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At least 1,099 records · Page 61

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗

On the numerical sensitivity of cellular automata grain structure predictions to large thermal gradients and cooling rates

Cellular automata (CA) models of as-solidified grain structure, originally developed and applied to casting, have become a common means of predicting grain structure resulting from Additive Manufacturing (AM) processes. The majority of these models are based on the decentered octahedron approach, which attempts to correct for the effect of grid anisotropy on the prediction of competitive solidification of dendritic grains. However, AM solidification occurs under cooling rates ($\dot{T}$) and thermal gradients (G) that are orders of magnitude larger than those encountered in casting, and no systematic investigation on the effect of the CA model cell size (Δx) and time step (Δt) on AM microstructure predictions has been performed. Here, in this study, such an investigation is first performed via simulation of individual grains of various crystallographic orientations with a fixed, unidirectional G, showing that CA prediction of the steady-state undercooling matched the expected values based on the interfacial response function at small G and deviated from the expected values at large G. Simulation of competitive growth of multiple grains showed a weakening of the predicted texture as G and Δx became large. Simulation of solidification under AM conditions, where G and $\dot{T}$ vary spatially across the melt pools, showed that not only does grain selection weaken and deviate from expectations at large Δx, but grains with crystallographic $\langle$100$\rangle$ aligned with the grid directions are more adversely affected by the temperature field discontinuities than grains with other crystallographic orientations. Despite the fact that the exact grain competition results depended on Δt, the overall texture development was notably less sensitive to Δt than Δx, provided that a reasonable value of Δt is selected based on the ratio of Δx to the maximum local solidification velocity in the simulation domain. Finally, from the directional solidification and AM simulation results, an analysis of computational cost compared to simulation resolution is performed based on an equation derived to quantify the relatively inaccuracy in grain selection based on the model and temperature field inputs. From this analysis, it is concluded that there is a need for algorithmic improvements to improve CA grain competition accuracy for large G processing conditions as sufficiently small Δx to resolve the necessary competition is intractable for many AM processing conditions.

36 MATERIALS SCIENCE↗

Microscale spatiotemporal patterns of water, soil organic carbon, and enzymes in plant litter detritusphere

Understanding biophysical and biochemical processes in detritusphere is critical to quantifying and modeling plant residue decomposition dynamics and subsequent soil organic carbon (C) accrual. The objectives of the study were to explore (i) micro-environmental conditions within the detritusphere formed around decomposing corn and soybean leaves, and (ii) the relationships between moisture distribution, enzyme activity, and C dynamics during decomposition. We assessed spatial and temporal dynamics of moisture distribution using X-ray and neutron computed tomography, and activities of β-glucosidase and chitinase, two enzymes involved in soil C and N processing, using zymography. We used 13 C labeled residue to track residue contribution to atmospheric CO 2 and soil organic C. Moisture redistribution pattern varied depending on the residue type. While the water was immediately absorbed by the corn leaves and maintained afterward, switchgrass leaves absorbed water more slowly and created water-deficient zones within ~1mm from the residue. This initial moisture depletion led to lower chitinase activity and residue-derived CO 2 emissions in switchgrass. In contrast to chitinase, β-glucosidase activity was influenced by a combination of vegetation history and residue type, and it was higher when the origin of the residue matched the vegetation history of the soil. Pore size had an opposite impact on the studied enzymes, supporting the notion that contrasting soil pore architecture can stimulate activities of different enzymes through a selection of dominant enzyme producers. We concluded that the decomposition dynamics of plant residues is not only a simple function of residue chemistry, but rather a combined effect of the vegetation history, in part through its effect on microbial community composition, the plant residue chemical and likely physical characteristics, and the soil pore structure in the detritusphere. Together, they create temporally dynamic micro-environmental conditions influencing decomposition. Specifically, our study demonstrated that the initial micro-environment formulated in detritusphere can play an important role in enzyme activities and consequent C dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing the initial state and dynamical evolution in XeXe and PbPb collisions using multiparticle cumulants

