Computational Physics
A Massively Scalable Ligand-Protein Dissociation Dynamic Database Derived from Atomistic Molecular Modelling
Maodong Li, Dechin Chen, Zhijun Pan et al. (+2 more)
Understanding the kinetics of drug-
protein interactions is paramount for drug design, yet the field lacks large-scale, dynamic data to move beyond static structural analysis. Here, we present DD-03B, a massively scalable database providing dynamic, all-atom dissociation trajectories for a broad set of ligand-
protein complexes. Utilising and extending a validated computational pipeline, we generated dissociation trajectories for 19,037 ligand-
protein complexes sourced from PDBbind+v2020R1, resulting in a repository of approximately 0.3 billion simulation frames totalling 40 TB in size. For these systems-which possess experimental binding affinities (kd) but typically lack measured koff rates-we computed and assigned dissociation rate constants through trajectory reweighting. Our analysis reveals that
protein-ligand complexes can be categorised into three mechanistic types (pathway-dominant, open-pocket, and
entropy-pocket systems), each requiring distinct strategies for accurate kinetic characterisation. Together with our previously released DD-13M, DD-03B forms the core of the expandable Dissociation Dynamic Database (DDD) project, which will be continuously augmented with new trajectories. This large-scale, publicly available resource establishes a critical foundation for training and benchmarking next-generation generative AI models to predict and optimise drug-
protein dissociation kinetics.
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All authors Maodong Li, Dechin Chen, Zhijun Pan, Zhe Wang, Yi Isaac Yang
Atmospheric and Oceanic Physics
Single Scattering Properties for an Ensemble of Randomly Oriented Convex Polyhedra in Geometrical Optics Regime
Quan Mu
To study how geometrical shape affect the light scattering properties for an ensemble of randomly orientated particles, the single scattering
matrices including complete polarization information are calculated statistically for a group of
crystals with random geometrical shape and a group of hexagonal prisms with various aspect ratios in geometrical optics approximation method. To compare, the single scattering
matrices for individual random irregular
crystal and individual hexagonal prism are also presented. It should be noted that all statistical simulation experiments in this study are restricted to the following conditions: diffraction and absorption effects are neglected, calculations are performed at a single fixed wavelength, particles are assumed to be randomly oriented, and the simulations are limited to the regime where the
geometric optics approximation is applicable. Using a unified computational framework for scattering
matrices of convex polyhedra, we carried out a series of statistical numerical simulations. The flexibility of this framework in modifying particle geometry enables a systematic investigation of shape-dependent scattering characteristics. The results demonstrate that regular and irregular particles exhibit noticeably different scattering
matrix signatures, and ensembles of irregular particles yield smooth and featureless non-zero
matrix elements. In contrast, ensembles of regular hexagonal particles with varying aspect ratios retain common
geometric scattering features.
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Instrumentation and Detectors
True Alternating Current Scanning Tunneling Microscope (ACSTM): tunneling on insulators
M.J. Rost
Scanning Tunneling Microscopy (STM) has revolutionized our atomic scale understanding of surfaces and accelerated progress in nanotechnology. This technique, however, is restricted to metal or semiconducting samples, as it requires a tiny current to stabilize the tip-sample distance with atomic scale precision. We developed a new imaging and feedback method that relies on true alternating current (AC) without any direct current (DC) component. This technique does not only enable the imaging on non-conducting surfaces with atomic step resolution, like (thin) glass and
oxides, it provides also access to high-frequency electronic signal coming from the sample. We demonstrate that it is possible to measure on 25nm thick silicon
oxide with 10 MHz tunneling current.
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Plasma Physics · Cross-listed from astro-ph.HE
Particle-acceleration mechanisms in multispecies relativistic plasmas
Claudio Meringolo, Mario Imbrogno, Alejandro Cruz-Osorio et al. (+2 more)
While collisionless
plasmas are ubiquitously present near astrophysical compact objects, the impact that their composition has on the high-energy emission is presently unknown. We present the first investigation of particle-acceleration mechanisms in kinetic, special-relativistic
turbulence, modeling electrons, positrons, and
protons with realistic mass ratios. Under global charge neutrality, we introduce a positron fraction and cover regimes ranging from an electron-
proton plasma over to pair-dominated
plasmas. Using a novel generalized Ohm's law for multispecies relativistic
plasmas, we analyze particle acceleration due to electric fields in reconnection events that self-consistently emerge from
turbulence. We demonstrate, for the first time, that energization occurs at reconnection current sheets driven by the divergence of the relativistic pressure tensor, which locally aligns with the particle velocity and leads to an efficient energy transfer. The imbalance between electrons and positrons systematically favors electron acceleration, highlighting the necessity of realistic multispecies modeling to capture the nonthermal contributions in
accretion flows and relativistic jets from black holes.
