Computational Physics · Cross-listed from cs.DC
A Precision Emulation Approach to the GPU Acceleration of Ab Initio Electronic Structure Calculations
Hang Liu, Junjie Li, Yinzhi Wang et al. (+2 more)
This study explores the use of INT8-based emulation for accelerating traditional FP64-based HPC workloads on modern GPU architectures. Through SCILIB-Accel automatic BLAS offload tool for cache-coherent Unified
Memory Architecture, we emulate FP64
matrix multiplications in the LSMS CPU application in the MuST suite without code changes. We find that accuracy depends on both arithmetic precision and the properties of the operator, which can be dealt with through tunable precision emulation. Unlike traditional mixed-precision approaches, this method preserves original
algorithms while optimizing hardware utilization. We showcase the potential of improving accuracy and performance at the same time. This work highlights the potential of AI-driven hardware to transform HPC, advocating for adaptive precision strategies in future scientific computing.
Read the full abstract ▾
All authors Hang Liu, Junjie Li, Yinzhi Wang, Niraj K. Nepal, Yang Wang
Chemical Physics · Cross-listed from cond-mat.mes-hall
Negative Electronic Friction and Non-Markovianity in Nonequilibrium Quantum Systems
Riley J. Preston, Samuel L. Rudge, Daniel S. Kosov et al. (+1 more)
We address the connection between negative electronic friction and non-Markovian effects in the nonadiabatic vibrational dynamics of molecules interacting with metal surfaces under nonequilibrium conditions. We show that a generic nonequilibrium mechanism leading to negative Markovian electronic friction, where molecular vibrations couple directly to inelastic electronic transitions, also introduces significant non-Markovian contributions to the electronic friction. To demonstrate these ideas, we investigate nonequilibrium charge transport through a molecular nanojunction containing a vibrationally coupled donor-acceptor model, where negative electronic friction reflects driving of the vibrational mode beyond standard Joule heating. By comparison to numerically exact, fully
quantum hierarchical equations of motion simulations, we verify that these non-Markovian effects have a significant impact on the nonequilibrium dynamics and even on the stability of the resulting Langevin equation.
Read the full abstract ▾
All authors Riley J. Preston, Samuel L. Rudge, Daniel S. Kosov, Michael Thoss
Chemical Physics
TD$\Delta$SCF: Time-Dependent Density Functional Theory with a Non-Aufbau Reference for near-degenerate states
Shuto Shibasaki, Fumiya Mohri and Takashi Tsuchimochi
Near-degenerate electronic structures remain a major challenge for conventional single-reference density functional theory (DFT). To address this problem, we propose time-dependent $\Delta$SCF (TD$\Delta$SCF), a novel linear-response scheme in which a non-Aufbau $\Delta$SCF determinant serves as the reference for a subsequent TDDFT calculation. In contrast to collinear
spin-flip (SF)-TDDFT, this formulation preserves the usual Coulomb and exchange-correlation response contributions while describing the target states from an electronically excited reference. We examine the performance of TD$\Delta$SCF for several prototypical problems involving near-degeneracy, including the torsional potential of ethylene, singlet–triplet gaps of representative diradicals, geometry optimizations of benzyne isomers, and bond-dissociation curves of hydrogen fluoride and F$_2$. Across these tests, TD$\Delta$SCF shows markedly weaker functional dependence than SF-TDDFT and often yields a more balanced description of challenging singlet states. In particular, it provides smooth torsional potentials, improved singlet–triplet gaps, a consistent monocyclic structure for singlet $m$-benzyne, and a more satisfactory description of bond dissociation without the spurious low-lying states found in SF-TDDFT. At the same time, the method exhibits a systematic tendency to overestimate singlet energies and can lose accuracy when the underlying $\Delta$SCF reference is not well suited to the final state. We also identify a numerical instability that can arise in non-Aufbau calculations and trace its origin to the exchange-correlation potential near uncompensated nodal regions. These results highlight both the promise and the practical limitations of TD$\Delta$SCF as a low-cost method for singlet states with near-degenerate electronic structures.
