Computational Physics · Cross-listed from physics.app-ph
Capacitance of Undoped Thin-Film Diodes
Oskar J. Sandberg, Mathias Nyman, Stefan Zeiske et al. (+3 more)
The capacitance of thin-film diodes based on undoped
semiconductors are dominated by injected charge carriers rather than doping-induced carriers. However, an analytical framework of the capacitance in these devices has remained elusive. Here, we derive an analytical description of the capacitance, fully accounting for injected charge carrier and electrode charge effects. Based on these findings, a method to extract the built-in voltage in these devices is presented. The theoretical framework is substantiated numerically by drift-
diffusion simulations and experimentally on organic solar
cells.
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All authors Oskar J. Sandberg, Mathias Nyman, Stefan Zeiske, Staffan Dahlstrom, Johannes Benduhn, Ardalan Armin
Computational Physics · Cross-listed from physics.flu-dyn
Physics-informed neural networks for viscoelastic fluid flows around a cylinder in a two-dimensional channel
Midhuna Suresh and Akanksha Gupta
Grid-based fluid dynamics solvers routinely struggle with exhaustive meshing demands and ill-posed inverse problems. A practical mesh-free alternative is given by Physics-informed neural networks (PINNs) but, applying them to highly elastic Oldroyd-B fluids results in many training failures. The High Weissenberg Number Problem (HWNP), driven by the exponential stress growth near stagnation points is a major issue, which causes standard PINN optimizers to diverge. To prevent the network from crashing, we apply a Cholesky decomposition to the conformation tensor. This mathematical constraint stabilizes the gradients by guaranteeing a positive-definite stress field. Beyond mathematical stability, the inherent spectral bias of deep learning models can hinder the network from accurately capturing the highly elastic wake structures. Therefore, we used sparse data assimilation to force the model toward the actual physical solution. By anchoring the physics loss with targeted CFD data points and accelerating training via transfer learning, we successfully pushed the network past non-physical local minima. We validated this Cholesky-PINN approach on flow past cylindrical geometries for Reynolds numbers (Re) between 5-25, for the single-cylinder setup. In addition, the relaxation time ({\lambda}) is increased from 0.1 to 0.5 to test the stability of the network. Finally, we scale the framework to a complex 3-cylinder array which proved our constructive solid geometry approach completely bypasses the tedious re-meshing steps of traditional CFD. The combined framework accurately captured sharp viscoelastic wakes, providing a stable computational tool for complex rheological modeling.
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Computational Physics · Cross-listed from cond-mat.soft
Valency-bounding correction potential for coarse-grained molecular dynamics simulations
Vladimir Dmitriev, Ankit Gupta and Anton Goloborodko
Many systems in soft and living matter bind through a limited number of bonds per particle:
proteins associate via discrete surface patches, nucleic acids form one-to-one contacts, and the phase behaviour of multivalent biomolecules is governed by the number of binding sites they carry. In simulations, valency limits are typically enforced with patchy particles, whose anisotropic potentials require integration of rotational degrees of freedom and combine hard cores with narrow patches, which forces small timesteps and commits the model to a fixed binding-site geometry that is often unknown, flexible or mobile. We introduce the valency-bounding correction (VBC), a many-body modification of generic short-range pairwise potentials that smoothly suppresses attraction once the neighbour count of either interacting particle exceeds a prescribed valency. The correction carries no angular degrees of freedom, applies on top of soft repulsive cores and evaluates in two passes over the neighbour list at the cost of a standard pairwise potential. The VBC drives the coordination number to the prescribed valency with low error, while its cluster statistics depart from Wertheim and Flory-Stockmayer predictions through unrestricted ring formation. A tuned variant exchanges bonded partners through ordinary molecular dynamics, reducing bond lifetimes at high saturation by an order of magnitude. On GPUs the cost of the correction is nearly independent of valency, reaching an almost tenfold advantage over a patchy-particle reference. We illustrate large-scale applications by reproducing the reentrant aggregation of repeat-expanded RNA, and show that the VBC also remedies the Fisher-Ruelle thermodynamic instability of soft-core potentials with attraction. The VBC is available as an open-source GPU plugin for HOOMD-blue.
