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At least 163 records · Page 9

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Solvent effects on extractant conformational energetics in liquid–liquid extraction: a simulation study of molecular solvents and ionic liquids

Extractant design in liquid–liquid extraction (LLE) is a research frontier of metal ion separations that typically focuses on the direct extractant–metal interactions. However, a more detailed understanding of energetic drivers of separations beyond primary metal coordination is often lacking, including the role of solvent in the extractant phase. In this work, we propose a new mechanism for enhancing metal-complexant energetics with nanostructured solvents. Using molecular dynamics simulations with umbrella sampling, we find that the organic solvent can reshape the energetics of the extractant's intramolecular conformational landscape. Here, we calculate free energy profiles of different conformations of a representative bidentate extractant, n-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four different solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]). By promoting reorganization of the extractant molecule into its binding conformation, our findings reveal how particular solvents can ameliorate this unfavorable step of the metal separation process. In particular, the charge alternating nanodomains formed in ILs substantially reduce the free energy penalty associated with extractant reorganization. Importantly, using alchemical free energy calculations, we find that this stabilization persists even when we explicitly include the extracted cation. These findings provide insight into the energetic drivers of metal ion separations and potentially suggest a new approach to designing effective separations using a molecular-level understanding of solvent effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

Significance Breakthrough technological advances such as Hi-C have enabled large-scale sequencing of pairwise genomic contacts. However, translating the 2D contacts to 3D spatial models remains challenging. Here we develop the “4DHiC” modeling method to infer 3D information from 2D datasets across time and construct a 3D model of the inactive X-chromosome (Xi). Our model not only demonstrates a spatial phase-separation between A/B and S1/S2 compartments to form “hemispheres,” but also reveals persistent smaller-scale structures hidden under the Xi superstructure. We also simulate Xist RNA spreading dynamics and deduce that the RNA spreads between hemispheres via both surface and core to establish the Xi. Our 4DHiC will serve a growing demand for data-driven methodologies that extract spatial information from biochemical interaction data.

Lappala, Anna↗

Stable Solid Molecular Hydrogen above 900 K from a Machine-Learned Potential Trained with Diffusion Quantum Monte Carlo

Here, we survey the phase diagram of high-pressure molecular hydrogen with path integral molecular dynamics using a machine-learned interatomic potential trained with quantum Monte Carlo forces and energies. Besides the HCP and C2/c–24 phases, we find two new stable phases both with molecular centers in the Fmmm–4 structure, separated by a molecular orientation transition with temperature. The high temperature isotropic Fmmm–4 phase has a reentrant melting line with a maximum at higher temperature (1450 K at 150 GPa) than previously estimated and crosses the liquid-liquid transition line around 1200 K and 200 GPa.

08 HYDROGEN↗

Electric Field’s Dueling Effects through Dehydration and Ion Separation in Driving NaCl Nucleation at Charged Nanoconfined Interfaces

Investigating nucleation in charged nanoconfined environments under electric fields is crucial for many scientific and engineering applications. Here we study the nucleation of NaCl from aqueous solution near charged surfaces using machine-learning-augmented enhanced sampling molecular dynamics simulations. Our simulations successfully drive phase transitions between the liquid and solid phases of NaCl. The solid phase is stabilized under electric fields, particularly at an intermediate surface charge density. We examine which physical characteristics drive the nucleation of NaCl from aqueous solutions and find that the removal of solvent water from Cl– at the solid precursor surface plays a more critical role than the accumulation of ions. Our simulations reveal the competing effects of electric fields on nucleation processes: they facilitate the removal of water, promoting nucleation, but also promote the separation of ion pairs, thereby hindering nucleation. Here, this work provides a framework for studying nucleation processes in nanoconfined environments under electric fields and provides physical insights for the design of electrochemistry materials.

Electric fields↗

Origin of Metal-Insulator Transition in Rare-Earth Nickelates

Rare-earth nickelates RNiO3 (R=rare-earth element) undergo coupled structural, metal-insulator, and magnetic changes as temperature is lowered. Because the metal-insulator transition often occurs together with a symmetry-lowering distortion, it is commonly viewed as lattice driven. Here we use QSGW calculations to separate the roles of spin and structure. In the high-symmetry Pbnm phase, imposing spin disproportionation already starts to open an electronic gap, although the undistorted lattice cannot stabilize a full insulating state in both spin channels. In the low-symmetry P21/n phase, removing the spin disproportionation destroys the insulating solution even though the bond disproportionation remains. These tests show that spin disproportionation is the primary electronic driver of gap formation, while structural disproportionation acts as the enabler that allows the inequivalent Ni states to become spatially separated and fully insulating. As an explicit finite-temperature example, machine-learned molecular dynamics for NdNiO3 at 220 K shows that a nominally high-symmetry Pbnm structure dynamically samples local Ni-O bond disproportionation, while retaining Pbnm symmetry on average. This illustrates a general structural channel by which thermal fluctuations in the high-symmetry phase can help stabilize locally spin-disproportionated states.

