsorption additive). The interactions between organic compounds were observed in traditional batch sorption and modified TCLP leachate tests for surrogate Cast Stone material with and without activated carbon addition. Specifically, phthalic acid (negatively charged) and 4-chloroaniline (polar) sorbed strongly to unmodified Cast Stone, while a group of three phenolic compounds (2,4,6-Trichlorophenol, Pentachlorophenol, o-Cresol) sorbed to and were retained by Cast Stone with a 1% activated carbon amendment. Mixtures of these compounds demonstrated visible retention of the organics within the matrix with a quantifiable affinity of the organics to the cement. This novel testing supports the notion that organics within Hanford tank waste would be retained onto the cement phase with the addition of simple materials easily added to the formulation as part of the treatment process. To further provide additional support to this claim, models employing Flory-Huggins theory in conjunction with macromolecular and organic molecule solubility parameters and species activity coefficients are being utilized to better understand these interactions. Within this context, Van Krevelen (VK) and Hansen organic and polymer solubility parameters were used to inform the Flory-Huggins interaction parameter, allowing for a quantifiable method of evaluating polymer-solvent compatibility and, by extension, interactions with proposed binding additives (e.g., activated carbon). These models and measurement should test the hypothesis for our systems understanding and applicability of Flory-Huggins theory, and whether the prediction of organics in the polymer phase versus the aqueous phase can be confidently made using this strategy. The estimation of the organic molecular activity coefficient in these high salt-saturated aqueous systems is another factor that will be assessed. This project aims to predict and understand complicated organic interactions in these heterogenous systems, guiding optimal treatment and stabilization methodologies.

Jolin, Will [Savannah River National Laboratory (S↗

Modeling and simulation of earthquake soil structure interaction excited by inclined seismic waves

Presented is an application of wave potential formulation (WPF) together with domain reduction method (DRM) to modeling earthquake soil structure interaction (ESSI) behavior in horizontally layered ground under inclined incident seismic waves. Wave potential formulation is used to develop a spatially varying, inclined seismic wave field from incident Primary (P) and Secondary (S) waves that propagate through layered ground. Developed seismic wave field is then used to develop effective forces for Domain Reduction Method that are then used for analyzing ESSI response of a soil structure system. Developed methodology, called WPF-DRM, is verified using analytic solution for a free field response of layered ground subjected to inclined incident waves. Developed WPF-DRM methodology is illustrated through analysis of an ESSI response of a deeply embedded structure, a small modular reactor (SMR) subjected to incident S wave polarized in vertical plane (SV) with variation in inclinations and frequencies. Presented example highlights the influences of incident wave inclination and frequency on ESSI response of analyzed SMR.

58 GEOSCIENCES↗

Analysis of phase stability and chemical segregation in the Mo-V alloys using a generalized embedded atom method potential

A new interatomic potential for the Mo-V system is introduced to facilitate the study of phase stability and mechanical properties at lower temperatures. This potential is based on a generalization of the embedded atom method and includes contributions from embedding energy, explicit two- and three-body interactions and nonlocal many-body interaction terms. The parameters of the potential are optimized by using data from ab initio density functional theory (DFT) calculations. The potential is rigorously validated across a range of physical properties, such as elastic constants, equation of states, phonon dispersion curves, point defect properties and melting temperatures for different compositions. Even though our potential is trained on a small dataset, its accuracy is comparable to available machine learning potentials for Mo and V. Furthermore, our results show that an ordered B2 phase is stable at low temperatures in alloys containing 50% V, but the solid solution phase is stable above 800 K. However, such long-range ordering is not observed in V-rich or Mo-rich alloys. In addition, our results show that V segregates to dislocation cores and grain boundaries.

36 MATERIALS SCIENCE↗

Quasiparticle Energy Relaxation in a Gas of One-Dimensional Fermions with Coulomb Interaction

We consider a system of charged one-dimensional spin-1/2 fermions at low temperature. We study how the energy of a highly excited quasiparticle (or hole) relaxes toward the chemical potential in the regime of weak interactions. The dominant relaxation processes involve collisions with two other fermions. We find a dramatic enhancement of the relaxation rate at low energies, with the rate scaling as the inverse sixth power of the excitation energy. Furthermore, this behavior is caused by the long-range nature of the Coulomb interaction.

