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At least 253 records · Page 14

Graphic contrastive learning analyses of discontinuous molecular dynamics simulations: Study of protein folding upon adsorption

A comprehensive understanding of the interfacial behaviors of biomolecules holds great significance in the development of biomaterials and biosensing technologies. In this work, we used discontinuous molecular dynamics (DMD) simulations and graphic contrastive learning analysis to study the adsorption of ubiquitin protein on a graphene surface. Our high-throughput DMD simulations can explore the whole protein adsorption process including the protein structural evolution with sufficient accuracy. Contrastive learning was employed to train a protein contact map feature extractor aiming at generating contact map feature vectors. Subsequently, these features were grouped using the k-means clustering algorithm to identify the protein structural transition stages throughout the adsorption process. The machine learning analysis can illustrate the dynamics of protein structural changes, including the pathway and the rate-limiting step. Our study indicated that the protein–graphene surface hydrophobic interactions and the π–π stacking were crucial to the seven-stage adsorption process. Upon adsorption, the secondary structure and tertiary structure of ubiquitin disintegrated. The unfolding stages obtained by contrastive learning-based algorithm were not only consistent with the detailed analyses of protein structures but also provided more hidden information about the transition states and pathway of protein adsorption process and structural dynamics. Our combination of efficient DMD simulations and machine learning analysis could be a valuable approach to studying the interfacial behaviors of biomolecules.

97 MATHEMATICS AND COMPUTING↗

Compact in-vacuum gamma-ray spectrometer for high-repetition rate PW-class laser–matter interaction

With the advent of high repetition rate laser facilities, novel diagnostic tools compatible with these advanced specifications are required. This paper presents the design of an active gamma-ray spectrometer intended for these high repetition rate experiments, with particular emphasis on functionality within a PW level laser-plasma interaction chamber’s extreme conditions. The spectrometer uses stacked scintillators to accommodate a broad range of gamma-ray energies, demonstrating its adaptability for various experimental setups. In addition, it has been engineered to maintain compactness, electromagnetic pulse resistance, and ISO-5 cleanliness requirements while ensuring high sensitivity. The spectrometer has been tested in real conditions inside the PW-class level interaction chamber at the BELLA center, LBNL. The paper further details the calibration process, which utilizes a 60 Co radioactive source, and describes the unfolding technique implemented through a stochastic minimization method.

47 OTHER INSTRUMENTATION↗

Topological spin/structure couplings in layered chiral magnet Cr 1/3 TaS 2 : The discovery of spiral magnetic superstructure

Significance Magnets in which chirality of crystal lattice gives rise to noncollinear spin orders are ideal playgrounds for studies of novel physical phenomena originating from the nontrivial topology of magnetic textures. Most studies have been focused on homochiral materials, while topological magnetic states of heterochiral magnets have rarely been explored. Here, we report a layered chiral helimagnet with highly tunable topological heterochiral states. Tuning the chiral domain density, we have observed a topological magnetic texture that has the form of a spiral unfolding in the radial direction. In weak in-plane fields, this spiral magnetic superstructure transforms into a nonspiral array of concentric rings. Our results open a horizon for studies of tunable topological magnetic textures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex

The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA + ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3–REV7 binary and fused SHLD2–SHLD3–REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2–SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2–SHLD3–REV7–TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex.

59 BASIC BIOLOGICAL SCIENCES↗

A unified understanding of minimum lattice thermal conductivity

Here, we propose a first-principles model of minimum lattice thermal conductivity ($κ^{min}_L$) based on a unified theoretical treatment of thermal transport in crystals and glasses. We apply this model to thousands of inorganic compounds and find a universal behavior of $κ^{min}_L$ in crystals in the high-temperature limit: The isotropically averaged $κ^{min}_L$ is independent of structural complexity and bounded within a range from ~0.1 to ~2.6 W/(m K), in striking contrast to the conventional phonon gas model which predicts no lower bound. We unveil the underlying physics by showing that for a given parent compound, $κ^{min}_L$ is bounded from below by a value that is approximately insensitive to disorder, but the relative importance of different heat transport channels (phonon gas versus diffuson) depends strongly on the degree of disorder. Moreover, we propose that the diffuson-dominated $κ^{min}_L$ in complex and disordered compounds might be effectively approximated by the phonon gas model for an ordered compound by averaging out disorder and applying phonon unfolding. With these insights, we further bridge the knowledge gap between our model and the well-known Cahill–Watson–Pohl (CWP) model, rationalizing the successes and limitations of the CWP model in the absence of heat transfer mediated by diffusons. Finally, we construct graph network and random forest machine learning models to extend our predictions to all compounds within the Inorganic Crystal Structure Database (ICSD), which were validated against thermoelectric materials possessing experimentally measured ultralow κ L . Our work offers a unified understanding of $κ^{min}_L$, which can guide the rational engineering of materials to achieve .

