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At least 361 records · Page 20

Path sampling of recurrent neural networks by incorporating known physics

Recurrent neural networks have seen widespread use in modeling dynamical systems in varied domains such as weather prediction, text prediction and several others. Often one wishes to supplement the experimentally observed dynamics with prior knowledge or intuition about the system. While the recurrent nature of these networks allows them to model arbitrarily long memories in the time series used in training, it makes it harder to impose prior knowledge or intuition through generic constraints. In this work, we present a path sampling approach based on principle of Maximum Caliber that allows us to include generic thermodynamic or kinetic constraints into recurrent neural networks. We show the method here for a widely used type of recurrent neural network known as long short-term memory network in the context of supplementing time series collected from different application domains. These include classical Molecular Dynamics of a protein and Monte Carlo simulations of an open quantum system continuously losing photons to the environment and displaying Rabi oscillations. Our method can be easily generalized to other generative artificial intelligence models and to generic time series in different areas of physical and social sciences, where one wishes to supplement limited data with intuition or theory based corrections.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding the Effect of Chiral NN Parametrization on Nuclear Shapes From an Ab Initio Perspective

The ab initio symmetry-adapted no-core shell model naturally describes nuclear deformation and collectivity, and is therefore well-suited to studying the dynamics and coexistence of shapes in atomic nuclei. For the first time, we analyze how these features in low-lying states of 6 Li and 12 C are impacted by the underlying realistic nucleon-nucleon interaction. We find that the interaction parametrization has a notable but limited effect on collective shapes in the lowest 6 Li and 12 C states, while collective structures in the excited 2 + state of 12 C are significantly more sensitive to the interaction parameters and exhibits emergent shape coexistence.

Becker, Kevin S. [Louisiana State University, Bato↗

Landscape-scale characterization of Arctic tundra vegetation composition, structure, and function with a multi-sensor unoccupied aerial system

The Arctic is experiencing some of the most rapid climate change on Earth, with strong impacts on tundra ecosystems that are characterized by high land-surface and vegetation heterogeneity. Previous studies have explored this complexity using satellite remote sensing, however these typically coarse spatial resolution data have generally missed sub-pixel heterogeneity, leaving critical gaps in our understanding of tundra vegetation dynamics from the community to landscape scales. To address these gaps, we collected very high-resolution (1-5 cm) optical, structural, and thermal data at three low-Arctic tundra sites on the Seward Peninsula, Alaska, using a multi-sensor unoccupied aerial system (UAS). We examined the application of these data to studying tundra vegetation dynamics, by quantifying (1) canopy height and thermoregulation (leaf-air temperature) of representative plant functional types (PFTs), (2) fine-scale patterns of vegetation composition across landscapes, and (3) impacts of fine-scale vegetation composition on landscape-scale variation of canopy height and thermoregulation. Our results show that deciduous tall shrubs (those that can potentially grow >2 m) had a strong cooling effect, with canopy temperatures significantly lower than local air temperatures and other PFTs. Increased cover of tall shrubs also had the potential to reduce the cover of low-stature PFTs across the landscape, potentially associated with their closed canopy (i.e., increased light competition) and strong thermoregulation. To understand the connections between fine-scale vegetation composition and large-scale ecosystem processes, we produced a random forest model which showed that fine-scale PFT composition accounted for 86.8% and 74.2% of the landscape-scale variation in canopy height and thermoregulation, respectively. These findings highlight the importance of spatially detailed characterization of tundra PFTs to improve our ecological understanding and model representation of tundra vegetation, also transcend our study to show the need for continued collection of similar datasets to better understand the impacts of surface heterogeneity on the mapping and modeling of tundra ecosystem dynamics, as well as assist with conservation management and biodiversity monitoring strategies.

