Prediction of yield surface of single crystal copper from discrete dislocation dynamics and geometric learning
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Materials Science↗
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Numerical methodology for treating static and dynamic dislocation problems near a free surface
Abstract Simulation of dislocation dynamics enables researchers and scientists to explore the plastic behavior of crystalline materials under loading. Analytic solutions for the stress field due to a linear dislocation segment near a free surface are case-specific, e.g. dealing with either a horizontal segment or a vertical segment, and therefore hard to implement in time-dependent dislocation dynamics simulations as different dislocation segments could be differently oriented. This article presents a generalized numerical framework to find the stress field beneath a free surface due to the presence of a dislocation segment. The framework can be expanded to non-flat surfaces. Also, three-dimensional discrete dislocation dynamics simulations are performed here, which clearly show the effect of free surfaces on the flow stress of a material.
Siddique, Abu Bakar↗
Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape: Modeling Archive
This modeling archive is in support of the Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) publication "Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape", by Murphy et al. (2025). This archive contains model input files and outputs from landscape-scale simulations conducted using ELM, the land model component of the Department of Energy’s Energy Exascale Earth System Model (E3SM), at the Council NGEE Arctic field site (Council Road mile marker 71) on Alaska’s Seward Peninsula. Input data and model output from two sets of ELM simulations are provided. The first set of simulations were conducted with the two default ELM Arctic plant functional types (PFTs; broadleaf deciduous boreal shrub and a C3 grass) and the second set of simulations were conducted with a set of nine Arctic-specific PFTs including nonvascular mosses and lichens, graminoids, forbs, evergreen dwarf shrubs, three height classes of deciduous shrubs (dwarf, low, and low to tall), and deciduous alder shrubs (Sulman et al., 2021). Parameter names and major parameter changes in the Arctic-specific PFT configuration are described in Sulman et al. (2021) and archived in the Sulman et al. (2021) dataset (see below). Simulations were spatially explicit, covering an approximately 6.4X3.3 km domain at the Council site with a spatial resolution of 100 m for a total of 2,112 simulated grid cells under each ELM PFT configuration. The modeling archive contains meteorological forcing (seven *.nc files and one *.txt file), a domain definition file (one *.nc files), land surface configuration files (two *.nc files), parameter files (two *.nc files), annual ELM output files spanning 1980-2014 (68 *.nc files), and a User’s Guide (*pdf file). Additional information on the provided files is in the “Modeling Archive Contents” section of the User’s Guide. Model outputs are aggregated to the column scale (i.e. PFT-specific outputs are not provided here).
Murphy, Bailey [ORNL] (ORCID:0000000203995221)↗
Assessing factors that determine adatom migration and clustering on a thin film oxide; Pt 1 and Rh 1 on the “29” Cu x O/Cu(1 1 1) surface
The dynamical nature of single-site catalysts under non-equilibrium conditions poses significant challenges in the full characterization of their active sites. The “29” oxide is a thin Cu x O film grown on Cu(111) which provides a well-defined surface on which to study the structure and chemistry of atomically dispersed precious metals. A combination of experimental and first-principles approaches is used to investigate the factors that influence the mobility of metal adatoms and their clustering tendencies. Our work elucidates how a homogenous coordination environment of neutral single-atoms can be obtained when its tendency to break oxide bonds within its vicinity is low. Herein we demonstrate that this in turn affects the chemical atomically dispersed species on thin-film oxides, as defects on the oxide would in fact allow such species to be more accessible to CO. We thus highlight the importance of understanding the relationship between defects and atomically dispersed active sites upon designing single-site catalysts.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Effect of graphitic anode surface functionalization on the structure and dynamics of electrolytes at the interface
Surface termination on a graphitic surface and the type of electrolytes in lithium-ion batteries (LIBs) play an important part in determining the structure, composition, and thus, the quality of the emergent solid electrolyte interphase. In this paper, we analyze the structure and dynamics of electrolyte molecules in multi-component electrolyte with varying species compositions combinatorially paired with four different graphitic surfaces terminated with hydrogen, hydroxyl, carbonyl, and carboxyl to explore the interplay between surface chemistry and electrolyte dynamics at electrode/electrolyte interfaces. Addition of dimethyl carbonate and fluoroethylene carbonate brought substantial changes in the ethylene carbonate (EC) and LiPF6 surface population density for hydroxyl and carbonyl surfaces. Strong density oscillation and drastic slowing of the dynamics of the electrolyte molecules at the interface are reported for all the systems. While these observations are universal, carboxyl surfaces have the strongest local and long-range effects. Characterization of the average dipole direction at the interface shows strong orientational preferences of ethylene carbonate molecules. EC molecules are preferred to be oriented either almost parallel or perpendicular to the hydroxyl surface, are tilted between parallel and perpendicular with a higher angle of incidence of the dipole vs surface normal on the carbonyl surface than on the hydroxyl surface, and are oriented perpendicularly against the carboxyl surface. These differences highlight the significant effect of graphite surface termination on the dynamics of the electrolytes and provide insight into the complex interplays between electrolyte species and graphite anode in LIBs.