For the first time, correlations among mixed-order moments of two or three flow harmonics —( v n k , v m l ) and ( v n k , v m l , v p q ), with k, l, and q denoting the respective orders—are measured in xenon–xenon (XeXe) collisions and compared with lead–lead (PbPb) results, providing a novel probe of collective behavior in heavy ion collisions. These measurements compare a nearly spherical, doubly-magic 208 Pb nucleus to a triaxially deformed 129 Xe nucleus, emphasizing the sensitivity to initial-state geometry fluctuations arising from nuclear deformation. The dependence of these results (v n , n = 2 , 3 , 4 ) on the shape and size of the nuclear overlap region is studied. Comparisons between v 2 , v 3 , and v 4 demonstrate the importance of v 3 and v 4 in exploring the nonlinear hydrodynamic response of the quark-gluon plasma (QGP) to the initial spatial anisotropy. The results constrain initial-state model parameters that influence the evolution of the QGP. The CMS detector was used to collect XeXe and PbPb data at nucleon-nucleon center-of-mass energies of S N N = 5.44 and 5.36 TeV, respectively. Correlations are extracted using multiparticle mixed-harmonic cumulants (up to eight-particle cumulants) with charged particles in the pseudorapidity range |η| < 2.4 and transverse momentum range 0.5 < p T < 3 GeV/c.

CMS↗

Probabilistic Context Neighborhood model for lattices

Here we present the Probabilistic Context Neighborhood model designed for two-dimensional lattices as a variation of a Markov random field assuming discrete values. In this model, the neighborhood structure has a fixed geometry but a variable order, depending on the neighbors’ values. Our model extends the Probabilistic Context Tree model, originally applicable to one-dimensional space. It retains advantageous properties, such as representing the dependence neighborhood structure as a graph in a tree format, facilitating an understanding of model complexity. Furthermore, we adapt the algorithm used to estimate the Probabilistic Context Tree to estimate the parameters of the proposed model. We illustrate the accuracy of our estimation methodology through simulation studies. Additionally, we apply the Probabilistic Context Neighborhood model to spatial real-world data, showcasing its practical utility.

97 MATHEMATICS AND COMPUTING↗

A Robust Estimate of Continental-Scale Terrestrial Carbon Sinks Using GOSAT XCO 2 Retrievals

Satellite XCO 2 retrievals could improve the estimates of surface carbon fluxes, but it remains unknown on what scales these estimates are robust. Here, we use the time-dependent Bayesian synthesis top-down method and prior net ecosystem exchanges (NEEs) from 12 terrestrial biosphere models (TBMs) to infer the monthly carbon fluxes of 51 land regions with constraints by GOSAT XCO 2 retrievals. We find that the uncertainty (standard deviation of 12 TBMs) reduction rates (uncertainty reduction rate (URR)) decrease significantly at decreasing spatial scales. On the continental-scale, the mean URR is about 57%, and the annual and seasonal cycle estimates of NEE are rather robust. The evaluation shows that the posterior CO 2 concentrations are significantly improved at the continental scale. Our study suggests that the GOSAT XCO 2 can only promise a robust continental-scale NEE estimate and improving the XCO 2 accuracy is an effective way to achieve robust estimates on smaller scales under current spatial coverage.

58 GEOSCIENCES↗

Observation of plaid-like spin splitting in a noncoplanar antiferromagnet

Spatial, momentum and energy separation of electronic spins in condensed matter systems guides the development of novel devices where spin-polarized current is generated and manipulated. Recent attention on a set of previously overlooked symmetry operations in magnetic materials leads to the emergence of a new type of spin splitting, enabling giant and momentum-dependent spin polarization of energy bands on selected antiferromagnets. Despite the ever-growing theoretical predictions, the direct spectroscopic proof of such spin splitting is still lacking. Here, we provide solid spectroscopic and computational evidence for the existence of such materials. In the noncoplanar antiferromagnet MnTe 2 , the in-plane components of spin are found to be antisymmetric about the high-symmetry planes of the Brillouin zone, comprising a plaid-like spin texture in the antiferromagnetic (AFM) ground state. Such an unconventional spin pattern, further found to diminish at the high- temperature paramagnetic state, stems from the intrinsic AFM order instead of spin- orbit coupling (SOC). Furthermore, our finding demonstrates a new type of quadratic spin texture induced by time-reversal breaking, placing AFM spintronics on a firm basis and paving the way for studying exotic quantum phenomena in related materials.