1-dimensional systems↗

Modeling PAH Mixture Interactions in a Human In Vitro Organotypic Respiratory Model

One of the most significant challenges in human health risk assessment is to evaluate hazards from exposure to environmental chemical mixtures. Polycyclic aromatic hydrocarbons (PAHs) are a class of ubiquitous contaminants typically found as mixtures in gaseous and particulate phases in ambient air pollution associated with petrochemicals from Superfund sites and the burning of fossil fuels. However, little is understood about how PAHs in mixtures contribute to toxicity in lung cells. To investigate mixture interactions and component additivity from environmentally relevant PAHs, two synthetic mixtures were created from PAHs identified in passive air samplers at a legacy creosote site impacted by wildfires. The primary human bronchial epithelial cells differentiated at the air–liquid interface were treated with PAH mixtures at environmentally relevant proportions and evaluated for the differential expression of transcriptional biomarkers related to xenobiotic metabolism, oxidative stress response, barrier integrity, and DNA damage response. Component additivity was evaluated across all endpoints using two independent action (IA) models with and without the scaling of components by toxic equivalence factors. Both IA models exhibited trends that were unlike the observed mixture response and generally underestimated the toxicity across dose suggesting the potential for non-additive interactions of components. Overall, this study provides an example of the usefulness of mixture toxicity assessment with the currently available methods while demonstrating the need for more complex yet interpretable mixture response evaluation methods for environmental samples.

3D in vitro models↗

Development of an interatomic potential for the Ta–Li system

A new interatomic potential for the Ta–Li system is introduced to facilitate the study of phase stability, mechanical properties and non-equilibrium dynamics after Li implantation in Ta. Here, this potential is based on a generalization of the embedded atom method (GEAM) and includes contributions from embedding energy, explicit two- and three-body interactions, and nonlocal many-body interaction terms. The parameters of the potential are optimized using energies and atomic forces for a wide range of configurations obtained from ab initio density functional theory (DFT) calculations. The potential is rigorously validated across a range of physical properties, including elastic constants, equations of state, phonon dispersion curves, point defect properties, and melting temperatures for different compositions. Although our potential is trained on a small dataset, its accuracy is comparable to that of available machine learning potentials for Li and Ta. Our simulations show that at temperatures below 500 K, Li atoms in Ta–Li alloys form clusters separated by Ta-rich domains, and we find no evidence of ordered phase formation. For Li concentrations below a few percent, Li atoms preferentially segregate to surfaces and grain boundaries. However, in alloys containing more than ~10% Li, the accumulation of Li in symmetric-tilt grain boundaries can lead to one of the following effects: formation of amorphous-like regions, changes in grain boundary structural units, or lateral movement of the grain boundary.

GEAM potential↗

Leveraging Triphenylphosphine-Containing Polymers to Explore Design Principles for Protein-Mimetic Catalysts

Complex interactions between noncoordinating residues are significant yet commonly overlooked components of macromolecular catalyst function. While these interactions have been demonstrated to impact binding affinities and catalytic rates in metalloenzymes, the roles of similar structural elements in synthetic polymeric catalysts remain underexplored. Using a model Suzuki–Miyuara cross-coupling reaction, we performed a series of systematic studies to probe the interconnected effects of metal–ligand cross-links, electrostatic interactions, and local rigidity in polymer catalysts. To achieve this, a novel bifunctional triphenylphosphine acrylamide (BisTPPAm) monomer was synthesized and evaluated alongside an analogous monofunctional triphenylphosphine acrylamide (TPPAm). In model copolymer catalysts, increased initial reaction rates were observed for copolymers untethered by Pd complexation (BisTPPAm-containing) compared to Pd-cross-linked catalysts (TPPAm-containing). Further, incorporating local rigidity through secondary structure-like and electrostatic interactions revealed nonmonotonic relationships between composition and the reaction rate, demonstrating the potential for tunable behavior through secondary-sphere interactions. Lastly, through rigorous cheminformatics featurization strategies and statistical modeling, we quantitated relationships between chemical descriptors of the substrate and reaction conditions on catalytic performance. Collectively, these results provide insights into relationships among the composition, structure, and function of protein-mimetic catalytic copolymers.