36 MATERIALS SCIENCE↗

Effects of Asymmetric Molecular Architecture on Chain Stretching and Dynamics in Miktoarm Star Copolymers

We use broad-band dielectric spectroscopy (BDS) and small-angle X-ray scattering (SAXS) to investigate the impact of architectural asymmetry in the miktoarm star copolymer on the dielectric polymer relaxations. The miktoarm copolymers studied contain one or two polystyrene (PS) chains of constant molecular weight and two identical poly(cis-1,4-isoprene) (PI) chains with varied molecular weights. Using the chains in the PI block as dielectric probes, we find that the architecturally asymmetric miktoarm star copolymer systems (PSPI 2 ) feature distributions in chain relaxation times and dielectric relaxation strengths that are not dependent on molecular weight or morphology, in stark contrast to the effects of morphological confinement observed for symmetric diblock systems (PS-b-PI or PS 2 PI 2 ). Along with evidence from the SAXS measurements regarding phase separation, these results are attributed to influences from chain stretching within the framework of the Gaussian chain model for block copolymer systems. As such, the molecular architecture in block copolymers happens to be a versatile handle to control polymer chain dynamics and, ultimately, the macroscopic physicochemical properties in architecturally complex polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Compositional phase stability of correlated electron materials within DFT+DMFT

Predicting the compositional phase stability of strongly correlated electron materials is an outstanding challenge in condensed matter physics, requiring precise computations of total energies. In this work, we employ the density functional theory plus dynamical mean-field theory (DFT+DMFT) formalism to address local correlations due to transition metal $\textit{d}$ electrons on compositional phase stability in the prototype rechargeable battery cathode material Li x CoO 2 , and detailed comparisons are made with the simpler DFT+$\textit{U}$ approach (i.e., the Hartree-Fock solution of the DMFT impurity problem). Local interactions are found to strongly impact the energetics of the band insulator LiCoO 2 , most significantly via the $E_g$ orbitals, which are partially occupied via hybridization with $\textit{O p}$ states. We find CoO 2 and Li 1/2 CoO 2 to be moderately correlated Fermi liquids with quasiparticle weights of 0.6–0.8 for the $T_{2g}$ states, which are most impacted by the interactions. Further, as compared to DFT+$\textit{U}$, DFT+DMFT considerably dampens the increase in total energy as $\textit{U}$ is increased, which indicates that dynamical correlations are important to describe this class of materials despite the relatively modest quasiparticle weights. Unlike DFT+$\textit{U}$, which can incorrectly drive Li x CoO 2 toward spurious phase separating or charge-ordered states, DFT+DMFT correctly captures the system's phase stability and does not exhibit a strong charge-ordering tendency. Most importantly, the error within DFT+$\textit{U}$ varies strongly as the composition changes, challenging the common practice of artificially tuning $\textit{U}$ within DFT+$\textit{U}$ to compensate the errors of Hartree-Fock. DFT+DMFT predicts the average intercalation voltage decreases relative to DFT, opposite to the result of DFT+$\textit{U}$, which would yield favorable agreement with experiment in conjunction with the overprediction of the voltage by the strongly constrained and appropriately normed DFT functional.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Toward Intelligent Multimodal Holography for Real-Time Chemical Imaging of Dynamic Ion Separation

