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DOE OSTI2024

BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules

A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Variational deep learning of equilibrium transition path ensembles

Here, we present a time-dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off of the variational path sampling methodology by approximating the time-dependent commitment probability within a neural network ansatz. The reaction mechanisms inferred through this approach are elucidated by a novel decomposition of the rate in terms of the components of a stochastic path action conditioned on a transition. This decomposition affords an ability to resolve the typical contribution of each reactive mode and their couplings to the rare event. The associated rate evaluation is variational and systematically improvable through the development of a cumulant expansion. We demonstrate this method in both over- and under-damped stochastic equations of motion, in low-dimensional model systems, and in the isomerization of a solvated alanine dipeptide. In all examples, we find that we can obtain quantitatively accurate estimates of the rates of the reactive events with minimal trajectory statistics and gain unique insights into transitions through the analysis of their commitment probability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Emergent facilitation and glassy dynamics in supercooled liquids

In supercooled liquids, dynamical facilitation refers to a phenomenon where microscopic motion begets further motion nearby, resulting in spatially heterogeneous dynamics. This is central to the glassy relaxation dynamics of such liquids, which show super-Arrhenius growth of relaxation timescales with decreasing temperature. Despite the importance of dynamical facilitation, there is no theoretical understanding of how facilitation emerges and impacts relaxation dynamics. Here, we present a theory that explains the microscopic origins of dynamical facilitation. We show that dynamics proceeds by localized bond-exchange events, also known as excitations, resulting in the accumulation of elastic stresses with which new excitations can interact. At low temperatures, these elastic interactions dominate and facilitate the creation of new excitations near prior excitations. Using the theory of linear elasticity and Markov processes, we simulate a model, which reproduces multiple aspects of glassy dynamics observed in experiments and molecular simulations, including the stretched exponential decay of relaxation functions, the super-Arrhenius behavior of relaxation timescales as well as their two-dimensional finite-size effects. The model also predicts the subdiffusive behavior of the mean squared displacement (MSD) on short, intermediate timescales. Furthermore, we derive the phonon contributions to diffusion and relaxation, which when combined with the excitation contributions produce the two-step relaxation processes, and the ballistic–subdiffusive–diffusive crossover MSD behaviors commonly found in supercooled liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Validation of Fault Displacements from Dynamic Rupture Simulations against the Observations from the 1992 Landers Earthquake

ABSTRACT Coseismic fault displacements in large earthquakes have caused significant damage to structures and lifelines on and near fault lines. Coseismic displacements represent a real threat, especially to distributed infrastructure systems. For infrastructure systems that can not avoid active faults, engineering displacement demands are defined using probabilistic fault-displacement hazard analyses (PFDHA). However, PFDHA models are sparse and poorly constrained partly due to the scarcity of detailed fault-displacement observations. Advancements in dynamic rupture simulation methods make them an attractive approach to address this important issue. Because fault displacements can be simulated for various geologic conditions as constrained by current knowledge about earthquake processes, they can be used to supplement the observation datasets. In addition to providing on-fault displacements, when used with appropriate constitutive models for the bulk medium, they can capture off-fault distributed inelastic deformations as well. For viable extrapolation, simulations must first be validated against data. In this article, we summarize the calibration and validation of the dynamic rupture model against the observations of the well-documented 1992 Landers earthquake. We defined a preferred model that reproduces several first-order fault-displacement metrics such as the on-fault partition of the total displacement, the mean fault-zone width, and the location of the peak displacement. Simulated ground motions consistent with the observations ensure that all physics important to modeling have been properly parameterized. For the extrapolation, we generated a suite of dynamic rupture models to quantify expected fault-displacement metrics, their intercorrelations, and magnitude dependencies, which are in part supported by the Landers and other recent earthquakes. Our validation and extrapolation exercise paves the way for using dynamic rupture modeling to quantitatively address fault-displacement hazard on a broader scale. The results are promising and are expected to be useful to inform PFDHA model development.

