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645 records · Page 4

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology

Reflection and refraction of directrons at the interface

Reflection and refraction are ubiquitous phenomena with extensive applications, yet minimizing energy loss and information distortion during these processes remains a significant challenge. This study examines the behavior of structurally stable solitons, known as directrons, in nematic liquid crystals interacting with an interface where the director field orientation changes, despite identical physical properties, external potentials, and boundary anchoring in the two regions. During reflection and refraction, the directrons maintain nearly constant structure and velocity, ensuring energy conservation and information integrity. Microscopic analyses of the director field and macroscopic evaluations of effective potential are employed to elucidate the dependence of reflection and refraction probabilities on the directron’s incident angle and the orientation difference across the interface. The findings provide valuable insights into the dynamics of solitary waves in structured liquid crystal systems, offering significant implications for the development of tunable photonic devices, reconfigurable optical systems, and nanoscale material engineering.

Science & Technology - Other Topics

Ultrafast Nanoimaging of Carrier Funneling in Composition-Graded Semiconductor Nanowires

Recent advances in bandgap engineering of low-dimensional semiconductors have enabled high-efficiency carrier transport in miniaturized electronic and optoelectronic devices. The physical properties and functionalities of these materials are governed by complex carrier dynamics coupled with multiple transport mechanisms in tailored band structures. Here, we report ultrafast nanoimaging of carrier funneling and recombination in composition-grade CdSxSe1-x nanowires using pump-probe near-field nanoscopy. Leveraging the high resolution of this technique in both space and time, we resolve nanoscale local carrier dynamics along composition-graded nanowires, revealing the local variation of composition-dependent carrier mobilities and lifetimes that significantly differ from their uniform composition counterparts. Furthermore, we demonstrate a length-dependent behavior wherein shorter nanowires exhibit enhanced funneling effects, accelerating carrier transport by up to 33%. Our findings provide direct visualization of nanoscale carrier transport while supporting an effective approach for investigating complex carrier interactions in inhomogeneous semiconductor nanostructures, with implications for optimizing next-generation optoelectronic devices.

Yang, Rundi

The Future Polarized Target Program at Jefferson Lab

Polarized targets have played a crucial role in Jefferson Lab's exploration of nuclear structure over the past four decades. The three original experimental halls have seen 19 separate installations of polarized solid or gas targets for use in the particle physics scattering experiments, and this trend will continue in the next decade. Five polarized target systems are in preparation for use at JLab in the coming years. Hall B will see the use of two solid polarized targets, one longitudinally polarized to the beam, the other transversely, as well as a novel 3He gas polarized target. In Hall C, new experiments will augment the tensor polarization in dynamically polarized solids. Plans are under development to bring a polarized solid target to Jefferson Lab's photon beam hall, Hall D, for the first time. To support these efforts, the JLab polarized target group is building a test laboratory to develop dynamic nuclear polarization techniques, as well as an apparatus to irradiate target material using electrons from JLab's injector test facility. In this talk, we will explore the development progress and plans for each of these efforts.

Maxwell, James [Thomas Jefferson National Accelera

SODAs: sparse optimization for the discovery of differential and algebraic equations

Differential-algebraic equations (DAEs) integrate ordinary differential equations (ODEs) with algebraic constraints, providing a fundamental framework for developing models of dynamical systems characterized by time-scale separation, conservation laws and physical constraints. While sparse optimization has revolutionized model development by allowing data-driven discovery of parsimonious models from a library of possible equations, existing approaches for dynamical systems assume DAEs can be reduced to ODEs by eliminating variables before model discovery. This assumption limits the applicability of such methods for DAE systems with unknown constraints and time scales. We introduce sparse optimization for differential-algebraic systems (SODAs), a data-driven method for the identification of DAEs in their explicit form. By discovering the algebraic and dynamic components sequentially without prior identification of the algebraic variables, this approach leads to a sequence of convex optimization problems. It has the advantage of discovering interpretable models that preserve the structure of the underlying physical system. To this end, SODAs improves since SODAs is singular numerical stability when handling high correlations between library terms, caused by near-perfect algebraic relationships, by iteratively refining the conditioning of the candidate library. We demonstrate the performance of our method on biological, mechanical and electrical systems, showcasing its robustness to noise in both simulated time series and real-time experimental data.