Molecular-level visualization of ion transport and separation dynamics in complex environments is crucial for advancing energy systems, water purification, and critical materials recovery. Achieving this requires imaging platforms that combine structural sensitivity, chemical specificity, and real-time operation. Digital off-axis holography (DOAH) provides high-throughput, label-free quantitative phase imaging but inherently lacks chemical selectivity. Integrating DOAH with complementary spectroscopic channels such as fluorescence or hyperspectral imaging introduces the needed molecular specificity, while also creating challenges in multimodal data fusion, synchronization, and computational throughput. Artificial intelligence offers a powerful route to address these limitations by uniting physics-based reconstruction with data-driven interpretation. In this Perspective, we outline a framework for intelligent multimodal holography and demonstrate its potential using a preliminary AI-driven test case. Raw DOAH holograms of lanthanide solutions subjected to magnetic field gradients were analyzed using multi-agent AI workflows that autonomously selected reconstruction tools, extracted NMF components, and generated scientific claims consistent with true paramagnetic and diamagnetic behavior. This demonstration shows how AI-enabled reasoning can deliver real-time chemical–structural interpretation directly from raw holograms. Together, these advances define a path toward adaptive, intelligent holography platforms capable of supporting in situ chemical separations, dynamic ion transport analysis, and next-generation interfacial science.

Ricchiuti, Giovanna↗

Nonadiabatic Phase Transition with Broken Chiral Symmetry

We explore nonadiabatic quantum phase transitions in an Ising spin chain with a linearly time-dependent transverse field and two different spins per unit cell. Such a spin system passes through critical points with gapless excitations, which support nonadiabatic transitions. Nevertheless, we find that the excitations on one of the chain sublattices are suppressed in the nearly adiabatic regime exponentially. Furthermore, we reveal a coherent mechanism to induce exponentially large density separation for different quasiparticles.

1-dimensional spin chains↗

Barriers to carriers: faults and recombination in non-stoichiometric perovskite scintillators

Abstract Tuning the efficiency and speed of charge carrier recombination in inorganic scintillators can potentially improve their performance in diverse applications. Recent work suggests that this maybe be achieved via a two-phase scintillator AB that naturally phase separates into A -rich and B -rich domains. In addition, a favorable electronic structure and band-edge alignment such that the charge carriers are confined or are thermodynamically driven to preferentially accumulate in one of the two domains, might lead to an improved radiative recombination rate. Here, we use density functional theory computations and ab initio molecular dynamics (AIMD), including non-adiabatic molecular dynamics (NAMD) simulations, to examine an alternative phase structure and its potential impact on recombination. Using a model perovskite SrTiO $$_3$$ 3 system with one-, two- and three-dimensional Ruddlesden–Popper (RP) phases, we demonstrate that RP faults induce band structure changes in the material that can act as barriers to carrier transport. Our AIMD/NAMD simulations indicate competing effects of a lower mean free path (potentially enhancing the desired radiative recombination and overall scintillating efficiency) and faster non-radiative recombination (undesired) due to enhanced electron–phonon coupling in the faulted system. Full exploitation of such a rational design approach would require tuning of the effective scintillation efficiency by varying the perovskite chemistry using appropriate arrangements of RP faults in the bulk material. Finally, other effects, such as the tendency of point defects to segregate at the interface, that might affect the overall performance, are briefly discussed. We expect the basic results found here to apply to other nanostructured scintillators. Graphical Abstract

36 MATERIALS SCIENCE↗

Observation of stacking engineered magnetic phase transitions within moiré supercells of twisted van der Waals magnets

Abstract Recent demonstrations of moiré magnetism, featuring exotic phases with noncollinear spin order in the twisted van der Waals (vdW) magnet chromium triiodide CrI 3 , have highlighted the potential of twist engineering of magnetic (vdW) materials. However, the local magnetic interactions, spin dynamics, and magnetic phase transitions within and across individual moiré supercells remain elusive. Taking advantage of a scanning single-spin magnetometry platform, here we report observation of two distinct magnetic phase transitions with separate critical temperatures within a moiré supercell of small-angle twisted double trilayer CrI 3 . By measuring temperature-dependent spin fluctuations at the coexisting ferromagnetic and antiferromagnetic regions in twisted CrI 3 , we explicitly show that the Curie temperature of the ferromagnetic state is higher than the Néel temperature of the antiferromagnetic one by ~10 K. Our mean-field calculations attribute such a spatial and thermodynamic phase separation to the stacking order modulated interlayer exchange coupling at the twisted interface of moiré superlattices.