Geochemistry & Geophysics↗

DOE OSTI2025

Extending TOUGH + HYDRATE with a parallel particle transport simulator: numerical investigation of sand production during gas production from hydrate deposits

A new parallel code for simulating particle transport in porous media is integrated with the TOUGH + HYDRATE simulator to investigate sand production associated with gas production from unconsolidated gas hydrate-bearing sediments (HBS). Here, the parallel coupled simulator is named THMPT and uses the integral finite difference method to describe the Darcian and non-Darcian flow of fluids and heat transport, the finite element method to describe the associated geomechanical changes, and the discrete element method to track the trajectory of individual sand particles within the HBS. The THMPT simulator is written in Fortran, incorporates multiple optimized algorithms, and can comprehensively address the coupled flow, thermal, chemical, geomechanical, and particle transport processes that characterize the system behaviors during gas production from HBS. The simulator can capture all processes involved in sand particle transport in porous media, including sand detachment, collision, clogging (i.e., bridging), and migration. A benchmark case study of sand production in the course of depressurization-induced gas production from a representative HBS reveals various distinct microscopic particle migration mechanisms and the adverse impact of sand particle detachment, transport, and clogging. The numerical investigation also examines the effect of bottomhole pressure on mitigating sand production. The simulation results indicate that sand clogging near the wellbore significantly reduces permeability, decreasing gas production by at least 50%. Lastly, the efficiency of gravel packing in mitigating sand production is numerically evaluated, revealing that the structure of the porous media appears to profoundly influence the macroscopic motion behavior of sand particles and sand clogging characteristics.

discrete element method↗

DOE OSTI2020

Uncovering the Functional Role of Coherent Phonons during the Photoinduced Phase Transition in a Molecular Crystal

The atomic motions that make up phonons and molecular vibrations in molecular crystals influence their photophysical and electronic properties, including polaron formation, carrier mobility, and phase transitions. Discriminating between spectator and driving motions is a significant challenge hindering optimization. Unlocking this information and developing fine-tuned controls over actively participating phonon modes would not only lead to a stronger understanding of photochemistry but also provide a significant new tool in controlling solid state chemistry. We present a strategy using rationally designed double pulses to unveil the unique function of specific excited state phonon modes. Using ultrafast spectroscopy, we identified 50 and 90 cm –1 phonons involved in modulating the photoinduced spin-Peierls melting of potassium tetracyanoquinodimethane crystals. Here, we show that the 50 cm –1 phonon specifically corresponds to the coherent nuclear wavepacket involved in the charge transfer component of the overall spin-Peierls phase melting process, while the 90 cm –1 phonon facilitates the phase transition component.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2025

Probabilistic flux limiters

The stable numerical integration of shocks in compressible flow simulations relies on the reduction or elimination of Gibbs phenomena (unstable, spurious oscillations). A popular method to virtually eliminate Gibbs oscillations caused by numerical discretization in under-resolved simulations is to use a flux limiter. A wide range of flux limiters have been studied in the literature, with recent interest in their optimization via machine learning methods trained on high-resolution datasets. The common use of flux limiters in numerical codes as plug-and-play blackbox components makes them key targets for design improvement. Even for deterministic dynamical models, numerical uncertainty is introduced via coarse-graining required by insufficient computational power to solve all scales of motion. Conventional flux limiters are deterministic and lack the capacity to address uncertainties, both aleatoric (inherent randomness) and epistemic (modeling uncertainty due to limited knowledge), which arise in coarse-grained numerical simulations. Here, we introduce a conceptually distinct type of flux limiter that is designed to handle the effects of randomness in the model and uncertainty in model parameters. Unlike traditional single-function flux limiters, these new probabilistic flux limiters incorporate multiple flux limiting functions, each applied with a learned probability drawn from high-resolution data to mitigate the effects of uncertainty in numerical simulations. This approach departs from traditional single-function limiters by explicitly modeling and incorporating uncertainty into the shock capturing process. Using the example of Burgers' equation as a testbed, we show that a machine learned, probabilistic flux limiter may be used in a shock capturing code to more accurately capture shock profiles. In particular, we show that our probabilistic flux limiter outperforms standard limiters and can be successively improved upon (up to a point) by expanding the set of probabilistically chosen flux limiting functions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Fluid Flow Observations of The Spray Near-Field Using High-Speed X-Ray Imaging

