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At least 73 records · Page 4

Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions

The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREB TAD ) construct. The CREB TAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. In conclusion, our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.

59 BASIC BIOLOGICAL SCIENCES↗

Polymorphous nature of cubic halide perovskites

Many common crystal structures can be described by a single (or very few) repeated structural motif (“monomorphous structures”) such as octahedron in cubic halide perovskites. Interestingly, recent accumulated evidence suggests that electronic structure calculations based on such macroscopically averaged monomorphous cubic ($\textit{Pm} – 3m$) halide perovskites obtained from x-ray diffraction, show intriguing deviations from experiment. These include systematically too small band gaps, dielectric constants dominated by the electronic, negative mixing enthalpy of alloys, and significant deviations from the measured pair distribution function. We show here that a minimization of the systems $\textit{T}$ = 0 internal energy via density functional theory reveals a distribution of different low-symmetry local motifs, including tilting, rotations, and B-atom displacements (“polymorphous networks”). This is found only if one allows for larger-than-minimal cell size that does not geometrically exclude low symmetry motifs. As the (super) cell size increases, the energy is lowered relative to the monomorphous cell, and stabilizes after ~32 formula units (≥160 atoms) are included. Being a result of nonthermal energy minimization in the internal energy without entropy, this correlated set of displacements must represent the intrinsic geometry preferred by the underlying chemical bonding (lone pair bonding), and as such has a different origin than the normal, dynamic thermal disorder modeled by molecular dynamics. Indeed, the polymorphous network, not the monomorphous ansatz, is the kernel structure from which high temperature thermal agitation develops. The emerging physical picture is that the polymorphous network has an average structure with high symmetry, yet the local structural motifs have low symmetries. In this work we find that, compared with monomorphous counterparts, the polymorphous networks have significantly lower predicted total energies, larger band gaps, and ionic dominated dielectric constants, and agree much more closely with the observed pair distribution functions. An analogous polymorphous situation is found in the paraelectric phase of a few cubic oxide perovskites where local polarization takes the role of local displacements in halide perovskites, and in the paramagnetic phases of a few 3 d oxides where the local spin configuration takes that role.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

B56$δ$ long-disordered arms form a dynamic PP2A regulation interface coupled with global allostery and Jordan’s syndrome mutations

Intrinsically disordered regions (IDR) and short linear motifs (SLiMs) play pivotal roles in the intricate signaling networks governed by phosphatases and kinases. B56δ (encoded by PPP2R5D) is a regulatory subunit of protein phosphatase 2A (PP2A) with long IDRs that harbor a substrate-mimicking SLiM and multiple phosphorylation sites. De novo missense mutations in PPP2R5D cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Our single-particle cryo-EM structures of the PP2A-B56δ holoenzyme reveal that the long, disordered arms at the B56δ termini fold against each other and the holoenzyme core. This architecture suppresses both the phosphatase active site and the substrate-binding protein groove, thereby stabilizing the enzyme in a closed latent form with dual autoinhibition. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is coupled to an allosteric network responsive to phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations increase the holoenzyme activity and perturb the phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the normal variant.

59 BASIC BIOLOGICAL SCIENCES↗

Non-Equilibrium relaxation, aging scaling, and critical depinning dynamics of skyrmions in disordered magnetic films. Final Report

Technical applications of type-II superconductors, especially high-Tc compounds, in external magnetic fields require an effective flux pinning mechanism to reduce Ohmic losses due to flux creep and flow. Naturally abundant point defects, dislocations, and twin boundaries as well as artificially introduced disorder may serve as effective pinning centers for magnetic vortices. The properties of interacting flux lines subject to strong thermal fluctuations and point-like or extended pinning centers have therefore been a major research focus in condensed matter physics, and considerable progress has been achieved in the characterization and mathematical description of the equilibrium phases and non-equilibrium steady states of vortex matter. Detailed studies of the rich phase diagrams that reveal novel glassy states as well as the associated complex dynamical phenomena have in turn enriched the theoretical understanding of condensed matter systems, elucidating specifically the kinetics of elastic objects driven through disordered media and the important role of topological defects such as vortices and dislocations in various materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Vibrational relaxation dynamics in layered perovskite quantum wells