54 ENVIRONMENTAL SCIENCES↗

Dynamic Nanocrystal Superlattices with Thermally Triggerable Lubricating Ligands

The size-dependent and collective physical properties of nanocrystals (NCs) and their self-assembled superlattices (SLs) enable the study of mesoscale phenomena and the design of metamaterials for a broad range of applications. However, the limited mobility of NC building blocks in dried NCSLs often hampers the potential for employing postdeposition methods to produce high-quality NCSLs. In this study, we present tailored promesogenic ligands that exhibit a lubricating property akin to thermotropic liquid crystals. The lubricating ability of ligands is thermally triggerable, allowing the dry solid NC aggregates deposited on the substrates with poor ordering to be transformed into NCSLs with high crystallinity and preferred orientations. The interplay between the dynamic behavior of NCSLs and the molecular structure of the ligands is elucidated through a comprehensive analysis of their lubricating efficacy using both experimental and simulation approaches. Coarse-grained molecular dynamic modeling suggests that a shielding layer from mesogens prevents the interdigitation of ligand tails, facilitating the sliding between outer shells and consequently enhancing the mobility of NC building blocks. Further, the dynamic organization of NCSLs can also be triggered with high spatial resolution by laser illumination. The principles, kinetics, and utility of lubricating ligands could be generalized to unlock stimuli-responsive metamaterials from NCSLs and contribute to the fabrication of NCSLs.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Investigation of the yielding transition in concentrated colloidal systems via rheo-XPCS

We probe the microstructural yielding dynamics of a concentrated colloidal system by performing creep/recovery tests with simultaneous collection of coherent scattering data via X-ray Photon Correlation Spectroscopy (XPCS). This combination of rheology and scattering allows for time-resolved observations of the microstructural dynamics as yielding occurs, which can be linked back to the applied rheological deformation to form structure–property relations. Under sufficiently small applied creep stresses, examination of the correlation in the flow direction reveals that the scattering response recorrelates with its predeformed state, indicating nearly complete microstructural recovery, and the dynamics of the system under these conditions slows considerably. Conversely, larger creep stresses increase the speed of the dynamics under both applied creep and recovery. The data show a strong connection between the microstructural dynamics and the acquisition of unrecoverable strain. By comparing this relationship to that predicted from homogeneous, affine shearing, we find that the yielding transition in concentrated colloidal systems is highly heterogeneous on the microstructural level.

42 ENGINEERING↗

Machine learning prediction of glass transition temperature of conjugated polymers from chemical structure

Predicting the glass transition temperature (T g ) is of critical importance as it governs the thermomechanical performance of conjugated polymers (CPs). Here, we report a predictive modeling framework to predict T g of CPs through the integration of machine learning (ML), molecular dynamics (MD) simulations, and experiments. With 154 T g data collected, an ML model is developed by taking simplified “geometry” of six chemical building blocks as molecular features, where side-chain fraction, isolated rings, fused rings, and bridged rings features are identified as the dominant ones for T g . MD simulations further unravel the fundamental roles of those chemical building blocks in dynamical heterogeneity and local mobility of CPs at a molecular level. The developed ML model is demonstrated for its capability of predicting T g of several new high-performance solar cell materials to a good approximation. The established predictive framework facilitates the design and prediction of T g of complex CPs, paving the way for addressing device stability issues that have hampered the field from developing stable organic electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Trapped-ion quantum simulation of collective neutrino oscillations

It is well known that the neutrino flavor in extreme astrophysical environments changes under the effect of three contributions: the vacuum oscillation, the interaction with the surrounding matter, and the collective oscillations due to interactions between different neutrinos. The latter adds a nonlinear contribution to the equations of motion, making the description of their dynamics complex. In this work we study various strategies to simulate the coherent collective oscillations of a system of N neutrinos in the two-flavor approximation using quantum computation. This was achieved by using a pair-neutrino decomposition designed to account for the fact that the flavor Hamiltonian, in the presence of the neutrino-neutrino term, presents an all-to-all interaction that makes the implementation of the evolution dependent on the qubit topology. We analyze the Trotter error caused by the decomposition demonstrating that the complexity of the implementation of time evolution scales polynomially with the number of neutrinos and that the noise from near-term quantum device simulation can be reduced by optimizing the quantum circuit decomposition and exploiting a full-qubit connectivity. We find that the gate complexity using second order Trotter-Suzuki formulas scales better with system size than with other decomposition methods such as quantum signal processing. In conclusion, we finally present the application and the results of our algorithm on a real quantum device based on trapped-ion qubits.