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All authors Claudio Meringolo, Mario Imbrogno, Alejandro Cruz-Osorio, Sergio Servidio, Luciano Rezzolla
Optics · Cross-listed from cond-mat.supr-con
Nonlinear phononics in LaFeAsO: Optical control of the crystal structure toward possible enhancement of superconductivity
Shu Kamiyama, Tatsuya Kaneko, Kazuhiko Kuroki et al. (+1 more)
Nonlinear phononics provides a route to control
crystal structures through light-induced
phonon excitation. In this study, we apply nonlinear phononics to an iron-based
superconductor, LaFeAsO, with the aim of tuning its
crystal structure toward the ideal one to enhance superconductivity. We simulate light-induced
phonon dynamics on the anharmonic
lattice potential determined by first-principles calculations. We find that the anion height $h$, a key structural parameter in iron-based
superconductors, approaches its ideal value when an appropriate infrared-active
phonon mode is selectively excited. This result suggests the possibility of controlling
crystal structures and enhancing superconductivity in iron-based
superconductors based on the concept of nonlinear phononics.
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All authors Shu Kamiyama, Tatsuya Kaneko, Kazuhiko Kuroki, Masayuki Ochi
Data Analysis and Statistics · Cross-listed from cond-mat.mes-hall
Resolving Single-Peptide Phosphorylation Dynamics in Plasmonic Nanopores using Physics-Informed Bi-Path Model
Mulusew W. Yaltaye, Yingqi Zhao, Kuo Zhan et al. (+2 more)
Protein phosphorylation provides a dynamic readout of cellular signaling yet remains difficult to detect at low abundance and stoichiometry. Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) using particle-in-pore plasmonic nanopores offers label-free molecular detection with submolecular sensitivity. However, reliable identification of subtle post-translational modifications (PTMs) is hindered by the
stochastic nature of SM-SERS signals, partial excitation of peptide residues within the plasmonic hotspot, and background interference. Here, we introduce a physics-informed deep learning framework to decode complex SM-SERS dynamics and identify single-peptide PTMs. The model integrates multiple-instance learning with a temporal encoder combining temporal convolutional networks and bidirectional gated recurrent units to capture both local spectral variability and long-range blinking dynamics. To address
diffusion-driven spectral heterogeneity, long spectral trajectories are segmented using Pearson-correlation, enabling weakly supervised training under label ambiguity. This framework robustly distinguishes single peptide phosphorylation despite strong background interference and
stochastic signal fluctuations. By coupling nanoplasmonic confinement with spatiotemporal deep learning, our approach enables high-fidelity detection of single-molecule phosphorylation events and advances ultrasensitive phosphoproteomic analysis.