Rustam, Sabiha (ORCID:0000000224248153)↗
Excited state dynamics of cis,cis-1,3-cyclooctadiene: Non-adiabatic trajectory surface hopping
We have performed trajectory surface hopping dynamics for cis,cis-1,3-cyclooctadiene to investigate the photochemical pathways involved after being excited to the S 1 state. Our calculations reveal ultrafast decay to the ground state, facilitated by conical intersections involving distortions around the double bonds. The main distortions are localized on one double bond, involving twisting and pyramidalization of one of the carbons of that double bond (similar to ethylene), while a limited number of trajectories decay via delocalized (non-local) twisting of both double bonds. The interplay between local and non-local distortions is important in our understanding of photoisomerization in conjugated systems. The calculations show that a broad range of the conical intersection seam space is accessed during the non-adiabatic events. Several products formed on the ground state have also been observed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Achieving Realistic Runoff in the Western United States with a Land Surface Model Forced by Dynamically Downscaled Meteorology
Abstract In this study, we calibrate a regional climate model’s (RCM) underlying land surface model (LSM). In addition to providing a realistic representation of runoff across the hydroclimatically diverse western United States, this is done to take advantage of the RCM’s ability to physically resolve meteorological forcing data in ungauged regions, and to prepare the calibrated hydrologic model for tight coupling, or the ability to represent land surface–atmosphere interactions, with the RCM. Specifically, we use a 9-km resolution meteorological forcing dataset across the western United States, from the fifth generation ECMWF Reanalysis (ERA5) downscaled by the Weather Research Forecasting (WRF) regional climate model, as an offline forcing for Noah-Multiparameterization (Noah-MP). We detail the steps involved in producing an LSM capable of accurately representing runoff, including physical parameterization selection, parameter calibration, and regionalization to ungauged basins. Based on our model evaluation from 1954 to 2021 for 586 basins with daily natural streamflow, the streamflow bias is reduced from 24.2% to 4.4%, and the median daily Nash–Sutcliffe efficiency (NSE) is improved from 0.12 to 0.36. When validating against basins with monthly natural streamflow data, we obtain a similar reduction in bias and a median monthly NSE improvement from 0.18 to 0.56. In this study, we also discover the optimal setup when using a donor-basin method to regionalize parameters to ungauged basins, which can vary by 0.06 NSE for unique designs of this regionalization method. Significance Statement This study provides useful guidance for improving a land surface model to accurately represent runoff across a spatially extensive and hydroclimatically diverse region (the western United States). The land surface model is updated to represent runoff more accurately at gauged basins, and then additionally updated for basins without observational data using a mathematical approach called the donor-basin method. We make use of a regional climate model’s reanalysis-derived meteorological data and its underlying land surface model to achieve realistic runoff. The calibrated land surface model can thus be tightly coupled in subsequent studies in a manner that should more accurately reflect runoff conditions. Findings from this study will serve as a useful reference for the atmospheric (and hydrologic) modeling communities and their ability to represent large-scale hydrology accurately.