42 ENGINEERING↗

Pseudogap in electron-doped cuprates: Strong correlation leading to band splitting

The pseudogap phenomena have been a long-standing mystery of the cuprate high-temperature superconductors. The pseudogap in the electron-doped cuprates has been attributed to band folding due to antiferromagnetic (AFM) long-range order or short-range correlation. We performed an angle-resolved photoemission spectroscopy study of the electron-doped cuprates Pr 1.3−x La 0.7 Ce x CuO 4 showing spin-glass, disordered AFM behaviors, and superconductivity at low temperatures and, by measurements with fine momentum cuts, found that the gap opens on the unfolded Fermi surface rather than the AFM Brillouin zone boundary. The gap did not show a node, following the full symmetry of the Brillouin zone, and its magnitude decreased from the zone-diagonal to (π,0) directions, opposite to the hole-doped case. These observations were reproduced by cluster dynamical-mean-field-theory calculation, which took into account electron correlation precisely within a (CuO 2 ) 4 cluster. In conclusion, the present experimental and theoretical results are consistent with the mechanism that electron or hole doping into a Mott insulator creates an in-gap band that is separated from the upper or lower Hubbard band by the pseudogap.

74 ATOMIC AND MOLECULAR PHYSICS↗

Acclimation to high and low diurnal light is flexible in Chlamydomonas reinhardtii

Chlamydomonas acclimates to repeated low (LL) or high light (HL) days by changing the abundance of photosynthetic complexes and the ultrastructure of its thylakoid membranes. These phenotypes persist through the night phases, suggesting a readiness for the daylight environment that is routinely experienced despite the intervening dark periods [S. Dupuis et al., Plant Cell 37, koaf086 (2025), 10.1093/plcell/koaf086]. Here, we investigate how prior acclimation impacts algal fitness upon a change in daylight intensity and how quickly Chlamydomonas can reprogram its photoprotective strategy in a diurnal context. We performed a systems analysis of synchronized populations acclimated to diurnal LL when subjected to HL days and of populations acclimated to diurnal HL when subjected to LL days. In the latter case, diurnal photoacclimation decreased fitness during the first day at a new light intensity: HL-acclimated cells barely increased in size over the first LL period, and they failed to complete a cell cycle. However, although LL-acclimated cells showed severe photodamage after 6 h of HL, they recovered chloroplast form and function later that afternoon and successfully divided at nightfall. These cells rapidly altered their thylakoid membrane ultrastructure, increased their photoprotective quenching capacity, and decreased their inventory of photosystem and antenna proteins by the end of the first HL day. Transcriptomic and proteomic analyses revealed rapid induction of thousands of genes, including those encoding proteases, chaperones, and other proteins involved in the chloroplast unfolded protein response. These results show that the alga is highly flexible and competent to rapidly acclimate to changes in diurnal light intensity.

Diel↗

Advances in Operando Electrocatalysis with High-Resolution Hard X-Ray Spectroscopy

Electrocatalysis unfolds at the interface—where solids, liquids, and gases meet to exchange charge, transform molecules, and set the foundation for technologies like CO 2 conversion, and water splitting. These interfacial regions are inherently dynamic, chemically diverse, and structurally heterogeneous. How atoms rearrange, oxidize, coordinate ligands, or adsorb reaction intermediates under electro-chemical potential defines a catalyst’s performance. Furthermore, capturing these changes with element specificity and electronic sensitivity under operando conditions remains one of the most critical challenges in the field.

Garcia-Esparza, Angel T. [SLAC National Accelerato↗

Tensor decompositions for count data that leverage stochastic and deterministic optimization

There is growing interest to extend low-rank matrix decompositions to multi-way arrays, or tensors. One fundamental low-rank tensor decomposition is the canonical polyadic decomposition (CPD). The challenge of fitting a low-rank, nonnegative CPD model to Poisson-distributed count data is of particular interest. Several popular algorithms use local search methods to approximate the maximum likelihood estimator (MLE) of the Poisson CPD model. Here, this work presents two new algorithms that extend state-of-the-art local methods for Poisson CPD. Hybrid GCP-CPAPR combines Generalized Canonical Decomposition (GCP) with stochastic optimization and CP Alternating Poisson Regression (CPAPR), a deterministic algorithm, to increase the probability of converging to the MLE over either method used alone. Restarted CPAPR with SVDrop uses a heuristic based on the singular values of the CPD model unfoldings to identify convergence toward optimizers that are not the MLE and restarts within the feasible domain of the optimization problem, thus reducing overall computational cost when using a multi-start strategy. We provide empirical evidence that indicates our approaches outperform existing methods with respect to converging to the Poisson CPD MLE.

