Computational Physics · Cross-listed from cond-mat.mtrl-sci
Local Response Theory of Electrified Interfaces from Screened Effective Charges
Nicolas G. Hörmann, Nicolas Bergmann and Karsten Reuter
First-principles, electronic-structure simulations provide direct access to ground-state, global system properties. In the context of computational electrochemistry these are, e.g., bias-dependent energies, free energies, work functions, and capacitances. However, a comparably systematic local description of how these quantities respond to biasing via interfacial charging is still missing. Here, we introduce the screened electrochemical Born effective charge (SEBEC), a mixed total-energy derivative that measures the force response of an atomic degree of freedom to interfacial charging under electrochemical boundary conditions. SEBECs play the role for electrochemistry that Born effective charges play in the modern theory of polarization: they provide an unambiguous decomposition of global response and generate the same formal structures for structural relaxation, capacitance, and electrochemical Stark tuning that are familiar from solid-state response theory. The broader implication is a local response framework that brings electrochemical interfaces closer to the conceptual rigor long established for insulating solids.
Read the full abstract ▾
Computational Physics · Cross-listed from physics.bio-ph
Protein eXplosion Imaging (PXI): Protein Structures from Laser-Driven Explosions
Alfredo Bellisario, Tomas André, Carl Caleman et al. (+1 more)
We investigate the structural information retained in the distribution of explosion ion trajectories from
proteins subjected to strong ionization. Using molecular-dynamics simulations and machine-learning analysis benchmarked against an analytical approach, we show that low-resolution structural information can be retrieved from the explosion distributions alone. An ensemble of convolutional neural networks trained on simulated spherical ion maps recovers the radius of gyration and the three semi-axes of an ellipsoidal molecular envelope with prediction errors of 1.2 Å and 1.5 Å, respectively, while an analytical ellipsoid charge model returns similar estimates and performs best for globular structures. We further investigate how higher-level structural information and
symmetries can be extrapolated from ion measurements. This study supports the viability for structural determination of single
proteins without large-scale X-ray facilities.
Read the full abstract ▾
All authors Alfredo Bellisario, Tomas André, Carl Caleman, Nicuşor Tîmneanu
Computational Physics · Cross-listed from math.NA
Global convergence of an efficient splitting method for the defocusing Gross–Pitaevskii ground state problem
Jiaxing Li, Shixin Zheng and Xiangxiong Zhang
For computing the ground state of the defocusing Gross–Pitaevskii energy, we propose and analyze two efficient schemes based on the Davis–Yin three-operator splitting, which treats the potential and interaction terms explicitly, and the kinetic energy by a resolvent. One iteration costs one inversion of $I-\gamma\Delta$ for the first scheme, and of $I-\gamma\Delta+\gamma V_1$ for the second, with $V_1$ denoting the separable part of the potential, and on structured meshes both operators can be inverted by simple fast GPU solvers. For monotone discrete
Laplacians, including the second-order finite difference scheme and the lumped linear finite element method on simplicial meshes with suitable angle conditions, we prove global convergence to the unique positive discrete ground state, for every positive normalized initial vector, for any constant step size below an explicit threshold. In contrast, the methods previously proven to converge globally to the ground state all invert a more difficult elliptic operator that depends on the iteration variable. In three-dimensional tests with up to $999^3$ unknowns on one GPU, a simple variable step size rule makes the proposed splitting schemes efficient in practice, comparable in wall-clock time to Riemannian conjugate gradient methods that also invert only a shifted
Laplacian operator, and much more robust with respect to the choice of the initial guess.
Read the full abstract ▾
Computational Physics · Cross-listed from physics.flu-dyn
A conservative Godunov-type mesh-free hydrodynamics scheme for weakly compressible multiphase flows
Fabian Fritz, Stefan Adami and Nikolaus A. Adams
We present a Godunov-type mesh-free hydrodynamics scheme for the numerical simulation of weakly compressible single- and multiphase flows. The method employs a consistent second-order spatial reconstruction of the primitive variables at the inter-particle interface, applies slope limiting, and solves the moving Riemann problem using a subsonic HLLC approximate Riemann solver. Particles are advected with a quasi-Lagrangian material velocity incorporating an inherent self-relaxation mechanism that suppresses the formation of anisotropic particle distributions. Near material interfaces, one-sided renormalized gradients are used to handle density discontinuities and slope limiting is applied for each phase independently. The Lagrangian character of material interfaces is preserved by constraining the relaxation mechanism to act tangentially to the interface. For same-phase particle interactions, the Riemann problem is centered at the arithmetic mean of the two material velocities. For cross-phase interactions, it is centered at the contact-wave velocity. This choice naturally eliminates spurious mass fluxes across phase boundaries. The methodology is validated on a set of challenging
benchmarks, including the inviscid Taylor-Green
vortex, material interface advection, surface
gravity waves near hydrostatic
equilibrium, the Kelvin-Helmholtz instability, and the Rayleigh-Taylor instability under gravitational stratification.