Meteorology & Atmospheric Sciences↗
Spontaneous crack healing in calcite reveals the influence of dynamic strain evolution and surface chemistry
The mechanics of fracture healing in calcite remain poorly constrained yet are fundamental to managing fluid transport in geothermal reservoirs and hydrocarbon systems. Here, we apply microfocused synchrotron Laue X-ray diffraction and infrared spectroscopy to investigate subcritical crack healing in a 1 mm-thick calcite crystal subjected to controlled loading in a double-torsion device. Over a 44-hour period following load removal, we map the evolution of residual strain fields surrounding the crack tip and observe a progressive increase in compressive strain perpendicular to the crack plane accompanied by infrared spectroscopic signatures that reveal enhanced accumulation of water at the healed interface. The correlation between strain evolution and surface chemistry suggests that spontaneous crack healing in calcite is driven by dynamic anelastic relaxation coupled with irreversible fluid-mineral interactions. These findings offer insight into time-dependent crack closure processes in carbonates and highlight the role of chemically-mediated plasticity in subsurface fracture evolution.
materials science↗
Distinguishing Bulk and Surface Recombination By Measuring and Modeling Ultrafast Carrier Dynamics
Distinguishing Bulk and Surface Recombination By Measuring and Modeling Ultrafast Carrier Dynamics The combination of modeling with TRTS and TRPL under multiple excitation conditions improves accuracy and precision of parameter estimation. Ultrafast carrier dynamics can link materials, processing, and device performance to direct the design of more efficient solar cells.
14 SOLAR ENERGY↗
Description and Demonstration of the Coupled Community Earth System Model v2 – Community Ice Sheet Model v2 (CESM2‐CISM2)
Abstract Earth system/ice‐sheet coupling is an area of recent, major Earth System Model (ESM) development. This work occurs at the intersection of glaciology and climate science and is motivated by a need for robust projections of sea‐level rise. The Community Ice Sheet Model version 2 (CISM2) is the newest component model of the Community Earth System Model version 2 (CESM2). This study describes the coupling and novel capabilities of the model, including: (1) an advanced energy‐balance‐based surface mass balance calculation in the land component with downscaling via elevation classes; (2) a closed freshwater budget from ice sheet to the ocean from surface runoff, basal melting, and ice discharge; (3) dynamic land surface types; and (4) dynamic atmospheric topography. The Earth system/ice‐sheet coupling is demonstrated in a simulation with an evolving Greenland Ice Sheet (GrIS) under an idealized high CO 2 scenario. The model simulates a large expansion of ablation areas (where surface ablation exceeds snow accumulation) and a large increase in surface runoff. This results in an elevated freshwater flux to the ocean, as well as thinning of the ice sheet and area retreat. These GrIS changes result in reduced Greenland surface albedo, changes in the sign and magnitude of sensible and latent heat fluxes, and modified surface roughness and overall ice sheet topography. Representation of these couplings between climate and ice sheets is key for the simulation of ice and climate interactions.
Muntjewerf, Laura↗
Operando characterization and regulation of metal dissolution and redeposition dynamics near battery electrode surface
Mn dissolution has been a longstanding, ubiquitous issue that negatively impacts the performance of Mn-based battery materials. Mn dissolution involves complex chemical and structural transformations at the electrode-electrolyte interface. The continuously evolving electrodeelectrolyte interface has posed great challenges for characterizing the dynamic interfacial process and quantitatively establishing the correlation with battery performance. In this study, we visualize and quantify the temporally and spatially resolved Mn dissolution/redeposition (D/R) dynamics of electrochemically operating Mn-containing cathodes. The particle-level and electrode-level analyses reveal that the D/R dynamics is associated with distinct interfacial degradation mechanisms at different states of charge. Our results statistically differentiate the contributions of surface reconstruction and Jahn-Teller distortion to the Mn dissolution at different operating voltages. Introducing sulfonated polymers (Nafion) into composite electrodes can modulate the D/R dynamics through trapping the dissolved Mn species and rapidly establishing the local Mn D/R equilibrium. This work represents an inaugural effort to pinpoint the chemical and structural transformations responsible for Mn dissolution via an operando synchrotron study and develops an effective method to regulate Mn interfacial dynamics for improving battery performance.