Read the full abstract ▾
Applied Physics · Cross-listed from cond-mat.mtrl-sci
Molecular beam epitaxy of wafer-scale O-band InAs/InGaAs quantum dots on GaAs for quantum photonics
Pavel S. Avdienko, Lukas Hanschke, Quirin Buchinger et al. (+13 more)
We report a scalable molecular beam epitaxy strategy to achieve a low density of O-band electrically tunable InAs/InGaAs
quantum dots (QDs) on GaAs(001) substrates. Our approach is based on a gradient deposition of InAs in the sub-ML regime and subsequent capping with an InGaA strain-reducing layer to
redshift the emission wavelength. For different growth conditions, we investigate the optical properties of the dots using photoluminescence mapping and correlate with structural properties determined by scanning transmission electron microscopy. Using a surface roughness modulation technique and synchronizing InAs sub-monolayer deposition cycles with substrate rotation, we control the dot density and position low-density regions (< 1 QD per um^2) on the substrate. Hyperspectral imaging is used to map the spatial and spectral characteristics of many individual dots in the low-density region, confirming that our approach is universally applicable to conventional MBE growth on (001) surfaces. Finally, we tune the QD emission wavelength within the O-band using electric fields and demonstrate single-
photon emission with g(2)(0) = 0.020(14).
Read the full abstract ▾
All authors Pavel S. Avdienko, Lukas Hanschke, Quirin Buchinger, Nikolai Bart, Hubert Riedl, Bianca Scaparra, Yu Xia, Ziria Herdegen, Knut Müller-Caspary, Gregor Koblmüller, Tobias Huber-Loyola, Arne Ludwig, Andreas Pfenning, Sven Höfling, Kai Müller, Jonathan J. Finley
Data Analysis and Statistics
Growth-rate distributions at stationarity
Edgardo Brigatti
We propose new analytical tools for describing growth-rate distributions generated by stationary time-series. Our analysis shows how deviations from normality are not pathological behaviour, as suggested by some traditional views, but instead can be accounted for by clean and general statistical considerations. In contrast, strict normality is the effect of specific modelling choices. Systems characterized by stationary Gamma or heavy-tailed abundance distributions produce log-growth-rate distributions well described by a generalized logistic distribution, which can describe tent-shaped or nearly normal
datasets and serves as a useful null model for these observables. These results prove that, for large enough time lags, in practice, growth-rate distributions cease to be time-dependent and exhibit finite variance. Based on this analysis, we identify some key stylized macroecological patterns and specific
stochastic differential equations capable of reproducing them. A pragmatic workflow for heuristic selection between these models is then introduced. This approach is particularly useful for systems with limited data-tracking quality, where applying sophisticated inference methods is challenging.
Read the full abstract ▾
Instrumentation and Detectors
The Instrumented Baffle at the Input Mode Cleaner of Advanced Virgo Plus: Four years of Successful Operation as a Monitor of Stray Light
Dounia Nanadoumgar-Lacroze, Monica Seglar-Arroyo, Mario Martinez et al. (+2 more)
The suspended end mirror of the Input Mode Cleaner cavity in the Advanced Virgo Plus interferometer was equipped with an instrumented baffle in Spring 2021, serving as a demonstrator of the technology in preparation for the installation of large instrumented baffles in the main arms of the interferometer. This baffle includes tens of sensors positioned near the mirror to enable monitoring of stray light within the cavity. In this contribution, we assess the stability and performance of the instrument after four years of operation. After introducing the main characteristics of the baffle, we study the distribution of stray light and show that the instrumented baffle can be used to monitor
laser stability and
alignment within the cavity. Finally, we perform a noise level assessment with data from the final stages of the O4b commissioning and conclude that the baffle does not introduce any additional disturbance to the normal operation of the interferometer.
Read the full abstract ▾
All authors Dounia Nanadoumgar-Lacroze, Monica Seglar-Arroyo, Mario Martinez, Lluïsa-Maria Mir, Otger Ballester
Chemical Physics
Gap edge eigenpairs from density matrix purification using moments of the Dirac distribution
Lionel Alexandre Truflandier
In this work, we propose a simple method to resolve the eigenstates located at the band gap edges of an electronic eigenspectrum using only the quasi-purified one-particle density
matrix as input. The theoretical framework relies on the decomposition of the occupation number variance into a particle and a hole moment. These moments, when purified using power narrowing iterations, allow us to isolate the highest occupied and lowest unoccupied single-state projectors, \colp{giving ready access} to the corresponding eigenpairs. We demonstrate that when degeneracy is encountered, power narrowing remains able to deliver relevant mixed states. From a
benchmark of selected molecules, we show that the method is robust and efficient since it requires from four to sixteen
matrix-
matrix multiplications in the worst case. The possibility of reducing the computational cost using the Lanczos subspace approach is discussed. The
algorithm simplicity of power narrowing makes it very easy to implement in electronic structure codes or libraries already featuring
Fermi operator expansion or density
matrix purification.
