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Results for “Pairwise interaction model”

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.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Experimental realization of classical Z 2 spin liquids in a programmable quantum device

We build and probe a Z 2 spin liquid in a programmable quantum device, the D-Wave DW-2000Q. Specifically, we observe the classical eight-vertex and six-vertex (spin ice) states and transitions between them. To realize this state of matter, we design a Hamiltonian with combinatorial gauge symmetry using only pairwise-qubit interactions and a transverse field, i.e., interactions which are accessible in this quantum device. The combinatorial gauge symmetry remains exact along the full quantum annealing path, landing the system onto the classical eight-vertex model at the endpoint of the path. The output configurations from the device allow us to directly observe the loop structure of the classical model. Moreover, we deform the Hamiltonian so as to vary the weights of the eight vertices and show that we can selectively attain the classical six-vertex (ice) model, or drive the system into a ferromagnetic state. Additionally, we present studies of the classical phase diagram of the system as a function of the eight-vertex deformations and effective temperature, which we control by varying the relative strengths of the programmable couplings, and we show that the experimental results are consistent with theoretical analysis. Finally, we identify additional capabilities that, if added to these devices, would allow us to realize Z 2 quantum spin liquids on which to build topological qubits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Unconventional nonlinear Hall effects in twisted multilayer 2D materials

We present the first investigation of unusual nonlinear Hall effects in twisted multilayer 2D materials. Contrary to expectations, our study shows that these nonlinear effects are not merely extensions of their monolayer counterparts. Instead, we find that stacking order and pairwise interactions between neighboring layers, mediated by Berry curvatures, play a pivotal role in shaping their collective nonlinear optical response. By combining large-scale Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) simulations with model Hamiltonian analyses, we demonstrate a remarkable second-harmonic transverse response in hexagonal boron nitride four-layers, even in cases where the total Berry curvature cancels out. Furthermore, our symmetry analysis of the layered structures provides a simplified framework for predicting nonlinear responses in multilayer materials in general. Our investigation challenges the prevailing understanding of nonlinear optical responses in layered materials and opens new avenues for the design and development of advanced materials with tailored optical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Development and application of a uranium mononitride (UN) potential: Thermomechanical properties and Xe diffusion

We report that atomic-scale modeling of thermophysical and defect properties of uranium mononitride (UN) plays an important role in establishing a better understanding and improved models of UN fuel performance. Having an accurate interatomic potential is crucial for generating reliable data at finite temperatures using molecular dynamic simulations. We report a new interatomic potential for UN, based on a combination of many-body and pairwise interactions, a simple form that we later show could be easily adapted to include Xe-U and Xe-N interactions, i.e., generating a U-N-Xe interatomic potential. The potential was fitted to experimental thermal expansion and single crystal elastic constants, as well as Frenkel, Schottky, anti-Schottky, and antisite pair reaction energies from density functional theory (DFT) calculations. Using the potential, we successfully reproduced experimental lattice parameters, thermal expansion, single crystal elastic constants, and temperature dependent heat capacity. The potential also performs reasonably well in reproducing the energy of the aforementioned stoichiometric defect reactions and defect migration barriers calculated using DFT. However, the potential underestimates the energy difference between the tetrahedral and dumbbell uranium interstitials, and a more complex potential form might be needed to overcome this issue. The potential was also used to predict UN single crystal elastic constants and elastic properties at different temperatures, showing that UN becomes softer and more compressible with increasing temperature. We also compare our potential against literature data from previous empirical potentials, demonstrating similar or better behavior depending on the property of interest. To enable the simulation of Xe in UN a Buckingham potential has been fitted to DFT-derived Xe incorporation energies. The potential was then used to determine the activation energy for Xe diffusion due to various Xe-containing defects, with {XeU : VU} exhibiting the lowest activation energy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM’s Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM’s Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen’s early Nobel prize winning experiments by using OpenMM’s Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Lagrangian and Eulerian drag models that are consistent between Euler-Lagrange and Euler-Euler (two-fluid) approaches for homogeneous systems