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All authors Mulusew W. Yaltaye, Yingqi Zhao, Kuo Zhan, Vahid Farrahi, Jian-An Huang
Chemical Physics · Cross-listed from cond-mat.dis-nn
Projector, Neural, and Tensor-Network Representations of $\mathbb{Z}_N$ Cluster and Dipolar-cluster SPT States
Seungho Lee, Daesik Kim, Hyun-Yong Lee et al. (+1 more)
The $\mathbb{Z}_N$ cluster-state wavefunction, a paradigmatic example of
symmetry-protected topological (SPT) order with $\mathbb{Z}_N \times \mathbb{Z}_N$
symmetry, is expressed in various equivalent ways. We identify the projector-based scheme called the $P$-representation as the efficient way to express cluster and dipolar cluster state's wavefunctions. Employing the restricted Boltzmann machine scheme to re-write the interaction
matrix in the $P$-representation in terms of neural weight
matrices allows us to develop the neural
quantum state (NQS) and the
matrix product state (MPS) representations of the same state. The NQS and MPS representations differ only in the way the weight
matrices are split and grouped together in a
matrix product. For both $\mathbb{Z}_N$ cluster and dipolar cluster states, we derive in closed form the weight function $W(s,h)$ that couples physical
spins $s$ to hidden variables $h$, generalizing the previous construction for $Z_2$ cluster states to $\mathbb{Z}_N$. For the dipolar cluster state protected by two charge and two dipole
symmetries, the procedure we have developed leads to the tensor product state (TPS) representation of the wavefunction where each local tensor carries three virtual indices connecting a given site to two nearest neighbors and one further neighbor. We
benchmark the resulting TPS construction against conventional MPS representation using density-
matrix renormalization group simulations and argue that the TPS could offer a more efficient representation for some modulated SPT states. As a by-product of the investigation, we generalize the previous $Z_2$
matrix product operator construction of the Kramers-Wannier (KW) operator to $\mathbb{Z}_N$ and interprets it as the dipolar generalization of the discrete
Fourier transform on $\mathbb{Z}_N$ variables. The new interpretation naturally explains why the KW map is non-invertible.
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All authors Seungho Lee, Daesik Kim, Hyun-Yong Lee, Jung Hoon Han
Optics
Attosecond quantum spectroscopy with entangled photon pairs
Zijian Lyu, Fengxiao Sun, Sili Yi et al. (+6 more)
Bright squeezed light from parametric down-conversion in the infrared (IR) frequency range has triggered the emergence of attosecond
quantum optics – a new research field at the interface of
quantum optics, strong-field physics, and attosecond technology. Two challenges arise at this interface: transferring
quantum features of the IR light sources to the ultraviolet (UV) and extreme ultraviolet (XUV) frequency range via strong-field nonlinearities, and exploiting
quantum optical properties of the nonlinear optical response as a new probe in ultrafast dynamics. Here, we address both by driving high-harmonic generation (HHG) in solids with entangled
photon pairs either in degenerate or non-degenerate frequency modes. In the degenerate mode, single-shot measurements of harmonics up to the 10th order reveal strong
photon bunching whose $g^{(2)}$ first grows and then decreases with the harmonic order. We show that this behavior tracks different microscopic mechanisms responsible for harmonic emission, demonstrating the potential of attosecond
quantum optical spectroscopy. In the non-degenerate case, the harmonics retain
quantum-induced correlations, verified by wavelength-resolved second-order cross-correlation maps. Our findings demonstrate transfer of
quantum photon correlations into the XUV domain and open a pathway toward
quantum-enhanced attosecond spectroscopy and control of ultrafast dynamics in solids.
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All authors Zijian Lyu, Fengxiao Sun, Sili Yi, Jingze Li, Haodong Liu, Qiongyi He, Qihuang Gong, Misha Ivanov, Yunquan Liu
Geophysics · Cross-listed from astro-ph.EP
Variable Earth's Rotation Speed in the 14th to 16th Centuries: New {\Delta}T Constraints from Chinese Eclipse Records
Hisashi Hayakawa, Mitsuru Sôma and Naiqi Li
Total
solar eclipses are not only astronomical spectacles but also great astrophysical laboratories. Their historical records are particularly helpful for assessing the past variability of the Earth's rotation speed. Chinese records played a key role for such analyses. However, Chinese eclipse records from the Míng period have not been used for {\Delta}T reconstructions, partially because most of the contemporaneous eclipse reports are found not in official histories but in local treatises. This study examines eclipse records in the (quasi-)contemporaneous local treatises, concentrating on what explicitly mentioned eclipse totality on the day of a total
solar eclipse and what were compiled during the Míng Dynasty. On their basis, our study revised the {\Delta}T constraint in 1361 to -408 s =< {\Delta}T =< 601 s and set new {\Delta}T constraints of 277 s =< {\Delta}T =< 890 s in 1514, -328 s =< {\Delta}T =< 332 s in 1542, and -1762 s =< {\Delta}T =< 1091 s in 1575, respectively. We also revised most of the existing {\Delta}T constraints in the 14th to 16th centuries, using the ephemeris data of the NASA JPL DE 441. Overall, our {\Delta}T constraints generally tighten the {\Delta}T variations more than what M+21 fit for their {\Delta}T spline curve, requiring downward modification and upward modifications for the {\Delta}T reconstructions around 1361 and 1542, respectively. Our results suggest that the {\Delta}T decrease between 1514 and 1567 was slightly steeper than previously considered.
