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DOE OSTI2026

From bulk to surface: Structure and dynamics of amorphous alumina from deep potential molecular dynamics

Understanding the atomic-scale structure and dynamics of amorphous oxide surfaces is essential for interpreting their chemical reactivity, mechanical stability, and interfacial behavior, yet direct experimental characterization remains challenging. We employ Deep Potential (DP) molecular dynamics to generate large-scale, ab initio -quality models of amorphous Al 2 O 3 bulk glasses and melt-quenched free surfaces, enabling a quantitative analysis of both structure and relaxation dynamics with statistical confidence inaccessible to direct ab initio simulation. The trained DP model reproduces experimental liquid and glass structure, captures the cooling-rate dependence of the bulk glass transition, and corrects systematic biases in the polyhedral populations predicted by widely used classical force fields. At the free surface, mass density recovers to bulk values over ~10 Å, while local coordination requires a slightly wider subsurface region to fully converge. The outermost layer is oxygen-enriched, exhibits altered polyhedral connectivity with contracted Al–O bonds, and hosts a broad population of under-coordinated motifs (notably AlO 3 and OAl 2 ) whose abundances are governed by glass stability. These under-coordinated surface motifs exhibit distinct vibrational signatures and occur as locally paired Lewis acid and Brønsted base sites consistent with bond-valence compensation, yet remain spatially dispersed rather than aggregating into extended clusters. Despite this pronounced structural heterogeneity, surface relaxation and the glass-transition temperature remain comparable to their bulk counterparts, suggesting that the disordered surface is kinetically stable once formed. Together, these results establish a molecular-level picture of amorphous alumina surfaces and demonstrate the capability of machine-learned potentials to resolve structure–property relationships in disordered oxide interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Universal progression of structure and dynamics in colloidal nanocrystal gels during salt-accelerated aging

Controlling the structure and function of colloidal gels requires a detailed understanding of how the various components govern network formation and aging. In particular, molecular additives like salts are widely used to tune interparticle interactions, yet their influence on gelation pathways in complex systems such as colloidal nanocrystal gels remains inadequately understood. Here, we investigate how noncoordinating salts modulate the evolution of gels formed using chemically linked tin-doped indium oxide nanocrystals. Through combined structural, dynamic, and kinetic analyses, we demonstrate that increasing salt concentration accelerates gelation. When rescaled by salt-dependent characteristic times, the evolution collapses onto universal trajectories, revealing a time-salt superposition principle. The universality extends across length scales, suggesting a consistent salt-dependent mechanism that controls both local structuring and macroscopic network formation. This observed salt modulation of structure and dynamics provides a predictive basis for controlling the kinetics of nonequilibrium nanocrystal gel assembly, enhancing the rational design of functional nanomaterials with tunable properties.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Probing potential energy landscapes via electron-beam-induced single atom dynamics

Structure, bonding, and chemical dynamics of reactions at surfaces and interfaces, and therefore most material properties are intrinsically tied to the energetic landscape in which each atom resides. Here, we demonstrate that a moving atom under electron beam excitation can be used to probe the energy landscape along (confined) step edges, providing information about atomic-scale potentials. In conclusion, the techniques for experimentally exploring atomic potentials holds promise for predictive atom-by-atom fabrication using electron beams.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Photoinduced structural recovery dynamics of rare-earth nickelate thin films

Photoinduced structural dynamics of rare-earth nickelate thin films, NdNiO 3 and SmNiO 3 , grown on (001) oriented SrTiO 3 were studied using time-resolved x-ray diffraction. The evolution of the (002) Bragg peak was tracked following laser excitation. The recovery pathways were found to be strongly dependent on laser fluence for NdNiO 3 and distinct for the two rare-earth nickelates. The recovery of the (002) peak shifts was modeled using a one-dimensional thermal diffusion model which showed that the recovery processes are non-thermal at high fluences. For NdNiO 3 , the timescales for the recovery of the (002) peak shift were found to be closely related to Ni magnetism recovery, potentially indicating magneto-structural coupling. Moreover, the evolution of integrated intensity and full-width-half-maximum points towards the presence of a structural phase separation during recovery. In conclusion, our studies highlight structural recovery pathways in nickelates by comparing the distinct responses of the photoinduced metal-insulator transition in NdNiO 3 and SmNiO 3 .