CPAPR↗

Results from the last DD and DT JET campaigns in the framework of the EUROfusion Tokamak Exploitation Work Package activity

JET, the only tokamak capable of operating with deuterium–tritium (D–T) fuel (since TFTR was shutdown in 1999), has provided essential experimental data to support ITER and DEMO design and operation. Within the EUROfusion Tokamak Exploitation Work Package, JET completed its final campaigns (2022–2023), culminating in the third D–T campaign (DTE3). These experiments addressed key challenges in plasma scenarios, exhaust control, and tritium management under reactor-relevant conditions. Significant progress was achieved in demonstrating ITER-like integrated scenarios with impurity seeding, achieving partial divertor detachment and high confinement ($H_{98}(y,2)$ ≈ 0.85) at 3 MA in D–T plasmas. Advanced exhaust regimes such as quasi-continuous exhaust (QCE) and X-point radiator (XPR) were successfully achieved first in D–D and then extended to D–T operation, confirming their relevance for mixed isotope operation. Operational milestones included a new world record of 69 MJ fusion energy in tritium-rich hybrid plasmas and long-pulse H-mode operation up to 60 s, contributing with unique data to the CICLOP database. Physics studies focused on peeling-limited pedestals in support of ITER and improved understanding of edge stability and impurity screening in metallic environments. Extensive usage of the shattered pellet injector (SPI) on JET provided critical information for the design of the ITER disruption mitigation system (DMS). Real-time control systems for D/T ratio control and plasma exhaust were deployed and demonstrated in D–D and D–T, while energetic particle physics investigations unfolded the role of fast ions in turbulence suppression mechanisms. Comprehensive tritium retention studies using gas balance method, post-mortem analysis, and ITER-relevant laser induced desorption spectroscopy (LIDS) diagnostics provided essential input for tritium accountancy strategies. These results are validating the ITER operational concepts, inform DEMO design, and deliver critical experience in nuclear operation and scenario integration.

disruptions↗

Measurements of $\overline{\nu}_{\mu}$ and $\overline{\nu}_{\mu} + \nu_{\mu}$ charged-current cross-sections without detected pions or protons on water and hydrocarbon at a mean anti-neutrino energy of 0.86 GeV

We report measurements of the flux-integrated $\overline{\nu}_\mu$ and $\overline{\nu}_\mu+\nu_\mu$ charged-current cross-sections on water and hydrocarbon targets using the T2K anti-neutrino beam with a mean beam energy of 0.86 GeV. The signal is defined as the (anti-)neutrino charged-current interaction with one induced $\mu^\pm$ and no detected charged pion or proton. These measurements are performed using a new WAGASCI module recently added to the T2K setup in combination with the INGRID Proton Module. The phase space of muons is restricted to the high-detection efficiency region, $p_{\mu}>400~{\rm MeV}/c$ and $\theta_{\mu}<30^{\circ}$, in the laboratory frame. An absence of pions and protons in the detectable phase spaces of $p_{\pi}>200~{\rm MeV}/c$, $\theta_{\pi}<70^{\circ}$ and $p_{\rm p}>600~{\rm MeV}/c$, $\theta_{\rm p}<70^{\circ}$ is required. In this paper, both the $\overline{\nu}_\mu$ cross-sections and $\overline{\nu}_\mu+\nu_\mu$ cross-sections on water and hydrocarbon targets and their ratios are provided by using the D’Agostini unfolding method. The results of the integrated $\overline{\nu}_\mu$ cross-section measurements over this phase space are $\sigma_{\rm H_{2}O}=(1.082\pm0.068(\rm stat.)^{+0.145}_{-0.128}(\rm syst.)) \times 10^{-39}\,{\rm cm^{2} / nucleon}$, $\sigma_{\rm CH}=(1.096\pm0.054(\rm stat.)^{+0.132}_{-0.117}(\rm syst.)) \times 10^{-39}\,{\rm cm^{2} / nucleon}$, and $\sigma_{\rm H_{2}O}/\sigma_{\rm CH} = 0.987\pm0.078(\rm stat.)^{+0.093}_{-0.090}(\rm syst.)$. The $\overline{\nu}_\mu+\nu_\mu$ cross-section is $\sigma_{\rm H_{2}O} = (1.155\pm0.064(\rm stat.)^{+0.148}_{-0.129}(\rm syst.)) \times 10^{-39}\,{\rm cm^{2} / nucleon}$, $\sigma_{\rm CH}=(1.159\pm0.049(\rm stat.)^{+0.129}_{-0.115}(\rm syst.)) \times 10^{-39}\,{\rm cm^{2} / nucleon}$, and $\sigma_{\rm H_{2}O}/\sigma_{\rm CH}=0.996\pm0.069(\rm stat.)^{+0.083}_{-0.078}(\rm syst.)$.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Transient local secondary structure in the intrinsically disordered C‐term of the Albino3 insertase

