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At least 307 records · Page 17

High-Performance Semiempirical Excited-State Molecular Dynamics Powered by Graphics Processing Units

Here, this Letter introduces excited-state molecular dynamics in PYSEQM, a GPU-accelerated semiempirical quantum chemistry engine implemented in PyTorch. The new module enables Born–Oppenheimer molecular dynamics (BOMD) using configuration-interaction singles and random phase approximation for excited states, allowing long trajectories and large statistical ensembles to be simulated efficiently on a single GPU. We also implement an extended Lagrangian excited-state BOMD (XL-ESMD) scheme that propagates auxiliary electronic variables, enabling relaxed ground and excited-state convergence thresholds without compromising energy conservation. The excited-state BOMD implementation scales smoothly from small chromophores to a nearly 900-atom dendrimer (taking 6.5 s per MD step). PYSEQM also supports batched execution, allowing many geometries or trajectories to be evaluated in a single GPU launch, substantially increasing throughput and making ensemble-based protocols routine. As a demonstration, we compute absorption, emission, and infrared spectra from trajectories propagated on the ground and first excited states. The XL-ESMD scheme yields identical spectra at significantly lower computational cost, establishing the role of extended Lagrangian based dynamics for efficient excited-state BOMD simulations. Beyond raw performance, PYSEQM’s PyTorch foundation provides automatic differentiation for forces, efficient GPU batching, and seamless interfacing with machine learning models. These capabilities position PYSEQM as a practical platform for machine learning-augmented excited-state dynamics and lay the foundation for future data-driven nonadiabatic excited-state dynamics modeling of ultrafast spectroscopic probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model: Modeling Archive

This archive contains the data and Python scripts required to reproduce the analyses and figures in the study: Gomez-Velez, J. D., Rathore, S. S., Cohen, M. J., & Painter, S. L. (2025). Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model. Submitted to Water Resources Research. The analysis utilizes the subgrid model Advection Dispersion Equation with Lagrangian Subgrids (ADELS) implemented in the Advanced Terrestrial Simulator (ATS; https://amanzi.github.io/ats/stable/). In this case, the ATS and Amanzi versions are (1) ATS version 1.5.1_f5ba18f8 and (2) Amanzi version 1.6-dev_53444cca4. The repository includes a Jupyter Notebook and the necessary data (Pandas DataFrames stored as pickle files) to generate the figures for the manuscript. Additionally, it contains Python scripts to create ATS input files, run the ATS simulations, and post-process the results. Finally, it provides routines for parameter estimation using the Single-Station Metabolism (SSM) model with the Differential Evolution Adaptive Metropolis (DREAM) Markov Chain Monte Carlo (MCMC) algorithm with ZS enhancements (DREAM-ZS).

54 ENVIRONMENTAL SCIENCES↗

Balancing moisture and oxygen can match the crystallization dynamics of inert halide perovskite processing

Understanding crystallization in ambient environments is essential for scaling the fabrication of halide perovskite solar cells. Antisolvent-free perovskite deposition offers improved compatibility with high-throughput processing but introduces distinct crystallization dynamics relative to the more ubiquitous use of antisolvents in lab-scale perovskite fabrication. These dynamics are driven by interactions between solutes, solvent and the deposition environment. Using in situ wide-angle X-ray scattering during spin-coating and annealing, we demonstrate how relative humidity (RH) and oxygen, can be tuned to drive polytype evolution during ambient crystallization of formamidinium lead iodide to match that of inert synthesis and achieve comparable film and device quality. In an inert (N 2 ) environment, we find that perovskite films follow a well-established 2H → 3C phase transformation with a short period of coexistence of the 4H and 6H phase during heating. During crystallization in dry air (RH 0%), the added presence of oxygen leads to the dominance of 4H intermediate for an extended duration, establishing a 2H → 4H → 3C pathway. Introducing low humidity (RH 10%) suppresses the 4H phase to a short-lived intermediate above 100 °C, facilitating a more direct transition to the desired 3C phase and almost replicating the crystallization behavior observed under inert conditions. Interestingly, films crystallized under RH 10% show a lower onset temperature for the perovskite 3C phase than under N 2 . At higher humidity (RH 40%), the strong interaction of oxygen and moisture with iodoplumbates appears to stabilize higher order polytypes (4H and 6H). Devices fabricated under RH 10% achieve higher efficiency and enhanced stability compared to those produced under inert atmosphere. These findings provide mechanistic insight into crystallization pathways in different environments and provide a framework to transfer processes from inert to ambient conditions. The results highlight the critical role of controlled humidity in tuning antisolvent-free perovskite crystallization for scalable processing.