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Computational Physics · Cross-listed from cs.LG
Latent-MoE: Domain-Aware Mixture-of-Experts for PDEs with Multi-Regime Physics
Hanwen Wang and Paris Perdikaris
Physics-informed neural networks (PINNs) struggle on PDEs whose governing physics varies across the domain. We trace this to a structural property of standard coordinate networks: their neural tangent kernel (NTK) is translation-variant and lets training points of large coordinate magnitude disproportionately influence predictions elsewhere, producing long-range coupling and gradient conflict during training. We show analytically and empirically that mixture-of-experts (MoE) architectures with centered, compact-support routers yield a uniformly banded NTK whose kernel-regression weights decay exponentially with distance, localizing the learning. Building on this, we propose Latent-MoE, which interleaves domain-aware MoE blocks within a shared backbone. Unlike FB-PINNs or X-PINNs, which rigidly partition both the domain and the parameters so that the parameters on different subdomains are updated independently, Latent-MoE is designed to preserve the localization benefit of domain-aware routing while allowing capacity to flow across regions through the shared backbone. On standard homogeneous-physics
benchmarks Latent-MoE is competitive with established baselines; on
benchmarks with multi-stage time-variable physics, where global models and rigid domain decompositions both fall into spurious solutions, it improves over them by more than an order of magnitude, with markedly reduced gradient conflict during training.
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Computational Physics · Cross-listed from physics.ins-det
Real-time blind indexing by cross-frame consensus
Stefano Marchesini and Yuan Ni
Classical crystallography determines orientation and unit-
cell geometry from a rotation series collected from a single specimen, whereas serial crystallography acquires one still exposure from each of many randomly oriented microcrystals and must reconstruct a complete
dataset by pooling partial measurements across the ensemble. In serial experiments, each frame typically contains only a subset of reflections, and frames with few reliable peaks (the small-N regime) are especially difficult to index blindly, because multiple incorrect
lattices or orientations can explain sparse observations. The approach implemented in GLINT addresses this small-N regime by treating the
dataset, rather than the individual frame, as the unit of inference. Candidate solutions are generated for many frames, weak but recurrent
lattice hypotheses are pooled across the ensemble to identify a shared unit
cell, and each frame is then registered against that consensus
cell through a known-
cell orientation search with lower dimensionality than blind indexing. In
benchmark tests, GLINT matched the strongest blind indexer in the comparison on indexing yield at roughly 40x lower per-frame blind-indexing latency against XGANDALF's fastest configuration, and batched known-
cell registration ran entirely on one GPU, allowing
cell discovery on the fly during serial data collection. On experimental serial data, frames indexed blind by GLINT merged to crystallographic quality (CC* = 0.90), while the method rejected non-
crystal images rather than forcing unsupported indexing assignments. These results demonstrate that indexing performance can be evaluated not only by indexing yield and throughput, but also by the quality of the resulting merged crystallographic data.
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Computational Physics · Cross-listed from quant-ph
Geometric inflation of deviations challenges neural quantum states in dynamics of quantum Ising models
Wladislaw Krinitsin, Jonas B. Rigo, Mohammad Abedi et al. (+1 more)
Neural
quantum states (NQS) have emerged as a powerful framework for simulating non-
equilibrium dynamics in strongly correlated
quantum systems, offering scalable variational representations of highly entangled states. Yet, accurate NQS simulations have been found to be surprisingly challenging in some physical regimes of limited complexity. Here, we address paradigmatic quench dynamics of a one-dimensional
quantum Ising model as a controlled
benchmark. Through supervised state reconstruction we establish substantially tighter empirical upper bounds on the required parameter count than previous estimates, ruling out representational limitations as the key obstruction. Instead, we uncover a
geometric inflation of small deviations as a hitherto overlooked challenge for accurate solutions of the infinitesimal time-dependent variational principle (TDVP): the dynamical rotation of the kernel of the
quantum geometric tensor (QGT) can suddenly lend physical significance to previously irrelevant parameter deviations. The stability of
matrix product state solutions of the same TDVP suggests that the non-linearity of the neural network ansatz is the origin of the sensitivity. These results identify QGT-null-space rotation as a
geometric diagnostic of sensitive NQS dynamics and as a concrete target for improving TDVP
algorithms
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All authors Wladislaw Krinitsin, Jonas B. Rigo, Mohammad Abedi, Markus Schmitt
Computational Physics · Cross-listed from hep-ex
Reducing simulation-related emissions in rare-event searches through optimised event biasing
P. Knights, L. J. Milligan and K. Nikolopoulos
Rare-event search experiments continue to extend their sensitivities to unprecedented levels. This requires increasingly small backgrounds, and shielding schemes that can suppress external backgrounds by several orders of magnitude. Moreover, detailed simulations are required to attain a good understanding of these experimental backgrounds. Studies have suggested, however, that simulations and computing-related tasks contribute approximately 10% to the average particle physicist's carbon footprint. With backgrounds frequently below 0.01 counts per kg of target per keV of energy, simulations require more computing resources; growing a rare-event researcher's computing-related carbon footprint. Event biasing is often applied in shielding simulations as a remedy, yet there is a lack of systematic guidance on how to maximally benefit from them. An optimisation study for the importance-splitting biasing technique is discussed, focused on balancing statistical precision with simulation CPU-time, and how this can benefit the average researcher's carbon footprint.