Read the full abstract ▾
Computational Physics · Cross-listed from cond-mat.mtrl-sci
Symmetry- and Property-Aware Crystal Generation with Reinforcement Learning for Inverse Materials Design
Ting-Wei Hsu, Arun Bansil and Qimin Yan
The inverse design of crystalline materials ultimately seeks structures with desired physical properties. However, for many functional responses, a favorable numerical value is meaningful only when supported by the
symmetry of the underlying
crystal. Without the appropriate crystallographic constraints, an apparent response may be ill defined, accidental, or not
symmetry protected. Here we introduce SPARC, a
symmetry- and property-aware reinforcement learning framework that optimizes physical objectives while preserving the structural conditions required for their realization. We demonstrate SPARC on two complementary tasks. The first targets strong uniaxial dielectric anisotropy, a tensorial response that is well defined only within appropriate
crystal classes. The second maximizes the spectroscopic limited maximum efficiency, a scalar device-level objective without a prescribed
symmetry class, allowing the framework to identify favorable crystallographic motifs. These results show that
symmetry is not merely an additional design constraint, but a physical foundation for generating candidates with meaningful, robust, and realizable functional properties.
Read the full abstract ▾
Computational Physics · Cross-listed from cond-mat.mes-hall
Topological classification through knotted graphs: Fermi surface dispersions and Lifshitz transitions
Hakan Akgün, Xianquan Yan and Ching Hua Lee
Knot theory has provided a rich topological taxonomy for band structures, but its reach is fundamentally limited:
knot invariants classify only 1D nodal lines at gap closure, and cannot encode the full dispersion or rich Fermi surface structure of realistic materials. Here we show that knotted graphs (
knots that admit graph-like intersections in 3D space) - which have so far been elusive in condensed matter literature - provide a unified topological
language for classifying the entire band dispersion, and even the eigenstate
topology in some contexts. We propose a new framework beyond the existing Yamada
polynomials that can topologically characterize the intricacies of realistic Fermi surfaces completely, crucially including how their multiple disconnected pieces are nested. This yields the Yamada set, a boundary-resolved extension which organizes the full topological
evolution across energy into a Yamada sequence: a compact dispersion-level fingerprint directly tied to experimental signatures of Lifshitz transitions. Our framework is demonstrated with DFT-based band structures of real materials. Beyond dispersion-level classifications, this framework can be extended to non-Hermitian exceptional surfaces, where Berry-
curvature flux further equips the knotted-graph skeleton with a directed Abelian edge flow that also captures the eigenstate
topology.
Read the full abstract ▾
Computational Physics · Cross-listed from physics.chem-ph
Can Autonomous LLM Agents Execute Multireference Quantum Chemistry Calculations?
Victor Chang Lee and James M. Rondinelli
Multireference electronic-structure calculations remain difficult to automate because critical workflow decisions, including active-space selection, state averaging, convergence recovery, and state identification, traditionally rely on expert judgment. Here, we investigate whether an autonomous large
language model (LLM)
agent can perform these tasks without human intervention. The
agent selects active spaces using literature-grounded analogies or explicitly documented chemical
reasoning, generates and submits ORCA calculations, analyzes outputs, and records all decisions in an auditable
reasoning log. Benchmarking against 558 vertical transition energies (VTEs) from QUESTDB shows that an unguided baseline
agent achieves 24.9% coverage with a mean absolute error (MAE) of 0.373 eV. Introducing a structured decision ladder increases coverage to 44.1% while reducing the MAE to 0.339 eV. The largest gains are observed for double and Rydberg excitations, demonstrating that expert-informed procedural guidance substantially improves active-space construction and state identification. When provided with complete workflow information, the
agent successfully reproduces published QUEST calculations with an MAE of only 23 meV, resolving 75% of target configurations within seven attempts. These results demonstrate that contemporary LLM
agents can autonomously execute and reproduce complex multireference
quantum-chemical workflows, while highlighting the importance of structured
reasoning frameworks for achieving reliable high-throughput and high-fidelity electronic-structure calculations.