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Data Analysis and Statistics · Cross-listed from hep-ex
Biases in the Determination of Correlations Between Underground Muon Flux and Atmospheric Temperature
Bangzheng Ma, Katherine Dugas, Kam-Biu Luk et al. (+3 more)
The underground rates of
cosmic-ray
muons exhibit seasonal variations correlated with effective atmospheric temperature, quantified via a single coefficient. We compare two analysis methods for studying the correlation: the standard Unbinned Method, where all rate-temperature data points are fit simultaneously via linear regression, and the Binned Method, where data points with similar temperatures are first grouped into bins before fitting. We find that while both methods are unbiased in the limit of negligible temperature uncertainties, the Binned Method develops significant bias when temperature uncertainties are present, due to binning-induced distortions. In contrast, the Unbinned Method remains robust if the uncertainties are accurately known. To address the widely encountered issue of imprecise uncertainty estimation, we propose a novel procedure that assesses correlation stability by varying the time intervals and their assigned uncertainties. This approach resolves methodological tensions in studies of seasonal modulation of the
muon rate and provides a practical framework for robust correlation estimation under real-world conditions.
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All authors Bangzheng Ma, Katherine Dugas, Kam-Biu Luk, Juan Pedro Ochoa-Ricoux, Bedřich Roskovec, Qun Wu
Atomic Physics
Strong-field ionization of atoms with bright squeezed vacuum light
Haodong Liu, Xiaoxiao Long, Peizeng Li et al. (+2 more)
Strong-field ionization is the cornerstone of attosecond physics, which has been extensively studied under coherent-state driving. Recently, the interface between attosecond physics and
quantum optics has emerged as a new frontier. Yet, owing to experimental limitations, the role of the
quantum nature of light in atomic strong-field ionization has remained unexplored. Here, we demonstrate strong-field ionization of xenon atoms driven by bright squeezed
vacuum (BSV) with average pulse energy up to 10 \textmu J. We show that, as a nonclassical state with zero mean field and strong intensity fluctuations, BSV selectively enhances the spider-like
holographic structures in the photoelectron momentum distributions. Using a
quantum-light-corrected
quantum-trajectory Monte Carlo (q-QTMC) model, we attribute this effect to the intrinsic coherence of trajectory pairs emitted within the same subcycle field fluctuation. These dynamically correlated paths exhibit enhanced phase stability and remain robust against dephasing, whereas asynchronous paths are filtered out by field noise. Our results reveal a
quantum-fluctuation-induced mechanism for coherence protection in strong-field processes, positioning BSV as an effective coherence filter and establishing a new regime of
quantum-enabled noise-resilient ultrafast dynamics.
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All authors Haodong Liu, Xiaoxiao Long, Peizeng Li, Zijian Lyu, Yunquan Liu
Plasma Physics
Development of a Simple Stellarator using Tilted Circular Toroidal Field Coils
Ashit Kumar Nath and Yasuhiro Suzuki
This study investigates a simplified stellarator configuration employing circular coils, in which rotational transform is generated by tilting the toroidal field (TF) coils. A pair of axisymmetric poloidal field (PF) coils is introduced to compensate for the vertical
magnetic field component produced by the tilted TF coils, together forming the three-dimensional
magnetic configuration. The existence of clear, nested
magnetic flux surfaces is confirmed through
magnetic field-line tracing, and the corresponding
vacuum free-boundary
equilibrium is computed using the DESC solver. The coil set is partially optimized by varying the TF coil radius and tilt angle to reduce neoclassical transport and enhance alpha-particle confinement. The optimized configuration is compared with fully optimized stellarators such as W7-X and LHD in terms of alpha-particle confinement and the Gamma_C proxy. The neoclassical transport coefficient D11 is evaluated and found to be low. Collisionless guiding-center orbit calculations for 100 eV
protons and 3.5 MeV alpha particles further demonstrate favorable confinement properties.