Electronic devices↗

Valley filtering in strain-induced α-$\mathcal{T}_3$ quantum dots

We test the valley filtering capabilities of a quantum dot inscribed by locally straining an α-$\mathcal{T}_3$ lattice. Specifically, we consider an out-of-plane Gaussian bump in the center of a four-terminal configuration and calculate the generated pseudo-magnetic field having opposite direction for electrons originating from different valleys, the resulting valley-polarized currents, and the conductance between the injector and collector situated opposite one another. Depending on the quantum dot’s width and width-to-height ratio, we detect different transport regimes with and without valley filtering for both the α-$\mathcal{T}_3$ and Dice lattice structures. In addition, we analyze the essence of the conductance resonances with high valley polarization in terms of related (pseudo) Landau levels, the spatial distribution of the local density of states and the local current densities. The observed local charge and current density patterns reflect the local inversion symmetry-breaking by the strain, besides the global inversion symmetry breaking due to the scaling parameter α. By this way we can also filter out different sublattices

36 MATERIALS SCIENCE↗

Model-Free Measurement of Local Entropy Production and Extractable Work in Active Matter

Time-reversal symmetry breaking and entropy production are universal features of nonequilibrium phenomena. Despite its importance in the physics of active and living systems, the entropy production of systems with many degrees of freedom has remained of little practical significance because the high dimensionality of their state space makes it difficult to measure. Here, in this work, we introduce a local measure of entropy production and a numerical protocol to estimate it. We establish a connection between the entropy production and extractability of work in a given region of the system and show how this quantity depends crucially on the degrees of freedom being tracked. We validate our approach in theory, simulation, and experiments by considering systems of active Brownian particles undergoing motility-induced phase separation, as well as active Brownian particles and E.coli in a rectifying device in which the time-reversal asymmetry of the particle dynamics couples to spatial asymmetry to reveal its effects on a macroscopic scale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

ITreeForeCast: An integrated modeling software to simulate tree level growth and forest carbon storage

Healthy trees in forest act as a natural carbon sink, capturing carbon. As they grow, they store carbon in their trunks, leaves and roots. Not all trees store carbon at the same rate, or in the same quantities, as it depends on a variety of biophysical and climatic factors. Furthermore, although carbon estimation in trees can be complex, the precision of estimates is tightly linked to trees growth, both in diameter and height. However, the simulation of carbon uptake by forest and forest growth has each been modeled separately, and independently at differing levels of detail and spatial resolution. In this paper, we introduce ITreeForeCast, a simulation model combining the two types of modeling on a unified platform, enabling the investigation of impacts of management strategies on carbon sequestration and wood products. ITreeForeCast is a user-extendable framework that offers new opportunities to model, simulate, and visualize the dynamics of individual trees in a forest, simulate management strategies over time, and carbon uptake.

09 - BIOMASS FUELS↗

Explore Spatio‐Temporal Learning of Large Sample Hydrology Using Graph Neural Networks

Abstract Streamflow forecasting over gauged and ungauged basins play a vital role in water resources planning, especially under the changing climate. Increased availability of large sample hydrology data sets, together with recent advances in deep learning techniques, has presented new opportunities to explore temporal and spatial patterns in hydrological signatures for improving streamflow forecasting. The purpose of this study is to adapt and benchmark several state‐of‐the‐art graph neural network (GNN) architectures, including ChebNet, Graph Convolutional Network (GCN), and GraphWaveNet, for end‐to‐end graph learning. We explicitly represent river basins as nodes in a graph, learn the spatiotemporal nodal dependencies, and then use the learned relations to predict streamflow simultaneously across all nodes in the graph. The efficacy of the developed GNN models is investigated using the Catchment Attributes and MEteorology for Large‐sample Studies (CAMELS) data set under two settings, fixed graph topology (transductive learning), and variable graph topology (inductive learning), with the latter applicable to prediction in ungauged basins (PUB). Results indicate that GNNs are generally robust and computationally efficient, achieving similar or better performance than a baseline model trained using the long short‐term memory (LSTM) network. Further analyses are conducted to interpret the graph learning process at the edge and node levels and to investigate the effect of different model configurations. We conclude that graph learning constitutes a viable machine learning‐based method for aggregating spatiotemporal information from a multitude of sources for streamflow forecasting