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Computational Physics · Cross-listed from cond-mat.stat-mech
Emergent Equilibrium Structure Along a Critical Cluster Recursion
Shuo Wei, Abbas Ali Saberi and Youjin Deng
Critical universality does not determine the microscopic conditional structure of a probability measure. We study a bicolored cluster recursion constrained to remain critical at every generation, with no
equilibrium spin measure or fixed coupling imposed. In both two and three dimensions, the resulting history-dependent sequence develops a common Ising/Fortuin–Kasteleyn (FK) compatibility structure: the second-shell dependence of a one-site conditional law is strongly suppressed, nearest-neighbor effective couplings move progressively toward one another near the critical Ising value, and cluster and interface observables organize around the corresponding FK geometry. An exact cluster-coloring factorization singles out $q=2$ as the point where the residual connectivity weight disappears from the two-color
spin marginal. Thus
equilibrium-compatible conditional structure can emerge along a trajectory that remains critical throughout.
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Computational Physics · Cross-listed from cs.LG
Constitutive State-Space Modeling of Path-Dependent Plasticity: A Resolution-Consistent and Parallelizable Computational Framework
Rui Barreira, Taylan Soydan, Francesco Scipione et al. (+2 more)
Data-driven constitutive models for path-dependent plasticity are commonly formulated using nonlinear recurrent neural networks, whose sequential state
evolution limits parallel training and whose predictions may depend on the discretization of the applied strain path. We introduce a Constitutive State Space (CSS) model that reformulates structured state-space dynamics as an incremental constitutive operator. The strain increment is decomposed into magnitude and direction: the loading direction drives the latent state-space system, while the increment magnitude enters the zero-order-hold discretization of its continuous-time linear recurrence. This mechanics-tailored construction guarantees stationarity under zero increments, strongly reduces sensitivity to strain-path resolution, and retains the parallel-scan structure of S5 for efficient training on long constitutive histories. The CSS and Minimal State
Cell (MSC) architectures are compared for four multiaxial path-dependent material models including isotropic J2 plasticity, pressure-sensitive foam plasticity, and combined isotropic-kinematic hardening. CSS matches or exceeds the prediction accuracy of the MSC, including one order of magnitude lower validation losses for the plastically incompressible materials. Importantly, CSS maintains low errors across large changes in strain-path discretization, whereas the MSC error increases substantially when evaluated at coarser resolutions than used for training. CSS trains substantially faster and requires fewer strain-stress pairs to attain comparable or better accuracy. Analysis of the learned state further reveals latent structure consistent with the dimensionality of the underlying physical constitutive models. These results establish mechanics-tailored structured state-space dynamics as a computational framework for efficient and discretization-robust data-driven constitutive modeling.
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All authors Rui Barreira, Taylan Soydan, Francesco Scipione, Miguel A. Bessa, Dirk Mohr
Computational Physics · Cross-listed from physics.chem-ph
Mixed quantum-classical evolution in open molecular systems
Michael Galperin and Abraham Nitzan
We consider a mixed
quantum-classical formulation for open nonequilibrium molecular systems. We employ the pseudoparticle nonequilibrium Green's function (PP-NEGF) method as a fully
quantum description and a starting point for introducing classical nuclear dynamics for an open system. We use this formulation to derive a density-
matrix equation of motion describing the
quantum-classical
evolution. We compare our results with previous formulations and highlight important differences related to the nonequilibrium and open character of the molecular system. We also analyze the approximations needed to reduce full
quantum-classical dynamics to the fewest-switches surface hopping (FSSH) method and show that these approximations are unreasonable when adiabatic surfaces come close to each other.