The undisturbed flow of a particle is of fundamental importance since it controls both the undisturbed flow force and the perturbation force (which includes quasisteady, added-mass, and history forces). Here we use the pairwise interaction extended point particle framework to evaluate the undisturbed flow of each particle through superposition of the perturbation flow induced by all its neighbors. This approach allows calculation of various statistics related to undisturbed fluid velocity under conditions of both stationary and nonstationary particles. In a random distribution of stationary particles, while the macroscale undisturbed flow is slowly varying, the microscale undisturbed flow that arises due to the perturbation flow of neighbors varies substantially from one particle to another and this in turn leads to large variation in the hydrodynamic force exerted on the particles. The effect of particle motion is generally to increase the particle-to-particle variation in the undisturbed fluid velocity of the particles. We observe that this increase is greater for the transverse component than for the streamwise component. As a result, with increasing random particle motion, the distribution of undisturbed fluid-velocity fluctuation becomes isotropic. Three different normalized forces are defined: $Φ^L$ is the Lagrangian normalized force on an individual particle suitable for application in a microscale-informed Euler-Lagrange simulation, $Φ^E$ is the Eulerian normalized average force suitable for application in an Euler-Euler simulation, and $Φ^{LE}$ is the Lagrangian normalized force on an individual particle suitable for application in the standard Euler-Lagrange simulation. In this work, we establish precise relations between these different definitions. The drag laws developed based on particle-resolved direct numerical simulation results and experiments are appropriate for application only as the Eulerian normalized average force. We introduce the force consistency relation and use it to obtain an expression for $Φ^L$, which when applied to each particle and averaged over all the particles equals $Φ^E$. The results are first obtained in the limit of stationary particles and then extended to the general case of nonstationary particles.

42 ENGINEERING↗
DOE OSTI2024

Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning

Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the β-lactamase enzyme and quantitated the function of variants against two β-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A two-stage optical fusion framework for wildfire severity mapping across the conterminous United States

Accurate wildfire severity mapping (WSM) is essential for post-fire recovery planning, erosion risk assessment, ecosystem monitoring, and disaster risk reduction. Although Landsat and Sentinel optical imagery have been widely used for burn severity assessment, the added value of fusing multiple optical sensors has not been sufficiently quantified across diverse fire events, particularly since the launch of Landsat-9. This study evaluates whether multisensor optical fusion improves wildfire severity mapping relative to single-sensor baselines using Sentinel-2, Landsat-8, and Landsat-9 imagery across 40 wildfire events in the conterminous United States. We tested a two-stage fusion framework that combines feature-level fusion with pixel-level dimensionality reduction. First, feature-level fused datasets were created through early fusion by combining standardized post-fire bands from each sensor into a single predictor stack. Both raw reflectance bands and pairwise spectral transforms were retained to capture within- and cross-sensor spectral interactions. Second, Linear Discriminant Analysis was applied to both single-sensor and fused datasets to produce comparable low-dimensional feature spaces. Six machine-learning classifiers were then used to benchmark model performance with repeated spatially buffered train–test splits. Results show that Landsat-9 was the strongest single-sensor baseline. Among the fusion strategies, Sentinel-2 + Landsat-9 produced the most consistent improvement and reduced performance variability. Landscape-condition analysis further showed that this fusion was most beneficial in shrubland-dominated and high-terrain fires, where it achieved the highest overall mean accuracy and the fewest failures. In contrast, its benefits were less reliable in evergreen forests, mixed vegetation, and low- to moderate-elevation terrain. In operational settings, the Sentinel-2 + Landsat-9 configuration offers a practical solution for post-fire recovery planning, erosion-risk assessment, watershed management, and ecological monitoring when field observations are available and timely satellite-based information is needed.

Landsat↗
DOE OSTI2025

Competition and cooperation: The plasticity of bacterial interactions across environments

Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By computationally simulating thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This modeling approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions in response to the availability of environmental resources.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Design and Development of Stable Nanocrystalline High‐Entropy Alloy: Coupling Self‐Stabilization and Solute Grain Boundary Segregation Effects