Catalysts↗

Preliminary Analysis of Advanced Reactors Storage, Transportation, and Disposal

Based on the higher interest in Advanced Reactor (AR) deployment (e.g., ARDP[1]) for potential new fuel cycles, the Spent Fuel & Waste Science and Technology (SFWST) Program has begun to evaluate the possible implications of long-term management and final disposition of potential Advance Reactor spent nuclear fuels (SNF) that would be generated in potential advanced reactors. Safely managing and dispositioning the potential future AR SNF, and any other associated radioactive wastes, is the primary focus of this initial preliminary assessment of those. This paper summarizes the efforts by the Spent Fuel & Waste Science and Technology (SFWST) in evaluating characteristics and packaging options for advanced reactor spent nuclear fuel forms. The fuel forms were categorized into three types: (1) tristructural isotropic (TRISO), (2) metallic, and (3) fuel salt. This work emphasized TRISO and metallic SNF and waste streams because of the near-term anticipated operation of the Xe-100 and the Natrium reactors as advanced-reactor demonstrations. Preliminary information for the spent-fuel salts discharged from molten-salt reactors (MSRs) is also examined to provide a baseline for future efforts. All calculations and assumptions used publicly available information. The following characteristics are calculated or estimated for use in the preliminary assessments: SNF volume and mass, radiation/activity levels through time, thermal conditions through time, potential radionuclide source terms, chemical interactions and evolutions, disposal inventories, and waste-form lifetime. Using those characteristics, calculations to determine the applicability of existing canister designs were performed. These evaluations included geometric (e.g., dimension, volume) and mass/weight considerations, known operational approaches and loading procedures, physical and chemical considerations/conditions for storage environments, as-loaded radiation, thermal, and criticality analyses to identify constraints for storage, transportation, and disposal. The paper also includes a literature review and analysis on the storage, transportation, and disposal evaluations and experiences from reactors with similar fuel forms. Advanced-reactor vendors cite past experiences with Fort St. Vrain for TRISO and the Experimental Breeder Reactor II (EBR-II) for metallics that have major influences on fuel design. Finally, the paper includes preliminary concepts of operation for advanced-reactor SNF. This encompasses storage, transportation, potential treatment, and disposal activities from both a per-canister and systems-integration perspective.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Enhancing Early Systems R&D Capabilities with Systems —Theoretic Process Analysis

Systems engineering today faces a wide array of challenges, ranging from new operational environments to disruptive technological — necessitating approaches to improve research and development (R&D) efforts. Yet, emphasizing the Aristotelian argument that the “whole is greater than the sum of its parts” seems to offer a conceptual foundation creating new R&D solutions. Invoking systems theoretic concepts of emergence and hierarchy and analytic characteristics of traceability, rigor, and comprehensiveness is potentially beneficial for guiding R&D strategy and development to bridge the gap between theoretical problem spaces and engineering-based solutions. In response, this article describes systems–theoretic process analysis (STPA) as an example of one such approach to aid in early-systems R&D discussions. STPA—a ‘top-down’ process that abstracts real complex system operations into hierarchical control structures, functional control loops, and control actions—uses control loop logic to analyze how control actions (designed for desired system behaviors) may become violated and drive the complex system toward states of higher risk. By analyzing how needed controls are not provided (or out of sequence or stopped too soon) and unneeded controls are provided (or engaged too long), STPA can help early-system R&D discussions by exploring how requirements and desired actions interact to either mitigate or potentially increase states of risk that can lead to unacceptable losses. This article will demonstrate STPA's benefit for early-system R&D strategy and development discussion by describing such diverse use cases as cyber security, nuclear fuel transportation, and US electric grid performance. Together, the traceability, rigor, and comprehensiveness of STPA serve as useful tools for improving R&D strategy and development discussions. In conclusion, leveraging STPA as well as related systems engineering techniques can be helpful in early R&D planning and strategy development to better triangulate deeper theoretical meaning or evaluate empirical results to better inform systems engineering solutions.

42 ENGINEERING↗

Characterizing Supernovae Neutrinos in MARLEY

This summer I worked on characterizing the uncertainties in neutrino-argon interactions due to the optical model potential. Functionally, this was a great deal of new experience coding in C++. I wrote a script using MARLEY(Gardiner 2019) to compute both the branching ratios and exclusive cross sections for a whole host of different decay processes from the unstable Potassium nucleus created by a v+Ar charged current interaction. These decays were computed through MARLEY, governed by a global parametrization of the Optical Model potential(Koning-Delaroche 2003). Helpfully, Pruitt+ 2023 provided public supplemental material outlining 400 separate "universes" for the optical model potential parameters. These "universes" represent uncertainties on the optical potential itself, and I wrote code to incorporate them into the MARLEY framework and quantify their impact on the predictions of neutrino-argon cross sections. This stands as the first computation of nuclear de-excitation systematic errors on cross sections in this energy band for v+Ar interactions, a critical step to understanding the science we can do with DUNE in the tens-of-MeV band.