Sprays are important to may industrial processes, but the near-field region where spray formation takes place is difficult to visualize and characterize through visible light imaging because this region is typically optically dense. X-ray imaging is one technique that can penetrate this optically dense region and provide unique observations of the spray formation process. This study uses high-speed white beam X-ray imaging conducted at the Advanced Photon Source to capture spray formation dynamics from a canonical airblast atomizer. In this work, a range of momentum flux ratios are visualized by varying the gas flow rate while the liquid flow rate is held constant. The use of X-rays show overlapping flow structures including bags, ligaments, mushrooms, and webs. Air bubbles are captured within the liquid regions, and a very dynamic crown forms at the liquid needle exit at higher momentum flux ratios. Finally, at the highest momentum flux ratios, air bubbles and liquid droplets are observed migrating upstream in the center of the crown, and this motion is attributed to a toroidal recirculation cell at the nozzle exit.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Reinforcement Learning-Guided Long-Timescale Simulation of Hydrogen Transport in Metals

Diffusion in alloys is an important class of atomic processes. However, atomistic simulations of diffusion in chemically complex solids are confronted with the timescale problem: the accessible simulation time is usually far shorter than that of experimental interest. In this work, long-timescale simulation methods are developed using reinforcement learning (RL) that extends simulation capability to match the duration of experimental interest. Two special limits, RL transition kinetics simulator (TKS) and RL low-energy states sampler (LSS), are implemented and explained in detail, while the meaning of general RL are also discussed. As a testbed, hydrogen diffusivity is computed using RL TKS in pure metals and a medium entropy alloy, CrCoNi, and compared with experiments. The algorithm can produce counter-intuitive hydrogen-vacancy cooperative motion. We also demonstrate that RL LSS can accelerate the sampling of low-energy configurations compared to the Metropolis–Hastings algorithm, using hydrogen migration to copper (111) surface as an example.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Satellites, core hole excitations, and spin-resolved electronic structure in the spectroscopy of half-metallic CrO 2

Photoelectron satellites—the structures appearing on the low kinetic or high binding-energy side of the “main” or “elastic” photopeak—betray the complex many-body interactions set in motion by the sudden creation of the core hole. In this work, we demonstrate, using the technologically important ferromagnetic half-metal CrO 2 , how such satellites can manifest themselves in other core-level spectroscopies of the material and how they can reveal important details pertinent to its electronic structure. Specifically, we identify a fluorescence satellite in the Cr 𝐿 3 resonant x-ray-emission spectra that radiates at a constant emission energy across the Cr 𝐿 3 x-ray edge with energy ≈1.3 eV above the ordinary valence fluorescence. Here, we provide evidence that this feature arises from the valence recombination of the Cr 2⁢𝑝 core hole “dressed” by the same shakeup charge-transfer process present in both the Cr x-ray photoelectron and the Cr x-ray absorption spectra with its energy uniquely measuring the exchange splitting of the Cr 3⁢𝑑 level. Further analysis of the x-ray emission data reveals three additional features that radiate at constant loss energy that are attributed to combinations of Cr 3⁢𝑑⁢(𝑡 2⁢𝑔 ) → Cr 3⁢𝑑⁢(𝑡 2⁢𝑔 ), charge-transfer O 2⁢𝑝→Cr 3⁢𝑑, and crystal-field Cr⁢ 3⁢𝑑⁡(𝑡 2⁢𝑔 )→Cr⁢ 3⁢𝑑⁡(𝑒 𝑔 ) excitations. These assignments and their energies are supported by density-functional theory calculations, the accuracy of which we demonstrate by hard x-ray valence-photoemission measurements. Atomic multiplet calculations, which include crystal-field effects, help interpret x-ray photoelectron and x-ray absorption spectra of the covalently mixed Cr ion. Resonant Cr K-𝐿 2,3 ⁢𝐿 2,3 Auger-electron emission spectra support a ligand-to-metal nature of the charge-transfer process while highlighting the charge sensitivity differences between photon-in/electron-out and photon-in/photon-out spectroscopies.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Longitudinal double helicity asymmetry $A_{LL}$ from direct photon, jet and charged pion production in polarized $\vec{p}+\vec{p}$ collisions