DAE

Probing the role of local tunnel variations in early-stage lithiation of α-MnO₂ nanowires via in situ TEM

Understanding lithium-ion transport in tunnel-structured manganese oxides is essential for designing high-performance lithium-ion battery electrode materials. Here, we elucidate the early-stage lithiation mechanism of potassium-stabilized α-MnO 2 nanowires using in situ transmission electron microscopy (TEM) coupled with electron energy-loss spectroscopy (EELS), high-resolution TEM (HRTEM), and geometric phase analysis (GPA). Real-time TEM imaging reveals clear volume expansion at the reaction front, while EELS analysis uncovers lithium-ion diffusion far beyond this region, where no visible expansion is observed, indicating fast, defect-assisted transport. GPA and HRTEM analyses show that localized tensile and compressive strain fields, originating from pre-existing local tunnel structural variations, persist after lithiation. The tensile-strained regions enable lithium-ion insertion with minimal lattice distortion, offering additional free volume that facilitates rapid lithium-ion accommodation ahead of the structural transformation. Our results demonstrate a local tunnel variation-mediated fast diffusion pathway that precedes bulk reaction, underscoring the critical role of local strain in enabling early-stage lithium transport. Given the structural versatility of MnO 2 and its ability to accommodate diverse atomic arrangements beyond the well-known tunnel phases (β-, γ-, δ-, λ-, R-phases), our findings highlight the importance of understanding and engineering local structural environments. This work provides fundamental insights into the interplay between defects, strain, and ion dynamics, and presents defect engineering as a promising approach to enhance both rate performance and structural stability in manganese-based cathodes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

The CP-PAW Code Package for First-Principles Calculations from a User’s Perspective

CP-PAW is a combined electronic structure and ab initio molecular dynamics code to perform mixed quantum and classical simulations of atomistic condensed phase systems, such as solids, liquids, and molecular systems. As the name suggests, the CP-PAW code unifies the all-electron projector augmented-wave (PAW) method with the Car–Parrinello (CP) approach to determine not only the electronic and nuclear ground states of condensed matter but also to study their properties and dynamics. In addition to briefly outlining the underlying theory, the focus will be on the unique aspects of CP-PAW and how to correctly employ them as a user. How to install CP-PAW using the new build system will also be briefly mentioned.

Blöchl, Peter E [Institute for Theoretical Physic

Learning Nonlinear Reduced Models from Data with Operator Inference

This review discusses Operator Inference, a nonintrusive reduced modeling approach that incorporates physical governing equations by defining a structured polynomial form for the reduced model, and then learns the corresponding reduced operators from simulated training data. The polynomial model form of Operator Inference is sufficiently expressive to cover a wide range of nonlinear dynamics found in fluid mechanics and other fields of science and engineering, while still providing efficient reduced model computations. The learning steps of Operator Inference are rooted in classical projection-based model reduction; thus, some of the rich theory of model reduction can be applied to models learned with Operator Inference. This connection to projection-based model reduction theory offers a pathway toward deriving error estimates and gaining insights to improve predictions. Furthermore, through formulations of Operator Inference that preserve Hamiltonian and other structures, important physical properties such as energy conservation can be guaranteed in the predictions of the reduced model beyond the training horizon. This review illustrates key computational steps of Operator Inference through a large-scale combustion example.

Mechanics

Tunable magnetic excitations in the honeycomb antiferromagnet (Co,Ni)⁢TiO3

The solid solution of the honeycomb antiferromagnet (AFM) Co0.5⁢Ni0.5⁢TiO3 (CNTO) was synthesized by mixing a 1:1 molar ratio of CoTiO3 (CTO) and NiTiO3 (NTO). Powder neutron scattering was used to determine the structure and magnetic spectrum, where the nuclear and magnetic structures resemble those of the end members. The Néel temperature (T𝑁 = 27 ± 1 K), the ordered magnetic moment (M = 2.29 ± 0.03 𝜇𝐵 per magnetic ion), and lattice parameters are intermediate between those of the two. From inelastic neutron scattering, it is observed that the magnon density of states (MDOS) extends up to 13 meV, and the interaction can be described by an XXZ-type magnetic Hamiltonian. Above 15 meV, spin-orbit excitons (SOEs) are observed similarly to those in CTO, but with modified spin-orbit crystal-field splitting because of the substitution of Ni at Co sites, and the disorder induced by the Ni substitution modifies the spin-orbit crystal field. Thus, the magnetic dynamics of the CNTO cannot be described as a simple average of the two parent compounds.