Albino3 (Alb3) is an integral membrane protein fundamental to the targeting and insertion of light‐harvesting complex (LHC) proteins into the thylakoid membrane. Alb3 contains a stroma‐exposed C‐terminus (Alb3‐Cterm) that is responsible for binding the LHC‐loaded transit complex before LHC membrane insertion. Alb3‐Cterm has been reported to be intrinsically disordered, but precise mechanistic details underlying how it recognizes and binds to the transit complex are lacking, and the functional roles of its four different motifs have been debated. Using a novel combination of experimental and computational techniques such as single‐molecule fluorescence resonance energy transfer, circular dichroism with deconvolution analysis, site‐directed mutagenesis, trypsin digestion assays, and all‐atom molecular dynamics simulations in conjunction with enhanced sampling techniques, we show that Alb3‐Cterm contains transient secondary structure in motifs I and II. The excellent agreement between the experimental and computational data provides a quantitatively consistent picture and allows us to identify a heterogeneous structural ensemble that highlights the local and transient nature of the secondary structure. This structural ensemble was used to predict both the inter‐residue distance distributions of single molecules and the apparent unfolding free energy of the transient secondary structure, which were both in excellent agreement with those determined experimentally. We hypothesize that this transient local secondary structure may play an important role in the recognition of Alb3‐Cterm for the LHC‐loaded transit complex, and these results should provide a framework to better understand protein targeting by the Alb3‐Oxa1‐YidC family of insertases.

Okoto, Patience S.↗

Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC

AbstractThe folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

Zhao, Yanyan (ORCID:0000000323021763)↗

Electronic structures and pseudogap nature of the strongly correlated Kondo semimetals and insulators CeNiSn and CeRhX(X=As, Sb)

Employing temperature (T)-dependent angle-resolved photoemission spectroscopy (ARPES) near the Ce 4d absorption edge, we have investigated the electronic structures of the strongly correlated Kondo insulators (KIs) and/or Kondo semimetals of CeNiSn and CeRhX (X=As, Sb), which also belong to potential topological KIs (TKIs). Good agreement is found between the Fermi surfaces (FSs) measured at the Ce 4d→4f on resonance and those calculated and unfolded into the Ce-only Brillouin zone, supporting the crucial Ce 4f contribution to the Fermi-edge states in them. While the FSs of CeRhSb and CeNiSn are similar to each other, they are quite different from those of CeRhAs, which is understood to originate from the semimetallic Kondo ground states of CeNiSn and CeRhSb in contrast to the insulating Kondo ground state of CeRhAs. T-dependent ARPES demonstrates the existence of the Kondo resonance above the Fermi level (EF) and its T-driven decoherence in CeNiSn and CeRhSb, and the existence of the Ce 4f Kondo-like peak well below EF with a pseudogap in CeRhAs. With increasing T, the tail of the Kondo resonance in CeNiSn and CeRhSb loses its coherence, whereas the Ce 4f Kondo-like peak in CeRhAs persists up to T≥200 K. The Kondo temperatures (TKs) are estimated via the analysis of T-dependent ARPES, yielding TK≈80 K (CeNiSn), TK≈180 K (CeRhSb), and TK≫200 K (CeRhAs). High-resolution, low-T ARPES confirms the Kondo resonance just above EF in CeNiSn and CeRhSb Kondo semimetals and the KI ground state of CeRhAs with a pseudogap of Δ≈30 meV, demonstrating the importance of the coherent Kondo states in determining their potential topological properties. The differences in the T-dependent ARPES of CeNiSn and CeRhSb suggest the weaker f-c hybridization in CeNiSn than in CeRhSb (c: conduction electron), which is likely due to the more localized Ni 3d orbitals than the delocalized Rh 4d orbitals. The differences between the T-dependent ARPES of CeNiSn/CeRhSb Kondo semimetals and those of CeRhAs Kondo insulator are likely due to the smaller volume of CeRhAs than those of CeNiSn/CeRhSb.