Understanding the proton spin composition from the quarks and gluons spin polarization and their motion is important to test various kinds of sum rules and nonperturbative properties of hadrons. At the Relativistic Heavy Ion Collider (RHIC), we collide longitudinally polarized proton beams and measure the double helicity asymmetry A_{LL} A L L , which is an important physical quantity for extracting the polarized parton distribution functions (PDFs) of the proton. Direct photon, jet and charged pion production are good channels to probe the gluon spin polarization inside the proton, with the ability to probe also the sign of the gluon spin. Direct photon production is the theoretically ``cleanest’’ channel, with little fragmentation contribution, but limited by statistics. On the other hand, jet and charged pion production have more statistics, but include more hard processes and hadronization effects. I will present the recent measurements of direct photon, jet and charged pion A_{LL} A L L s at PHENIX and show their complementary roles in extracting the gluon spin.

Ji, Zhongling↗

DOE OSTI2023

Determination of single crystal thermal expansion in Uranium-6wt%Niobium shape memory alloy using in-situ diffraction and modeling of textured polycrystalline samples

In-situ neutron diffraction and ex-situ dilatometry experiments were performed on a chemically banded, quenched uranium-6wt% niobium shape memory alloy to study the impact of deformation-(detwinning-) induced texture on the evolution of thermally induced strains (and associated stresses). Thermal heating and cooling cycles between 5K and 473K were performed in-situ with neutron diffraction, and the lattice strain evolution is reported for the observed monoclinic α" phase. Comparisons between the measured diffraction strains and macroscopic dilatometry experiments reveal relationships between micro- and macro-level thermal expansion. Softening of the texture during heating suggests that twin boundary motion can accommodate the large internal thermal strains which are approximately 2% greater than that typically observed during the 175K heating interval used to age more randomly oriented polycrystalline material. Assuming weak constraint of neighboring grains in randomly textured polycrystals, the single crystal thermal expansion tensor is extracted from measurements of lattice strains over the range 5K to 473K. Predictions of polycrystalline thermal expansion, based upon this single crystal thermal expansion tensor, are shown to compare favorably with bulk thermal expansion observations of the as quenched microstructure. However, such a lower-bound estimate is insufficient to explain all aspects of the behavior of the textured material, where the matrix is not isotropic. In conclusion, it is hypothesized that relaxation processes which occur within the quenched microstructure during heating are responsible for the distinct thermal expansion behavior observed during the initial heating cycle compared to cooling and subsequent cycling.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Control-Affine Schrödinger Bridge and Generalized Bohm Potential

From a stochastic control perspective, the Schrödinger bridge is a density-valued continuous curve parameterized by time that connects a given pair of initial and terminal probability densities via minimum effort controlled Brownian motion. The control-affine Schrödinger bridge extends this idea to a generic control-affine Itô diffusion, possibly with an additive state cost. Here, in this letter, we recast the necessary conditions of optimality for the control-affine Schrödinger bridge problem as a two point boundary value problem for a quantum mechanical Schrödinger PDE with complex potential. This complex-valued potential is a generalization of the real-valued Bohm potential in quantum mechanics. Our derived potential is akin to the optical potential in nuclear physics where the real part of the potential encodes elastic scattering (transmission of wave function), and the imaginary part encodes inelastic scattering (absorption of wave function). The key takeaway is that the process noise that drives the evolution of probability densities induces an absorbing medium in the evolution of wave function. These results make new connections between control theory and non-equilibrium statistical mechanics through the lens of quantum mechanics.