Rathnayaka, Srimal [University of Virginia, Charlo

Atomistic Simulation of Glasses and Amorphous Materials: Challenges and Opportunities for the Next Decade

Atomistic simulations have become indispensable tools for understanding glass structure, dynamics, and properties, yet persistent challenges limit their predictive power. This perspective examines three interconnected issues, namely glass formation procedures, interatomic potential development, and machine learning applications, which emerged from the 5th International Workshop on Challenges of Atomistic Simulations of Glasses and Amorphous Materials. We identify convergent community priorities for (i) standardized validation protocols, (ii) curated benchmark datasets with complete metadata, and (iii) open repositories for glasses. A systematic was forward is provided by a hierarchical validation framework for assessing the structural fidelity, property prediction, and behavioral realism of simulation techniques. Looking ahead, transformative advances are promised by the fusion of classical techniques with machine learning based approaches, for instance, by integrating swap Monte Carlo with machine-learning (ML) potentials, leveraging foundation models through transfer learning, and finetuning ML potentials with experimental data. Progress depends on the community committing to validated models, reproducible protocols, and sustained data sharing.

Krishnan, N. M. Anoop

Generative learning of densities on manifolds

A generative modeling framework is proposed that combines diffusion models and manifold learning to efficiently sample data densities on manifolds. The approach utilizes Diffusion Maps to uncover possible low-dimensional underlying (latent) spaces in the high-dimensional data (ambient) space. Two approaches for sampling from the latent data density are described. The first is a score-based diffusion model, which is trained to map a standard normal distribution to the latent data distribution using a neural network. The second one involves solving an Itô stochastic differential equation in the latent space. Additional realizations of the data are generated by lifting the samples back to the ambient space using Double Diffusion Maps , a recently introduced technique typically employed in studying dynamical system reduction; here the focus lies in sampling densities rather than system dynamics. The proposed approaches enable sampling high dimensional data densities restricted to low-dimensional, a priori unknown manifolds. The efficacy of the proposed framework is demonstrated through a benchmark problem and a material with multiscale structure.

Double diffusion maps

A parametric study of slow dynamic nonlinear elasticity with comparisons to models

Several phenomenological models that aspire to quantitative description of anomalous nonlinear mesoscopic elasticity are reviewed and compared with laboratory measurements. This class of nonlinearity, best known perhaps for slow dynamics and aging, is seen widely in imperfectly consolidated granular solids but is not well understood. Typical slow dynamic tests show that a modest conditioning oscillatory "pump" strain depresses material stiffness, which then recovers like the logarithm of time after conditioning ceases. Several phenomenological models based on physical arguments have been proposed that predict the material stiffness response to arbitrary pump strain histories during conditioning and recovery. Approximate closed form and numerical solutions to the models are presented that predict the quantitative influence of three key pump parameters: the pump's strain amplitude, the pump's strain rate, and the pump’s duration. Laboratory measurements on Berea sandstone, concrete and a confined single aluminum bead find that slow dynamic responses are linear in pump strain and independent of pump frequency. Measurements also show that, after pump-off, stiffness recovers over times far longer than the pump duration. These observations and others are compared to model predictions. One of the considered models, based on a picture of fast brittle damage and slow healing, successfully matches all these behaviors.

36 MATERIALS SCIENCE

Uncovering obscured phonon dynamics from powder inelastic neutron scattering using machine learning

The study of phonon dynamics is pivotal for understanding material properties, yet it faces challenges due to the irreversible information loss inherent in powder inelastic neutron scattering spectra and the limitations of traditional analysis methods. In this study, we present a machine learning framework designed to reveal obscured phonon dynamics from powder spectra. Using a variational autoencoder, we obtain a disentangled latent representation of spectra and successfully extract force constants for reconstructing phonon dispersions. Notably, our model demonstrates effective applicability to experimental data even when trained exclusively on physics-based simulations. The fine-tuning with experimental spectra further mitigates issues arising from domain shift. Analysis of latent space underscores the model’s versatility and generalizability, affirming its suitability for complex system applications. Furthermore, our framework’s two-stage design is promising for developing a universal pre-trained feature extractor. This approach has the potential to revolutionize neutron measurements of phonon dynamics, offering researchers a potent tool to decipher intricate spectra and gain valuable insights into the intrinsic physics of materials.

domain adaptation