Read the full abstract ▾
Physics and Society · Cross-listed from q-bio.NC
Copy-Spread-Annihilate Dynamics in Degree-Assortative Networks
Yan Hao, Daniel J. Graham and Marc-Thorsten Hütt
In many systems, communication proceeds by broadcasting rather than single source-target routing, but network structures that maximize signal lifetime are not well understood. Degree correlations are known to influence robustness and spreading, yet their effect on signal persistence has remained unclear. Here we introduce Copy-Spread-Annihilate dynamics, a minimal synchronous broadcasting model with annihilation. We show that signal lifetimes vary non-monotonically with assortativity and are maximized near neutral assortativity, where hub-driven amplification is strong but annihilation via short cycles is still limited. Applying this framework to the mouse connectome suggests assortativity as a structural control parameter for broadcast signal persistence in
brain-like and other complex networks.
Read the full abstract ▾
Chemical Physics
Short-lived memory in multidimensional spectra encodes full signal evolution
Thomas Sayer, Ethan H. Fink, Zachary R. Wiethorn et al. (+9 more)
Ultrafast multidimensional spectroscopies are powerful tools that can access charge and energy flow in complex materials, shifting chemical kinetics, and even many-body interactions in correlated matter. However, current implementations typically involve complex apparatuses and long averaging times. As a result, these methods have been limited to detailed mechanistic investigations of a few samples, precluding the broad characterization of molecular systems and/or the optimization of material ones. For example, converging the statistical noise in 2D spectra becomes exponentially expensive with increasing waiting times, and extended
laser exposure heightens the probability of sample degradation. We address this fundamental challenge by developing a new technique, the spectral generalized master equation (GME), that enables one to employ short-waiting time 2D spectra to determine the full
evolution of 2D spectra over arbitrary waiting times with high temporal resolution. In addition to reducing the cost of experiments by multiple orders of magnitude, our approach accurately removes statistical noise, reducing the need for time averaging, while circumventing the increasing convergence costs with longer waiting times. We provide a rigorous theoretical footing for the spectral GME and demonstrate its applicability on theoretically generated and experimentally measured 2D electronic and 2D infrared spectra. We anticipate that this advance has the potential to enable the investigation of systems that are too delicate for study with current multidimensional spectroscopies and accelerate the progress of 2D spectroscopy-based microscopies that can offer highly resolved excitation dynamics with spatial resolution over heterogeneous environments.
Read the full abstract ▾
All authors Thomas Sayer, Ethan H. Fink, Zachary R. Wiethorn, Devin R. Williams, Anthony J. Dominic III, Luke Guerrieri, Yi Ji, Veronica Policht, Jennifer Ogilvie, Gabriela Schlau-Cohen, Amber Krummel, Andrés Montoya-Castillo
Physics and Society
Urban mobility enables deprivation bubble breaking in Indian and Mexican cities
Yuan Liao, Federico Delussu, Sílvia de Sojo et al. (+2 more)
Urban deprivation is traditionally measured using static, residence-based indicators, capturing the socioeconomic, demographic, and spatial conditions of neighborhoods. However, this approach overlooks how daily movement allows residents to navigate the city, potentially exposing them to opportunities that differ significantly from their residential environments. To bridge this gap, we quantify the extent of bubble breaking - travel to less deprived areas - by analyzing mobile phone mobility networks combined with satellite-derived deprivation indices across 64 cities in India and Mexico. We find that residents of deprived areas systematically travel to better-off locations to meet daily needs, exhibiting a compensatory mobility pattern that significantly exceeds expectations derived from
gravity models based on population and road networks. This residual bubble breaking (the part
gravity models can not explain) is associated with a tension in the built environment: while high local amenity diversity allows residents to satisfy needs locally, high amenity density and positive spillovers from neighboring areas is associated with movement across socioeconomic boundaries. Overall, residual bubble breaking reflects the extent to which residents rely on cross-neighborhood mobility to overcome local amenity deficits, a dimension of spatial inequality that residence-based measures leave unobserved.
Read the full abstract ▾
All authors Yuan Liao, Federico Delussu, Sílvia de Sojo, Laura Alessandretti, Antonio Desiderio
Optics
Strongly Nonlinear Slow Light Polaritons in Subwavelength Modulated Waveguides
Amir Rahmani, Maciej Dems and Michał Matuszewski
Slow light is a regime of reduced group velocity, resulting in increased
photon density in optical pulses and enhanced nonlinear effects. Here, we propose the realization of slow light in the regime of strong light-matter interaction between waveguide
photons and
semiconductor excitons. We design a dielectric superlattice structure with a nearly-flat band characterized by low group velocity and group velocity dispersion, both required for enhancing nonlinear effects with ultrashort pulses. Furthermore, by applying this general framework to a perovskite-based structure, we demonstrate an enhancement of the single-particle phase shift by a factor of more than 20, representing a significant step toward the few-
photon quantum regime. Our results provide a blueprint for accessible strong interactions in solid-state integrated optics.