Markov processes↗

DOE OSTI2022

Random Walks and Sticky Surfaces: Single-Molecule Measurements of Solute Diffusion in Ethanol/Water-Filled Anodic Alumina Nanopores

Nanoporous anodic aluminum oxide (AAO) membranes are now being explored for use in advanced chemical separations, including in the dehydration of biofuels such as ethanol. Optimization of membrane performance requires an in-depth understanding of how solvent mixtures and solutes behave under nanoconfinement. In this work, the diffusion of rhodamine B (RhB) dye through 10 nm and 20 nm AAO nanopores filled with a series of ethanol/water mixtures (0 - 33% water) is explored by fluorescence correlation spectroscopy (FCS). RhB was found to diffuse through the pores by two distinct mechanisms with mean diffusion coefficients, $D_f$ and $D_s$, reflecting fast and slow diffusive motions, respectively, with values that differ by nearly two orders of magnitude. Further, both $D_f$ and $D_s$ increased with pore size and were significantly smaller than $D_b$, the RhB diffusion coefficient in bulk liquid. Mean $D_f$ values follow a composition-dependent trend that closely mimics the viscosity dependence of $D_b$. Additional slowing of fast RhB diffusion is attributed to both hydrodynamic drag and electrostatic interactions with the nanopore surface. The mean $D_s$ values exhibit a different trend with increasing water content, revealing an increase in $D_s$ and a decrease in the contributions of slow diffusion to the observed dynamics. The fluorescence time transient data used in the analysis show that the slow diffusion process is strongly hindered and likely involves frequent adsorption of RhB to the pore surfaces. These results provide new insights into the detailed molecular-level mechanisms of mass transport in nanoporous AAO membranes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Unconventional solitonic high-temperature superfluorescence from perovskites

Fast thermal dephasing limits macroscopic quantum phenomena to cryogenic conditions and hinders their use at ambient temperatures. For electronic excitations in condensed media, dephasing is mediated by thermal lattice motion. Therefore, taming the lattice influence is essential for creating collective electronic quantum states at high temperatures. Although there are occasional reports of high-T c quantum effects across different platforms, it is unclear which lattice characteristics and electron–lattice interactions lead to macroscopically coherent electronic states in solids. Here we studied intensity fluctuations in the macroscopic polarization during the emergence of superfluorescence in a lead halide perovskite and showed that spontaneously synchronized polaronic lattice oscillations accompany collective electronic dipole emission. We further developed an effective field model and theoretically confirmed that exciton–lattice interactions lead to a new electronically and structurally entangled coherent extended solitonic state beyond a critical polaron density. The analysis shows a phase transition with two processes happening in tandem: incoherent disordered polaronic lattice deformations establish an order, while macroscopic quantum coherence among excitons simultaneously emerges. Recombination of excitons in this state culminates in superfluorescence at high temperatures. Our study establishes fundamental connections between the transient superfluorescence process observed after the impulsive excitation of perovskites and general equilibrium phase transitions achieved by thermal cooling. By identifying various electron–lattice interactions in the perovskite structure and their respective role in creating collectively coherent electronic effects in solids, our work provides unprecedented insight into the design and development of new materials that exhibit high-temperature macroscopic quantum phenomena.