79 ASTRONOMY AND ASTROPHYSICS↗

Exploring entanglement and spectral split correlations in three-flavor collective neutrino oscillations

In environments with prodigious numbers of neutrinos, such as core-collapse supernovae, neutron star mergers, or the early Universe, neutrino-neutrino interactions are dynamically significant. They can dominate neutrino flavor evolution and force it to be nonlinear, causing collective neutrino oscillations. Such collective oscillations have been studied numerically, for systems with up to millions of neutrinos, using mean-field or one-particle effective approximations. However, such a system of interacting neutrinos is a quantum many-body system, wherein quantum correlations could play a significant role in the flavor evolution—thereby motivating the exploration of many-body treatments that follow the time evolution of these correlations. In many-body flavor evolution calculations with two neutrino flavors, the emergence of spectral splits in the neutrino energy distributions has been found to be correlated with the degree of quantum entanglement across the spectrum. In this work, for the first time, we investigate the emergence of spectral splits in the three-flavor many-body collective neutrino oscillations. We find that the emergence of spectral splits resembles the number and location found in the mean-field approximation but not in the width. Moreover, unlike in the two-flavor many-body calculations, we find that additional degrees of freedom make it more difficult to establish a correlation between the location of the spectral splits and the degree of quantum entanglement across the neutrino energy spectrum. The observation from the two-flavor case, that neutrinos nearest to the spectral split frequency exhibit the highest level of entanglement, is more difficult to ascertain in the three-flavor case because of the presence of multiple spectral splits across different pairwise combinations of flavor and/or mass states. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

97 MATHEMATICS AND COMPUTING↗

Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

Tree growth and survival differ strongly between canopy trees (those directly exposed to overhead light), and understory trees. However, the structural complexity of many tropical forests makes it difficult to determine canopy positions. The integration of remote sensing and ground-based data enables this determination and measurements of how canopy and understory trees differ in structure and dynamics. Here we analyzed 2 cm resolution RGB imagery collected by a Remotely Piloted Aircraft System (RPAS), also known as drone, together with two decades of bi-annual tree censuses for 2 ha of old growth forest in the Central Amazon. We delineated all crowns visible in the imagery and linked each crown to a tagged stem through field work. Canopy trees constituted 40% of the 1244 inventoried trees with diameter at breast height (DBH) > 10 cm, and accounted for ~70% of aboveground carbon stocks and wood productivity. The probability of being in the canopy increased logistically with tree diameter, passing through 50% at 23.5 cm DBH. Diameter growth was on average twice as large in canopy trees as in understory trees. Growth rates were unrelated to diameter in canopy trees and positively related to diameter in understory trees, consistent with the idea that light availability increases with diameter in the understory but not the canopy. The whole stand size distribution was best fit by a Weibull distribution, whereas the separate size distributions of understory trees or canopy trees > 25 cm DBH were equally well fit by exponential and Weibull distributions, consistent with mechanistic forest models. The identification and field mapping of crowns seen in a high resolution orthomosaic revealed new patterns in the structure and dynamics of trees of canopy vs. understory at this site, demonstrating the value of traditional tree censuses with drone remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗

2D reactive transport model of shale chemical weathering and biogeochemical fluxes along a mountainous hillslope, East River Watershed, Colorado: Input files and simulation results

This data package contains input files and simulation results for a two-dimensional (2D) reactive transport model used to quantitatively analyze the coupled hydrological and biogeochemical processes governing shale weathering and associated biogeochemical fluxes under realistic environmental conditions in the high-elevation East River Watershed. These data support the conclusions presented in Stolze et al. (Water Resources Research, under review), "Model-based interpretation of solute exports and carbon partitioning during shale weathering in a mountainous hillslope". The model simulates atmospheric-subsurface gas exchange, subsurface water flow, and shale weathering processes under dynamic, year-scale conditions along a shale-underlain hillslope located in the East River watershed. The simulations were performed using the PFLOTRAN flow and reactive transport code and executed on the Perlmutter supercomputer to leverage its large-scale parallel computing capabilities. The data package contains two zipped folders, "model_input_files" and "simulation_results", and one readme.txt file. "model_input_files" contains the necessary input files to run the calibrated base-base model presented in Stolze et al. (Water Resources Research, under review). "simulation_results" contains a single hdf5 file ("Output_2D_hillslope_model.h5") which includes the results of simulation performed using the base-case model. This file can be opened with HDFView 3.1.4, Python, or MATLAB. "readme.txt" contains relevant information about the base-case model and provides guidelines on how to run the associated input files provided in the folder "model_input_files". Furthermore, readme.txt provides information regarding the model results provided in "Output_2D_hillslope_model.h5" such as matrix dimensionality and output units. Field datasets used to evaluate model performance were collected at three monitoring wells located along a hillslope transect (PLM1, PLM2, and PLM3). Dissolved ion concentration data were collected from November 2016 to October 2021 for Ca, Mg, DIC, Na, K, SO4 (Dong et al., 2025 - dic_npoc_data_2014_2024.zip - DOI:10.15485/1660459; Williams et al., 2025 - anion_data_2014_2024.zip - DOI:10.15485/1668054; Dong et al., 2025 - cation_data_2014_2024.zip - DOI:10.15485/1668055). Note that we used the files named er_PLM1_xx_yy, er_PLM2_xx_yy, and er_PLM3_xx_yy where xx stands for the name of the aqueous species and yy stands for the depth where the measurements were performed. Soil water content ([0 - 1] m) and water table depth were collected from November 2016 to October 2021 (Wan et al., 2024 - Dynamic_water_table__depthsFig2b.csv and Soil_water_content_Fig4e.csv - DOI:10.15485/2322567). Gaseous CO2 concentration were collected from October 2020 to December 2021(Wan et al., 2024 - Soil_CO2_concentrations_Fig4h.csv - DOI:10.15485/2322567) Gaseous CO2 flux from the subsurface to the atmosphere were collected in the vicinity of PLM2 from October 2019 to May 2022 (Wu et al., 2025). Soil microbial biomass concentration was measured from August 2016 to June 2017 (Sorensen et al., 2019 - 2017_East_River_Pumphouse_Microbial_Biomass__1_.csv - DOI:10.15485/1577267) All field data are published as CSV files compatible with Microsoft Excel, MATLAB, and Python, or as text files. The coordinates of the monitoring wells and the CO2(g) flux sensor in the coordinate system WGS84 are: -PLM1: [38.9197710 ; -106.9492750] -PLM2: [38.9201580 ; -106.9487170] -PLM3: [38.9207843 ; -106.9483668] -PLM4: 38.9210060 ; -106.9479528] -CO2(g) flux sensor: [38.9199180 ; -106.9489906] ------------------------------------------------------------------------------------------- This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility using NERSC award BER-ERCAP 23980, BER-ERCAP 28550, and BER-ERCAP 33789.