Abu El-Haj, Luca↗

Quantum model learning agent: characterisation of quantum systems through machine learning

Accurate models of real quantum systems are important for investigating their behaviour, yet are difficult to distil empirically. Here, we report an algorithm—the quantum model learning agent (QMLA)—to reverse engineer Hamiltonian descriptions of a target system. We test the performance of QMLA on a number of simulated experiments, demonstrating several mechanisms for the design of candidate Hamiltonian models and simultaneously entertaining numerous hypotheses about the nature of the physical interactions governing the system under study. QMLA is shown to identify the true model in the majority of instances, when provided with limited a priori information, and control of the experimental setup. Our protocol can explore Ising, Heisenberg and Hubbard families of models in parallel, reliably identifying the family which best describes the system dynamics. We demonstrate QMLA operating on large model spaces by incorporating a genetic algorithm to formulate new hypothetical models. The selection of models whose features propagate to the next generation is based upon an objective function inspired by the Elo rating scheme, typically used to rate competitors in games such as chess and football. In all instances, our protocol finds models that exhibit F 1 score ≥ 0.88 when compared with the true model, and it precisely identifies the true model in 72% of cases, whilst exploring a space of over 250 000 potential models. By testing which interactions actually occur in the target system, QMLA is a viable tool for both the exploration of fundamental physics and the characterisation and calibration of quantum devices.

97 MATHEMATICS AND COMPUTING↗

Exotic Photonic Molecules via Lennard-Jones-like Potentials

Ultracold systems offer an unprecedented level of control of interactions between atoms. An important challenge is to achieve a similar level of control of the interactions between photons. Towards this goal, we propose a realization of a novel Lennard-Jones-like potential between photons coupled to the Rydberg states via electromagnetically induced transparency (EIT). This potential is achieved by tuning Rydberg states to a Förster resonance with other Rydberg states. In this work, we consider few-body problems in 1D and 2D geometries and show the existence of self-bound clusters (“molecules”) of photons. We demonstrate that for a few-body problem, the multibody interactions have a significant impact on the geometry of the molecular ground state. This leads to phenomena without counterparts in conventional systems: For example, three photons in two dimensions preferentially arrange themselves in a line configuration rather than in an equilateral-triangle configuration. Our result opens a new avenue for studies of many-body phenomena with strongly interacting photons.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Instantons in chiral magnets

In this work, we exhaustively construct instanton solutions and elucidate their properties in one-dimensional antiferromagnetic chiral magnets based on the $\textit{O}(3)$ nonlinear sigma model description of spin chains with the Dzyaloshinskii-Moriya (DM) interaction. By introducing an easy-axis potential and a staggered magnetic field, we obtain a phase diagram consisting of ground-state phases with two points (or one point) in the easy-axis dominant cases, a helical modulation at a fixed latitude of the sphere, and a tricritical point allowing helical modulations at an arbitrary latitude. We find that instantons (or skyrmions in two-dimensional Euclidean space) appear as composite solitons in different fashions in these phases: temporal domain walls or wall-antiwall pairs (bions) in the easy-axis dominant cases, dislocations (or phase slips called merons) with fractional instanton numbers in the helical state, and isolated instantons and calorons living on the top of the helical modulation at the tricritical point. We also show that the models with DM interaction and an easy-plane potential can be mapped into those without them, providing a useful tool to investigate the model with the DM interaction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Predicting nucleon-nucleus scattering observables using nuclear structure theory

Developing a predictive capability for inelastic scattering will find applications in multiple areas. Experimental data for neutron-nucleus inelastic scattering is limited and thus one needs a robust theoretical framework to complement it. Charged-particle inelastic scattering can be used as a surrogate for ( n, γ ) reactions to predict capture cross sections for unstable nuclei. Our work uses microscopic nuclear structure calculations for spherical nuclei to obtain nucleon-nucleus scattering potentials and calculate cross sections for these processes. We implement the Jeukenne, Lejeune, Mahaux (JLM) semi-microscopic folding approach, where the medium effects on nuclear interaction are parameterized in nuclear matter to obtain the nucleon-nucleon ( NN ) interaction in a medium at positive energies. We solve for the nuclear ground state using the Hartree-Fock-Bogliubov (HFB) many-body method, assuming the nucleons within the nucleus interact via the Gogny-D1M potential. The vibrational excited states of the target nucleus are calculated using the quasi-particle random phase approximation (QRPA). We demonstrate our approach for spherical nuclei in the medium-mass region, showing scattering results for the 90 Zr nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