36 MATERIALS SCIENCE↗

Conservation laws and effective hadronization models

Hadronization models based on local string-breaking dynamics are typically Markovian by construction, yet the physical ensemble of final states is shaped by global constraints that couple the entire fragmentation trajectory. Recasting hadronization as a conditioned stochastic diffusion process provides a precise mathematical resolution to this tension. In particular, this language reveals explicitly that constraints stemming from conservation laws induce non-Markovian correlations between otherwise independent fragmentation steps, and that these correlations can be absorbed exactly into a renormalization of the local dynamics through a Doob $h$-transform. We develop this formalism for a $q\bar{q}$ string in the chiral limit, where the longitudinal-transverse factorization of the Lund kernel becomes exact, enabling systematic power counting and clean ultraviolet (UV)/infrared (IR) separation. The dynamics organize naturally into a tower of effective theories distinguished by the remaining string mass, spanning a UV fixed point with scale-invariant transport coefficients, an intermediate regime where transverse phase space induces controlled running, and an IR boundary layer where non-local effects enter at leading order. The tower exhibits genuine Wilsonian structure, including $β$-functions, anomalous dimensions, and systematic matching conditions. The resulting framework achieves a clean factorization of universal microscopic fragmentation dynamics from infrared constraint effects, and opens new directions for both the theoretical analysis and practical simulation of hadronization.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗

Vanishing dynamic strength measured in a transient high-pressure phase of tin

This work reports two independent experimental estimations of the dynamic strength of the body-centered tetragonal (bct) 𝛾 phase of tin, which occurs at pressures above about 9 GPa and transforms promptly back to the ambient 𝛽 phase upon pressure release. Measuring strength in such a transient high-pressure phase is challenging. One measurement used free-surface Richtmyer-Meshkov instabilities generated with gas gun impact. Another set of measurements used ramp-release loading in a pulsed-power facility. Strength estimations came from comparison to simulations using a comprehensive multiphase modeling framework that includes equation of state, shear moduli, and strength separately for each phase, and treats mixed-phase regions. Both experimental methods found the 𝛾-phase strength to be very low, within experimental uncertainty of zero. The existing literature on other materials, by contrast, almost universally reports higher strength in transient high-pressure phases compared with ambient phases. Recent Molecular-Dynamics simulations on tin in the literature showed almost zero deviatoric strength during a deformation-induced bct → bct transformation in which one of the 𝛾-phase 𝑎 axes “flips” to the 𝑐 axis. This reorientation currently provides the most plausible explanation for the low observed strength in 𝛾-phase tin.

36 MATERIALS SCIENCE↗

RELAP-7 Application and Enhancement for FLEX Strategies and ATF Behavior under Extended Loss of AC Power Conditions

This report summarizes the results of a three-year research project sponsored by the U.S. Department of Energy (DOE) Nuclear Energy University Program (NEUP) to enhance and apply the RELAP-7 code by adding and improving several important components (e.g., a mechanistic Reactor Core Isolation Cooling (RCIC) system model) for thermal hydraulic studies of LWRs under ELAP conditions and evaluating the time available for transition to portable FLEX equipment. The project team included University of Massachusetts–Lowell, The Ohio State University, Texas A&M University, Idaho National Laboratory and Oak Ridge National Laboratory. In the Fukushima accident, it was found that the RCIC system played a crucial role in delaying core meltdown by almost three days in Fukushima Daiichi Unit 2, because of self-regulated operation of the steam driven RCIC turbine-pump injection system. Steam flow in the convergent-divergent nozzles of the RCIC Terry turbine is two-phase non-equilibrium transonic flow with homogenous nucleation condensation. To more accurately predict the dynamic process and behavior of the transonic compressible steam flow, a one-dimensional transient two-phase analytical model is presented. A simplified four-fluid model was employed in the present work with the consideration of four separate fluid fields: vapor, liquid film, entrained droplets and condensed droplets. The mass, momentum and energy interactions between the fluids were considered and modeled. An extended seven-equation non-equilibrium critical flow model was developed to obtain the critical pressure and velocities of each phase at the nozzle throat. To predict the wetness in the divergent section, a mechanistic nucleation condensation model was integrated in the nozzle analysis model, considering the generation and consequent growth of droplets. The governing differential equations on a staggered grid were discretized using the second-order Lax-Wendroff scheme with a flux limiter, and the Semi-Implicit Method for Pressure-Linked Equation (SIMPLE) algorithm was employed to solve the discrete linear system. To demonstrate the predictability and reliability of the physical models and the numerical method proposed in the present work, three representative nozzles were modeled and simulated. The results show good agreement with the available experimental data, even for condensation shock. Then, the 1D nozzle model was employed to obtain nozzle flow tables of the Terry turbine nozzle for different working pressures which can cover the operation pressure range of the RCIC system. A mechanistic RCIC turbine-pump system model was developed and implemented in the system code TRACE to simulate dynamic responses of the RCIC system under Beyond Design Basis Accident (BDBA) conditions. The turbine-pump governing equations are based on the control volume approach of the angular momentum balance. The physics based mechanistic RCIC model was developed using the TRACE control system components (i.e., signal variables, control blocks, and tables), and incorporated into a TRACE boiling water reactor (BWR) model. The TRACE model in this report has a detailed nodalization of the reactor pressure vessel (RPV), and all of the major flow paths and system components, including the safety relief valves (SRVs) and the containment suppression pool and drywell. Based on the nozzle flow tables generated from the 1D nozzle model developed, the turbine drive torque can be calculated from table lookup. Since the detailed specifications of the RCIC pump are unavailable, the homologous curves for a Bingham pump were used in the current pump component. A station black-out (SBO) accident test problem was selected to demonstrate the TRACE RCIC model. The short-term SBO simulations were performed for two cladding materials: Zircaloy and FeCrAl, to demonstrate the effect of the accident tolerant fuel cladding on fuel heat-up under BDBA accident conditions. The wetwell plays a vital safety role in SBO and other BWR accident scenarios in that it can reduce containment pressure and supply additional core make-up water. The suppression pool temperature distribution has a very large impact on both RPV and containment pressure. Thus, another novel contribution of the project comes mainly from an improved, systems-level wetwell model which can capture buoyancy-induced thermal stratification effects due to steam injection and condensation. A two-zone stratified wetwell model has been implemented in RELAP-7 and some results from that model are presented. This wetwell model is capable of simulating thermal stratification due to a low steam mass injection rate. With a low mass flow rate, the model assumes that all the steam condenses within the pipe and the resulting plume can be approximated with a purely buoyant, heat-source driven model. The wetwell model developed with these assumptions is adequate to simulate slow transients such as extended SBO transients.