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Optics
Steady-State Statistical Modeling of Digitally Stabilized Laser Frequency with Markov-State Feedback
Swarnav Banik, Elliot Greenwald and Xing Pan
Laser frequency stabilization is conventionally analyzed using continuous-time control theory, which accurately models analog feedback but is insufficient for digital implementations where quantization, sampling, and
stochastic noise shape the dynamics. In modern digital
laser systems, such as Photonic Integrated
Circuit (PIC)-based
lasers, finite discriminator and actuator resolution, sampling delays, and measurement noise introduce
stochastic behavior that deterministic models do not capture. We present a discrete-time Markov-state framework that models the
evolution of the quantized actuator in a digital
laser frequency lock, with state-transition probabilities determined by the frequency discriminator response, noise statistics, and implemented digital control logic. The steady-state actuator and locked-
laser frequency distributions are obtained directly from the unit-
eigenvalue solution of the transition
matrix, providing immediate access to key stability metrics without long time-domain simulations. For white frequency noise, we show that the Markov formulation is exact under decorrelated sampling and update schemes, while correlated discriminator sampling introduces a predictable inflation of actuator variance without shifting the operating point. In the presence of colored noise, long-range temporal correlations induce sampling-dependent deviations in both actuator mean and variance, defining the regime of validity of the memoryless Markov description. This framework provides a compact and physically transparent tool for analyzing and optimizing digitally stabilized
lasers in integrated photonic systems.
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Optics
Ultra-wideband electrically-tuned mid-infrared on-chip parametric oscillator
Alexander Y. Hwang, Hubert S. Stokowski, Luke Qi et al. (+7 more)
Developing compact, broadband mid-infrared coherent sources for applications in spectroscopy and sensing remains a pressing challenge in photonics. However, material limitations and integration constraints have restricted the accessible wavelengths and operation bandwidths of current mid-infrared
lasers. Here, we address these challenges by developing a nonlinear integrated photonic device that converts a fixed-wavelength near-infrared pump
laser into broadly tunable mid-infrared light. Our device, an optical parametric oscillator (OPO) integrated on thin-film lithium niobate, generates 22 THz of multi-milliwatt, voltage-tunable radiation from 2.7-3.4 microns, a region typically difficult to access but vital for environmental, chemical, and biological sensing. By introducing an on-chip-tunable OPO architecture taking advantage of the Vernier effect, we obtain electrical control of the emission wavelengths from coarse, multi-THz scales down to continuous, sub-100-GHz mode-hop-free tuning ranges. This work establishes a robust platform for a new class of compact, widely tunable mid-infrared sources with potential for future scaling.
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All authors Alexander Y. Hwang, Hubert S. Stokowski, Luke Qi, David K. Concepcion, Geun Ho Ahn, Ethan Rosenfeld, Taewon Park, Devin J. Dean, Martin M. Fejer, Amir H. Safavi-Naeini
Medical Physics · Cross-listed from eess.IV
4D Vessel Reconstruction for Benchtop Thrombectomy Analysis
Ethan Nguyen, Javier Carmona, Arisa Matsuzaki et al. (+2 more)
Introduction: Mechanical thrombectomy can cause vessel deformation and procedure-related injury. Benchtop models are widely used for device testing, but time-resolved, full-field 3D vessel-motion measurements remain limited. Methods: We developed a nine-camera, low-cost multi-view workflow for benchtop thrombectomy in silicone middle cerebral artery phantoms (2160p, 20 fps). Multi-view
videos were calibrated, segmented, and reconstructed with 4D Gaussian Splatting. Reconstructed point clouds were converted to fixed-connectivity edge graphs for region-of-interest (ROI) displacement tracking and a relative surface-based stress proxy. Stress-proxy values were derived from edge stretch using a Neo-Hookean mapping and reported as comparative surface metrics. A synthetic Blender pipeline with known deformation provided
geometric and temporal validation. Results: In synthetic bulk translation, the stress proxy remained near zero for most edges (median $\approx$ 0 MPa; 90th percentile 0.028 MPa), with sparse outliers. In synthetic pulling (1-5 mm), reconstruction showed close