Abstract Grain growth is prevalent in nanocrystalline (NC) materials at low homologous temperatures. Solute element addition is used to offset excess energy that drives coarsening at grain boundaries (GBs), albeit mostly for simple binary alloys. This thermodynamic approach is considered complicated in multi‐component alloy systems due to complex pairwise interactions among alloying elements. Guided by empirical and GB‐segregation enthalpy considerations for binary‐alloy systems, a novel alloy design strategy, the “ pseudo‐binary thermodynamic ” approach, for stabilizing NC‐high entropy alloys (HEAs) and other multi‐component‐alloy variants is proposed. Using Al 25 Co 25 Cr 25 Fe 25 as a model‐HEA to validate this approach, Zr, Sc, and Hf, are identified as the preferred solutes that would segregate to HEA‐GBs to stabilize it against growth. Using Zr, NC‐Al 25 Co 25 Cr 25 Fe 25 HEAs with minor additions of Zr are synthesized, followed by annealing up to 1123 K. Using advanced characterization techniques— in situ X‐ray diffraction (XRD), scanning/transmission electron microscopy (S/TEM), and atom probe tomography, nanograin stability due to coupling self‐stabilization and solute‐GB segregation effects is reported in HEAs up to substantially high temperatures. The self‐stabilization effect originates from the preferential GB‐segregation of constituent HEA‐elements that stabilizes NC‐Al 25 Co 25 Cr 25 Fe 25 up to 0.5 T m ( T m –melting temperature). Meanwhile, solute‐GB segregation originates from Zr segregation to NC‐Al 25 Co 25 Cr 25 Fe 25 GBs; this results in further stabilization of the phase and grain‐size (≈14 nm) up to ≈0.58 and ≈0.64 T m , respectively.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1989

Pressure broadening and line coupling in bending bands of CO2

The pressure broadening and line coupling cross sections in the Fano-Ben Reuven theory of line shapes are calculated for bending bands of CO2 in a bath of He atoms. Molecular collision dynamics are simplified by invoking the infinite order sudden (IOS) approximation for molecular rotational and vibrational angular momentum in a manner similar to but not identical with the method developed by Clary and shown to be accurate for CO2-He. Numerical values are obtained using a pairwise additive interaction potential developed by Clary. Predictions are in good accord with data for various infrared bands and pure rotational Raman spectra. It is found that all pressure broadening and state-to-state cross sections depend on only a few dynamical factors (generalized IOS cross sections) and are therefore closely interrelated. Results are used to assess models developed previously to analyze line shapes in this and similar systems.

Green, Sheldon↗
DOE OSTI2023

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes

Motivation: Alignment of protein–protein interaction networks can be used for the unsupervised prediction of functional modules, such as protein complexes and signaling pathways, that are conserved across different species. To date, various algorithms have been proposed for biological network alignment, many of which attempt to incorporate topological similarity between the networks into the alignment process with the goal of constructing accurate and biologically meaningful alignments. Especially, random walk models have been shown to be effective for quantifying the global topological relatedness between nodes that belong to different networks by diffusing node-level similarity along the interaction edges. However, these schemes are not ideal for capturing the local topological similarity between nodes. Results: Here, we propose MONACO, a novel and versatile network alignment algorithm that finds highly accurate pairwise and multiple network alignments through the iterative optimal matching of ‘local’ neighborhoods around focal nodes. Extensive performance assessment based on real networks as well as synthetic networks, for which the ground truth is known, demonstrates that MONACO clearly and consistently outperforms all other state-of-the-art network alignment algorithms that we have tested, in terms of accuracy, coherence and topological quality of the aligned network regions. Furthermore, despite the sharply enhanced alignment accuracy, MONACO remains computationally efficient and it scales well with increasing size and number of networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

FriendlyNets

FriendlyNets provides a method for assessing the promotion/inhibition effect on a microbe of a microbial community using a network of community interactions. At its core, FriendlyNets judges how much a network promotes or inhibits one of its nodes. It does this by assuming a set of dynamical systems represented by the network and using the resulting dynamics. FriendlyNets is also packaged with functions for generating a network from a set of genome-scale metabolic models (commonly called GSMs or GEMs) by simulating pairwise growth.

Brunner, James↗
NASA NTRS1997

The Growth of Planets From Planetesimals

Modern theories of star and planet formation, which are based upon observations of the Solar System and of young stars and their environments, state that planets grow from circumstellar disks of gas and dust. Interstellar dust and/or disk condensates settle towards the midplane of the disk and agglomerate into kilometer-sized solid bodies known as planetesimals. These planetesimals then interact with one another via gravitational forces and collisions. Terrestrial planets are believed to grow via pairwise accretion until the spacing of planetary orbits becomes large enough that the configuration is stable for the age of the system. Giant planets begin their growth in the same manner as do terrestrial planets, but they become -massive enough that they are able to accumulate substantial amounts of gas before the protoplanetary disk dissipates. Models for the formation of our Solar System and of the giant planets found in recent radial velocity searches are discussed.