36 MATERIALS SCIENCE↗

DOE OSTI2020

An in situ shearing x-ray measurement system for exploring structures and dynamics at the solid–liquid interface

Revealing interfacial structure and dynamics has been one of the essential thematic topics in material science and condensed matter physics. Synchrotron-based x-ray scattering techniques can deliver unique and insightful probing of interfacial structures and dynamics, in particular, in reflection geometries with higher surface and interfacial sensitivity than transmission geometries. We demonstrate the design and implementation of an in situ shearing x-ray measurement system, equipped with both inline parallel-plate and cone-and-plate shearing setups and operated at the advanced photon source at Argonne National Laboratory, to investigate the structures and dynamics of end-tethered polymers at the solid-liquid interface. With a precise lifting motor, a micrometer-scale gap can be produced by aligning two surfaces of a rotating upper shaft and a lower sample substrate. A torsional shear flow forms in the gap and applies tangential shear forces on the sample surface. The technical combination with nanoscale rheology and the utilization of in situ x-ray scattering allow us to gain fundamental insights into the complex dynamics in soft interfaces under shearing. In this work, we demonstrate the technical scope and experimental capability of the in situ shearing x-ray system through the measurements of charged polymers at both flat and curved interfaces upon shearing. Furthermore, through the in situ shearing x-ray scattering experiments integrated with theoretical simulations, we aim to develop a detailed understanding of the short-range molecular structure and mesoscale ionic aggregate morphology, as well as ion transport and dynamics in soft interfaces, thereby providing fundamental insight into a long-standing challenge in ionic polymer brushes with a significant technological impact.

36 MATERIALS SCIENCE↗

DOE OSTI2023

RNA structures and dynamics with Å resolution revealed by x-ray free-electron lasers

RNA macromolecules, like proteins, fold to assume shapes that are intimately connected to their broadly recognized biological functions; however, because of their high charge and dynamic nature, RNA structures are far more challenging to determine. We introduce an approach that exploits the high brilliance of x-ray free-electron laser sources to reveal the formation and ready identification of angstrom-scale features in structured and unstructured RNAs. Previously unrecognized structural signatures of RNA secondary and tertiary structures are identified through wide-angle solution scattering experiments. With millisecond time resolution, we observe an RNA fold from a dynamically varying single strand through a base-paired intermediate to assume a triple-helix conformation. While the backbone orchestrates the folding, the final structure is locked in by base stacking. This method may help to rapidly characterize and identify structural elements in nucleic acids in both equilibrium and time-resolved experiments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Multinucleon structure and dynamics via quantum computing

We propose a framework for computing the structure and dynamics for second-quantized many-nucleon Hamiltonians on quantum computers. We develop an oracle-based Hamiltonian input model that computes the many-nucleon states and nonzero Hamiltonian matrix elements of the many-nucleon system. With our Fock-state based input model, we show how to implement the sparse matrix simulation algorithms to calculate the dynamics of the second-quantized many-nucleon Hamiltonian. Based on the dynamics simulation methods, we also present the methodology for structure calculations of the many-nucleon system. In this work, we provide an explicit circuit design of our input model of the second-quantized Hamiltonian within a direct encoding scheme that maps the occupation of each available single-particle state in the many-nucleon state to the state of specific qubit in a quantum register. Here, we analyze our method and provide the asymptotic cost in computing resources for structure and dynamics calculations of many-nucleon systems. For pedagogical purposes, we demonstrate our input model with two model problems in restricted model spaces.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Lattice Dynamics and Structural Phase Transitions in Eu 2 O 3