54 ENVIRONMENTAL SCIENCES↗

The DREAM Endstation at the Linac Coherent Light Source

Free-electron lasers (FEL), with their ultrashort pulses, ultrahigh intensities, and high repetition rates at short wavelength, have provided new approaches to Atomic and Molecular Optical Science. One such approach is following the birth of a photo electron to observe ion dynamics on an ultrafast timescale. Such an approach presents the opportunity to decipher the photon-initiated structural dynamics of an isolated atomic and molecular species. It is a fundamental step towards understanding single- and non-linear multi-photon processes and coherent electron dynamics in atoms and molecules, ultimately leading to coherent control following FEL research breakthroughs in pulse shaping and polarization control. A key aspect for exploring photoinduced quantum phenomena is visualizing the collective motion of electrons and nuclei in a single reaction process, as dynamics in atoms/ions proceed at femtosecond (10 –15 s) timescales while electronic dynamics take place in the attosecond timescale (10 –18 s). Here, we report on the design of a Dynamic Reaction Microscope (DREAM) endstation located at the second interaction point of the Time-Resolved Molecular and Optical (TMO) instrument at the Linac Coherent Light Source (LCLS) capable of following the photon–matter interactions by detecting ions and electrons in coincidence. The DREAM endstation takes advantage of the pulse properties and high repetition rate of LCLS-II to perform gas-phase soft X-ray experiments in a wide spectrum of scientific domains. With its design ability to detect multi-ions and electrons in coincidence while operating in step with the high repetition rate of LCLS-II, the DREAM endstation takes advantage of the inherent momentum conservation of reaction product ions with participating electrons to reconstruct the original X-ray photon–matter interactions. In this report, we outline in detail the design of the DREAM endstation and its functionality, with scientific opportunities enabled by this state-of-the-art instrument.

47 OTHER INSTRUMENTATION↗

More relaxed intracluster gas than galaxies in clusters in quasi-equilibrium

ABSTRACT During cluster mergers, the intracluster gas and member galaxies undergo dynamic evolution, but at different time-scales and reach different states. We collect 24 galaxy clusters in quasi-equilibrium state as indicated by the X-ray image, and calculate the cluster orientations and three kinds of dynamical parameters, i.e. the normalized centroid offset, the sphere index, and the ellipticity, for these clusters from the distributions of member galaxies and also the intracluster gas. We find consistent alignments for the orientations estimated from the two components. However, the three kinds of dynamical parameters indicated by member galaxies are systematically larger than those derived from the gas component, suggesting that the gas component is more relaxed than member galaxies. Differences of dynamical features between the intracluster gas and member galaxies are independent of cluster mass and concentration. We conclude that the intracluster gas reaches the dynamic equilibrium state earlier than the almost-collisionless member galaxies.