25 ENERGY STORAGE↗
Effect of Solvents on Lignin–Surface Interactions via Molecular Dynamics Simulations
Lignin, an essential building block of lignocellulosic biomass, is a potential abundant source of aromatic monomers for the polymer and chemical industry. Reductive catalytic fractionation (RCF) is one promising process that can produce high yields of phenolic monomers and oligomers from lignin under different catalytic conditions. An important choice in optimizing RCF is the selection of solvent; however, detailed insights into solvent effects on lignin behaviors and interactions remain limited. Here, in this work, we perform all-atom molecular dynamics simulations to study the solvation of lignin, solvent-mediated conformational changes, and the interaction of solvated lignin oligomers with model surfaces. We focus on the behavior of an oligomeric lignin model compound in methanol, ethanol, a binary mixture of ethanol and water, and water at both the RCF reaction temperature (473 K) and room temperature. Analysis of structural features of lignin suggests that these three organic solvent systems favorably solvate lignin, resulting in a more extended conformation suitable for catalytic conversion to valuable chemicals. We further introduce model palladium (Pd) and carbon (C) surfaces to understand how solvent choice impacts adsorption onto a representative catalytic surface and support, and to quantify the competition among the reactant and solvent molecules for the surface. Unbiased simulations suggest strong adsorption of lignin on both Pd and C surfaces at 473 K, with notable solvent-mediated differences in adsorption energies. Additionally, our findings indicate that lignin adsorption is promoted by the entropy change resulting from the displacement of solvent molecules from the surface. This study provides a molecular perspective of adsorption of lignin onto varying surfaces, which is a step towards understanding and optimizing the catalytic conversion of lignin into valuable chemicals.
adsorption↗
Mixed quantum–classical approach to model non-adiabatic electron–nuclear dynamics: Detailed balance and improved surface hopping method
We develop a density matrix formalism to describe coupled electron–nuclear dynamics. To this end, we introduce an effective Hamiltonian formalism that describes electronic transitions and small (quantum) nuclear fluctuations along a classical trajectory of the nuclei. Using this Hamiltonian, we derive equations of motion for the electronic occupation numbers and for the nuclear coordinates and momenta. We show that, in the limit, when the number of nuclear degrees of freedom coupled to a given electronic transition is sufficiently high (i.e., the strong decoherence limit), the equations of motion for the electronic occupation numbers become Markovian. Furthermore, the transition rates in these (rate) equations are asymmetric with respect to the lower-to-higher energy transitions and vice versa. In thermal equilibrium, such asymmetry corresponds to the detailed balance condition. We also study the equations for the electronic occupations in the non-Markovian regime and develop a surface hopping algorithm based on our formalism. To treat the decoherence effects, we introduce additional “virtual” nuclear wave packets whose interference with the “real” (physical) wave packets leads to the reduction in coupling between the electronic states (i.e., decoherence) as well as to the phase shifts that improve the accuracy of the numerical approach. Remarkably, the same phase shifts lead to the detailed balance condition in the strong decoherence limit.
74 ATOMIC AND MOLECULAR PHYSICS↗
Equation of state for He bubbles in W and model of He bubble growth and bursting near W{100} surfaces derived from molecular dynamics simulations
Abstract Molecular dynamics (MD) simulations are performed to derive an equation of state (EOS) for helium (He) bubbles in tungsten (W) and to study the growth of He bubbles under a W(100) surface until they burst. We study the growth as a function of the initial nucleation depth of the bubbles. During growth, successive loop-punching events are observed, accompanied by shifts in the depth of the bubble towards the surface. Subsequently, the MD data are used to derive models that describe the conditions that cause the loop punching and bursting events. Simulations have been performed at 500, 933, 1500, 2000, and 2500 K to fit the parameters in the models. To compute the pressure in the bubble at the loop punching and bursting events from the models, we derive an EOS for He bubbles in tungsten with an accompanying volume model to compute the bubble volume for a given number of vacancies ( $$N_\text {V}$$ N V ), He atoms ( $$N_\text {He}$$ N He ), and temperature ( T ). To derive the bubble EOS, we firstly derive the EOS for a free He gas. The derived free-gas EOS can accurately predict all MD data included in the analysis (which span up to 54 GPa at 2500 K). Subsequently, the bubble EOS is derived based on the free-gas EOS by correcting the gas density to account for the interaction between He and W atoms. The EOS for the bubbles is fitted to data from MD simulations of He bubbles in bulk W that span a wide range of gas density and sizes up to about 3 nm in diameter. The pressure of subsurface bubbles at the loop punching events as calculated using the bubble-EOS and the volume model agrees well with the pressure obtained directly from the MD simulations. In the loop punching model, for bubbles consisting of $$N_\text {V}$$ N V vacancies and $$N_\text {He}$$ N He helium atoms, the $$N_\text {He}/N_\text {V}$$ N He / N V ratio that causes the event, the resulting increase in $$N_\text {V}$$ N V , and the associated shift of the bubble depth are formulated as a function of $$N_\text {V}$$ N V and T . In the bursting model, a bubble must simultaneously reach a certain depth and $$N_\text {He}/N_\text {V}$$ N He / N V ratio in order to burst. The burst depth and $$N_\text {He}/N_\text {V}$$ N He / N V are also modeled as a function of $$N_\text {V}$$ N V and T . The majority of the loop punching events occur at bubble pressures between 20 and 60 GPa, depending on the bubble size and temperature. The larger the bubble and the higher the temperature, the lower the bubble pressure. Furthermore, our results indicate that at a higher temperature, a bubble can burst from a deeper region.