Significance Halide perovskites, especially layered perovskites, offer a number of advantages to creating bright and efficient light-emitting devices and other optoelectronic applications. The organic–inorganic hybrid layered perovskite features complex lattice dynamics due to the ionic character of the crystal and the softness arising from noncovalent bonds between molecular moieties and the inorganic network. Especially, the packing geometry of the organic barriers leads to a structural deformation of inorganic octahedral, which strongly affects the properties that are crucial for device applications. In this work, we use high-resolution resonant impulsive stimulated Raman spectroscopy of a variety of ligand substitutions in layered perovskites. We find the composition of organic ligands can substantially change the dephasing rate of optical phonons and their temperature dependence, due to varying degrees of anharmonicity in the lattice and dynamic structural disorder.

36 MATERIALS SCIENCE↗

Coarsening dynamics of Ising-nematic order in a frustrated Heisenberg antiferromagnet

We study the phase ordering dynamics of the classical antiferromagnetic 𝐽 1 −𝐽 2 (nearest-neighbor and next-nearest-neighbor couplings) Heisenberg model on the square lattice in the strong frustration regime (𝐽 2 /𝐽 1 > 1/2). While thermal fluctuations preclude any long-range magnetic order at finite temperatures, the system exhibits a long-range spin-driven nematic phase at low temperatures. The transition into the nematic phase is further shown to belong to the two-dimensional Ising universality class based on the critical exponents near the phase transition. Our large-scale stochastic Landau-Lifshitz-Gilbert simulations find a two-stage phase ordering when the system is quenched from a high-temperature paramagnetic state into the nematic phase. In the early stage, collinear alignments of spins lead to a locally saturated Ising-nematic order. Once domains of well-defined Ising order are developed, the late-stage relaxation is dominated by curvature-driven domain coarsening, as described by the Allen-Cahn equation. The characteristic size of Ising-nematic domains scales as the square root of time, similar to the kinetic Ising model described by the time-dependent Ginzburg-Landau theory. Our results confirm that the late-stage ordering kinetics of the spin-driven nematic, which is a vestigial order of the frustrated Heisenberg model, belongs to the dynamical universality class of a nonconserved Ising order. Interestingly, the system shows no violation of the superuniversality hypothesis under weak bond disorder. The dynamic scaling invariance is preserved in the presence of weak bond disorder. Here, we also discuss possible applications of our results to materials for which vestigial Ising-nematic order is realized.

Antiferromagnets↗

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗

Statics and dynamics of skyrmions interacting with disorder and nanostructures

Magnetic skyrmions are topologically stable nanoscale particlelike objects that were discovered in 2009. Since that time, intense research interest in the field has led to the identification of numerous compounds that support skyrmions over a range of conditions spanning from cryogenic to room temperatures. Skyrmions can be set into motion under various types of driving, and the combination of their size, stability, and dynamics makes them ideal candidates for numerous applications. At the same time, skyrmions represent a new class of system in which the energy scales of the skyrmion-skyrmion interactions, sample disorder, temperature, and drive can compete. A growing body of work indicates that the static and dynamic states of skyrmions can be influenced strongly by pinning or disorder in the sample; thus, an understanding of such effects is essential for the eventual use of skyrmions in applications. The current state of knowledge regarding individual skyrmions and skyrmion assemblies interacting with quenched disorder or pinning is reviewed. Additionally, the microscopic mechanisms for skyrmion pinning, including the repulsive and attractive interactions that can arise from impurities, grain boundaries, or nanostructures, are outlined. This is followed by descriptions of depinning phenomena, sliding states over disorder, the effect of pinning on the skyrmion Hall angle, the competition between thermal and pinning effects, the control of skyrmion motion using ordered potential landscapes such as one- or two-dimensional periodic asymmetric substrates, the creation of skyrmion diodes, and skyrmion ratchet effects. Highlighted are the distinctions arising from internal modes and the strong gyrotropic or Magnus forces that cause the dynamical states of skyrmions to differ from those of other systems with pinning, such as vortices in type-II superconductors, charge density waves, or colloidal particles. Throughout this review future directions and open questions related to the pinning and dynamics in skyrmion systems are also discussed.