Read the full abstract ▾
Optics
High-Order Perfect Absorption in the Absence of Exceptional Point
Huisheng Xu, Luojia Wang, Luqi Yuan et al. (+1 more)
High-order perfect absorption of coherent input has recently attracted significant
attention due to its broadband absorption capacity. However, the realization of a high-order perfect absorber relies on the exceptional point (EP) to coalesce the scattering zeros. Here, we present a general scattering framework and achieve the high-order perfect absorber in the absence of EP. We consider the asynchronous coherent input, where a spatial delay introduces a momentum-dependent phase factor beyond the amplitude and phase control in synchronous coherent input. This new degree of freedom enables active control of the momentum dependent output, effectively reshaping the absorption line shape necessary for the high-order perfect absorber. Remarkably, despite the absence of EP, the proposed high-order perfect absorber exhibits significant response to the perturbations in the delay length. Our findings provide insights for the delay induced momentum-sensitive interference phenomenon and offer a new route for wave control.
Read the full abstract ▾
All authors Huisheng Xu, Luojia Wang, Luqi Yuan, Liang Jin
Atomic Physics
A criterion for an effective discretization of a continuous Schrödinger spectrum using a pseudostate basis
Tom Kirchner and Marko Horbatsch
We consider a
Hamiltonian $\hat H$ with a (partially) continuous spectrum and examine the zero-overlap condition which involves the projection onto exact continuum eigenstates of a set of pseudostates obtained from the diagonalization of $\hat H$ in a finite basis of square-integrable functions. For each projected pseudostate the condition implies the occurrence of zeros at all energies that correspond to the pseudo-continuum
matrix eigenvalues, except for the eigenenergy associated with that pseudostate. This feature was observed for the Coulomb continuum represented in a Laguerre basis [M. McGovern et al., Phys. Rev. A 79, 042707 (2009)] and later explained using special properties of the Laguerre functions [I. B. Abdurakhmanov et al., J. Phys. B 44, 075204 (2011)]. We establish that a sufficient condition for the zero-overlap condition to occur is that the image space of the operator $\hat Q \hat H \hat P$, where $\hat P$ is the projection operator onto the subspace spanned by the basis and $\hat Q = \hat 1 - \hat P$ its complement, has dimension one. We show that the condition is met for the one-dimensional free-particle problem by a basis of harmonic oscillator eigenstates and by a minimal set of simple momentum-space wave functions, and for the Coulomb problem by a Laguerre basis, thus offering an alternative proof for the latter case. The zero-overlap condition ensures that in, e.g., an ionizing collision or
laser-atom interaction process, transition probabilities obtained from the projection of a time-propagated pseudostate-expanded system wave function onto eigenstates of $ \hat H $ are asymptotically stable.
Read the full abstract ▾
Accelerator Physics
Data-Driven Optimisation of Superconducting Magnets at CEA Paris-Saclay
Damien F. G. Minenna, Guillaume Dilasser, Robin Penavaire et al. (+26 more)
Superconducting magnets for particle accelerators are particularly challenging to design because they involve a large number of coupled physical phenomena and the management of complex
datasets. Artificial Intelligence (AI), including machine learning and advanced optimisation techniques, offers promising approaches to address these challenges and accelerate the design process. This paper presents a new AI-based optimisation and data management platform, and highlights several ongoing applications of AI methods carried out at CEA Paris-Saclay, including multiphysics optimisation using active learning,
topology optimisation, holistic modelling of an Electron Cyclotron Resonance (ERC) ion source, and anomaly detection in quench events.
Read the full abstract ▾
All authors Damien F. G. Minenna, Guillaume Dilasser, Robin Penavaire, Valerio Calvelli, Thibault de Chabannes, Thibault Lecrevisse, Thomas Achard, Jason Le Coz, Christophe Berriaud, Benoît Bolzon, Antomne Caunes, Phillipe Fazilleau, Hélène Felice, Clément Genot, Antoine Guinet, Nikola Jerance, François-Paul Juster, Thibaut Lemercier, Gilles Lenoir, Clément Lorin, Yann Perron, Camille Pucheu-Plante, Étienne Rochepault, Damien Simon, Francesco Stacchi, Michel Segreti, Vincent Trauchessec, Olivier Tuske, Hajar Zgour
Atomic Physics · Cross-listed from cond-mat.quant-gas
Phase diagram of rotating Bose-Einstein condensates trapped in power-law and hard-wall potentials
G. M. Kavoulakis
We investigate the rotational phase diagram of a quasi-two-dimensional, weakly-interacting Bose-Einstein condensate confined in power-law and in hard-wall trapping potentials. For weak interactions, the system undergoes discontinuous transitions between multiply-quantized
vortex states as the rotation frequency of the trap increases. In contrast, stronger interactions induce continuous phase transitions toward mixed states involving both singly and multiply-quantized
vortex states. A central result is the qualitative (and experimentally observable) difference between power-law and hard-wall confinement: In hard-wall traps, the leading instability always involves states with nonzero density at the trap center, whereas in power-law traps the density vanishes as the rotation frequency increases. The two different types of confinement give rise to scaling properties in the derived phase diagrams.