36 MATERIALS SCIENCE↗

DOE OSTI2026

A collective trigger for widespread planetesimal formation revealed by accretion ages

The formation of planetesimals was an integral part of the cascading series of processes that built the terrestrial planets. To illuminate planetesimal formation, here we develop a refined thermal evolution model to calculate the formation ages of meteorite parent planetesimals. This model includes chemical reactions and phase changes during heating, as well as natural variations in the proportions of the constituent phases of these planetesimals. We find that the parent bodies of non-carbonaceous (NC) and carbonaceous (CC) iron meteorites start forming at very similar times ( ∼ 0.95 Myr after calcium-aluminium-rich inclusion [CAI] formation) and occupy overlapping time windows. NC and CC chondrite parent bodies formed later during non-overlapping periods. We combine these ages with proportions of isotopic end-members we recover from mixing models to construct records of motion throughout the protoplanetary disk. These records argue that NC and CC material traversed the barrier in the disk after ∼ 0.95 Myr after CAI formation. The onset of this motion coincided with planetesimal formation, indicating that the phenomenon that drove motion also triggered planetesimal formation. We argue that this feature also served as the semi-permeable barrier in the disk. Although its identity is uncertain, the effects this phenomenon had on the timing of planetesimal formation and motion through the disk can now serve as constraints on models of disk evolution. Models that reproduce these effects would elucidate the nature and implications of this phenomenon, which is key to unlocking a holistic model of terrestrial planet building.

Astronomy and AstroPhysics↗

DOE OSTI2025

The Effect of Core-Hole Shape on Attosecond Valence Electron Dynamics

Rapid X-ray ionization of a core electron is known to induce the attosecond motion of valence electrons; however, the effect of core-hole shape on the triggered dynamics remains relatively unknown. In this work, the sub-four fs response of prototypical functionalized/heterocyclic/polycyclic molecules was simulated using real-time time-dependent density functional theory (RT-TDDFT), a sudden approximation core-hole, and phenomenologically Auger–Meitner (AM) decay. These molecules included fluorobenzene, chlorobenzene, bromobenzene, phenol, thiophenol, pyridine, phosphorus, and azulene. It is observed that the valence electron dynamics are essentially independent of the core-hole created, provided that it is ionized from an inner-shell orbital and not an inner-valence orbital. This has broad implications for free-electron laser studies of X-ray pumped attosecond processes since the flexibility in edge allows for a wide range of experimental modalities, core-holes with longer AM lifetimes, and molecular targets.

aromatic compounds↗

DOE OSTI2025

XRISM spectroscopy on orbital modulation of Fe Ly α lines in Cygnus X-3

To understand physical processes such as mass transfer and binary evolution in X-ray binaries, the orbital parameters of the system are fundamental and crucial information. Cygnus X-3 is a high-mass X-ray binary composed of a compact object of unknown nature and a Wolf–Rayet star, which is of great interest in the context of wind-fed mass accretion and binary evolution. Here we present XRISM/Resolve high-resolution spectroscopy, focusing on the Fe Ly$\alpha$ lines when the source was in its hypersoft state. We perform an orbital phase-resolved spectral analysis of the lines to study the orbital modulation of the emission and absorption lines. It is found that the emission lines reflect the orbital motion of the compact object whose estimated velocity amplitude is $430^{+150}_{-140}$ km s$^{-1}$, while the absorption lines show a variation that can be interpreted as originating from the stellar wind. We discuss possible mass ranges for the binary components using the mass function with the estimated value of the velocity amplitude in this work, combined with the relation between the mass-loss rate and the orbital period derivative and the empirical mass and mass-loss rate relation for Galactic Wolf–Rayet stars. They are constrained to be (1.3–5.1) and (9.3–12) M$_\odot$, respectively, for the assumed inclination angle of $i =25^\circ$, and become more relaxed, (1.3–24) and (9.3–16) M$_\odot$, for $i = 35^\circ$. Thus, it remains unclear whether the system harbors a black hole or a neutron star.

X-rays: binaries↗