Lissauer, Jack J.↗
DOE OSTI2023

Pairwise‐Parallel Entangling Gates on Orthogonal Modes in a Trapped‐Ion Chain

Abstract Parallel operations are important for both near‐term quantum computers and larger‐scale fault‐tolerant machines because they reduce execution time and qubit idling. This study proposes and implements a pairwise‐parallel gate scheme on a trapped‐ion quantum computer. The gates are driven simultaneously on different sets of orthogonal motional modes of a trapped‐ion chain. This work demonstrates the utility of this scheme by creating a Greenberger‐Horne‐Zeilinger (GHZ) state in one step using parallel gates with one overlapping qubit. It also shows its advantage for circuits by implementing a digital quantum simulation of the dynamics of an interacting spin system, the transverse‐field Ising model. This method effectively extends the available gate depth by up to two times with no overhead when no overlapping qubit is involved, apart from additional initial cooling. This scheme can be easily applied to different trapped‐ion qubits and gate schemes, broadly enhancing the capabilities of trapped‐ion quantum computers.

Optics↗
DOE OSTI2020

Reconstruction of the interatomic forces from dynamic scanning transmission electron microscopy data

We explore the possibility for reconstruction of the generative physical models describing interactions between atomic units in solids from observational electron microscopy data. In this work, scanning transmission electron microscopy (STEM) is used to observe the dynamic motion of Si atoms at the edge of monolayer graphene under continuous electron beam illumination. The resulting time-lapsed STEM images represent the snapshots of observed chemical states of the system. We use two approaches: potential of mean force calculation using a radial distribution function and a direct fitting of the graphene–Si interatomic pairwise potentials with force matching, to reconstruct the force fields in the materials. These studies lay the foundation for quantitative analysis of materials energetics from STEM data through the sampling of the metastable states in the chemical space of the system.

42 ENGINEERING↗
DOE OSTI2020

Exploring the unknown Lambda-neutron interaction

No published \Lambda Λ n scattering data exist. A relativistic heavy-ion experiment has suggested that a \Lambda Λ nn bound state was seen. However, several theoretical analyses have cast serious doubt on the bound-state assertion. Nevertheless, there could exist a three-body \Lambda Λ nn resonance. Such a resonance could be used to constrain the \Lambda Λ n interaction. We discuss \Lambda Λ nn calculations using nn and \Lambda Λ n pairwise interactions of rank-one, separable form that fit effective range parameters of the nn system and those hypothesized for the as yet unobserved \Lambda Λ n system based upon four different \Lambda Λ N potentials. The use of rank-one separable potentials allows one to analytically continue the \Lambda Λ nn Faddeev equations onto the second complex energy plane in search of resonance poles, by examining the eigenvalue spectrum of the kernel of the Faddeev equations. Although each of the potential models predicts a \Lambda Λ nn sub-threshold resonance pole, scaling of the \Lambda Λ n interaction by as little as \sim ∼ 5% does produce a physical resonance. This suggests that one may use photo-(electro-)production of the \Lambda Λ nn system from tritium as a tool to examine the strength of the \Lambda Λ n interaction.

Gibson, Benjamin↗
DOE OSTI2021

Climate and multiple dimensions of plant diversity regulate ecosystem carbon exchange along an elevational gradient

The impacts of warming on communities and ecosystems are predicted to be significant in mountain ecosystems because physiological processes, including rates of carbon (C) cycling, are often more temperature-sensitive in colder environments. Plant biodiversity can also influence C exchange, yet few studies integrate how biotic and abiotic factors may directly or interactively impact ecosystem Cflux. Here, we examine the link between simultaneous changes in multiple dimensions of plant diversity and peak growing season ecosystem C uptake across a climatic gradient in the Rocky Mountains, Colorado, USA. We found that taxonomic diversity (species richness), functional diversity (functional evenness), and phylogenetic diversity (mean pairwise distance) were significantly and positively related to peak growing sea-son ecosystem C uptake (i.e., net ecosystem exchange) when considered independently. However, when abiotic and biotic factors were integrated in a structural equation model, only plant phylogenetic diversity was significantly related to C uptake. In addition, we found that actual evapotranspiration (AET - a measure that integrates precipitation and temperature) affected ecosystem C exchange indirectly via its impact on the three dimensions of plant diversity that we examined. These findings highlight complex relation-ships among key measures of biodiversity and ecosystem C uptake in a rapidly warming ecosystem, and the possible mechanisms that underlie relationships between biodiversity and ecosystem functioning. They also point to the need for integrating multiple dimensions of biodiversity into studies of community and ecosystem ecology.

54 ENVIRONMENTAL SCIENCES↗