36 MATERIALS SCIENCE↗

Disorder-induced excitation continuum in a spin- 1 2 cobaltate on a triangular lattice

A spin-1/2 triangular-lattice antiferromagnet is a prototypical frustrated quantum magnet, which exhibits remarkable quantum many-body effects that arise from the synergy between geometric spin frustration and quantum fluctuations. It can host quantum frustrated magnetic topological phenomena such as quantum spin liquid (QSL) states, highlighted by the presence of fractionalized quasiparticles within a continuum of magnetic excitations. Here, in this work, we use neutron scattering to study CoZnMo 3 O 8 , which has a triangular lattice of J eff = 1/2 Co 2+ ions with octahedral coordination. We found a wave-vector-dependent excitation continuum at low energy that disappears with increasing temperature. Although these excitations are reminiscent of a spin excitation continuum in a QSL state, their presence in CoZnMo 3 O 8 originates from magnetic intersite disorder-induced dynamic spin states with peculiar excitations. Our results, therefore, provide direct experimental evidence for the presence of a disorder-induced spin excitation continuum.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nonequilibrium DMFT + CPA for correlated disordered systems

We present a solution for the nonequilibrium dynamics of an interacting disordered system. The approach adapts the combination of the equilibrium dynamical mean-field theory and the equilibrium coherent potential approximation methods to the nonequilibrium many-body formalism, using the Kadanoff-Baym-Keldysh complex time contour, for the dynamics of interacting disordered systems away from equilibrium. We use our time domain solution to obtain the equilibrium density of states of the disordered interacting system described by the Anderson-Hubbard model, bypassing the necessity for the cumbersome analytical continuation process. We further apply the nonequilibrium solution to the interaction quench problem for an isolated disordered system. Here, the interaction is abruptly changed from zero (noninteracting system) to another constant (finite) value at which it is subsequently kept. We observe via the time dependence of the potential, kinetic, and total energies the effect of disorder on the relaxation of the system as a function of final interaction strength. Finally, the real-time approach has the potential to shed light on the fundamental role of disorder in the nonequilibrium dynamics of interacting quantum systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Thermal Disorder‐Induced Strain and Carrier Localization Activate Reverse Halide Segregation

The reversal of halide ions is studied under various conditions. However, the underlying mechanism of heat-induced reversal remains unclear. This work finds that dynamic disorder-induced localization of self-trapped polarons and thermal disorder-induced strain (TDIS) can be co-acting drivers of reverse segregation. Localization of polarons results in an order of magnitude decrease in excess carrier density (polaron population), causing a reduced impact of the light-induced strain (LIS – responsible for segregation) on the perovskite framework. Meanwhile, exposing the lattice to TDIS exceeding the LIS can eliminate the photoexcitation-induced strain gradient, as thermal fluctuations of the lattice can mask the LIS strain. Under continuous 0.1 W cm -2 illumination (upon segregation), the strain disorder is estimated to be 0.14%, while at 80 °C under dark conditions, the strain is 0.23%. However, in situ heating of the segregated film to 80 °C under continuous illumination (upon reversal) increases the total strain disorder to 0.25%, where TDIS is likely to have a dominant contribution. Therefore, the contribution of entropy to the system's free energy is likely to dominate, respectively. Various temperature-dependent in situ measurements and simulations further support the results. These findings highlight the importance of strain homogenization for designing stable perovskites under real-world operating conditions.

