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Reading and Steering Representations of Materials-Science Mechanisms in an Open-Weight Language Model

Large language models can answer scientific questions, yet a correct output does not reveal whether the model represents or uses the governing physics. Here, using three open-weight Gemma 4 models (google/gemma-4-E4B-it, google/gemma-4-12B-it, google/gemma-4-31B-it) we identify three experimentally separable signatures of materials-science mechanism information: selective concept readability, relational encoding of qualitative constitutive orientation, and causal, context-dependent control of constrained engineering answers. We combine matched direct and Jacobian vocabulary readouts, option-free state geometry, a 60-law counterfactual benchmark and causal interventions. In 50 held-out materials descriptions, three independently fitted Jacobian lenses reproduced concept ranks, and target-free word sets from both readouts enabled blinded identification of 9 of 10 mechanism families. A separate 72-prompt benchmark produced mechanism-specific hidden-state neighborhoods, but an exact graph audit showed that this apparent physical organization was equally explained by numerical comparison. We therefore compared otherwise identical prompts in which only the direction of the physical input was reversed, asking whether the resulting hidden-state movement followed the supplied constitutive law. These state transformations ordered direct, physically neutral and inverse laws across 60 frozen relations and correctly oriented 39 of 40 directional laws, whereas lexical controls were near chance. Bidirectional interventions shifted answer probabilities toward or away from the physically appropriate outcome across all 12 matched cases, while counterfactual state patches transferred opposing decision signals across mechanisms and answer formats. Physical relationships were therefore more visible in controlled state changes than in absolute states alone.

cs.AI

QArray+: A physics-informed GPU-accelerated simulator for quantum dot arrays

Semiconductor quantum-dot arrays are a compelling platform for scalable quantum technologies, yet their practical operation is hindered by the complexity of tuning large-scale devices. Existing automation tools rely on simplified physical models---such as constant-capacitance approximations and equilibrium Hubbard models---which assume instantaneous relaxation to a steady state. These frameworks fail in experimentally critical regimes where measurement rates exceed tunneling dynamics, necessitating more sophisticated non-equilibrium control strategies. To bridge this gap, we introduce QArray+, an extension of the QArray framework that incorporates gate-dependent tunnel coupling and a quantum open-system description of dissipative processes. This approach enables the unified simulation of coherent interdot charge-state hybridization and the non-equilibrium latching dynamics essential for training robust machine-learning models for automated device operation. Implemented in JAX with GPU acceleration, QArray+ scales across GPUs and multi-node systems. For example, a charge stability diagram for a 100X100 grid of gate voltages over 64 dots can be computed in $\sim0.17\,\mathrm{s}$ on multiple GPUs. Since interdot interactions are short-ranged and the corresponding tuning corrections are local, simulations at these scales capture the physics relevant to even larger devices. These capabilities support high-throughput dataset generation for automated device tuning.

cond-mat.mes-hall

Coarse-Graining Hidden Representations: Unsupervised Neuron Selection via Mapping Entropy

Overparameterized neural networks carry far more hidden units than a task nominally requires, raising the question of which neurons are essential and whether that distinction is legible in the representation itself, without labels or gradients. We cast neuron selection as the problem of coarse-graining the hidden layer by retaining a subset of its neurons, and score each putative selection by the mapping entropy (ME). This quantity measures the loss of discriminatory power inherent in discarding part of the network neurons, and the selection that minimises the ME is taken as particularly informative. This criterion is fully unsupervised, in that it depends only on hidden-activation statistics. In teacher-student networks, ME optimisation recovers the minimal teacher-consistent representation and retains extra units in proportion to the hidden layer's residual variability; in a non-linear Gaussian process task, it selects coherent functional-class mappings whose preferred class shifts across training. On this task and on translation-augmented MNIST, ME-selected subnetworks outperform random subsets of equal size, most clearly under strong compression - linking configurational distinguishability to predictive performance.

cs.LG

Percolation Dynamics in Optimization : Variance Cascades and Discrete Scale Invariance

We study the dynamics of Stochastic Gradient Descent (SGD), which is known to steer deep neural networks toward invariant sets that correspond to simpler subnetworks. How this steering unfolds over time remains poorly understood. We answer this by modeling the stochastic gradient flow (SGF) as a percolation process, in which architectural symmetries force subnetworks to merge in discrete simultaneous blocks rather than one at a time. These structural transitions register as variance spikes in a macroscopic order parameter, echoing physical phase transitions. We further show this trapping mechanism and its associated scaling cascade extend to Adam and AdamW under an explicit heavy-tailed noise model.