Read the full abstract ▾
Physics and Society
Globally distributed environmental justice resistance against extractive corporate networks
Dario Cottafava, José R. Nicolás-Carlock, Marcel Llavero-Pasquina et al. (+1 more)
Is environmental injustice driven by a global network of multinational companies? Is there a global environmental justice movement resisting extractivism? This study addresses these questions through a social network analysis of firms and Environmental Justice Organizations (EJOs) involved in socioenvironmental conflicts. Using Environmental Justice Atlas (EJAtlas) data, we examine 3,396 conflicts involving 6,244 companies and 11,231 EJOs. The findings reveal evident structural asymmetries. Corporations form cohesive, sector-specific global networks that support coordination across regions. Conversely, EJOs form a larger, decentralized, and self-organized network characterised by sparse localised interconnections that enable regional coordination across sectors. A limited number of international EJOs involved in many conflicts worldwide weaves a global environmental justice network to match the global spread of multinational corporations and supply chains. This research study shows that these contrasting network structures reflect the distinct purposes of their constituent actors: sectoral expansion for corporations and environmental and territorial defense for EJOs.
Read the full abstract ▾
All authors Dario Cottafava, José R. Nicolás-Carlock, Marcel Llavero-Pasquina, Joan Martínez Alier
Biological Physics
Nucleoid clustering drives stepwise expansion and segregation of replicating bacterial chromosomes
Giada Forte, Enzo Orlandini and Davide Marenduzzo
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a non-
equilibrium process that continuously generates new genetic material and reorganizes the nucleoid. Here, we investigate how replication-driven dynamics, combined with nucleoid-associated
protein (NAP) interactions, shape spatiotemporal chromosome organisation using a three-dimensional
polymer model that explicitly simulates DNA synthesis. We show that NAP-mediated interactions induce dynamic clustering of DNA, generating density fluctuations in the nucleoid. When coupled to replication, these clusters undergo cycles of stress buildup and release that produce stepwise expansion dynamics consistent with experimental observations. Chromosome segregation occurs naturally in this regime, but only within a finite range of interaction strengths: weak interactions fail to structure the nucleoid, whereas strong interactions hinder replication progression. Within this optimal balance, replication also promotes the spontaneous formation of replication factories. Our results demonstrate that bacterial chromosome organisation can be understood as a non-
equilibrium system in which the interplay between replication forces and
protein-mediated interactions generates nucleoid mechanics, dynamics, and segregation.
Read the full abstract ▾
Fluid Dynamics · Cross-listed from gr-qc
Towards Gravitational Wave Turbulence within the Hadad-Zakharov metric
Benoît Gay, Eugeny Babichev, Sébastien Galtier et al. (+1 more)
The theory of gravitational wave
turbulence describes the long-term statistical behaviour of a set of weakly nonlinear interacting waves. In this paper, we aim to study aspects of gravitational
turbulence within the framework of general relativity using the Hadad-Zakharov (HZ) metric. The latter is parameterised by four functions (the coefficients of a diagonal metric) that must satisfy seven non-trivial Einstein equations, six of which are independent. The issue of their mutual compatibility is therefore essential, yet it has so far been overlooked. In this work, we argue that these equations can be compatible in the weakly nonlinear regime under specific conditions. Our analytical investigation is complemented by direct numerical simulations performed with a new GPU-based code, TIGER. A comparative analysis of the
evolution of the
Ricci and Kretschmann scalars indicates that gravitational wave
turbulence corresponds to the propagation of a genuine physical degree of freedom. These numerical findings, however, must be interpreted with caution, given the difficulty of satisfying all seven Einstein equations simultaneously with sufficient accuracy. On the other hand, our simulations reproduce well the expected properties of the wave
turbulence regime, with the emergence of a dual cascade of energy and wave action, and for the latter the observation of the Kolmogorov-Zakharov spectrum. In addition, our analysis reveals that the canonical variables of the problem evolve towards a nearly Gaussian statistical distribution punctuated by intermittent coherent (spatially localised and long-living) structures. In contrast to the canonical variables, the structure functions of the gauge-invariant metric components exhibit monofractal behaviour, which is a classical property of wave
turbulence.