36 MATERIALS SCIENCE↗

Dynamic short-range correlation in photoinduced disorder phase transitions

Ultrafast photoexcitation can induce a nonequilibrium dynamic with electron-lattice interaction, offering an effective way to study photoinduced phase transitions (PIPTs) in solids. The issue that atomic displacements after photoexcitation belong to a coherent change or disordered process has become controversial in the PIPT community. Using real-time, time-dependent density functional theory (rt-TDDFT) simulations, we were able to obtained both the coherent and the disordered PIPTs (dimer dissociation) in IrTe 2 with different electronic occupations. More importantly, we found that in the disordered phase transition there exists a local correlation between different dimers regarding their dissociation status. We define these Ir-Ir dimers directly connected by Te atoms, including intralayer and vertically across the layers, as a group (group I). Other Ir-Ir dimers separated by five Ir atoms from Ir-Ir dimers in group I are divided into another group (group II). The dimers in the same group will dissociate in a correlated fashion; they either all dissociate or all do not dissociate. On the other hand, the dimers in neighboring groups will have an anticorrelation: If the dimers in one group dissociate, the dimers in the neighboring group tend not to be dissociated, and vice versa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Flexible machine-learning interatomic potential for simulating structural disordering behavior of Li 7 La 3 Zr 2 O 12 solid electrolytes

Batteries based on solid-state electrolytes, including Li 7 La 3 Zr 2 O 12 (LLZO), promise improved safety and increased energy density; however, atomic disorder at grain boundaries and phase boundaries can severely deteriorate their performance. Machine-learning (ML) interatomic potentials offer a uniquely compelling solution for simulating chemical processes, rare events, and phase transitions associated with these complex interfaces by mixing high scalability with quantum-level accuracy, provided that they can be trained to properly address atomic disorder. To this end, we report the construction and validation of an ML potential that is specifically designed to simulate crystalline, disordered, and amorphous LLZO systems across a wide range of conditions. The ML model is based on a neural network algorithm and is trained using ab initio data. Performance tests prove that the developed ML potential can predict accurate structural and vibrational characteristics, elastic properties, and Li diffusivity of LLZO comparable to ab initio simulations. As a demonstration of its applicability to larger systems, we show that the potential can correctly capture grain boundary effects on diffusivity, as well as the thermal transition behavior of LLZO. Here these examples show that the ML potential enables simulations of transitions between well-defined and disordered structures with quantum-level accuracy at speeds thousands of times faster than ab initio methods.

25 ENERGY STORAGE↗

Coordination Sphere of Lanthanide Aqua Ions Resolved with Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy

To resolve the fleeting structures of lanthanide Ln 3+ aqua ions in solution, we (i) performed the first ab initio molecular dynamics (AIMD) simulations of the entire series of Ln 3+ aqua ions in explicit water solvent using pseudopotentials and basis sets recently optimized for lanthanides and (ii) measured the symmetry of the hydrating waters about Ln 3+ ions (Nd 3+ , Dy 3+ , Er 3+ , Lu 3+ ) for the first time with extended X-ray absorption fine structure (EXAFS). EXAFS spectra were measured experimentally and generated from AIMD trajectories to directly compare simulation, which concurrently considers the electronic structure and the atomic dynamics in solution, with experiment. In this study, we performed a comprehensive evaluation of EXAFS multiple-scattering analysis (up to 6.5 Å) to measure Ln–O distances and angular correlations (i.e., symmetry) and elucidate the molecular geometry of the first hydration shell. This evaluation, in combination with symmetry-dependent L 3 - and L 1 -edge spectral analysis, shows that the AIMD simulations remarkably reproduces the experimental EXAFS data. The error in the predicted Ln–O distances is less than 0.07 Å for the later lanthanides, while we observed excellent agreement with predicted distances within experimental uncertainty for the early lanthanides. Our analysis revealed a dynamic, symmetrically disordered first coordination shell, which does not conform to a single molecular geometry for most lanthanides. This work sheds critical light on the highly elusive coordination geometry of the Ln 3+ aqua ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tetrahedral Tilting and Lithium‐Ion Transport in Halide Argyrodites Prepared by Rapid, Microwave‐Assisted Synthesis