Hossain, Maimur [Univ. of California, San Diego, C↗

Near-surface damage and mixing in Si-Cl 2 -Ar atomic layer etching processes: Insights from molecular dynamics simulations

Silicon-chlorine-argon (Si-Cl 2 -Ar) atomic layer etching (ALE) is simulated using classical molecular dynamics (MD). The simulations provide a detailed view into the near-surface region during ALE processing. Bombardment of Ar + ions creates a mixed amorphous region that significantly differs from the picture of ideal ALE. There is also a significant change in the Si etch yield and the etch product distribution as a function of Ar + ion fluence. The Si etch yield is the highest at the beginning of the bombardment step but eventually decays to the physical sputtering yield. Atomic Cl and silicon chlorides are major etch products at the start of an ion bombardment step, but quickly decay. Atomic Si yields remain relatively constant as a function of Ar + ion fluence. As a result, a new schematic of Si-Cl 2 -Ar ALE is presented in order to emphasize the complex behavior observed in MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accurate and efficient predictions of keyhole dynamics in laser materials processing using machine learning-aided simulations

The keyhole phenomenon has been widely observed in laser materials processing, including laser welding, remelting, cladding, drilling, and additive manufacturing. Keyhole-induced defects, primarily pores, dramatically affect the performance of final products, impeding the broad use of these laser-based technologies. The formation of these pores is typically associated with the dynamic behavior of the keyhole. So far, the accurate characterization and prediction of keyhole features, particularly keyhole depth, as a function of time, has been a challenging task. In situ characterization of keyhole dynamic behavior using the synchrotron X-ray technique is informative but complicated and expensive. Current simulations are generally hindered by their poor accuracy and generalization abilities in predicting keyhole depths due to the lack of accurate laser absorptance data. In this study, we develop a machine learning-aided simulation method that accurately predicts keyhole dynamics, especially in keyhole depth fluctuations, over a wide range of processing parameters. In two case studies involving titanium and aluminum alloys, we achieve keyhole depth prediction with a mean absolute percentage error of 10 %, surpassing those simulated using the ray-tracing method with an error margin of 30 %, while also reducing computational time. This exceptional fidelity and efficiency empower our model to serve as a cost-effective alternative to synchrotron experiments. Our machine learning-aided simulation method is affordable and readily deployable for a large variety of materials, opening new doors to eliminate or reduce defects for a wide range of laser materials processing techniques.

Computational fluid dynamics↗

Storage ring nonlinear dynamics optimization with multi-objective multi-generation Gaussian process optimizer

Nonlinear beam dynamics optimization is essential in a low emittance storage ring design. Multi-objective optimization algorithms are needed in order to simultaneously optimize the dynamic aperture and the momentum aperture. In this study we demonstrate the application of a highly efficient stochastic optimization algorithm, the multi-generation Gaussian process optimizer (MG-GPO), to storage ring nonlinear dynamics optimization by successfully applying the method to the SPEAR3 upgrade lattice. It is shown that the new method, owing to its capability of selecting high rank candidates from a large number of trial solutions, converges significantly faster than the commonly used traditional algorithms, multi-objective genetic algorithms (MOGA) and particle swarm optimization (PSO).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

In Situ Chemical Monitoring and Imaging of Contents within Microfluidic Devices Having a Porous Membrane Wall Using Liquid Microjunction Surface Sampling Probe Mass Spectrometry