42 ENGINEERING↗

Activated vortex lattice transition in a superconductor with combined sixfold and twelvefold anisotropic interactions

Abstract Numerical simulations are used to examine the transition dynamics between metastable and ground state vortex lattice phases in a system with combined sixfold and twelvefold contributions to the vortex–vortex interactions. The system is initially annealed using a twelvefold anisotropy, yielding domains of two different orientations and separated by grain boundaries. The vortex–vortex interaction is then suddenly changed to a sixfold anisotropy, rendering the twelvefold state metastable. Applying a drive that mimics an oscillating magnetic field causes the metastable state to decay, indicated by the structure factor that evolves from twelve to six peaks. The results fit the behavior seen in recent small-angle neutron scattering studies of the vortex lattice in MgB 2 . At higher drive amplitudes, the decay exhibits a two step process in which the initial fast decrease is followed by a slower regime where avalanches or bursts are correlated with dislocation annihilation events. The results are compared to other types of metastable systems with quenched disorder that decay under a periodic external drive.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Influence of Pore Water on the Fracture of Silica Sand at Particle Scale

The fracture of particles has a significant influence on the engineering behavior of granular materials. There are no reported conclusive answers in the literature to explain the influence of pore water on the fracture of sand, gravel, railroad ballast rock, aggregates, rockfill, and so on. Here, in this paper, two novel techniques were adopted to investigate the influence of pore water on the fracture of natural silica sand at the particle scale. The three-dimensional (3D) synchrotron microcomputed tomography (SMT) imaging technique was used to acquire and analyze multiple 3D images of specimens composed of wetted silica sand that were subjected to confined one-dimensional (1D) compression loading up to the fracture stage. A few representative particles were identified and digitally separated from the liquid water and gas phases. The 3D SMT images offer clear experimental evidence of the phase transition of water from liquid to gas within the opening cracks. In addition, a computational fluid dynamics numerical simulation framework for water flow into an opening crack was adopted and the results show that the fast opening of the crack induced cavitation, water phase transition, and water hammer effects. The results of the numerical simulations agree with the confined 1D compression experiments where the onset of the bubbles (gas phase) within the crack is mainly generated during the secondary cavitation stage, and the generated bubble near the crack mouth opening resulted from the primary cavitation, which was directly caused by the crack expansion. The results reported in this paper present a new cavitation phenomenon that occurs during particle fracture, which offers a physics-based explanation of why water-wetted sand fractures at smaller stresses than dry and can pave the way for more in-depth future studies on the fracture of water-wetted sand.

cavitation↗