Sun, Alexander Y.↗

Real-time laser ultrasonic monitoring of laser-induced thermal processes

Abstract Intra- and inter-layer integrity of components fabricated with advanced manufacturing techniques, such as laser powder bed fusion, is dependent upon rapid heating, melting, and solidification processes. There is a need for new techniques to provide in situ feedback of these processes. Here a laser-based ultrasonic technique to probe thermal effects induced by a high-power continuous wave laser in titanium samples is described. Numerical simulations were performed to show that, for a spatially uniform heating beam, laser-induced surface acoustic waves are strongly influenced by surface heating conditions, are dispersive in the case of rapid heating, and that an abrupt velocity reduction happens upon the onset of surface melting. Furthermore, laser-based ultrasound experimental results which monitor the transient change of surface wave travel time associated with high power laser surface heating are provided. A pulsed laser is used to generate high frequency surface acoustic waves that propagate through the laser-heated region and are detected using a photorefractive crystal-based interferometer. Qualitative agreement is observed between theory and experiment with both showing a rapid reduction in the surface wave velocity at the onset of illumination and further decrease in surface wave velocity associated with melting. It is demonstrated that changes in the surface wave velocity can be used to track local heating and detect the onset of surface melting in real time.

36 MATERIALS SCIENCE↗

Binary pseudo-random array (BPRA) for inspection and calibration for cylindrical wavefront interferometry

High-accuracy metrology is vitally important in manufacturing ultra-high-quality free-form mirrors designed to manipulate X-ray light with nanometer-scale wavelengths. However, surface topography measurements are instrument dependent, and without the knowledge of how the instrument performs under the practical usage conditions, the measured data contain some degree of uncertainty. Binary Pseudo Random Array (BPRA) “white noise” artifact are effective and useful for characterizing the Instrument Transfer Function (ITF) of surface topography metrology tools and wavefront measurement instrument. BPRA artifact contains features with all spatial frequencies in the instrument bandpass with equal weight. As a result, power spectral density of the patterns has a deterministic white-noise-like character that allows direct determination of the ITF with uniform sensitivity over the entire spatial frequency range. The application examples include electron microscopes, x-ray microscopes, interferometric microscopes, and large field-of-view Fizeau Interferometers. Furthermore, we will introduce the application of BPRA method to characterizing the ITF of Cylindrical Wavefront Interferometry (CWI), by developing the BPRA artifact which matches the radius of curvature of the cylindrical wavefront. The data acquisition and analysis procedures for different applications of the ITF calibration technique developed are also discussed.

Munechika, K↗

Molecular-Weight-Dependent Infiltration and Adsorption of Polymers into Nanochannels

The mesoporous silica shell coating hydrogenolysis nano-catalysts alters the molecular weight distributions of cleaved polymer chains compared to catalysts without a shell. The shell, composed of radially aligned narrow cylindrical nanopores, reduces the formation of low-valued gaseous products and increases the median molecular weight of the product, thus enhancing the value of the products for polymer upcycling. Here, to understand the role of the mesoporous shell, we have studied the spatial distribution of polystyrene chains, used as a model polymer, in the nanochannels in both the melt phase and solution phase. In the melt, we observed from small-angle X-ray scattering experiments that the infiltration rate of the polymer into the nanochannels is inversely proportional to the molecular weight, which is consistent with theory. In theta solution experiments using UV–vis spectroscopy, we found that the shell significantly enhances polymer adsorption compared to nanoparticles without pores. In addition, the degree of polymer adsorption is not a monotonic function of molecular weight but initially increases with the molecular weight before eventually decreasing. The molecular weight for the peak adsorption increases with the pore diameter. This adsorption behavior is rationalized as resulting from a balance between the mixing entropy gain by surface adsorption and the conformational entropy penalty incurred by chains confined in the nanochannels. The spatial distribution of polymer chains in the nanochannels is visualized by energy-dispersive X-ray spectroscopy (EDX), and inverse Abel-transformed data reveals a less uniform polymer distribution along the primary pore axis for longer chains.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visualizing temperature-dependent phase stability in high entropy alloys

High entropy alloys (HEAs) contain near equimolar amounts of five or more elements and are a compelling space for materials design. In the design of HEAs, great emphasis is placed on identifying thermodynamic conditions for single-phase and multi-phase stability regions, but this process is hindered by the difficulty of navigating stability relationships in high-component spaces. Traditional phase diagrams use barycentric coordinates to represent composition axes, which require ( N – 1) spatial dimensions to represent an N -component system, meaning that HEA systems with N > 4 components cannot be readily visualized. Here, we propose forgoing barycentric composition axes in favor of two energy axes: a formation-energy axis and a ‘reaction energy’ axis. These Inverse Hull Webs offer an information-dense 2D representation that successfully captures complex phase stability relationships in N ≥ 5 component systems. We use our proposed diagrams to visualize the transition of HEA solid-solutions from high-temperature stability to metastability upon quenching, and identify important thermodynamic features that are correlated with the persistence or decomposition of metastable HEAs.