geometric and temporal agreement with ground truth, with symmetric Chamfer distance of 1.714-1.815 mm and precision of 0.964-0.972 at $\tau = 1$ mm. In preliminary benchtop comparative trials (one trial per condition), cervical aspiration catheter placement showed higher max-median ROI displacement and stress-proxy values than internal carotid artery terminus placement. Conclusion: The proposed protocol provides standardized, time-resolved surface kinematics and comparative relative displacement and stress proxy measurements for thrombectomy benchtop studies. The framework supports condition-to-condition comparisons and methods validation, while remaining distinct from absolute wall-stress estimation. Implementation code and example data are available at https://ethanuser.github.io/vessel4D
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All authors Ethan Nguyen, Javier Carmona, Arisa Matsuzaki, Naoki Kaneko, Katsushi Arisaka
Atmospheric and Oceanic Physics
Global near-real-time daily emissions of atmospheric pollutants from power plants
Tao Li, Lixing Wang, Biqing Zhu et al. (+1 more)
The power sector is a major source of fossil fuel use and air pollutant emissions, making high-spatiotemporal-resolution emission accounting essential for effective mitigation policy and air quality management. Yet existing public inventories are often limited by low timeliness and coarse resolution. Here, we develop a global, plant-level, daily, multi-pollutant emission database for the power sector by integrating nearly 3 million hourly-to-daily near-real-time power generation records from 57 countries, representing about 81% of global fossil-fuel-based electricity generation, with fundamental information for more than 10,000 power plants worldwide, including location and installed capacity. The
dataset substantially improves the timeliness and granularity of global power-sector emission estimates. From 2019 to 2025, emissions of most pollutants increased, with 2025 daily mean emissions reaching 0.274 kt/d for BC, 45.1 kt/d for CO, 0.418 kt/d for NH3, 52.2 kt/d for NOx, 3.01 kt/d for NMVOC, 0.418 kt/d for OC, 6.76 kt/d for PM10, 5.11 kt/d for PM2.5, and 78.5 kt/d for SO2. Compared with 2019, NMVOC showed the largest increase, whereas SO2 was the only pollutant to decline overall. Coal remained the dominant source of sulfur-, nitrogen-, and particulate-related emissions, while gas and biomass contributed more to carbonaceous species and reduced nitrogen. The
dataset also captures pronounced seasonal, regional, and short-term variability. Against EDGAR for 2019-2022, our estimates agree well, with Pearson correlations of 0.92-0.99 and mean relative deviations of 8.8%-28.1%. This near-real-time, high-resolution
dataset provides a strong foundation for air pollution control, carbon mitigation, emission monitoring, and satellite-based inversion.
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All authors Tao Li, Lixing Wang, Biqing Zhu, Zhu Liu
Applied Physics
Single-Crystal, Single-Chirality, Single-Wall Carbon Nanotube Heterostructures for Optoelectronics: An Opinion
Ting-Wei Chang, Gustavo M. Rodriguez-Barrios, Andrey Baydin et al. (+1 more)
The extraordinary one-dimensional properties of carbon nanotubes have captivated scientists and engineers since their discovery in the early 1990s. In particular, semiconducting single-wall carbon nanotubes (SWCNTs) are highly promising for optoelectronic applications because of their diameter-dependent direct band gaps and strong, tunable light-matter interactions. However, the prevalence of structural disorder, misalignment, and chirality heterogeneity in macroscopic assemblies has hindered their practical applications. Recently, advanced assembly methods, combined with post-growth chirality separation techniques, have enabled the fabrication of wafer-scale, nearly crystalline films of highly aligned and densely packed SWCNTs with tailored properties. In this Opinion, we discuss how these films provide a transformative platform for engineering "Single$^3$"
heterostructures-assemblies that are simultaneously single-
crystal, single-chirality, and single-wall. Stacking these layers with nanometer-scale precision and tunable thicknesses allows for the realization of artificial
bilayer junctions,
quantum wells, and superlattices. We posit that these architectures will enable a new generation of high-performance devices, including
lasers, photodiodes,
solar cells, and single-
photon emitters.