Astronomy & Astrophysics↗

Wigner polarons probe the dynamics of a Wigner crystal in a monolayer semiconductor

Wigner crystals—lattices made purely of electrons—provide a platform for studying correlation-driven quantum phase transitions. Despite extensive research, accessing the internal dynamics of Wigner crystals has remained challenging, with most experiments probing only static order or collective motion. Here we demonstrate optical probing and the manipulation of zero-field Wigner crystals and elucidate their static and dynamic properties in the frequency domain. We observe optical resonances that we identify as Wigner polarons—quasiparticles formed when the electron lattice is locally distorted by exciton–Wigner crystal coupling. We further achieve all-optical control of spins in the Wigner crystal, thereby directly probing valley-dependent Wigner polaron scattering well above the magnetic ordering temperature and in the absence of any external magnetic field. Lastly, we show optical melting of the Wigner crystal and observe different responses of the umklapp (static) and Wigner polaron (dynamic) resonances to optical excitation. Our results provide an avenue for understanding electron dynamics and achieving ultrafast optical control of interaction-driven quantum phase transitions in strongly correlated electron systems.

2D materials↗

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases

Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Finally, our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.

59 BASIC BIOLOGICAL SCIENCES↗

Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae

Microbial metabolism is a fundamental cellular process that involves many biochemical events and is distinguished by its emergent properties. While the molecular details of individual reactions have been increasingly elucidated, it is not well understood how these reactions are quantitatively orchestrated to produce collective cellular behaviors. Here we developed a coarse-grained, systems, and dynamic mathematical framework, which integrates metabolic reactions with signal transduction and gene regulation to dissect the emergent metabolic traits of Saccharomyces cerevisiae. Our framework mechanistically captures a set of characteristic cellular behaviors, including the Crabtree effect, diauxic shift, diauxic lag time, and differential growth under nutrient-altered environments. It also allows modular expansion for zooming in on specific pathways for detailed metabolic profiles. Furthermore, this study provides a systems mathematical framework for yeast metabolic behaviors, providing insights into yeast physiology and metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Electron–Nuclear Dynamics Accompanying Proton-Coupled Electron Transfer

Although photoinduced proton-coupled electron transfer (PCET) plays an essential role in photosynthesis, a full understanding of the mechanism is still lacking due to the complex nonequilibrium dynamics arising from the strongly coupled electronic and nuclear degrees of freedom. Here we report the photoinduced PCET dynamics of a biomimetic model system investigated by means of transient IR and two-dimensional electronic–vibrational (2DEV) spectroscopies, IR spectroelectrochemistry (IRSEC), and calculations utilizing long-range-corrected hybrid density functionals. This collective experimental and theoretical effort provides a nuanced picture of the complicated dynamics and synergistic motions involved in photoinduced PCET. In particular, the evolution of the 2DEV line shape, which is highly sensitive to the mixing of vibronic states, is interpreted by accurate computational modeling of the charge separated state and is shown to represent a gradual change in electron density distribution associated with a dihedral twist that occurs on a 120 fs time scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stability of Calcium Ion Battery Electrolytes: Predictions from Ab Initio Molecular Dynamics Simulations

Multivalent batteries, such as magnesium-ion, calcium-ion, and zinc-ion batteries, have attracted significant attention as next-generation electrochemical energy storage devices to complement conventional lithium-ion batteries (LIBs). Among them, calcium-ion batteries (CIBs) are the least explored due to the difficult reversible Ca deposition-dissolution. In this work, we examined the stability of four different Ca salts with weakly coordinating anions and three different solvents commonly employed in existing battery technologies to identify suitable candidates for CIBs. By employing Born-Oppenheimer molecular dynamics (BOMD) simulations on salt-Ca and solvent-Ca interfaces, we find that the tetraglyme solvent and carborane salt are promising candidates for CIBs. Due to the strong reducing nature of the calcium surface, the other salts and solvents readily decompose. Further, we explain the microscopic mechanisms of salt/solvent decomposition on the Ca surface using time-dependent projected density of states, time-dependent charge-transfer plots, and climbing-image nudged elastic band calculations. Collectively, this work presents the first mechanistic assessment of the dynamical stability of candidate salts and solvents on a Ca surface using BOMD simulations, and provides a predictive path toward designing stable electrolytes for CIBs.

Born-Oppenheimer molecular dynamics↗