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Computational Physics · Cross-listed from cs.LG
PhysSAE: Mechanistic Interpretability of PINNs with Sparse Autoencoders
Nandita N. Patil, Eshwar R. A. and Gajanan V. Honnavar
Physics-Informed Neural Networks (PINNs) embed PDE residuals into neural network training, but their internal representations remain opaque: it is unknown what physical features their hidden layers encode or whether those features have a localized causal role. We present PhysSAE, a mechanistic interpretability framework that trains overcomplete sparse autoencoders (SAEs) on PINN penultimate-layer activations and evaluates dictionary atoms through direct causal intervention in the original frozen hidden state: $h_{\mathrm{cf}} = h - \alpha z_k d_k$, bypassing the SAE decoder entirely. Across six PDE families, with 3 PINN seeds and 3 SAE seeds each—we show that (i) Our discovered SAE atoms align with independently-defined physical observables (max Pearson $|r|=0.951$, always $\gg$ permutation null), (ii) the causal footprint of top-aligned atom ablation is 1.2–4.2$\times$ more spatially concentrated canonical than PCA or ICA interventions, and (iii) top-aligned atoms outperform matched random controls on causal localization for structured physical concepts (ESF$_{80}$ advantage 0.04-0.44). Two-atom bilateral representations improve concept regression R$^2$ by $\Delta R^2\!=\!0.05\text{-}0.15$ over single atoms, while random pairs decrease it by up to 0.60. These results demonstrate that PINNs develop sparse, physically structured latent representations that can be identified and causally interrogated post-hoc, opening a path toward interpretability-aware scientific machine learning.
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Computational Physics · Cross-listed from physics.soc-ph
Phase spaces of phase spaces: A method of constructing generalizable and topologically informed bases from time series demonstrated by reconstruction of the geometry of the macroeconomy
Maximilian Topel
Laws from physics to social science rest on a small, enumerable number of factors explaining variation in the systems they describe. While the orthodoxy of economics, physics and chemistry relies on a small number of analytically interpretable laws, large data models pursuing universality throw in all available data. Both fail in their extremes through the same flaw, an incorrect basis: too few orthogonal variables to describe system variation, or an explosion of dimensionality around fundamentally low dimensional but unknown dynamics. We propose and validate a framework that extracts an interpretable, mathematically sound, low dimensional and dynamically informed basis directly from arbitrary timeseries. Combining Takens' Delay
Embedding Theorem, dimensionality reduction and optimal transport, we produce a phase space of phase spaces (PSoPS) on which all interrelated dynamical series exist: barycenters formed from many phase spaces, together with the families of transport plans between individual phase spaces and the barycenter, yield a basis describing the relational geometry of each timeseries and the
topology of economic relationships. The macroeconomic PSoPS built from 281,536 series is a single connected object of effective dimension 7.3 +/- 0.2, into which the canonical laws (Phillips, Okun, Solow) embed as roughly 2-dimensional looped sub-attractors. The coupling between concept barycenters is directed, with the price of money and productivity as net sources and credit and output as sinks, recovering monetary transmission from geometry alone. IAAFT phase-randomized surrogates destroy 36-43% of the dimension across the three laws and 38% on the full corpus, so the basis is irreducibly nonlinear. We close with proposed extensions to fields whose dynamics share attractor geometries and to systems that are intrinsically low dimensional yet hard to navigate in raw coordinates.
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Computational Physics · Cross-listed from physics.atm-clus
Core-Level Spectroscopy Decodes Bond-Alternation Dynamics of Cyclo[18]Carbon
Minrui Wei, Zeyu Liu, Sheng-Yu Wang et al. (+4 more)
The advent of X-ray free-electron
lasers and high-harmonic generation has made time-resolved X-ray spectroscopy a powerful tool for probing local atomic environments, yet whether localized core excitations can report on global collective distortions remains open. Cyclo[18]carbon (C$_{18}$), with its polyynic ground state (D$_\text{9h}$) and cumulenic transition state (D$_\text{18h}$), provides an ideal model to address this long-standing issue in bond-length alternation (BLA) dynamics. Mapping two-dimensional potential energy surfaces by first-principles simulations, we find that core ionization symmetrizes the ground-state double-well potential along the BLA coordinate. Our calculated X-ray spectra reveal remarkable sensitivity to bond-length variations: C1s ionization potentials vary by up to 2.4~eV across the BLA coordinate (1.1–1.4~Å), with a 0.9~eV variation for minima predicted by different functionals, while NEXAFS $\pi^*$ peaks shift by up to 4~eV across the same coordinate. These predicted signatures provide a quantitative spectroscopy–structure dictionary for decoding transient structures in future ultrafast X-ray experiments and monitoring bond-alternation dynamics in real time.
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All authors Minrui Wei, Zeyu Liu, Sheng-Yu Wang, Jun-Rong Zhang, Lu Zhang, Guoyan Ge, Weijie Hua