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At least 1,729 records · Page 96

Geometrically frustrated interactions drive structural complexity in amorphous calcium carbonate

Amorphous calcium carbonate is an important precursor for biomineralization in marine organisms. Key outstanding problems include understanding the structure of amorphous calcium carbonate and rationalizing its metastability as an amorphous phase. Here we report high-quality atomistic models of amorphous calcium carbonate generated using state-of-the-art interatomic potentials to help guide fits to X-ray total scattering data. Exploiting a recently developed inversion approach, we extract from these models the effective Ca∙∙∙Ca interaction potential governing the structure. This potential contains minima at two competing distances, corresponding to the two different ways that carbonate ions bridge Ca 2+ -ion pairs. We reveal an unexpected mapping to the Lennard-Jones–Gauss model normally studied in the context of computational soft matter. The empirical model parameters for amorphous calcium carbonate take values known to promote structural complexity. We thus show that both the complex structure and its resilience to crystallization are actually encoded in the geometrically frustrated effective interactions between Ca 2+ ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase coexistence implications of violating Newton’s third law

Newton’s third law, action = reaction, is a foundational statement of classical mechanics. However, in natural and living systems, this law appears to be routinely violated for constituents interacting in a nonequilibrium environment. Here, we use computer simulations to explore the macroscopic phase behavior implications of breaking microscopic interaction reciprocity for a simple model system. We consider a binary mixture of attractive particles and introduce a parameter that is a continuous measure of the degree to which interaction reciprocity is broken. In the reciprocal limit, the species are indistinguishable, and the system phase separates into domains with distinct densities and identical compositions. Furthermore, increasing nonreciprocity is found to drive the system to explore a rich assortment of phases, including phases with strong composition asymmetries and three-phase coexistence. Many of the states induced by these forces, including traveling crystals and liquids, have no equilibrium analogs. By mapping the complete phase diagram for this model system and characterizing these unique phases, our findings offer a concrete path forward toward understanding how nonreciprocity shapes the structures found in living systems and how this might be leveraged in the design of synthetic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enhancement of phase change material hysteresis model: A case study of modeling building envelope in EnergyPlus

Nowadays, buildings are expected to offer demand side services to the power grid to enhance the electrical load flexibility, which leads to the concepts of grid-interactive efficient buildings (GEBs). Phase change material (PCM)-based thermal energy storage has seen increasing attention in recent years for peak load shifting of grid-interactive efficient buildings (GEBs). Numerical models are critical tools for design and evaluation of PCM-integrated systems. Most industrial-grade PCMs are reported to melt/freeze over a temperature range instead of at a unique temperature. Such thermal hysteresis effect significantly affects the reliability of simulation results because not only the heat transfer process depends on melting and freezing temperatures, the PCM thermal properties change significantly during the phase change process as well. This study is aimed to develop a model for the PCMs used in the building envelope with the capability to accurately simulate hysteretic behaviors. Further, this model is based on a two-phase assumption and is implemented in a whole building energy performance simulation program (i.e., EnergyPlus). A comparison between numerical results and experimental data shows that during a complete phase transition, the two-phase model could achieve a good agreement with the experimental data. During a partial phase transition, the two-phase model could lead to significant improvements compared to other alternative PCM models, including the existing PCM model in EnergyPlus. Last, whole building simulations were performed to study this model's performance regarding heating/cooling loads and zone mean air temperature of a given building. The results show that the difference in hourly heating/cooling loads introduced by the models was less than 1% in design conditions, while significant changes were observed in both hourly heating/cooling loads and zone mean air temperature when the PCM envelope underwent partial phase transition processes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Multi-trait multi-environment genomic prediction strategies for Miscanthus sacchariflorus

Genomic selection holds the potential to serve as a strategic tool to enhance the genetic gain of complex traits in Miscanthus breeding programs. The development of improved cultivars requires their assessment for various traits across diverse environments to ensure suitable overall performance. Hence, the multi-trait multi-environment (MTME) genomic prediction (GP) models offer an opportunity to improve selection accuracy. This study aims to evaluate the potential of five GP models: (1) three MTME models including genotype-by-trait-by-environment interaction (G×E×T) and (2) two single-trait multi-environment (STME) models (with and without G×E interaction). A Miscanthus sacchariflorus population comprising 336 genotypes evaluated in three environments and scored for four traits (biomass yield YDY, total culm number TCM, average internode length AIL, and culm node number CNN) was analyzed. The predictive ability of the models was evaluated considering three cross-validation schemes resembling realistic scenarios (CV1: predicting new genotypes, CVP: predicting missing traits in a given environment, and CV2: predicting partially observed genotypes). On average, in all cross-validation schemes compared to the STME the predictive ability of the MTME models was 10% to 70% higher for TCM and AIL. On the other hand, for YDY and CNN, both STME models performed similarly or slightly better (between 5 to 64%) than the MTME models in most environments. While the MTME models were not successful for all traits when compared to their STME counterparts, MTME models improved the prediction of the performance of genotypes that were untested across environments or lacked trait information in a specific environment. Overall, our study suggests that MTME GP models can be implemented in Miscanthus breeding programs to improve the predictive ability of the complex traits, shorten breeding cycles, and accelerate selection decisions.