The ability to observe dynamic chemical processes (e.g., signaling, transport, etc.) in vivo or in situ using nondestructive chemical imaging opens a new door to understanding the complex dynamics of developing biological systems. With the advent of “biology-on-a-chip” devices has come the ability to monitor dynamic chemical processes in a controlled environment, using these engineered habitats to capture key features of natural systems while allowing visual observation of system development. Having the capability to spatially and temporally map the chemical signals within these devices may yield new insights into the forces that drive biosystem development. Here, a porous membrane sealed microfluidic device was designed to allow normal microfluidic operation while enabling continuous, location specific sampling and chemical characterization by liquid microjunction surface sampling probe mass spectrometry (LMJ-SSP MS). LMJ-SSP was used to extract fluids with nL-to-μL/min flow rates directly from selected areas of the microfluidic device without negatively impacting the device function. These extracts were subsequently characterized using MS. This technique was used to acquire MS images of the entirety of several multi-input microfluidic devices having different degrees of fluid mixing. LMJ-SSP MS imaging visualized the spatial distribution of chemical components within the microfluidic channels and could visualize chemical reactions occurring in the device. These microfluidic devices with a porous membrane wall are wholly compatible with the construction of biology-on-a-chip devices. This ultimately would enable correlation of biosystem physical structure with an evolving chemical environment

47 OTHER INSTRUMENTATION↗

MODELLING OF ADDITIVE MANUFACTURING – COMPRESSION MOLDING PROCESS USING COMPUTATIONAL FLUID DYNAMICS

A computational fluid dynamics model has been developed to predict the behavior of a printed strands during a novel material extrusion additive manufacturing and compression molding process. While the traditional additive manufacturing process enables control over the fiber orientation within the part, it would also result in high void content. On the other hand, compression molding produces parts with low porosity levels at rapid processing cycle time but lacks control over the microstructure. The novel additive manufacturing – compression molding (AM-CM) integrating both these processes offers control over both the microstructure and porosity to manufacturing high performance composite parts. The numerical model developed here enables to analyze the effect of processing parameters on the behaviour of printed layer that is subsequently compressed and to determine the optimal printing parameters for high-performance composite part design.

Seta, Berin↗

Application of Peracetic Acid in Poultry Processing: Effects of Treatment Dynamics and Emerging Risk of Resistance Development in Salmonella spp.

Nontyphoidal Salmonella is a leading cause of foodborne illness, with poultry representing a major source. Peracetic acid (PAA), a widely adopted antimicrobial in poultry processing, offers advantages over traditional disinfectants but has sparked interest in its combined use with other antimicrobials and potential resistance. This review evaluates the efficacy of PAA in mitigating Salmonella in combination with other food-grade antimicrobials, explores possible synergism, efficacy under varying treatment parameters, resistance development against PAA, and its role in resistance evolution. While PAA demonstrates broad-spectrum efficacy, its performance varies with environmental parameters; higher temperatures generally enhance antimicrobial action but also accelerate PAA degradation. Organic matter diminishes PAA efficacy by reactive quenching. Variability in concentration and contact time further influences outcomes. Despite its oxidative mode of action and presumed low risk for resistance, emerging studies indicate that Salmonella can develop adaptive tolerance and potential cross/coresistance following repeated or sublethal exposure to PAA. These adaptations may involve genetic upregulation of oxidative stress response pathways, efflux systems, and modifications in cell membrane integrity, raising concerns about the long-term sustainability of PAA use. Additionally, combinatorial treatments (e.g., PAA with UV-C, enzymes, or organic acids) show promise in enhancing efficacy while mitigating resistance risks. Despite recognition of PAA's safety and effectiveness, knowledge gaps remain regarding standardized resistance definitions, serotype-specific tolerance, and optimal intervention strategies in commercial settings. Therefore, there is a need for standardized testing protocols, robust studies on potential resistance, and further exploration of synergistic PAA applications to ensure sustained poultry product safety and public health protection.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗

Structural and Dynamical Insights into the Formation Process of a Cross-Linked Polymer Network in Acrylic Adhesives During Thermal Curing