cs.LG

A unified geometric design framework for kirigami structures

In recent years, kirigami metamaterials have been widely studied and applied in science and engineering. While various two- and three-dimensional kirigami design methods have been developed, most of them are only applicable to a limited class of kirigami structures. In this work, we develop a unified framework for kirigami design that encompasses a wide range of 2D-to-2D, 2D-to-3D, and 3D-to-3D shape-morphing effects, as well as additional geometric and physical properties such as compact reconfigurability and rigid deployability. In particular, by reformulating the design task as a length-based constrained optimization problem and solving it simultaneously for multiple target states of the kirigami structure, our unified design framework enables greater design flexibility and stronger theoretical support. Experimental results with a wide range of shape-morphing effects are presented to demonstrate the effectiveness of our framework. We further present a rigorous theoretical analysis of several key aspects of kirigami design, covering inertia transposition, aspect-ratio law, and angle defects, thereby elucidating important design rules and limitations. Altogether, our work paves a new way for the design of shape-morphing mechanical metamaterials.

cond-mat.soft

FrOGS: Discrete Neural Sampler for Independent Alloy Configurations Across Chemical Conditions

Predicting the thermodynamic properties of an alloy requires sampling its configurations across many chemical conditions and recovering free energies on a common absolute scale. Markov chain Monte Carlo (MCMC) is the standard tool, but it requires separate simulations at different conditions, and auxiliary free-energy methods such as thermodynamic integration are used to place results on a common absolute scale. Modern discrete neural samplers typically use reverse KL divergence as the objective and can be mode-seeking or biased. We present Free energy Offering Generative Sampler (FrOGS), a hybrid discrete neural sampler that couples an autoregressive model to a continuous-time Markov chain (CTMC) to be trained jointly under a single shared loss. FrOGS draws i.i.d. configurations, returns an unbiased estimate of the partition function, and gives consistent estimates of thermodynamic observables. We train a single model across a wide range of chemical conditions to produce estimates on a common absolute free-energy scale. FrOGS matches exact finite-size results on the 2D Ising model and reference phase diagrams for AgPd and CuAu, without mode collapse. We additionally compare to SEGAL, a published autoregressive baseline, and find that only FrOGS recovers the stability range of the CuAu$_3$ phase.

cond-mat.mtrl-sci

Data Driven Equation Discovery for Phase-Ordering Dynamics : From Allen Cahn to the Ising Model

Data-driven discovery of governing equations from spatiotemporal data offers a promising route to obtaining coarse-grained descriptions of complex dynamical systems. Here, we investigate the performance of PDE-SINDy for discovering phase-ordering dynamics using the Allen--Cahn equation as a benchmark and the Ising model with Glauber spin-flip dynamics as a microscopic system. We systematically analyze the effects of data availability, size of the candidate library, and noise on the efficiency of the equation discovery. We find that stability-selection PDE-SINDy can robustly identify the relevant terms in the governing dynamics even under limited or noisy data, while the recovered coefficient values are substantially more sensitive to these factors. We further show that enlarging the candidate library can strongly affect both term identification and coefficient recovery. Incorporating library bagging with stability selection reduces this sensitivity and improves the efficiency of equation discovery. For the Glauber spin flip Ising model dynamics, the resulting coarse-grained equation reproduces the characteristic phase-separation and coarsening dynamics of the underlying microscopic system. Overall, our results demonstrate the potential of PDE-SINDy for phase-ordering systems while highlighting the importance of carefully assessing the factors that influence the efficiency of equation discovery.