Read the full abstract ▾
Computational Physics · Cross-listed from cs.CE
Extreme-Scale Linear-Scaling Kohn-Sham DFT at 100 Million Atoms: Bridging Quantum Simulations and Experiments
Qimen Xu, Yu Zhang, Dixing Ni et al. (+11 more)
Kohn-Sham density functional theory (DFT) remains the workhorse of ab initio materials simulation, yet cubic computational and quadratic
memory scaling have confined calculations to a few hundred to thousands of atoms, spanning only nanometers, far below experimentally relevant length scales. We introduce XLSDFT, a linear-scaling DFT framework based on divide-and-conquer decomposition of the one-particle density
matrix and Chebyshev-filtered subspace iteration, achieving linear computational and
memory scaling while retaining DFT accuracy. Deployed on the LineShine exascale supercomputer, XLSDFT reduces computational complexity by orders of magnitude, enabling unprecedented DFT scale: a 200-million-atom silicon
crystal, twentyfold beyond the prior record. Our implementation achieves 96.6% weak-scaling efficiency and sustained 157.9 Pflop/s (FP64) for a 100-million-atom scaling study. We further simulate an 11-million-atom all-solid-state battery interface of unprecedented complexity, 1,000 times beyond prior DFT for such systems, revealing how lithium metal reacts with the solid electrolyte at atomic resolution, in quantitative agreement with spectroscopy experiments.
Read the full abstract ▾
All authors Qimen Xu, Yu Zhang, Dixing Ni, Lei Gao, Guangnan Feng, Qinrui Zheng, Jianting Liu, Haitian Lu, Zhaopeng Jia, Wei Xue, Shriram Chandran, Torsten Hoefler, Haohuan Fu, Yutong Lu
Computational Physics
Physically Consistent 2D to 3D Pore Space Synthesis: 1. Dynamic Grain Packing Under Strict Morphology Constraints
Dmitry Kulygin, Andrey Ananev and Aleksey Khlyupin
The 3D digital reconstruction of multi-scale, heterogeneous porous media is traditionally limited by the resolution boundaries and artifacts of X-ray computed
tomography (XCT). This paper introduces a physically consistent 2D to 3D pore space synthesis framework that supersedes conventional
geometric shuffling with dynamic Newtonian gravitational deposition using a high-performance rigid-body mechanics engine. To honor strict physical contact mechanics, statistical 2D targets, and morphological constraints, we develop a two-stage dynamic packing pipeline that combines realistic 3D grain shapes with a virtual sub-particle insertion engine. The framework is validated against synthetic and natural core
benchmarks. First, we show that our stereological integral equation systematically converts size distributions; bypassing this inversion step induces a systematic 50% deviation in permeability predictions despite identical total porosities, independently altering flow channel
topology. Second, temporary virtual spheres serve as architectural placeholders to stabilize large non-
equilibrium dissolution voids, ensuring the reconstructed model satisfies target flow metrics within the prescribed tolerance. Finally, when applied to a fine-grained, weakly consolidated sandstone, the workflow exposes and suppresses systematic XCT artifacts, including phantom internal porosity. Ensembles of two-point correlation functions demonstrate that the hydrodynamically and structurally synthesized digital twins quantitatively exhibit closer structural proximity to the uncorrupted rock geometry than the reference XCT
dataset itself. This methodology establishes a scalable foundation for high-fidelity multi-phase rock reconstruction, with potential extensions toward complex amorphous cement phases.
Read the full abstract ▾
Computational Physics
Physics-enriched neural solvers for transient ice-flow simulation
Thomas Gregov, Sebastian Rosier, Brandon Finley et al. (+2 more)
Transient glacier simulations with higher-order ice flow require the repeated solution of a nonlinear problem as the geometry evolves. In the online mode of the Instructed Glacier Model, the velocity field is represented by a neural network whose weights are warm-started from the previous time step and updated with a few optimizer iterations. We show that supplying the network with inexpensive input fields derived from low-order ice-flow balances improves this online solver. Unlike residual-based physics-informed neural networks, which incorporate physics through governing-equation penalties in the loss, our approach leaves the governing energy objective unchanged, adding physical structure through the network inputs. Across three real-world glacier configurations, the enriched solver is markedly more robust to solver settings. On the two alpine cases, it also improves the tuned accuracy–runtime trade-off, reducing surface-velocity errors by factors of two to four at fixed runtime and reaching few-percent relative errors with only $10^4$–$10^5$ trainable parameters, far fewer than comparable raw-input baselines. A 300-year Aletsch simulation then completes in under one minute, and the larger Valais domain in about two minutes, on a single GPU—a budget once reserved for much simpler shallow-ice models. Gains are smaller for the fast marine-terminating glacier, where nonlocal stress coupling favors larger or spectral networks. More broadly, the results suggest that enriching a neural solver's inputs with reduced-order physics can make repeated higher-order solves much cheaper, with no training data and no offline training.