Abstract This study demonstrates a rapid, dry, microwave‐assisted (MW) synthesis method that enables preparation of halide argyrodites ( , , ) in less than 20 min. The structures and ion transport properties of the resulting materials are compared with those synthesized by conventional solid‐state synthesis methods. The microwave‐assisted method leads to increased site disorder and elevated Arrhenius prefactors (), which lead to an order of magnitude improvement in the 30 ionic conductivity of MW‐. X‐ray pair distribution function analysis (XPDF) reveals significant rotational disorder of the units, which is impacted by the synthesis method, choice of halide, and presence of / site disorder. These rotational displacements are strongly correlated with ion transport, specifically and entropy of migration (). Overall, this study demonstrates a rapid synthesis route for preparing high‐quality halide argyrodite solid‐state electrolytes in less than 20 min, and further unravels atomistic insights into the interplay of structural disorder, rotational dynamics, and ion transport mechanisms.

36 MATERIALS SCIENCE↗

Visualizing Crystallization Dynamics and Transformation Pathways of Disordered Rocksalt Oxides During Thermally Activated Sol–Gel Synthesis

Sol–gel synthesis is a wet-chemical processing route for fabricating functional materials with control over composition and microstructure at relatively low temperatures compared to conventional solid-state synthesis. While sol–gel process initiates with intermixed molecular precursors, the early-stage nucleation pathways are insufficiently understood. Here, in this study, the chemical and structural transformation of ion disordered rocksalt (DRX) Li 1.2 Mn 0.4 Ti 0.4 O 2 (LMTO), a promising cathode material for lithium batteries, is studied by multiscale characterizations. In situ heating transmission electron microscopy (TEM) using a liquid cell visualizes and identifies crystallization pathways at the nanoscale. While some regions follow a classical multi-step transition through thermodynamically stable intermediates, others exhibit a kinetic shortcut via a localized amorphous matrix to directly form the DRX structure. Macroscale Fourier transform infrared spectroscopy corroborates the findings and reveals that transition metal ions are more strongly incorporated into the acetate-coordinated network than lithium. Although in situ heating TEM captures diverse local transformation pathways, in situ synchrotron X-ray diffraction indicates that the macroscopic transformation proceeds predominantly through spinel LMTO and lithium titanates toward DRX-LMTO. The findings uncover the spatiotemporal chemical and structural transformations in sol–gel derived DRX-LMTO materials, and call for fine-tuning of such sol–gel chemistries to manipulate the crystallization pathways and achieve target material homogeneity more efficiently.

cathode material↗

All-Inorganic Halide Perovskites as Potential Thermoelectric Materials: Dynamic Cation off-Centering Induces Ultralow Thermal Conductivity

Halide perovskites are anticipated to impact next generation high performance solar cells because of their extraordinary charge transport and optoelectronic properties. However, their thermal transport behavior has received limited attention. In this work, we studied the thermal transport and thermoelectric properties of the CsSnBr 3–x I x perovskites. We find a strong correlation between lattice dynamics and an ultralow thermal conductivity for series CsSnBr 3–x I x reaching 0.32 Wm –1 K –1 at 550 K. The CsSnBr 3–x I x also possess a decent Seebeck coefficient and controllable electrical transport properties. The crystallography data and theoretical calculations suggest the Cs atom deviates from its ideal cuboctahedral geometry imposed by the perovskite cage and behaves as a heavy atom rattling oscillator. This off-center tendency of Cs, together with the distortion of SnX 6 (X = Br or I) octahedra, produces a highly dynamic and disordered structure in CsSnBr 3–x I x , which gives rise to a very low Debye temperature and phonon velocity. Moreover, the low temperature heat capacity data suggests strong coupling between the low frequency optical phonons and heat carrying acoustical phonons. In conclusion, this induces strong phonon resonance scattering that induces the ultralow lattice thermal conductivity of CsSnBr 3–x I x .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