cond-mat.soft

Unraveling the PFAS helix: A statistical approach

The extreme persistence of per- and polyfluoroalkyl substances (PFAS) in the environment is rooted in their three-dimensional molecular conformation. The helical twist adopted by perfluoroalkyl chains due to hyperconjugation involving their recalcitrant C-F bonds governs their resistance to degradation, yet a quantitative, continuous metric for helicity has remained absent. Here we introduce a data-driven framework that quantifies backbone helicity using three statistical descriptors: void-state (binary occupancy) spatial autocorrelations, local backbone principal component analysis, and persistent homology. We further validate each statistical descriptor against geometric dihedral benchmarks and DFT-calculated Vibrational Circular Dichroism (VCD) spectra. The framework is initially established on a homologous series of perfluorocarboxylic acids (FC2 through FC16) and their hydrogenated analogues, then extended across perfluorosulfonic acids, fluorotelomer alcohols, polyfluoroalkyl hexanoic acid analogues, and longer-chain PFOA and PFOS analogues. Agreement between statistical, geometric, and spectroscopic definitions of helicity is established for PFCAs and extended to structurally distinct subfamilies, including PFOA analogues of varying fluorine content and perfluorosulfonic acids, demonstrating that the descriptors are robust to changes in headgroup chemistry and fluorine substitution pattern. The framework provides a chemistry-agnostic toolset for incorporating backbone conformation into predictive models of PFAS environmental fate and degradation reactivity.

physics.chem-ph

Agentic programs: an emerging form of scientific software in computational materials science

Computational materials science has traditionally delegated algorithmic tasks to computers while leaving scientific judgments to humans. We argue that recent LLM-based agent harnesses enable an emerging form of scientific software, agentic programs, that combine deterministic algorithms with bounded LLM-based judgment, task-specific verification, episodic maturation, and complete delegation in production. We illustrate this concept with DeMARS, an agentic program for constructing atomistic models from experimentally measured disordered crystal structures.

cond-mat.mtrl-sci

Physical policy gradient theorem for in situ stochastic-adjoint training

In situ adjoint training extracts parameter gradients directly from measurement, but has so far been limited to reciprocal or restricted systems. Here, we introduce the physical counterpart of the policy gradient theorem: a stochastic-adjoint gradient estimator that lifts these constraints by trading reciprocity for nondegenerate diffusion. As validation, we train a nonlinear resonator network, whose own dynamics supply the policy, against antagonistic temporal modulations with gradients from measured stochastic trajectories alone, without finite differences or a separate adjoint experiment.

physics.optics

Quantum Circuit and Tensor Network Implementation of the 2D Acoustic Wave Equation

We present a cohesive framework for simulating seismic wave propagation utilizing quantum computing paradigms and their classical tensor network equivalents. We detail a quantum circuit-based formulation for the explicit finite-difference time-domain (FDTD) solution of the two-dimensional acoustic wave equation and map this quantum architecture onto a tensor train representation, namely for Matrix Product State (MPS). The MPS solver enables deterministic simulation of large-scale wavefield dynamics on classical high-performance computing systems. We demonstrate the MPS representation by computing 2D seismic wavefields on the Marmousi model. Our results indicate that the MPS representation is a viable direction for computing and scaling wavefield propagation.

quant-ph

Shortcomings and capacities of real-constrained neural networks in complex spaces

We find the asymptotic ratio between the storage capacities when enforcing real pre-activations in a complex hypothesis class as opposed to complex ones in the same class. We use weights drawn from the complex Gaussian, which converge asymptotically in norm to the square root of dimension almost surely. Our methods depend on Gardner volume-type comparisons at critical capacity. Our proof relies on an application of the Harish-Chandra-Itzykson-Zuber (HCIZ) formula, nonstandard in literature. With the HCIZ formula, we may obtain a more robust approximation for the final asymptotic ratio. This strategy is applicable to our work specifically since we integrate over the unitary and orthogonal compact manifolds, facilitated via the Weyl integration formula and the Haar measure.

cs.LG

The convergent laboratory: when AI reasoning, autonomous experiments, high performance and quantum computing reshape chemistry

This Comment emerges from TPC26 (https://tpc26.org), a conference convening leaders from academia, national laboratories, and industry who are reshaping materials science discovery. The meeting explored how AI, autonomous agents, self-driving labs, higher performance and quantum computing converge to amplify their individual impact on materials science discovery. The perspectives here reflect the firsthand experiences of researchers at these frontiers and capture the essence of this global endeavor. As AI-driven reasoning, autonomous agentic frameworks, self-driving laboratories, and fault-tolerant quantum processors mature simultaneously, we offer this Comment as a reference at what we believe is a tipping point of transformative advances and productive disruption in the chemical sciences.

cs.AI

Ab initio Modeling of MoS2/Oxide Device Interfaces with Machine Learned Electronic Structures