genomic prediction (GP)↗

Once-in-a-lifetime encounter models for neutrino media: From coherent oscillations to flavor equilibration

Collective neutrino oscillations are typically studied using the lowest-order quantum kinetic equation, also known as the mean-field approximation. However, some recent quantum many-body simulations suggest that quantum entanglement among neutrinos may be important and may result in flavor equilibration of the neutrino gas. In this work, we develop new quantum models for neutrino gases in which any pair of neutrinos can interact at most once in their lifetimes. A key parameter of our models is γ = μ Δ z , where μ is the neutrino coupling strength, which is proportional to the neutrino density, and Δ z is the duration over which a pair of neutrinos can interact each time. Our models reduce to the mean-field approach in the limit γ → 0 and achieve flavor equilibration in time t ≫ ( γ μ ) − 1 . These models demonstrate the emergence of coherent flavor oscillations from the particle perspective and may help elucidate the role of quantum entanglement in collective neutrino oscillations. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Machine Learning Assisted Development of a Model for the Populations of Convective and Stratiform Clouds

Abstract Traditional parameterizations of the interaction between convection and the environment have relied on an assumption that the slowly varying large‐scale environment is in statistical equilibrium with a large number of small and short‐lived convective clouds. They fail to capture nonequilibrium transitions such as the diurnal cycle and the formation of mesoscale convective systems as well as observed precipitation statistics and extremes. Informed by analysis of radar observations, cloud‐permitting model simulation, theory, and machine learning, this work presents a new stochastic cloud population dynamics model for characterizing the interactions between convective and stratiform clouds, with the goal of informing the representation of these interactions in global climate models. Fifteen wet seasons of precipitating cloud observations by a C‐band radar at Darwin, Australia are fed into a machine learning algorithm to obtain transition functions that close a set of coupled equations relating large‐scale forcing, mass flux, the convective cell size distribution, and the stratiform area. Under realistic large‐scale forcing, the derived transition functions show that, on the one hand, interactions with stratiform clouds act to dampen the variability in the size and number of convective cells and therefore in the convective mass flux. On the other, for a given convective area fraction, a larger number of smaller cells is more favorable for the growth of stratiform area than a smaller number of larger cells. The combination of these two factors gives rise to solutions with a few convective cells embedded in a large stratiform area, reminiscent of mesoscale convective systems.

54 ENVIRONMENTAL SCIENCES↗

A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior

Manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. We develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and predicts experimental conditions that allow the actuation temperature of the nano-hinge to be tuned over a range of temperatures from 30 °C to 45 °C. Additionally, the model identifies microscopic interactions that are important to the macroscopic behavior of the system, revealing surprising features of the system. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures or use strand binding interactions to control dynamic DNA origami behavior. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.

36 MATERIALS SCIENCE↗

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Abstract Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12 family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

Diverse fates of ancient horizontal gene transfers in extremophilic red algae

Abstract Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT‐derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the ‘Integrated HGT Model’ (IHM). To explore this concept further, we studied specialized HGT‐derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a ‘one gene‐one function’ model, resulting in an indivisible response. In contrast, the ars H gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling Dense Particle Flow in Multistage and Obstructed Flow Receivers Using High Fidelity Simulations

Particles are a leading contender for next-generation, concentrating solar power technologies, and the design of the particle receiver is critical to minimize the levelized cost of electricity. Falling particle receivers (FPRs) are a viable receiver concept, but many new designs feature complex particle obstructions that include dense discrete phase flows. This creates additional challenges for modeling as particle-to-particle interactions (i.e., collisions) and particle drag become more complex. To improve upon existing modeling strategies, a CFD-DEM simulation capability was created by coupling two independent codes: Sierra/Fuego and LAMMPS. A suitable receiver model was then defined using a traditional continuum-based model for the air and a granular model for the particle curtain. A sensitivity study was executed using this model to determine the relevance of different granular model inputs on important quantities of interest in obstructed flow FPRs: the particle velocity and curtain opacity. The study showed that the granular model inputs had little effect on the particle velocity magnitude and curtain opacity after an obstruction.