Many modern adhesives, sealants, and coatings rely on the controlled transition from a liquid to a solid state by forming a three-dimensional cross-linked polymer network, often referred to as curing. The curing process, which is initiated by the mixing of reactive components or an external trigger, defines the structure of a network and further controls the final mechanical properties of cured materials. However, the curing mechanism is not fully understood yet due to the lack of experimental tools capable of directly probing the structure and dynamics of a network over relevant time- and length scales. Here, in this paper, we report the curing process of a commercial two-component methyl methacrylate (MMA) adhesive using in operando X-ray photon correlation spectroscopy (XPCS), a method that closely simulates the target manufacturing environment of the adhesive. The results are then integrated with those obtained by rheology, differential scanning calorimetry (DSC), and transmission electron microscopy to establish the structure–dynamics–process–property relationship. The XPCS results identify four distinct stages in the curing process after the mixing, extrusion, and deposition of the acrylic adhesive: (i) At a cure time (or “aging time”, t age ) of less than 1 min, nanodomains of polymerized MMA are formed within a liquid monomeric MMA matrix. The average size is several nm and remains constant over t age , while the dynamics of the nanodomains are slowed down with t age due to an increase in the viscosity of the MMA matrix. (ii) After t age > 1 min, the size of the nanodomains increases with t age until the gel point (= 6.3 min after mixing as determined by rheology). The dynamics of the nanodomains also increase due to the heat generated by the exothermic reaction. (iii) At the gel point, the nanodomains begin to interconnect each other, resulting in a network structure with a characteristic length of about 100 nm. This characteristic network size does not change for the rest of the curing process up to t age = 500 min. The dynamics of the network structure, however, show a rapid slowing down with t age up to t age ≈ 12 min, corresponding to the onset of vitrification (as determined by rheology). (iv) At t age > 12 min, when the DSC and rheology data can no longer provide meaningful information, the XPCS data show a further slowing down of the network dynamics associated with vitrification. Our results provide rich and complex insights into the physics and material design of thermosets in commercially relevant processes, which are essential for future industrial applications.

36 MATERIALS SCIENCE↗

Hyporheic‐Zone Processes and Stream Oxygen Dynamics: Insights From a Multiscale Reactive Transport Model

Aquatic ecosystem metabolism encapsulates the daily fixation (gross primary production, GPP d ) and mineralization (ecosystem respiration, ER d ) of organic carbon. In fluvial systems, these are commonly estimated by inverse solutions to field observations using a model that describes oxygen concentrations varying in the water column in response to metabolic fluxes and air‐water gas exchange controlled by a rate coefficient (K 600 ). The most common conceptual model is the single‐station metabolism (SSM) model. The simplicity and flexibility of this conceptualization make it attractive; however, it implicitly assumes that all the processes that consume oxygen in fluvial systems can be lumped into a bulk estimate of respiration with poorly understood consequences for estimates of GPP d , ER d , and K 600 . Here, we focus on the implications of using SSM conceptualization when estimating metabolic fluxes from oxygen dynamics in channels where hyporheic exchange occurs. We use a new multiscale numerical model for reactive transport in streams that represents hyporheic exchange and streambed heterotrophic respiration. Nondimensionalization of this model reveals dimensionless groups that collectively control oxygen dynamics. Numerical experiments offer a mechanistic understanding of the impacts of hyporheic exchange on diel oxygen dynamics revealing that potential biases arise from neglecting mass transfer limitations. Specifically, we found that hyporheic exchange significantly affects diel oxygen dynamics, even for nonreactive streambed sediments. Moreover, while the SSM performs well in many situations, we find conditions where significant bias is produced by hyporheic exchange, even when oxygen data are well‐fitted. These situations pose a major challenge in the interpretation of metabolism assessment estimates.

Gomez‐Velez, Jesus D. [Oak Ridge National Laborato↗

Delineating magnetization dynamics in solution-processed doped yttrium iron garnet thin films

Here, in this work, thin films of ruthenium-doped and cerium-doped yttrium iron garnet were deposited on silicon using solgel chemistry. Doped YIG could be produced in phase pure form up to a precursor stoichiometry of Y 3 Ru 0.1 Fe 4.9 O 12 and Ce 0.7 Y 2.3 Fe 5 O 12 . Both dopants significantly increase the coercivity and anisotropy field of the materials either due to domain wall pinning or increased spin–orbit coupling from the dopant. To delineate these two effects, the dynamic magnetic properties were studied using strip line ferromagnetic resonance (FMR). The FMR linewidth was separated into intrinsic loss and inhomogeneous line broadening. Inhomogeneous line broadening was found to dominate the magnetic losses in all the films likely due to magnon scattering off grain boundaries, but the Gilbert damping remained fairly low. By comparing the two dopants, it was found that Gilbert damping increased more in Ce:YIG films than in Ru:YIG films. This finding was corroborated by changes in the anisotropy field of the films, indicating a larger contribution from spin–orbit coupling from cerium than from ruthenium. Surprisingly, while magnetic loss globally increased with higher substitution, adding a small amount of dopant actually reduced the inhomogeneous line broadening in both sets of films. This was corroborated by crystallite size. The damping in Ru:YIG also decreased with a small amount of the dopant, which has been predicted by Kittel for doped garnets. Thus, it follows that there is an ideal doping regime where solgel YIG can be doped at low levels without increasing magnetic loss.

