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At least 1,117 records · Page 62

Coarse-graining Hamiltonian systems using WSINDy

Abstract Weak form equation learning and surrogate modeling has proven to be computationally efficient and robust to measurement noise in a wide range of applications including ODE, PDE, and SDE discovery, as well as in coarse-graining applications, such as homogenization and mean-field descriptions of interacting particle systems. In this work we extend this coarse-graining capability to the setting of Hamiltonian dynamics which possess approximate symmetries associated with timescale separation. A smooth $$\varepsilon$$ ε -dependent Hamiltonian vector field $$X_\varepsilon$$ X ε possesses an approximate symmetry if the limiting vector field $$X_0=\lim _{\varepsilon \rightarrow 0}X_\varepsilon$$ X 0 = lim ε → 0 X ε possesses an exact symmetry. Such approximate symmetries often lead to the existence of a Hamiltonian system of reduced dimension that may be used to efficiently capture the dynamics of the symmetry-invariant dependent variables. Deriving such reduced systems, or approximating them numerically, is an ongoing challenge. We demonstrate that WSINDy can successfully identify this reduced Hamiltonian system in the presence of large perturbations imparted in the $$\varepsilon >0$$ ε > 0 regime, while remaining robust to extrinsic noise. This is significant in part due to the nontrivial means by which such systems are derived analytically. WSINDy naturally preserves the Hamiltonian structure by restricting to a trial basis of Hamiltonian vector fields. The methodology is computationally efficient, often requiring only a single trajectory to learn the global reduced Hamiltonian, and avoiding forward solves in the learning process. In this way, we argue that weak-form equation learning is particularly well-suited for Hamiltonian coarse-graining. Using nearly-periodic Hamiltonian systems as a prototypical class of systems with approximate symmetries, we show that WSINDy robustly identifies the correct leading-order system, with dimension reduced by at least two, upon observation of the relevant degrees of freedom. While our main contribution is computational, we also provide a contribution to the literature on averaging theory by proving that first-order averaging at the level of vector fields preserves Hamiltonian structure in nearly-periodic Hamiltonian systems. This provides theoretical justification for our approach as WSINDy’s computations occur at the level of Hamiltonian vector fields. We illustrate the efficacy of our proposed method using physically relevant examples, including coupled oscillator dynamics, the Hénon–Heiles system for stellar motion within a galaxy, and the dynamics of charged particles.

97 MATHEMATICS AND COMPUTING↗

Block segmentation in feature space for realtime object detection in high granularity images

Computer vision has applications in object detection, image recognition and classification, and object tracking. One of the challenges of computer vision is the presence of useful information at multiple distance scales. Filtering techniques may sacrifice details at small scales in order to prioritize the analysis of large-scale features of the image. We present a strategy for coarse-graining multidimensional data while maintaining fine-grained detail for subsequent analysis. The algorithm is based on fixed-size block segmentation in the feature space. We apply this strategy to solve the long-standing challenge of detecting particle trajectories at the Large Hadron Collider in real time.

Computer vision↗

Simulating nationwide coupled disease and fear spread in an agent-based model

Human cognitive responses, behavioral responses, and disease dynamics co-evolve over the course of any disease outbreak, and can result in complex feedbacks. We present a dynamic agent-based model that explicitly couples the spread of disease with the spread of fear surrounding the disease, implemented within the EpiCast simulation framework. EpiCast models transmission within a realistic synthetic population, capturing individual-level interactions. In our model, fear propagates through both in-person contact and broadcast media, prompting individuals to adopt protective behaviors that reduce disease spread. In order to better understand these coupled dynamics, we create and compare a range of compartmental models to ensure that introducing additional disease states does not prevent the emergence of multiple waves in these simpler models. Additionally, we compare a range of behavioral scenarios within EpiCast, varying the level and intensity of fear and behavior change. Our results show that the addition of asymptomatic, exposed, and pre-symptomatic disease states can impact both the rate at which an outbreak progresses and its overall trajectory in compartmental models. In EpiCast, the combination of non-local fear spread via broadcasters and strong behavioral responses by fearful individuals generally leads to multiple epidemic waves, an outcome that occurs only within a narrow parameter range when fear spreads purely through local contact. Accounting for the coupled spread of fear and disease is critical for understanding disease dynamics and designing timely, targeted responses to emerging infectious threats.