Mills, Brantley↗

Tunable plasmon-enhanced second-order optical nonlinearity in transition-metal dichalcogenide nanotriangles (Final Report for SC0008712)

The control of light-matter interaction at the nanoscale is a grand challenge that cuts across modern photonics, plasmonics, and optoelectronics. The development of simulation tools for predictive modeling of nanostructured light emitters and absorbers is critical to successfully tackling this grand challenge. Existing state-of-the-art tools are not suitable for the following reasons: a) Phenomenological models of materials, commonly employed in the full-wave solutions to Maxwell’s equations, are fit to experimental data for bulk materials and fall short when attempting to analyze nanostructures. b) Nonlinearities in optical response can arise solely from nanostructuring, and require time-dependent quantum electronic transport techniques to capture. c) Emergent materials with exotic and tunable physical properties are increasingly used, but their properties are very sensitive to the substrate, impurities, and edge termination, and require an accurate description of interband and intraband processes, as well as dissipation. d) Microscopic modeling of electronic transport usually employs simplified electrodynamics, and realistic models that couple full electronic transport with full-wave electrodynamics are needed for accurate photonics simulations. The objective of this project was to computational tools that will overcome the limitations faced by current modeling tools and provide an unprecedented level of accuracy for predictive modeling of light-matter interaction at the nanoscale.

36 MATERIALS SCIENCE↗

Energy Dependence in the Neutrino Scattering Data of MINERvA

As we prepare for lower neutrino energy beams where physics is highly energy-dependent, it is important to isolate factors that can contribute largely to these low energy neutrino experiments. The world of neutrino oscillation experiments uses a wide range of energies: from 0.7 GeV beam of T2K and MicroBooNE, 2 GeV beam of NOvA, to the 0.6 to 6.0 GeV beam produced by DUNE in the future. MINERvA’s data are currently the best place to test the upper end of the range for DUNE and can be extrapolated into both DUNE’s and NOvA’s oscillation maximum. The goal of the research is to constrain energy dependence in the neutrino scattering experiment using data from MINERvA and then determine what factors contribute to the observed energy dependence. The research is divided into two parts. First, I will analyze different theoretical models in different channels of interaction, such as the quasi-elastic and delta resonance channels, in terms of neutrino energy dependence. The goal is to study the models at the level of the structure functions, which emphasizes the W2 structure function (the C function for QE) dominates the MINERvA data, but the W3 is increasingly important for NOvA and DUNE. The second half of the research is data-driven and focuses on the different detectors and systematic effects. An experimental effect, the angle acceptance, is larger than the structure function effects. However, it is a detector geometry effect and is well measured and well modeled. Other effects such as the muon energy scale are small and localized. Additionally, the research will determine if the MINERvA GENIE model correctly predicts all of the energy dependence seen in the data, and identify the remaining unmodeled energy dependence between the MINERvA data and its best simulation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Scaling Outlooks on Integrated Energy Systems

The report provides research summaries of two developed theories: data projection to enable multi-scale facility digital interactions and introducing the Evaluation Model Development and Assessment Process (EMDAP) approach to Integrated Energy Systems (IES) design. For the data projection, a two-system scaling case including interactions between thermal storage and hydrogen production is provided. The corresponding facilities are the thermal energy distribution system (TEDS) facility and high temperature steam electrolysis (HTSE) facility at the Dynamic Energy Transport and Integration Laboratory (DETAIL) in Idaho National Laboratory (INL). For the EMDAP adaption to system design, a modified process of the EMDAP was developed and applied to indirect two-tank heat storage system design. System phenomena were identified, ranked, and scaled to discover helpful key relations that would determine the ideal component geometry.

08 HYDROGEN↗

Probing proton cross-shell excitations through the two-neutron removal from 38 Ca

Bound states of the neutron-deficient, near-dripline nucleus 36 Ca were populated in two-neutron removal from the ground state of 38 Ca, a direct reaction sensitive to the single-particle configurations and couplings of the removed neutrons in the projectile wave function. Final-state exclusive cross sections for the formation of 36 Ca and the corresponding longitudinal momentum distributions, both determined through the combination of particle and γ-ray spectroscopy, are compared to predictions combining eikonal reaction theory and shell-model two-nucleon amplitudes from the USDB, USDC, and ZBM2 effective interactions. The final-state cross-section ratio σ($2$$^{+}_{1}$) / σ (0 + ) shows particular sensitivity and is approximately reproduced only with the two-nucleon amplitudes from the ZBM2 effective interaction that includes proton cross-shell excitations into the pf shell. Characterizing the proton pf-shell occupancy locally and schematically, an increase of the sd – pf shell gap by 250 keV yields an improved description of this cross-section ratio and simultaneously enables a reproduction of the B(E2;$0$$^{+}_{1}$ → $2$$^{+}_{1}$) excitation strength of 36 Ca. Furthermore, this highlights an important aspect if a new shell-model effective interaction for the region was to be developed on the quest to model the neutron-deficient Ca isotopes and surrounding nuclei whose structure is impacted by proton cross-shell excitations.