We introduce a new ab initio approach to simulate semiconductor devices that integrates scalable machine-learned (ML) electronic structure models with an advanced quantum transport (QT) solver. The developed framework enables 10,000X speedups over density functional theory to produce the Hamiltonian matrix of devices made of >20,000 atoms, while offering high prediction accuracy. We use its unique features to investigate MoS2/oxide samples and single-layer MoS2 field-effect transistors, where the surrounding oxide layers, here, HfO2 or Al2O3, are explicitly included into the QT domain. In particular, we reveal that the presence of undercoordinated metal atoms (Hf or Al) close to the semiconductor-oxide interface significantly affects the magnitude of the electronic current and its propagation through MoS2.

cond-mat.mtrl-sci

On the Existence of Consistent Adversarial Attacks in High-Dimensional Linear Classification

What fundamentally distinguishes an adversarial attack from a misclassification due to limited model expressivity or finite data? In this work, we investigate this question in the setting of high-dimensional binary classification, where statistical effects due to limited data availability play a central role. We introduce a new error metric that precisely capture this distinction, quantifying model vulnerability to consistent adversarial attacks -- perturbations that preserve the ground-truth labels. Our main technical contribution is an exact and rigorous asymptotic characterization of these metrics in both well-specified models and latent space models, revealing different vulnerability patterns compared to standard robust error measures. The theoretical results demonstrate that as models become more overparameterized, their vulnerability to label-preserving perturbations grows, offering theoretical insight into the mechanisms underlying model sensitivity to adversarial attacks.

stat.ML

The thermodynamic freedom of a thermodynamic computer

Thermodynamic computers are stochastic physical devices designed to perform calculations at the thermal energy scale. Their operation is constrained by the equations of stochastic thermodynamics, among which are a set of bounds, known as speed limits, that relate a thermodynamic computer's run time to its computational progress and the heat it dissipates. Using the Wasserstein speed limit we assess the thermodynamic efficiency of a simulation model of a thermodynamic computer trained to perform a standard machine-learning classification task. On this task the thermodynamic computer is as capable as a simple multilayer perceptron. We show that different inference protocols allow the computer to operate within 40\% of the thermodynamic limit of efficiency without loss of accuracy, or to perform inference increasingly rapidly at fixed accuracy and thermodynamic efficiency. These results indicate that a thermodynamic computer designed for a particular task retains considerable freedom in its thermodynamic operation.

cond-mat.stat-mech

Breakdown of Edgeworth Expansion in Finite-Blocklength Regime and Exact Absorption via $q$-Deformation

This paper addresses the structural breakdown of the Edgeworth expansion in the finite-blocklength (FBL) regime, where conventional asymptotic approximations yield unphysical negative probabilities in the deep-tail region. We propose a $q$-deformed framework that resolves this inconsistency by replacing additive polynomial perturbations with a geometric deformation of the information density space. Motivated by the linearization of nonlinear dynamics, we prove that dynamically scaling the $q$-logarithmic parameter exactly absorbs the third-order skewness while preserving global nonnegativity. We establish a universal asymptotic matching, demonstrating that the framework encapsulates higher-order asymptotic scales. Numerical results confirm that the proposed method matches the state-of-the-art precision of the Cornish-Fisher bound without the risk of negative probabilities. The framework offers a robust and computationally stable foundation for evaluating operational limits in ultra-reliable communications such as 6G and URLLC.

cs.IT

Accelerating Atom Simulations with Variable-Block Sparse Matrix Library

Modern atomistic simulations increasingly employ localized orbitals to represent quantum operators, yielding sparse block matrices whose block shapes vary with chemical species and basis choice. Conventional scalar sparse formats store the entries of each block individually, obscuring this local structure and limiting the use of efficient block algorithms. We present VBCSR, a distributed sparse matrix library that preserves variable-size atomic blocks and accelerates the core linear algebra of large-scale atomistic simulations. A unified interface automatically maps scalar, uniform-basis, and multispecies operators to compressed sparse row (CSR), block sparse row (BSR), or variable-block compressed sparse row (VBCSR). Our advanced acceleration method groups blocks of equal shape and dispatches them to optimized dense kernels. In the reported benchmarks, VBCSR outperforms the tested Python-accessible reference implementations for several block-sparse benchmarks. We further demonstrate VBCSR in an InP nanoparticle application containing more than \(10^6\) atoms.

cond-mat.mtrl-sci