Read the full abstract ▾
All authors Benoît Gay, Eugeny Babichev, Sébastien Galtier, Karim Noui
Data Analysis and Statistics · Cross-listed from q-bio.QM
FcsIT: An Open-Source, Cross-Platform Tool for Correlation and Analysis of Fluorescence Correlation Spectroscopy Data
Tomasz Kalwarczyk
FcsIT is a platform-independent, open-source tool for calculating the correlation and fitting fluorescence correlation spectroscopy data. The software is written in Python and uses a powerful Dear PyGUI engine for its interface. It provides reading and correlating the TTTR data, as well as TCSPC filtering of the
photon time-trace data. The circular-block bootstrap method applied to the calculation of correlation data and its variance results in data quality comparable to that obtained with commercially available software. An intuitive fitting interface provides efficient analysis of large
datasets and includes nine predefined mathematical models for fitting correlation curves. Moreover, it allows users to add their own models in a user-friendly manner. Validation of the FcsIT tool against simulated FCS data and real FCS experiments confirms its usability and potential appeal to a wide variety of FCS users.
Read the full abstract ▾
Plasma Physics
Anisotropy-induced Inhomogeneous Melting in Finite Dust Clusters
Sushree Monalisha Sahu, Hirakjyoti Sarma, Ankit Dhaka et al. (+2 more)
We present the first experimental evidence of inhomogeneous melting in a finite dusty
plasma crystal confined in an anisotropic potential well. By systematically tuning the confinement anisotropy and applying controlled
laser heating, distinct melting patterns are observed. Spectral-mode analysis based on Singular Value Decomposition of particle trajectories reveals that increasing
laser power redistributes energy into specific collective modes, triggering localized structural destabilization. Molecular Dynamics simulations reproduce the observations and show that confinement-controlled mode coupling with
laser heating governs the melting dynamics. These results establish
geometric anisotropy as a key control parameter for inhomogeneous melting in finite coupled systems.
Read the full abstract ▾
All authors Sushree Monalisha Sahu, Hirakjyoti Sarma, Ankit Dhaka, Pintu Bandyopadhyay, Abhijit Sen
Chemical Physics
Investigating the Electrochemical Double Layer with Quantum-Chemical Simulations and Implicit Solvation Models
Alessandro Mangiameli and Christopher J. Stein
We assess the dielectrically consistent reference interaction site model (DRISM) as an implicit electrolyte framework for modeling the electrochemical double layer, and compare it with the Poisson-Boltzmann model and explicit molecular dynamics results from the literature. We use the gold-electrolyte interface as the main test case and analyze solvent and ionic density profiles, the differential capacitance, and the solvation contribution to CO adsorption. The results show a strong sensitivity to the Lennard-Jones parametrization of metal-ion and metal-water interactions. In particular, we find that the default Lorentz-Berthelot mixing rules to be inadequate and lead to excessive Na+ accumulation at the interface, which results in an increase of the differential capacitance at negative electrode potentials. We demonstrate that introducing pair-specific metal-ion parameters yields more symmetric charging behavior and provides greater flexibility. Our findings suggest that using pair-specific parameters, rather than relying on Lorentz-Berthelot mixing rules, improves the accuracy of the model and opens the way for future studies with this improved yet equally performant model.
Read the full abstract ▾
Optics
Efficiency limits in in-line imaging
Timur E. Gureyev, David M. Paganin and Harry M. Quiney
In-line phase-contrast imaging, also known as propagation-based imaging or Gabor holography, is capable of delivering significant gains in image quality, compared to attenuation-based imaging at the same radiation dose. Image quality metrics, including signal-to-noise ratio and spatial resolution, are considered, and their relationship to the amount of Shannon information in the image is discussed. It is demonstrated that it is possible to increase the image quality gain by combining known phase
retrieval methods with deconvolution of the point-spread function (PSF) of the imaging system, with the highest gain achieved using the Contrast Transfer Function correction method in combination with the PSF deconvolution. The ultimate limit of this gain is determined by the ratio of the real decrement to the imaginary part of the complex refractive index of the imaged sample. Analytical results for the image quality limits in in-line imaging are obtained using a Gaussian model for the detector PSF. A numerically simulated example confirming the theoretical results is also presented.