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All authors Ting-Wei Chang, Gustavo M. Rodriguez-Barrios, Andrey Baydin, Junichiro Kono
Medical Physics
Bayesian Aneurysm Growth Detection via Surface Displacement Modeling
Jorge A. Roa Castro, Abhishek Singh, Atharva Hans et al. (+5 more)
Clinical decisions for unruptured intracranial aneurysms depend on detecting growth on follow-up
magnetic resonance angiography (MRA). Growth is typically judged from manual 2D diameters on few slices, which vary across clinicians and frequently miss subtle 3D change. Even with 3D
segmentations, apparent differences can reflect resolution,
segmentation, surface processing, or registration mismatch rather than true growth; most criteria remain heuristic and binary. We show that a
Bayesian displacement-based model using the surrounding vessel as an internal reference achieves strong discrimination of aneurysm growth (AUC 0.86-0.87) and improves agreement with expert labels (Cohen's kappa up to 0.66 vs. 0.35 for volumetric criteria), while providing calibrated posterior probabilities with uncertainty bounds. The method registers baseline and follow-up surfaces, computes normal-directed displacements, and summarizes change as the difference between mean aneurysm displacement and mean displacement on the surrounding non-aneurysmal vessel segment. The vessel segment serves as an internal control for imaging and processing variability, assuming negligible structural change over the surveillance interval. We evaluate two cohorts spanning time-of-flight and contrast-enhanced longitudinal MRA studies: a public
dataset labeled from neuroradiologist-provided measurements and an institutional
dataset labeled by senior and junior raters. Performance is preserved when training on lower-expertise labels, indicating robustness to label variability. Calibrated probabilities may aid clinical decision-making in borderline cases, where high uncertainty can motivate repeat imaging. This framework provides interpretable probabilistic growth assessment from longitudinal MRA, reduces dependence on clinician expertise, and supports cross-center surveillance across scanners and angiography sequences.
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All authors Jorge A. Roa Castro, Abhishek Singh, Atharva Hans, Kostiantyn Kondratiuk, David Saloner, Vitaliy L. Rayz, Pavlos P. Vlachos, Ilias Bilionis
Optics
UV-enhanced SEM: towards orientation and electron work function imaging
Maciej Kretkowski, Haoran Mu, Hsin-Hui Huang et al. (+6 more)
Deep-UV ~ 250 nm (4.96 eV) tilted in-situ co-illumination of the sample under imaging by scanning electron microscope (SEM) is developed at a robust and practical instrument level. Precise mechanical control of the lateral position and tilt angle (within 6.5$^\circ$ from a 42$^\circ$ baseline) of the UV-C LED source is achieved using mechanisms external to the
vacuum chamber. The incorporated linear polariser (for s-pol. mode illumination) with external polarisation plane adjustment allows for modulation and tuning of tangential $E^{(t)}$ and normal $E^{(n)}$ electric field components and their enhancement for controlled directional electron emission from the surface of the sample. Numerical modelling of E-field enhancement corroborates the expected enhancement in the production of secondary electrons. This modality of SEM imaging does not require metal coatings, preserving sample integrity for subsequent analysis. The feasibility of having linearly polarised incident UV-C light with azimuthal orientation control in $(s,p)$-plane is modeled and discussed.
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All authors Maciej Kretkowski, Haoran Mu, Hsin-Hui Huang, Krishna Prasad Khakurel, Lukita Sari Ikhsan, Yu Masuda, Saulius Juodkazis, Wataru Inami, Yoshimasa Kawata
Fluid Dynamics
Modeling Ostwald Ripening Dynamics in Porous Microstructures
Md Zahidul Islam Laku, Mohammad Salehpour, Tian Lan et al. (+2 more)
Partially miscible ganglia trapped in a porous medium evolve through Ostwald ripening, driven by differences in interfacial
curvature. In practice, ganglia can span multiple pores and undergo discrete capillary events - invasion, snap-off, retraction, fragmentation, coalescence, and dislocation - that alter their
topology and induce local flow. Existing pore-network models (PNMs) for ripening are limited to single-pore ganglia, assume idealized pore shapes, and operate under quasi-static conditions that preclude flow. We present an image-based pore-network model (iPNM) that removes these limitations. Unlike existing PNMs, iPNM requires no idealization of pore shapes, as the effect on capillarity is encoded locally in
curvature-saturation curves computed via the pore-morphology method. iPNM couples two-phase flow, solute transport, and Ostwald ripening within a unified framework. We first verify iPNM against a prior quasi-static PNM, then validate it against recent high-resolution microfluidic experiments of hydrogen ripening in a sandstone-patterned micromodel over 15-24 days at 40C and 80C. Good agreement is obtained without adjustable parameters. Comparison with a continuum model shows that while macroscopic saturation is captured by both approaches, iPNM uniquely resolves population statistics, individual ganglion
curvatures, and pre-
equilibrium ripening dynamics within a representative elementary volume. Its computational efficiency over direct numerical simulation makes it suitable for guiding the development of improved theories of ripening in confined geometries.