60 APPLIED LIFE SCIENCES↗

Two-component dynamics in supercritical $\text {CO}_2$ from inelastic X-ray scattering

Supercritical fluids are characterized by unique thermodynamic properties. One of these properties is the existence of two-component dynamics that is associated with distinct low-frequency and high-frequency vibrational responses of the fluid. However, the origin of this behavior remains unknown. By combining inelastic X-ray scattering and molecular dynamics simulations, we show that this behavior can be connected to density heterogeneities arising from molecular clusters. Analyses of measurements and molecular trajectories suggest that the two-component dynamics emerges due to distinct momentum fluctuations of clustered and unbound molecules. This connection between clusters and two-component dynamics highlights the importance of molecular-structural heterogeneities in supercritical fluids, colloids, and condensed-matter systems.

biophysics↗

From peak to plummet: impending decline of the warm Arctic-cold continents phenomenon

Abstract This study assesses the projected trajectory of Warm Arctic-Cold Continent (WACC) events in East Asia and North America through large ensemble simulation for the upcoming decades. It analyses the evolution of the geographical boundaries of threshold cold temperatures, revealing a significant northward shift as a sign of global warming’s impact on the southward advancement of Arctic cold air. While validating the intensification of the WACC phenomenon until the 2020 s, echoing earlier studies, the findings indicate a marked decrease beginning in the 2030s. If warming is not curbed, this shift suggests a critical modification in the WACC pattern, prompting a re-evaluation of existing theories and models for extreme winter weather events. The results have major implications, spurring communities impacted by WACC to anticipate future changes and encouraging the climate forecasting community to update conceptual models for improved adaptation and mitigation approaches.

Meteorology & Atmospheric Sciences↗

CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling

Large-scale simulations with complex electron interactions remain one of the greatest challenges for atomistic modelling. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study technologically relevant phenomena. Here we present the Crystal Hamiltonian Graph Neural Network (CHGNet), a graph neural network-based machine-learning interatomic potential (MLIP) that models the universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory calculations of more than 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li x MnO 2 , the finite temperature phase diagram for Li x FePO 4 and Li diffusion in garnet conductors. We highlight the significance of charge information for capturing appropriate chemistry and provide insights into ionic systems with additional electronic degrees of freedom that cannot be observed by previous MLIPs.

36 MATERIALS SCIENCE↗

Upper troposphere dust belt formation processes vary seasonally and spatially in the Northern Hemisphere

Dust aerosols impact global energy balance substantially by acting as efficient ice nuclei to alter cold cloud properties. However, the estimate of dust indirect effect remains uncertain due to simulating dust distributions poorly and lacking reliable dust observations, especially in the upper-troposphere. Here, we characterize and understand upper-troposphere dust sources and transport with an improved dust dataset derived from A-train satellite lidar and radar measurements and an air parcel trajectory model. The distinct upper-troposphere dust belt over the northern hemisphere has seasonally varying base and top heights of 3.65 ± 2.84 and 8.35 ± 1.50 km above mean sea level and its column loading is strongest during spring (March-April-May). The out-of-phase annual cycles of mid-level dust concentration and westerly wind over source regions control the seasonal upper-tropospheric dust loading variations. African deserts contribute the most (46.3%) to the upper-troposphere dust belt in spring and the synoptic trough is the leading (49%) dust lifting mechanism.

54 ENVIRONMENTAL SCIENCES↗

Wildfire aerosol deposition likely amplified a summertime Arctic phytoplankton bloom

Summertime wildfire activity is increasing in boreal forest and tundra ecosystems in the Northern Hemisphere. However, the impact of long range transport and deposition of wildfire aerosols on biogeochemical cycles in the Arctic Ocean is unknown. Here, we use satellite-based ocean color data, atmospheric modeling and back trajectory analysis to investigate the transport and fate of aerosols emitted from Siberian wildfires in summer 2014 and their potential impact on phytoplankton dynamics in the Arctic Ocean. We detect large phytoplankton blooms near the North Pole (up to 82°N in the eastern Eurasian Basin). Our analysis indicates that these blooms were induced by the northward plume transport and deposition of nutrient-bearing wildfire aerosols. We estimate that these highly stratified surface waters received large amounts of wildfire-derived nitrogen, which alleviated nutrient stress in the phytoplankton community and triggered an unusually large bloom event. Our findings suggest that changes in wildfire activity may strongly influence summertime productivity in the Arctic Ocean.

54 ENVIRONMENTAL SCIENCES↗

Digital Twin for Chemical Science: a case study on water interactions on the Ag(111) surface

Directly visualizing chemical trajectories offers insights into catalysis, gas-phase reactions and photoinduced dynamics. Tracking the transformation of chemical species is best achieved by coupling theory and experiment. Here we developed Digital Twin for Chemical Science (DTCS) v.01, which integrates theory, experiment and their bidirectional feedback loops into a unified platform for chemical characterization. DTCS addresses a core question: given a set of experimental conditions, what is the expected outcome and why? It consists of a forward solver that takes a chemical reaction network and predicts spectra under experimental conditions, and an inverse solver that infers kinetics from measured spectra. We applied DTCS to ambient-pressure X-ray photoelectron spectroscopy measurements of the Ag–H2O interface as an example. This approach enables real-time knowledge extraction and guides experiments until a stopping condition is met based on accuracy and degeneracy. As a step toward autonomous chemical characterization, DTCS provides mechanistic knowledge in a verified, standardized manner.