Kang, J-S↗

Anomalous lattice relaxation dynamics in optimally doped La 2−𝑥⁢ Sr 𝑥 ⁢CuO 4

The atomic lattice plays a critical role in the emergence of high-𝑇 𝑐 superconductivity in cuprates. While the dynamics associated with electron-lattice coupling typically unfold on picosecond-to-femtosecond timescales, we present an x-ray photon correlation spectroscopy investigation on an optimally doped La-based cuprate that reveals a strong response of kilosecond-scale lattice relaxation dynamics to the superconducting state. Notably, an anomaly emerges around 𝑇 𝑐 : upon cooling into the superconducting state, the average atomic relaxation lifetime decreases, i.e., dynamics accelerate. This indicates a significant change in the local disorder-induced strain field dynamics at the superconducting transition, highlighting a remarkable coupling between superconductivity and the lattice on quasistatic timescales.

Petsch, A. N. [SLAC National Accelerator Laborator↗

Temperature dependence of electron-phonon interactions in vanadium

First-principles calculations were used to study the Fermi surface of body-centered cubic vanadium at elevated temperatures. Supercell calculations accounted for effects of thermal atom displacements on band energies, and band unfolding was used to project the spectral weight of the electron states into the Brillouin zone of a standard bcc unit cell. An electronic topological transition (ETT, or Lifshitz transition) occurred near the Γ point with increasing temperature, but the large thermal smearings from the atomic disorder and the Fermi-Dirac distribution reduced the effect of this ETT on the electron-phonon interactions. The phonon dispersions showed thermal stiffening of their Kohn anomalies near the Γ point and of the longitudinal N phonon mode. Finally, in general the effects of the ETT were overcome by the thermal smearing of the Fermi surface that reduces the spanning vector densities for anomalous phonon modes.

36 MATERIALS SCIENCE↗

Temperature-dependent angle-resolved photoemission spectroscopy study of the Ce 4f states in a possible topological Kondo insulator CeRhAs

The electronic structure of a possible topological Kondo insulator of CeRhAs has been investigated by employing temperature (T)-dependent angle-resolved photoemission spectroscopy (ARPES). Fermi surfaces (FSs) and band structures are successfully measured for three orthogonal crystallographic planes. The measured Fermi-edge states are found to have a three-dimensional (3D) character, contradictory to the proposed topological surface states of the 2 D character. The measured FSs due to the Ce 4f electrons agree well with those from the density functional theory band structures unfolded into the reduced Ce-only unit cell. The theoretically predicted hourglass-type bulk bands along $\bar{X}\bar{S}\bar{X}$ are not clearly resolved, in spite of the evident existence of those band features. Finally, T -dependent ARPES measurements reveal that the coherent Ce 4f states, having two pseudogap structures of Δ 1 ~ 80 meV and Δ 2 ~ 30 meV, persist to remain above 200 K, in agreement with the high Kondo temperature of CeRhAs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Strain-modulated helimagnetism and emergent magnetic phase diagrams in highly crystalline MnP nanorod films

Here, we explore strain-modulated helimagnetism in highly crystalline MnP nanorod films grown on Si(100) substrates using molecular beam epitaxy. The strained MnP film exhibits a paramagnetic to ferromagnetic (FM) phase transition at $T_C$ ~ 279 K, and the FM to helical phase transition at $T_N$ ~ 110 K. The value of $T_N$ is greater than $T_N$ ~ 47K for the MnP single crystal, indicating strong strain-modulated helimagnetic states in the MnP nanorod film. The presence of significant thermal hysteresis in the helical phase indicates the coexistence of competing magnetic interactions, leading to the first-order metamagnetic transition. Similar to its single-crystal counterpart, an anisotropic magnetic effect is observed in the MnP film, which is independently confirmed by magnetic hysteresis loop and radio-frequency transverse susceptibility (TS) measurements. The evolution of the screw to the cone and fan phases is precisely tracked from magnetization vs magnetic field/temperature measurements. The temperature dependence of the anisotropy fields, extracted from the TS spectra, yields further insight into the competing nature of the magnetic phases. Unfolding of the different helical phases at $\textit{T}$ < 120 K (~$T_N$) is analyzed by the temperature- and field-dependent magnetic entropy change. Based on these findings, the comprehensive magnetic phase diagrams of the MnP nanorod film are constructed for both the in-plane and out of plane magnetic field directions, revealing emergent strain/dimensionality-driven helical magnetic features that are absent in the magnetic phase diagram of the MnP single crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