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All authors Md Zahidul Islam Laku, Mohammad Salehpour, Tian Lan, Benzhong Zhao, Yashar Mehmani
Atmospheric and Oceanic Physics
A PMP-inspired Evaluation Framework for Assessing Deep-Learning Earth System Models
Giuliana Pallotta, Shiheng Duan, Céline Bonfils et al. (+3 more)
In recent years, Deep-Learning Earth System Models (DL-ESMs) have emerged as promising, computationally efficient complements to traditional Earth system models. Here, we present an evaluation framework for testing DL-ESMs from an Earth system model-development perspective using standardized diagnostics from the PCMDI Metrics Package (PMP). This framework allows DL-ESMs, including Ai2's ACE2 and Google's NeuralGCM, to be assessed with metrics that quantify their ability to reproduce climatology, major modes of variability, monsoons, and precipitation variability relative to observational reference
datasets and CMIP-class
benchmarks. By evaluating DL-ESMs with tools commonly used for traditional models, we extend their assessment beyond short-range forecast skill and toward longer Earth System-relevant applications. The results identify encouraging strengths in several large-scale fields and modes of variability, while also highlighting persistent challenges in precipitation, tropical variability, and long-run stability for some model versions. This evaluation is a critical step toward building trust in DL-ESMs, guiding future model development, and clarifying their fit-for-purpose for Earth system science applications.
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All authors Giuliana Pallotta, Shiheng Duan, Céline Bonfils, Jiwoo Lee, Seth Goodnight, Paul Ullrich
Fluid Dynamics · Cross-listed from math.AP
Global well-posedness of the one-phase Muskat problem with surface tension
Hongjie Dong and Hyunwoo Kwon
In this paper, we establish the global well-posedness of the one-phase Muskat problem with surface tension for small initial data. This problem describes the motion of the interface separating a wet region from a dry region within a porous medium, a process governed by Darcy's law. Although physically essential, the inclusion of surface tension introduces an additional challenge. We prove that if the initial free boundary is sufficiently small in $H^s$, $s>d/2+1$, then the problem admits a unique global strong solution. Moreover, the solution converges to zero in Lipschitz norm as $t\rightarrow\infty$. To the best of our knowledge, this work constitutes the first global well-posedness result for the one-phase Muskat problem with surface tension.
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Chemical Physics · Cross-listed from cond-mat.mtrl-sci
The effects of dispersion damping and three-body interactions for accurate layered-material exfoliation energies
Adrian F. Rumson, Kyle R. Bryenton and Erin R. Johnson
Accurate predictions of exfoliation energies and
lattice constants of layered materials hinge on a correct description of London dispersion physics. Modern a posteriori dispersion corrections in density-functional theory (DFT), such as the exchange-hole dipole moment (XDM) model, capture the proper asymptotic behaviour at long range while making use of damping functions to prevent unphysical divergence at short range. In the united-atom limit, the dispersion energy is damped to a finite, non-zero value by both the canonical Becke–Johnson (BJ) damping function and the new Z-damping function. XDM(BJ) has previously demonstrated exceptional accuracy for modelling layered materials, such as in the LM26
benchmark, which includes graphite, hexagonal boron nitride, lead(II)
oxide, and transition-metal dichalcogenides. This work presents the first assessment of XDM(Z) on the same
benchmark. We also show that inclusion of three-body interactions via the Axilrod–Teller–Muto (ATM) term further improves the computed exfoliation energies for both XDM(BJ) and XDM(Z), yielding the best performance achieved on LM26 using semi-local functionals to date, relative to reference data from the random-phase approximation.
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