20 ≤ A ≤ 38↗

Design and Closed‐Loop Motion Planning of an Untethered Swimming Soft Robot Using 2D Discrete Elastic Rods Simulations

Despite tremendous progress in the development of untethered soft robots in recent years, existing systems lack the mobility, model‐based control, and motion planning capabilities of their piecewise rigid counterparts. As in conventional robotic systems, the development of versatile locomotion of soft robots is aided by the integration of hardware design and control with modeling tools that account for their unique mechanics and environmental interactions. Here, a framework for physics‐based modeling, motion planning, and control of a fully untethered swimming soft robot is introduced. This framework enables offline co‐design in the simulation of robot parameters and gaits to produce effective open‐loop behaviors and enables closed‐loop planning over motion primitives for feedback control of a frog‐inspired soft robot testbed. This pipeline uses a discrete elastic rods (DERs) physics engine that discretizes the soft robot as many stretchable and bendable rods. On hardware, an untethered aquatic soft robot that performs frog‐like rowing behaviors is engineered. Hardware validation verifies that the simulation has sufficient accuracy to find the best candidates for sets of parameters offline. The simulator is then used to generate a trajectory library of the robot's motion in simulation that is used in real‐time closed‐loop path following experiments on hardware.

Huang, Xiaonan↗

Physics model validation of propane and methane for Hydrogen Plus Other Alternative Fuels Risk Assessment Models (HyRAM+)

HyRAM+ is a toolkit that includes fast-running models for the unconstrained (i.e., no wall interactions) dispersion and flames for non-premixed fuels. The models were developed for use with hydrogen, but the toolkit was expanded to include propane and methane in a recent release. Here, in this work we validate the dispersion and flame models for these additional fuels, based on reported literature data. The validation efforts spanned a range of release conditions, from subsonic to underexpanded jets and flames for a range of mass flow rates. In general, the dispersion model works well for both propane and methane although the width of the jet/plume is predicted to be wider than observed in some cases. The flame model tends to over-predict the induced buoyancy for low-momentum flames, while the radiative heat flux agrees with the experimental data reasonably well, for both fuels. The models could be improved but give acceptable predictions for propane and methane behavior for the purposes of risk assessment.

33 ADVANCED PROPULSION SYSTEMS↗

Open-system spin transport and operator weight dissipation in spin chains

Here, we use nonequilibrium steady states to study the effect of dissipation-assisted operator evolution (DAOE) on the scaling behavior of transport in one-dimensional spin chains. We consider three models in the XXZ family: the XXZ model with staggered anisotropy, which is chaotic; XXZ model with no external field and tunable interaction, which is Bethe-ansatz integrable and (in the zero interaction limit) free-fermion integrable; and the disordered XY model, which is free-fermion integrable and Anderson localized. We find evidence that DAOE's effect on transport is controlled by its effect on the system's conserved quantities. To the extent that DAOE preserves those symmetries, it preserves the scaling of the system's transport properties; to the extent it breaks those conserved quantities, it pushes the system towards diffusive scaling of transport.

1-dimensional spin chains↗

Uncertainty Visualization Challenges in Decision Systems with Ensemble Data & Surrogate Models: Preprint

Uncertainty visualization is a key component in translating important insights from ensemble data into actionable decision-making by visually conveying various aspects of uncertainty within a system. With the recent advent of fast surrogate models for computationally expensive simulations, users can interact with more aspects of data spaces than ever before. However, the integration of ensemble data with surrogate models in a decision-making tool brings up new challenges for uncertainty visualization, namely how to reconcile and communicate the new and different types of uncertainties brought in by surrogates and how to utilize these new data estimates in actionable ways. In this work, we examine these issues as they relate to high-dimensional data visualization, the integration of discrete datasets and the continuous representations of those datasets, and the unique difficulties associated with systems that allow users to iterate between input and output spaces. We assess the role of uncertainty visualization in facilitating intuitive and actionable interaction with ensemble data and surrogate models, and highlight key challenges in this new frontier of computational simulation.

ensemble visualization↗