Read the full abstract ▾
Fluid Dynamics
Instabilities in flow through and around a circular array of cylinders
Huaibao Zhang, Yongliang Yang, Guangxue Wang et al. (+1 more)
This paper presents results of two-dimensional direct numerical simulations (DNS) and global linear stability analyses (based on mean flow and base flow) of a viscous incompressible flow past a circular array of cylinders with six-fold rotational
symmetry. Six cylinder arrays, with varied patch density $\phi = N_c (d/D)^2$ (with $N_c$ cylinders of diameter $d$ within a patch of diameter $D$) is investigated by adjusting the $N_c$ and its arrangement. The simulations cover a wide parameter space, with $\phi$ ranging from $0.043$ to $0.315$, and the free-stream flow Reynolds numbers ($Re_D = U_{\infty} D / \nu = < 300$ based on $D$ and the uniform incoming velocity $U_{\infty}$ and the kinematic viscosity $\nu$). We focus on the onset of
vortex shedding with variant $\phi$, since the onset of global instabilities in such arrays has not been discussed earlier in the literature. For the patch diameters and solid volume fractions considered here,three distinct regimes are identified: (I) a low-$\phi$ regime where cylinders behave nearly independently, the flow is stable, forming steady wake without
vortex street; (II) an intermediate-$\phi$ regime where $Re_c$ varies logarithmically with $\phi$, resembling a porous medium; and (III) a high-$\phi$ regime where $Re_c$ approaches that of a solid cylinder ($\phi = 1$).
Read the full abstract ▾
All authors Huaibao Zhang, Yongliang Yang, Guangxue Wang, Mengqi Zhang
Physics and Society
A review on the use of complex networks in science education research
Paula Tuzón, Juan Antonio García-Castillo and Juan Fernández-Gracia
Network-based approaches have become increasingly prominent in science education research as tools for analysing relational structures in learning, teaching, and knowledge production. This review presents a PRISMA-informed scoping analysis of 82 articles published in nine leading science education journals, which are organised into four main categories: concept networks, social networks, bibliographic networks, and attitudes or behavioural networks. We observe a sustained exponential growth in the use of network methods, indicating a still-emerging and expanding research area. Concept networks dominate the literature, followed by social network analyses linking interaction structure to learning outcomes and persistence, while bibliographic and abilities-oriented networks provide complementary meta-level and practice-focused perspectives. In addition, analysis of the coauthorship network reveals a highly fragmented field, characterised by many small and weakly connected research groups, typically organised within single application categories. Complementary analysis of a citation network that includes all referenced authors shows that, despite this limited collaboration structure, the field is intellectually organised around several major traditions–network science methodology, learning sciences, and argumentation in science education–linked by a small number of bridging authors. Overall, the literature remains largely descriptive, relying on static, single-layer representations and a narrow set of network metrics. We identify substantial opportunities for advancing science education research through stronger theoretical integration and the adoption of dynamic, multilayer, and coevolutionary network frameworks.
Read the full abstract ▾
Fluid Dynamics
Self-scaling tensor basis neural network for Reynolds stress modeling of wall-bounded turbulence
Zelong Yuan and Yuzhu Pearl Li
Recent advances in data-driven
turbulence modeling have established tensor basis neural networks (TBNN) as a physically grounded framework for Reynolds-stress closure in Reynolds-averaged Navier-Stokes (RANS) simulations. However, their robustness in wall-bounded turbulent flows remains limited across Reynolds numbers and geometries due to the lack of an intrinsic scaling mechanism. In this work, we propose a self-scaling tensor basis neural network (STBNN) for Reynolds-stress modeling of wall-bounded
turbulence. The model incorporates an invariant velocity-gradient normalization derived from the first two invariants of the velocity-gradient tensor, providing an intrinsic and geometry-independent scale that balances strain and rotation effects without relying on empirical coefficients or wall-distance inputs. Owing to its frame-indifferent formulation, the approach preserves Galilean and rotational invariance while maintaining a physically interpretable representation of Reynolds-stress anisotropy. STBNN is evaluated through a priori and a posteriori studies using direct numerical simulation (DNS) data of canonical wall-bounded flows, including plane channel and periodic hill flows. In a priori tests, the model accurately reproduces Reynolds-stress anisotropy, with correlation coefficients exceeding 99% and relative errors below 10%, while capturing near-wall scaling and logarithmic-layer behavior. In a posteriori RANS simulations, STBNN predicts mean velocity profiles in close agreement with DNS and improves prediction of separation and reattachment compared with linear and quadratic eddy-viscosity models and the baseline TBNN. Notably, a model trained at low Reynolds numbers generalizes to higher Reynolds numbers and unseen geometries. These results demonstrate the effectiveness of the proposed framework for data-driven Reynolds-stress modeling in wall-bounded turbulent flows.