36 MATERIALS SCIENCE↗
Revealing subterahertz atomic vibrations in quantum paraelectrics by surface-sensitive spintronic terahertz spectroscopy
Understanding surface collective dynamics in quantum materials is crucial for advancing quantum technologies. For example, surface phonon modes in quantum paraelectrics are thought to be essential in facilitating interfacial superconductivity. However, detecting these modes, especially below 1 terahertz, is challenging because of limited sampling volumes and the need for high spectroscopic resolution. Here, we report surface soft transverse optical (TO1) phonon dynamics in KTaO 3 and SrTiO 3 by surface-sensitive spintronic terahertz spectroscopy that can sense the collective modes only a few nanometers deep from the surface. In KTaO 3 , the TO1 mode softens and sharpens with decreasing temperature, leveling off at 0.7 terahertz. In contrast, this mode in SrTiO 3 broadens substantially below the quantum paraelectric crossover and coincides with the hardening of a sub–milli–electron volt phonon mode related to the antiferrodistortive transition. These observations that deviate from their bulk properties may have implications for interfacial superconductivity and ferroelectricity. The developed technique opens opportunities for sensing low-energy surface collective excitations.
Chu, Zhaodong↗
Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study
A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.
59 BASIC BIOLOGICAL SCIENCES↗
Catalytic resonance theory for the kinetics of photon-promoted catalysis
The illumination of catalytic surfaces with a continuous or pulsed stream of photons dynamically modulates surface chemistry for faster rates, non-equilibrium conversion, or product selectivity control. To establish fundamental principles of dynamic photon-modulated catalysis, the photocatalytic conversion of a generic surface reaction was simulated using the kinetic Monte Carlo method to understand the kinetic implications of an independent stream of photons that promotes surface product desorption. The time-averaged photocatalytic rate at differential conditions for varying photon flux and temperatures indicated three kinetic regimes described by product thermal desorption control, surface reaction control, and an intermediate kinetic regime with a zero slope Arrhenius plot, consistent with a degree of rate control dominated by the photon arrival frequency (i.e., per-site photon flux). Here, the maximum photocatalytic rate occurred orders of magnitude above the Sabatier limit at the resonance frequency, identified as the photon arrival frequency matching the surface reaction rate constant.
Canavan, Jesse R. [University of Minnesota, Minnea↗
Hydrogen irradiation-driven computational surface chemistry of lithium oxide and hydroxide
We have investigated, using molecular dynamics, the surface chemistry of hydrogen incident on the amorphous and crystalline lithium oxide and lithium hydroxide surfaces upon being slowed down by a collision cascade and retained in the amorphous surface of either Li 2 O or LiOH. We looked for the bonding of H to the resident structures in the surface to understand a possible chain of chemical reactions that can lead to surface transformation upon H atom impact. Our findings, using Density-Functional Theory (DFT) trained ReaxFF force field/electronegativity equalization method potentials, stress the importance of inclusion of polarization in the dynamics of a Li–O–H system, which is also illustrated by DFT energy minimization and quantum–classical molecular dynamics using tight binding DFT. The resulting polar-covalent chemistry of the studied systems is complex and very sensitive to the instantaneous positions of all atoms as well as the ratio of concentrations of various resident atoms in the surface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