Using the density functional theory, we study the structural and lattice dynamical properties of europium sesquioxide (Eu 2 O 3 ) in the cubic, trigonal, and monoclinic phases. The obtained lattice parameters and energies of the Raman modes show a good agreement with the available experimental data. The Eu-partial phonon density of states calculated for the cubic structure is compared with the nuclear inelastic scattering data obtained from a 20 nm thick Eu 2 O 3 film deposited on a YSZ substrate. A small shift of the experimental spectrum to higher energies results from a compressive strain induced by the substrate. On the basis of lattice and phonon properties, we analyze the mechanisms of structural transitions between different phases of Eu 2 O 3 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Collaborative Proposal: Improving understanding of the internal structure and dynamics of deep convection using ARM observations and large eddy simulations

Recent observational and large eddy simulation (LES) modeling studies have nearly unanimously supported the view of deep cumulus convection being composed of a series of quasi-spherical bubbles of buoyant air, known as moist thermals. Despite the prevalence of moist thermals in deep convection, a comprehensive theory for the dynamics of these structures is lacking. Most current conceptual models for cumulus convection are based on canonical scaling theories for dry thermals or plumes; however, there is considerable evidence that the behavior of moist thermals differs markedly from these theories. Furthermore, the theoretical basis for most cumulus parameterizations originates from the plume conceptual model, and therefore these parameterizations are inconsistent with the real structure of moist convection. Motivated by the aforementioned knowledge gaps, this “end-to-end” research effort use theory, observations, numerical simulations, and direct improvements to the Zhang-McFarlane (ZM) convection scheme in the global climate Community Atmosphere Model (CAM) to address the following research questions: What key environmental parameters determine whether or not shallow convection will transition into deep convection, in the context of thermal-like updrafts? What factors regulate the size of thermals within cumulus updrafts? How does vertical wind shear influence thermal behavior, and as a consequence, vertical velocity and mass flux profiles and the shallow-to-deep convective transition? What are the critical processes that determine updraft vertical velocities and their connection to the vertical mass flux profile for thermal-like updrafts? Idealized LES modeling will be used in conjunction with theoretical models for the core properties of thermal-like updrafts to better understand key processes that regulate thermal ascent rates and entrainment properties. Thermal-tracking procedures will be used to characterize the behavior of thermals within the LES, and recently developed direct measures of entrainment and detrainment will be used to quantify entrainment/detrainment rates. Building from these results, we will analyze the structure of moist thermals from hemispheric range-height indicator scans taken during the Atmospheric Radiation Measurement Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign, and from “real case” LES of CACTI events. This combined modeling and observational analysis will provide essential validation for the existing body of research on moist thermal dynamics, which is based primarily on modeling studies. With the insight gained from the aforementioned activities, we will modify the Zhang-McFarlane convection scheme to improve its representation of updraft vertical velocity and entrainment rate profiles. These process-level changes will be tested in the Community Atmosphere Model to assess the impact on global climate simulations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Community Fabric: Visualizing communities and structure in dynamic networks

We present Community Fabric, a novel visualization technique for simultaneously visualizing communities and structure within dynamic networks. In dynamic networks, the structure of the network is continuously evolving throughout time and these underlying topological shifts tend to lead to communal changes. Community Fabric helps the viewer more easily interpret and understand the interplay of structural change and community evolution in dynamic graphs. To achieve this, we take a new approach, hybridizing two popular network and community visualizations. Community Fabric combines the likes of the Biofabric static network visualization method with traditional community alluvial flow diagrams to visualize communities in a dynamic network while also displaying the underlying network structure. Our approach improves upon existing state-of-the-art techniques in several key areas. We describe the methodologies of Community Fabric, implement the visualization using modern web-based tools, and apply our approach to three example data sets.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Structure and dynamics of $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquids close to Earth's liquid core conditions

Using an artificial neural-network machine learning interatomic potential, we have performed molecular dynamics simulations to study the structure and dynamics of $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquid close to the Earth's liquid core conditions. Here, the simulation results reveal that the short-range structural order (SRO) in the $\mathrm{Fe_{90}}$$\mathrm{Si_3}$$\mathrm{O_7}$ liquid is very strong. About 80% of the atoms are arranged in crystallinelike SRO motifs. In particular, ~ $70$% of Fe-centered clusters can be classified as either hexagonal-close-packed-like or icosahedrallike SRO motifs. The SRO clusters centered on Fe, Si, or O atoms are strongly intermixed and homogenously distributed throughout the liquid. The atomic structure of the liquid and the fractions of dominant SRO clusters are not sensitive to pressure/temperature used in the simulations except that the SRO of the O-centered clusters is enhanced close to inner core pressures. The O-diffusion coefficient is about two to three times larger than the Fe and Si ions and increases more rapidly in the deeper core regions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Thermodynamics, dynamics, and structure of supercritical water at extreme conditions