Chemistry↗

Community RNA-Seq: multi-kingdom responses to living versus decaying roots in soil

Abstract Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (“community RNA-Seq”) and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group’s more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.

Nuccio, Erin E. (ORCID:000000030189183X)↗

Electrification pathways for U.S. passenger vehicles

As electric vehicle (EV) adoption continues to accelerate, we explore the implications of different adoption trajectories that achieve a full transition to EVs by 2050 for U.S. light-duty passenger vehicles (LDVs). Using a vetted transportation system model, we find that achieving 100% EV sales by 2040 would decrease tailpipe greenhouse gases (GHGs) by 90% between 2022 and 2050, leaving about 45 million gasoline vehicles on the road. Achieving 100% sales by 2035, tailpipe emissions decrease 93%, with about 28 million gasoline vehicles on the road in 2050 (9% of stock). Slower EV adoption, reaching 100% sales by 2045, would result in 69 million gasoline vehicles on the road in 2050. Fully electrifying passenger vehicles by 2050 would require a full transition to EVs sales in the 2030s coupled with either changes to mobility, or an accelerated stock turnover in the 2040s with additional 19–30% annual LDV sales.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Theoretical H + O 3 rate coefficients from ring polymer molecular dynamics on an accurate global potential energy surface: assessing experimental uncertainties

Thermal rate coefficients and kinetic isotope effects have been calculated for an important atmospheric reaction H/D + O 3 → OH/OD + O2 based on an accurate permutation invariant polynomial-neural network potential energy surface, using ring polymer molecular dynamics (RPMD), quasi-classical trajectory (QCT) and variational transition-state theory (VTST) with multidimensional tunneling. The RPMD approach yielded results that are generally in better agreement with experimental rate coefficients than the VTST and QCT ones, especially at low temperatures, attributable to its capacity to capture quantum effects such as tunneling and zero-point energy. Additionally, the theoretical results support one group of existing experiments over the other. In addition, rate coefficients for the D + O 3 → OD + O 2 reaction are also reported using the same methods, which will allow a stringent assessment of future experimental measurements, thus helping to reduce the uncertainty in the recommended rate coefficients of this reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular latent space simulators

Latent space simulators learn kinetic models for atomistic simulations and generate novel trajectories at six orders of magnitude lower cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep learning for characterizing the self-assembly of three-dimensional colloidal systems

Creating a systematic framework to characterize the structural states of colloidal self-assembly systems is crucial for unraveling the fundamental understanding of these systems’ stochastic and non-linear behavior. The most accurate characterization methods create high-dimensional neighborhood graphs that may not provide useful information about structures unless these are well-defined reference crystalline structures. Dimensionality reduction methods are thus required to translate the neighborhood graphs into a low-dimensional space that can be easily interpreted and used to characterize non-reference structures. We investigate a framework for colloidal system state characterization that employs deep learning methods to reduce the dimensionality of neighborhood graphs. The framework next uses agglomerative hierarchical clustering techniques to partition the low-dimensional space and assign physically meaningful classifications to the resulting partitions. In this work, we first demonstrate the proposed colloidal self-assembly state characterization framework on a three-dimensional in silico system of 500 multi-flavored colloids that self-assemble under isothermal conditions. We next investigate the generalizability of the characterization framework by applying the framework to several independent self-assembly trajectories, including a three-dimensional in silico system of 2052 colloidal particles that undergo evaporation-induced self-assembly.

36 MATERIALS SCIENCE↗

Lithium oxidation and electrolyte decomposition at Li-metal/liquid electrolyte interfaces

In this work, we examine the evolution of events occurring when a Li metal surface is in contact with a 2 M solution of a Li salt in a solvent or mixture of solvents, via classical molecular dynamics simulations with a reactive force field allowing bond breaking and bond forming. The main events include Li oxidation and electrolyte reduction along with expansion of the Li surface layers forming a porous phase that is the basis for the formation of the solid-electrolyte interphase (SEI) components. Nucleation of the main SEI components (LiF, Li oxides, and some organics) is characterized. The analysis clearly reveals the details of these physical–chemical events as a function of time, during 20 nanoseconds. The effects of the chemistry of the electrolyte on Li oxidation and dissolution in the liquid electrolyte, and SEI nucleation and structure are identified by testing two salts: LiPF 6 and LiCF 3 SO 3 , and various solvents including ethers and carbonates and mixtures of them. The kinetics and thermodynamics of Li 6 F, the core nuclei in the LiF crystal, are studied by analysis of the MD trajectories, and via density functional theory calculations respectively. The SEI formed in this computational experiment is the “native” film that would form upon contact of the Li foil with the liquid electrolyte. As such, this work is the first in a series of computational experiments that will help elucidate the intricate interphase layer formed during battery cycling using metal anodes.