Chemistry↗

A Multi-Model Framework for Assessing Long- and Short-Term Climate Influences on the Electric Grid

Climate change influences many aspects of the electric grid, but prior work and industry practices often ignore the potential effects of changing climate, or they only consider a single effect or individual effects in isolation. Challenges vary with each grid and include adapting to long-term trends such as changing temperature and precipitation or shorter-term events such as drought or storms that could increase in frequency or intensity. Here we present a multi-model framework designed to analyze the effects of long and short-term climate impacts in combination. This framework couples capacity expansion and production cost models with hydrologic models and future climate scenario data to analyze alternative climate and energy futures at high spatial, temporal, and process resolutions. Furthermore, we constructed and evaluated the results of a suite of simulated scenarios exploring climate impacts on capacity investment and stress-tested the resulting future infrastructures using hourly dispatch modeling under alternative drought and load conditions. We demonstrate the approach through a case study of the U.S. Western Interconnection, where climate impacts depend on interactions between temperature-induced load, water availability for hydropower, technology competitiveness, and demand flexibility. Changes in 2038 generating capacity range from -8.5-16.6 GW, and changes in 2038 transmission capacity range from -1-2 GW. Capacity increases are driven by higher load from higher temperatures, while capacity reductions can be achieved in scenarios with higher future hydropower availability and increased demand flexibility. Scenarios requiring additional capacity cost an additional $\$5$-$\$17$ billion (discounted) from 2018 to 2038; however, scenarios with capacity reductions cost $\$1$-$\$18$ billion less. Stress tests on four 2038 infrastructures demonstrated that the identified systems were able to serve at least 99.999% of load and 99.96% of reserves. However, drought and unexpected high-load conditions can result in reduced capacity to respond to contingency events we did not model. Although these results are system and scenario specific, they highlight the importance of considering multiple climate change impacts simultaneously in long-term planning efforts and demonstrate a multi-model, multiscale approach that can be flexibly applied to any system and set of climate change concerns.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Experimental characterization of discharge plasma dynamics in a square capillary for prospective applications in laser wakefield acceleration

Research on plasma generated by electrical discharge in gas-filled capillaries plays an important role in advancing laser wakefield accelerators. We present a comprehensive study of the temporal and spatial distribution of plasma density within a short, 1 cm long, square-shaped capillary filled with hydrogen gas. Two transverse capillary sizes, 500 μm and 300 μm, were investigated achieving peak plasma densities of 0.9 × 10 18 cm −3 and 2.5 × 10 18 cm −3 , respectively, at the capillary center. In addition, we explore how these distributions depend on discharge parameters, specifically discharge current and gas flow through the capillary. Plasma density was determined by analyzing the Stark broadening of the hydrogen Balmer-alpha line. The results obtained were compared with the theoretical models and simulations. The comparison between the model predictions and the experimental data at the transient ionization stage of the discharge reveals a discrepancy of a factor of ∼1.3–2.1, depending on the capillary size, which is thoroughly discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Resolving the dynamic correlated disorder in KTa 1- x Nb x O 3

Understanding the complex temporal and spatial correlations of ions in disordered perovskite oxides is critical to rationalize their functional properties. Here, in this study, we provide new insights into the longstanding controversy regarding the off-centering of transition metal ions in the archetypal ferroelectric alloy KTa 1-x Nb x O 3 (KTN). By mapping the full energy (E) and wavevector (Q) dependence of the dynamical structure factor S(Q, E) using neutron scattering, and rationalizing our observations with atomistic simulations leveraging machine learning, we fully resolve the static vs dynamic nature of diffuse scattering sheets, as well as their composition (x) and temperature dependence. Our first-principles simulations, extended with machine-learning molecular dynamics, reproduce both inelastic neutron spectra and diffuse features, and establish how dynamically-correlated transition metal off-centerings couple to phonons, unifying local and collective viewpoints. This study sheds new light into an exemplary ferroelectric systems and shows the importance of mapping the full S(Q, E) to reveal critical spatio-temporal correlations of atomic disorder from which functional properties emerge.

42 ENGINEERING↗