Molecular dynamics (MD) simulations to understand the thermodynamic, dynamic, and structural changes in supercritical water across the Frenkel line and the melting line have been performed. The two-phase thermodynamic model [J. Phys. Chem. B(2010), 114(24), 8191-8198] and the velocity autocorrelation functions are used to locate the Frenkel line and to calculate the thermodynamic and dynamic properties. The Frenkel lines obtained from the two-phase thermodynamic model and the velocity autocorrelation criterion do not agree with each other. Structural characteristics and the translational diffusion dynamics of water suggest that this inconsistency could arise from the two oscillatory modes in water, which are associated with the bending of hydrogen bonds and intermolecular collisions inside the first coordination shell. Finally, the overall results lead us to conclude that the universality of the Frenkel line as a dynamic crossover line from rigid to nonrigid fluids is preserved in water.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Explicit solvent machine-learned coarse-grained model of sodium polystyrene sulfonate to capture polymer structure and dynamics

In this article, strongly charged polyelectrolytes (PEs) demonstrate complex solution behavior as a function of chain length, concentrations, and ionic strength. The viscosity behavior is important to understand and is a core quantity for many applications, but aspects remain a challenge. Molecular dynamics simulations using implicit solvent coarse-grained (CG) models successfully reproduce structure, but are often inappropriate for calculating viscosities. To address the need for CG models which reproduce viscoelastic properties of one of the most studied PEs, sodium polystyrene sulfonate (NaPSS), we report our recent efforts in using Bayesian optimization to develop CG models of NaPSS which capture both polymer structure and dynamics in aqueous solutions with explicit solvent. We demonstrate that our explicit solvent CG NaPSS model with the ML-BOP water model [Chan et al. Nat Commun 10, 379 (2019)] quantitatively reproduces NaPSS chain statistics and solution structure. The new explicit solvent CG model is benchmarked against diffusivities from atomistic simulations and experimental specific viscosities for short chains. We also show that our Bayesian-optimized CG model is transferable to larger chain lengths across a range of concentrations. Overall, this work provides a machine-learned model to probe the structural, dynamic, and rheological properties of polyelectrolytes such as NaPSS and aids in the design of novel, strongly charged polymers with tunable structural and viscoelastic properties

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2024

Solvent structure and dynamics over Brønsted acid MWW zeolite nanosheets

In the liquid phase of heterogeneous catalysis, solvent plays an important role and governs the kinetics and thermodynamics of a reaction. Although it is often difficult to quantify the role of the solvent, it becomes particularly challenging when a zeolite is used as the catalyst. This difficulty arises from the complex nature of the liquid/zeolite interface and the different solvation environments around catalytically active sites. Here, we use ab initio molecular dynamics simulations to probe the local solvation structure and dynamics of methanol and water over MWW zeolite nanosheets with varying Brønsted acidity. We find that the zeolite framework and the number and location of the acid sites in the zeolite influence the structure and dynamics of the solvent. In particular, methanol is more likely to be in the vicinity of the aluminum (Al 3+ ) at the T4 site than at T1 due to easy accessibility. The methanol oxygen binds strongly to the Al at the T4 site, weakening the Al–O for the bridging acid site, which results in the formation of the silanol group, significantly reducing the acidity of the site. The behavior of methanol is in direct contrast to that of water, where protons can easily propagate from the zeolite to the solvent molecules regardless of the acid site location. Furthermore, our work provides molecular-level insights into how solvent interacts with zeolite surfaces, leading to an improved understanding of the catalytic site in the MWW zeolite nanosheet.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

All-Atom Simulations Uncover Structural and Dynamical Properties of STING Proteins in the Membrane System