25 ENERGY STORAGE↗

Dissociative electron attachment to 5-bromo-uracil: non-adiabatic dynamics on complex-valued potential energy surfaces

Electron induced dissociation reactions are relevant to many fields, ranging from prebiotic chemistry to cancer treatments. However, the simulation of dissociation electron attachment (DEA) dynamics is very challenging because the auto-ionization widths of the transient negative ions must be accounted for. We propose an adaptation of the ab initio multiple spawning (AIMS) method for complex-valued potential energy surfaces, along the lines of recent developments based on surface hopping dynamics. Our approach combines models for the energy dependence of the auto-ionization widths, obtained from scattering calculations, with survival probabilities computed for the trajectory basis functions employed in the AIMS dynamics. The method is applied to simulate the DEA dynamics of 5-bromouracil in full dimensionality, i.e., taking all the vibrational modes into consideration. The propagation starts on the $π_{2}^{*}$ resonance state and describes the formation of Br - anions mediated by non-adiabatic couplings. The potential energies, gradients and non-adiabatic couplings were computed with the fractional-occupancy molecular orbital complete-active-space configuration-interaction method, and the calculated DEA cross section are consistent with the observed DEA intensities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Incorporating concentration-dependent sediment microbial activity into methylmercury production kinetics modeling

We report in anoxic environments, anaerobic microorganisms carrying the hgcAB gene cluster can mediate the transformation of inorganic mercury (Hg(II)) to monomethylmercury (MMHg). The kinetics of Hg(II) transformation to MMHg in periphyton from East Fork Poplar Creek (EFPC) in Oak Ridge, TN have previously been modeled using a transient availability model (TAM). The TAM for Hg(II) methylation combines methylation/demethylation kinetics with kinetic expressions for processes that decrease Hg(II) and MMHg availability for methylation and demethylation (multisite sorption of Hg(II) and MMHg, Hg(II) reduction/Hg(0) oxidation). In this study, the TAM is used for the first time to describe MMHg production in sediment. We assessed MMHg production in sediment microcosms using two different sediment types from EFPC: a relatively anoxic, carbon-rich sediment with higher microbial activity (higher CO 2 production from sediment) and a relatively oxic, sandy, carbon-poor sediment with lower microbial activity (lower CO 2 production from sediment). Based on 16s rRNA sequencing, the overall microbial community structure in the two sediments was retained during the incubations. However, the hgcA containing methanogenic Euryarchaeota communities differed between sediment types and their growth followed different trajectories over the course of incubations, potentially contributing to the distinct patterns of MMHg production observed. The general TAM paradigm performed well in describing MMHg production in the sediments. However, the MMHg production and ancillary data suggested the need to revise the model structure to incorporate terms for concentration-dependent microbial activity over the course of the incubations. We modified the TAM to include Monod-type kinetics for methylation and demethylation and observed an improved fit for the carbon-rich, microbially active sediment. Overall our work shows that the TAM can be applied to describe Hg(II) methylation in sediments and that including expressions accounting for concentration-dependent microbial activity can improve the accuracy of the model description of the data in some cases.

54 ENVIRONMENTAL SCIENCES↗

Multichannel photodissociation dynamics in CS 2 studied by ultrafast electron diffraction

In this study, the structural dynamics of photoexcited gas-phase carbon disulfide (CS 2 ) molecules are investigated using ultrafast electron diffraction. The dynamics were triggered by excitation of the optically bright 1 B 2 ( 1 Σ u + ) state by an ultraviolet femtosecond laser pulse centred at 200 nm. In accordance with previous studies, rapid vibrational motion facilitates a combination of internal conversion and intersystem crossing to lower-lying electronic states. Photodissociation via these electronic manifolds results in the production of CS fragments in the electronic ground state and dissociated singlet and triplet sulphur atoms. The structural dynamics are extracted from the experiment using a trajectory-fitting filtering approach, revealing the main characteristics of the singlet and triplet dissociation pathways. Finally, the effect of the time-resolution on the experimental signal is considered and an outlook to future experiments provided.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