Read the full abstract ▾
All authors Thomas Gregov, Sebastian Rosier, Brandon Finley, Andreas Vieli, Guillaume Jouvet
Computational Physics · Cross-listed from cond-mat.str-el
Diversifying time evolution of matrix product states using BUGs
Kornél Kapás, Dominik Sulz, Charlotte Verhoeven et al. (+3 more)
Time
evolution of tensor-network states is a central tool for studying nonequilibrium dynamics in strongly correlated
quantum systems. In the past decade, using the time-dependent variational principle (TDVP) discretized by projector-splitting has become the gold standard for evolving
matrix product states (MPS) with long-range
Hamiltonians. More recently, a conceptually different class of discretizations of the TDVP, the class of Basis Update and Galerkin (BUG) integrators, has been developed within the framework of dynamical low-rank approximation, offering an alternative, more flexible approach. In this work, we formulate two BUG integrators explicitly for MPS. The BUG integrators result in "single-site" MPS integrators that are robust with respect to small singular values, avoid backward-in-time substeps, and naturally allow for the adaptive choice of bond dimensions. We consider the augmented BUG integrator of first order and the midpoint BUG integrator of second order and clarify their relation to the projector-splitting discretization of the TDVP. Using representative models of strongly correlated
quantum systems, like the XY
spin model with long-range interaction and two-dimensional
lattice models of
fermions and
spins of various lengths, we perform a systematic numerical comparison between BUG and projector-splitting time discretizations of the continuous-time TDVP, focusing on scalability, numerical complexity, and accuracy. We find that BUG integrators, due to their reduced numerical cost and the flexibility of the concept, provide a competitive and, in certain regimes, advantageous alternative to the well-established time-stepping by projector-splitting in TDVP, especially in models with large local dimensions, and in cases where observables are extracted with high temporal resolution.
Read the full abstract ▾
All authors Kornél Kapás, Dominik Sulz, Charlotte Verhoeven, Miklós Antal Werner, Örs Legeza, Christian Lubich
Computational Physics
Physics Based Triple Debye Dielectric Modeling and Multi Layer ADE FDTD Simulation of Terahertz Pulse Reflection for Breast Cancer Detection
Ali Asghar Molavi Choobini and Mehran Shahmansouri
Terahertz (THz) imaging has emerged as a promising non-ionizing modality for breast cancer assessment owing to its intrinsic sensitivity to tissue hydration. However, existing dielectric descriptions of biological tissue, largely restricted to single- or double-Debye models, fail to capture the multiscale relaxation dynamics governing broadband THz dispersion and absorption, thereby limiting the quantitative interpretation of reflected pulse signatures.Here, a physics based triple Debye dielectric framework is developed to quantitatively predict broadband THz-tissue interactions. The proposed model explicitly incorporates three physically distinct relaxation processes associated with free-water rotational dynamics, bound-water relaxation ({\tau}_2), and ultrafast interfacial/macromolecular polarization ({\tau}_3). Model parameters are obtained by nonlinear least-squares fitting to experimentally measured refractive-index data digitized from published THz time-domain spectroscopy measurements of ex vivo human breast tissue. Compared with conventional Debye formulations, the proposed model substantially improves the fitting accuracy, reducing the root-mean-square error from 0.7773 (single Debye) and 0.2976 (double Debye) to only 0.0199 for the triple-Debye model. Fullwave FDTD ADE simulations of realistic multilayer breast structures further demonstrate that reflected THz pulses encode tissue hydration through reproducible temporal signatures, including increased reflection amplitude, delayed pulse arrival, and enhanced waveform broadening in malignant tissue. Polarization and angle resolved Fresnel analysis further indicates that hydration-dependent pseudo-Brewster minima provide an additional contrast mechanism by selectively suppressing reflections from low hydration normal and adipose tissues.
Read the full abstract ▾
Computational Physics · Cross-listed from cs.IT
Error-Rate Reduction in LDPC Decoding via Bit-Aligned Temporal Reinforcement in Parallel Probabilistic-Bit Dynamics
Naoya Onizawa and Takahiro Hanyu
Probabilistic bits (p-bits) provide a physical and algorithmic primitive for
stochastic inference, but highly parallel updates can alter their collective dynamics. We study the decoding of random-regular (3, 6) low-density parity-check (LDPC) codes using Jacobi-type p-bit annealing with
stochastic partial activation. An additive response-path rule stores each bit's saturated response and reuses it before
stochastic readout. High-statistics simulations with independent parameter optimization for each method show pooled bit-error-rate reductions of 33.5%, 74.8%, and 81.8% relative to memoryless probabilistic simulated annealing (pSA) for representative codes of block lengths 96, 192, and 288, respectively. Static gain, normalized averaging, response shuffling, and same-bit binary-state feedback with only its coefficient tuned under the same nonmemory parameters do not reproduce the full saturated-response benefit. Trajectory analysis links the improvement to acquisition of the channel-consistent valid-codeword basin and enhanced post-acquisition stability; the acquisition advantage persists from random and channel-hard-decision starts under the tested conditions. Across all 30 independent code realizations, fixed additive parameter-and-readout packages achieve lower bit- and frame-error rates than separately optimized pSA-specific packages, with neither package retuned for individual codes. These results show that the computational effect of temporal state depends on the retained quantity and its reinjection into
stochastic dynamics.
Read the full abstract ▾