Recent studies have shown that the stimulator of interferon gene (STING) protein plays a central role in the immune system by facilitating the production of type I interferons in cells. The STING signaling pathway is also a prominent activator of cancer-killing T cells that initiate a powerful adaptive immune response. Since biomolecular signaling pathways are complicated and not easily identified through traditional experiments, molecular dynamics (MD) has often been used to study structural and dynamical responses of biological pathways. In this work, we carried out MD simulations for full-length chicken and human STING (chSTING and hSTING) proteins. Specifically, we investigated ligand-bound closed (holo) and ligand-unbound open (apo) forms of STING in the membrane system by comparing their conformational and dynamical differences. Our research provides clues for understanding the mechanism of the STING signaling pathway by uncovering detailed insights for the examined systems: the residues from each chain in the binding pocket are strongly correlated to one another in the open STING structure compared with those in the closed STING structure. Ligand-bound closed STING displays ~174° rotation of the ligand-binding domain (LBD) relative to the open STING structure. The dynamical analysis of residue Cys148 located in the linker region of hSTING does not support the earlier hypothesis that Cys148 can form disulfide bonds between adjacent STING dimers. We also demonstrate that using the full-length proteins is critical, since the MD simulations of the LBD portion alone cannot properly describe the global conformational properties of STING.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

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↗

DOE OSTI2026

Imaging Three-Dimensional Molecular Structure and Dynamics with Multiparticle Covariance and Cumulant Coulomb Explosion Analysis

Coulomb explosion imaging (CEI) provides a direct means of imaging molecular geometry by correlating fragment ion momenta following the fragmentation of a molecular polycation. Here, we demonstrate the use of three-body covariance and four-body cumulant analysis to extract three-dimensional (3D) structural information from the X-ray-induced Coulomb explosion of tert-butyl iodide (C4H9I). Site-selective ionization at the iodine 4d edge with intense femtosecond soft X-ray pulses from an X-ray free-electron laser (XFEL) enables rapid charge buildup and molecular breakup. By correlating ionic fragments in the molecular frame, we isolate complete dissociation channels and reveal subtle structural changes, such as umbrella-type motion of the branched alkyl chain, during the ionization process. Comparison with point-charge simulations of the Coulomb explosion shows close agreement, validating the approach. Furthermore, these results establish covariance/cumulant mapping as a powerful strategy for imaging complex three-dimensional molecular structures and point the way toward time-resolved CEI using both XFEL and tabletop sources for capturing ultrafast structural dynamics.

Imaging↗

DOE OSTI2021

Structure and dynamical properties of two-dimensional dusty plasmas on one-dimensional periodic substrates

In the presence of the substrate, various structural and dynamical properties of two-dimensional dusty plasma (2DDP) were investigated using Langevin dynamical simulations. This paper reviews a series of results of the structural and dynamical properties of 2DDP modified by one-dimensional periodic substrates (1DPSs) as follows. First, when the depth of the 1DPS increases gradually, it is found that the static structural order of 2DDP along each potential well of the 1DPS increases first, and then decreases gradually. When the width of the 1DPS increases gradually, the particle arrangement in each potential well of the 1DPS changes from one straight row gradually to two rows, including the stable zigzag structure. Second, when there are two rows in each potential well of the 1DPS, the phonon spectra are split into two branches, corresponding to the breathing and sloshing modes, respectively. In addition, due to the pure repulsion between dust particles, from the obtained phonon spectra, the sloshing wave propagates backward at small wave numbers. Third, the calculated mean-square displacement (MSD) shown that, at the intermediate timescale between the initial ballistic and final diffusive motions, the particle motion tends to be more subdiffusive while the depth of the 1DPS increases. While the width of the 1DPS increases gradually, the long-time diffusive motion first increases, then decreases, and finally increases again, exhibiting the oscillation-like diffusion, due to the stable zigzag structure. Finally, when an external direct-current driving force is applied on all particles of 2DDP, three different depinning phases are discovered, which are the pinned, disordered plastic flow, and moving ordered states, respectively, as the driving force increases from zero. In addition, the continuous/discontinuous property of the phase transition between these different depinning states is investigated, showing that the transition property is modulated by the depth of the applied 1DPS

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