36 MATERIALS SCIENCE↗

Laboratory and field studies of ice-nucleating particles from open-lot livestock facilities in Texas

Abstract. In this work, an abundance of ice-nucleating particles (INPs) from livestock facilities was studied through laboratory measurements from cloud-simulation chamber experiments and field investigation in the Texas Panhandle. Surface materials from two livestock facilities, one in the Texas Panhandle and another from McGregor, Texas, were selected as dust proxies for laboratory analyses. These two samples possessed different chemical and biological properties. A combination of aerosol interaction and dynamics in the atmosphere (AIDA) measurements and offline ice spectrometry was used to assess the immersion freezing mode ice nucleation ability and efficiency of these proxy samples at temperatures above −29 ∘C. A dynamic filter processing chamber was also used to complement the freezing efficiencies of submicron and supermicron particles collected from the AIDA chamber. For the field survey, periodic ambient particle sampling took place at four commercial livestock facilities from July 2017 to July 2019. INP concentrations of collected particles were measured using an offline freezing test system, and the data were acquired for temperatures between −5 and −25 ∘C. Our AIDA laboratory results showed that the freezing spectra of two livestock dust proxies exhibited higher freezing efficiency than previously studied soil dust samples at temperatures below −25 ∘C. Despite their differences in composition, the freezing efficiencies of both proxy livestock dust samples were comparable to each other. Our dynamic filter processing chamber results showed on average approximately 50 % supermicron size dominance in the INPs of both dust proxies. Thus, our laboratory findings suggest the importance of particle size in immersion freezing for these samples and that the size might be a more important factor for immersion freezing of livestock dust than the composition. From a 3-year field survey, we measured a high concentration of ambient INPs of 1171.6 ± 691.6 L−1 (average ± standard error) at −25 ∘C for aerosol particles collected at the downwind edges of livestock facilities. An obvious seasonal variation in INP concentration, peaking in summer, was observed, with the maximum at the same temperature exceeding 10 000 L−1 on 23 July 2018. The observed high INP concentrations suggest that a livestock facility is a substantial source of INPs. The INP concentration values from our field survey showed a strong correlation with measured particulate matter mass concentration, which supports the importance of size in ice nucleation of particles from livestock facilities.

58 GEOSCIENCES↗

Neutron spin echo spectroscopy

Neutron spin echo (NSE) spectroscopy is a powerful technique used to probe the internal dynamics and diffusion processes within matter, allowing researchers to quantify how materials respond to changes in external conditions. To fully understand the bulk properties of a material, it is often crucial to investigate dynamic processes occurring on nanometre length scales and nanosecond timescales. NSE spectroscopy provides an exceptional capability to measure such dynamics across a broad spectrum of condensed matter systems, ranging from proteins and quantum magnets to catalysts. In this Primer, we present an overview of NSE spectroscopy, highlighting the instruments used, methods of data collection and representative applications in both soft-matter and hard-matter sciences.

Czakkel, Orsolya [Institut Max von Laue-Paul Lange↗

Processes controlling helium bubble dynamics at varying temperatures in simulated radioactive materials

Alpha-radiation damage is known to degrade materials exposed to harsh radiation environments via swelling and embrittlement by nano-scale helium bubbles. How these bubbles grow under varying temperature is essential to understanding and predicting material failure and optimization. Using in situ X-ray scattering, we probed ≈1012 bubbles before, during and after annealing at different temperatures in He-implanted aluminum to reveal a critical growth activation temperature that depends strongly on the helium implantation conditions. An analysis of the data aided by our molecular dynamics simulations identifies multiple temperature-dependent bubble growth mechanisms above and below the critical growth activation temperature. Moreover, the irreversible bubble growth that occurs after annealing for ≈4 h was evaluated using dislocation dynamics and found to negligibly affect the yield strength but may affect subsequent bubble growth at temperature. These in situ results provide valuable insight into bubble growth never observed before and reveal, for the first time, bubble shrinkage after cooling.

36 MATERIALS SCIENCE↗