Read the full abstract ▾
Plasma Physics · Cross-listed from astro-ph.SR
Multi-hierarchy simulation of Riemann problem for reconnection exhausts
Keita Akutagawa, Shinsuke Imada and Munehito Shoda
Magnetic reconnection drives a wide range of astrophysical
plasma phenomena, including
solar flares, by converting
magnetic energy into
plasma energy through changes in
magnetic field
topology. Petschek reconnection is a magnetohydrodynamic (MHD) model in which
magnetic field lines reconnect within a localized
diffusion region, and a pair of switch-off slow shocks forms outside this region, enabling efficient energy conversion. Whether this picture remains valid when kinetic effects are included remains an open question. In this study, we examine the formation and properties of slow shocks associated with reconnection exhausts by solving a two-dimensional Riemann problem using a multi-hierarchy framework that couples MHD and particle-in-
cell (PIC) simulations. We find that a slow shock close to the switch-off limit forms in the MHD domain even when slow shock formation is suppressed in the PIC domain, and that this behavior is insensitive to the size of the PIC domain. The formation of the slow shock further promotes
plasma isotropization within the PIC domain. These results suggest that Petschek-like reconnection remains viable in collisionless-collisional systems, such as
solar flares, where temperature anisotropy appears to be relaxed far from the reconnection region.
Read the full abstract ▾
Biological Physics · Cross-listed from cond-mat.soft
The continuum limit of the Poland-Scheraga DNA denaturation model
Richard Dengler
Using a field theory equivalent to a
lattice version of the Poland-Scheraga model, the phase diagram for a long DNA molecule is derived in closed form. For the generalized model with excluded-volume interactions a one-loop renormalization group calculation shows that there are two stable fixed points. At both fixed points, the excluded-volume effect plays a role. At the fixed point reached when the original excluded-volume effect is weak, the phase transition is continuous. At the other fixed point, the phase transition is first order.
Read the full abstract ▾
Data Analysis and Statistics · Cross-listed from nucl-th
A systematic approach to Covariance matrix formulation in charged particle activation experiments
Tanmoy Bar
This work presents a detailed covariance and correlation
matrix analysis for experimentally measured cross sections obtained using the activation technique. Both statistical and systematic contributions to the covariance
matrix were explicitly calculated using sensitivity coefficients. The detector efficiency was determined by refitting standard source data with an exponential function, and the associated covariance
matrix of the fitted parameters was propagated to estimate the uncertainty in efficiency at the relevant $\gamma$-ray energy. The cross sections and the corresponding experimental parameters, such as beam flux, target thickness, $\gamma$-ray intensity, and decay corrections, were taken from previously published measurements and are used here for the purpose of illustrating the covariance formalism. The resulting covariance and correlation
matrices provide a comprehensive representation of uncertainties and their interdependencies. This formalism demonstrates the importance of including correlated uncertainties for reliable interpretation and comparison of experimental cross section data.
Read the full abstract ▾
Computational Physics · Cross-listed from math.NA
Solving the (Navier-)Stokes equations with space and time adaptivity using deal.II
Peter Munch, Marc Fehling, Martin Kronbichler et al. (+2 more)
In this article, we solve the Stokes and Navier-Stokes equations with the deal$.$II finite-element library. In particular, we use its multigrid, adaptive-mesh, and
matrix-free infrastructures to design efficient linear and nonlinear iterative solvers, respectively. We solve the stationary Stokes equations on hp-adaptive meshes with a hp-multigrid approach, the transient Stokes equations with space-time finite elements and space-time multigrid, and, finally, the stabilized incompressible Navier-Stokes equations on locally refined meshes with a monolithic multigrid solver. The selected examples underline the flexibility and modularity of the multigrid infrastructure of deal$.$II.
Read the full abstract ▾
All authors Peter Munch, Marc Fehling, Martin Kronbichler, Nils Margenberg, Laura Prieto Saavedra
Instrumentation and Detectors
Design, Fabrication and Characterization of Microwave Multiplexing SQUID Prototype
Mengjie Song, Yixian Deng, Zhengwei Li et al. (+14 more)
The readout system with a high multiplexing ratio has become a bottleneck limiting the application of large-scale Transition Edge Sensor (TES) detector arrays. In recent years, the microwave superconducting
quantum interference device (SQUID) multiplexer has emerged as a key technology for effectively reading large-scale cryogenic detector arrays. Currently, the microwave SQUID multiplexer is being adopted by an increasing number of experiments due to its capability of achieving a multiplexing ratio of 2000:1 within the readout bandwidth. In this study, we developed and fabricated a 32-channel microwave SQUID multiplexer prototype. And we measured 8 channels of the prototype. The measured equivalent noise current of the prototype reached 42 pA/$\sqrt{Hz}$.
Read the full abstract ▾
All authors Mengjie Song, Yixian Deng, Zhengwei Li, He Gao, Zhouhui Liu, Yudong Gu, XiangXiang Ren, Nan Li, Guofu Liao, Qinglei Xiu, Yu Xu, Mengqi Jiang, Xufang Li, Yaqiong Li, Shibo Shu, Yongjie Zhang, Congzhan Liu