Generative Nested Sampling of Atomistic Thermodynamic Landscapes

Nested sampling (NS) resolves the thermodynamics of an atomistic system from a single simulation, but its practical reach is limited by the Markov-chain updates needed to decorrelate walkers within each likelihood-constrained ensemble. Flow-based NS has removed this bottleneck for gravitational-wave (GW) inference, yet its transfer to atomistic systems is not merely a change of application. Comparing a GW150914-like binary-black-hole likelihood with an eight-particle two-dimensional Lennard-Jones (LJ) system of comparable dimensionality, we show that the two landscapes differ fundamentally: atomistic multimodality is discrete and combinatorial, generated by particle permutations separated by hard collision walls, and its coordinate coupling is dense and collective, whereas the GW posterior exhibits smooth degeneracies and localized parameter coupling. Guided by this diagnosis, we introduce NS-Flows: a single conditional normalizing flow, conditioned on the NS energy bound and trained on a sliding window of recent live sets, that replaces MCMC by direct parallel draws corrected by importance-weighted rejection resampling. Live sets supply data self-consistently, allowing flow training without structured priors or a pre-existing dataset. For LJ disks in PBC, the algorithm reduces energy evaluations by over two orders of magnitude and wall-clock time by roughly one third, an advantage that becomes increasingly favorable as the cost of the potential grows. The flow's generation efficiency further acts as a physical diagnostic: it varies non-monotonically along the annealing trajectory, is lowest in the dense disordered regime, and is quantitatively captured by the constrained ensemble's internal mode complexity together with target drift across the training window, identifying liquid-like ensembles, rather than prior-target separation, as the hard case for current flow architectures.

Unsupervised Thermodynamics of Molecular Diffusion Models: Action-Operator Semantics and Auditable Free-Energy Readout

Diffusion models are increasingly utilized for modeling molecular structures and conformational ensembles, yet the thermodynamic meaning of their learned representations and scores remains elusive. To resolve this ambiguity, we introduce a mathematically consistent action-operator framework natively compatible with diffusion models. By defining a fixed molecular environment as a base action $S_0(x)$ and an alchemical perturbation as an operator $O(x)$, standard diffusion noising induces effective noised actions and operators whose gradients and alchemical derivatives are directly represented by the model's learned fields. This rigorous self-consistency enables a ``noisy operator bridge'' capable of reading out free-energy differences ($ΔF$) from endpoint ensembles and per-frame evaluations. In controlled experiments on alanine dipeptide systems, we show that incorporating physical inductive biases enables partial recovery of the base action and perturbation operator. When applied to a challenging C6-H to C6-F ligand-pocket nonbonded perturbation (185L/IND) with negligible phase-space overlap, our supervised bridge estimates the alchemical $ΔF$ within approximately $1\ k_\mathrm{B}T$ of a stable 19-state MBAR reference. Finally, we demonstrate that endpoint coordinates and binary labels alone are sufficient to partially recover the operator shape and a centered free-energy scale without any force or action supervision. This work provides a rigorous path toward transforming generative molecular diffusion models from black-box coordinate samplers into auditable thermodynamic estimators.

Thermodynamic Measure of Intelligence

Can intelligence be measured? We propose that intelligence can be defined as the lawful amplification of rare but valid futures: a system increases the probability of outcomes that would be unlikely under passive dynamics but remain admissible under the constraints of the domain. We start with the premise that an intelligent system must model the world and its own place within it. Because the system is part of the world it models, this leads naturally to recursive self-simulation: the system represents futures in which its own actions are part of the trajectory. Our central results give a necessity statement and a conditional near-sufficiency statement connecting this architecture to a precise thermodynamic measure of lawful amplification of rare-valid futures: high rare-valid lift is impossible unless the internal simulation identifies rare-valid futures with high fidelity; conversely, when rare-valid fidelity is high and the simulation contains an effective policy, the achievable lift approaches the actuation-limited optimum. Thus recursive self-simulation is not merely a plausible feature of intelligence but, under the stated assumptions, is necessary and nearly sufficient for high thermodynamic intelligence. The resulting framework makes intelligence measurable on a universal scale, from passive matter and feedback controllers, large language models, and humans as text generators to Maxwell-demon-like information engines.

GENERIC-FNO: Embedding Energy Conservation and Entropy Production into Fourier Neural Operators

We introduce GENERIC-FNO, the first neural operator to embed the full GENERIC (metriplectic) structure of nonequilibrium thermodynamics -- reversible, energy-conserving dynamics and irreversible, entropy-producing dynamics coupled through the degeneracy conditions -- directly in function space. Existing structure-preserving neural operators enforce at most a single conservation law or reversible (Hamiltonian) structure, while thermodynamically consistent learning has been confined to finite-dimensional, graph, or particle systems. GENERIC-FNO closes this gap: it learns the energy and entropy functionals as neural operators and parameterizes the Poisson and friction operators as diagonal Fourier multipliers sandwiched between rank-one projections that enforce the degeneracy conditions exactly, by construction, with no penalty term, update projection, or residual. The degeneracy identities hold to machine precision (residuals ~10^-13) for any initialization, dimension, or resolution, so the continuous-time dynamics conserve the learned energy and produce entropy exactly; the explicit time stepping adds only a small O(dt^2) drift (per-step residual ~10^-6). We further note that the (E,S,L,M) decomposition of a given flow is not unique, and introduce a gauge-invariant dissipation diagnostic separating reversible from dissipative dynamics independently of the learned functionals. Across three operator backbones (1D/2D FNOs and DeepONet) and four PDEs spanning reversible, dissipative, and mixed regimes, GENERIC-FNO preserves its exact structural guarantees zero-shot across a 4x super-resolution range (64 to 256), recovers the ground-truth ordering of physical dissipation, and is competitive with strong unconstrained and energy-penalized baselines, outperforming them on several dissipative and mixed problems at comparable or fewer parameters.

GPT-Micro: A large language paradigm for accelerated, inexpensive, and thermodynamics-consistent discovery of constitutive models in manufacturing

Constitutive modeling of the relationship between process-imposed material states and fundamental material properties is critical to control of material microstructure in manufacturing processes. The limited accuracy resulting from the typical reliance on fallible human expertise and intuition for postulation and revision of the models functional form results in incremental and time consuming model discovery. Conventional Machine Learning (ML) incurs significant cost and time of data generation. Model discovery using Large Language Models (LLMs) suffers from the above issues and/or ignores the inviolability of fundamental thermodynamics laws. This work creates a novel GPT-Micro paradigm for autonomous, data sparse, and thermodynamics-compliant discovery of de-novo constitutive models. This framework seamlessly integrates semantic knowledge extraction from literature, enforcement of thermodynamics-based conservation laws, and sparse datasets, with LLM-driven generation and refinement of model hypotheses. Validation is performed for a long-intractable constitutive modeling problem in a printed electronics process testbed. This reveals significant and simultaneous advantages over the state-of-the-art including: (a) More than 70 percent reduction in data burden relative to ML-based modeling without loss in accuracy; (b) 400X reduction in discovery time after data generation, from months to hours, relative to human-driven modeling; (c) Discovery of models with novel functional forms without subjective human choice of a starting hypothesis; (d) Enhanced physics-rooted trustworthiness, human interpretability, and mechanistic insight via synthesis of compact, conservation-compliant, and physically complete analytical models. The potential of GPT-Micro to realize rapid, low-cost, physically trustworthy, and interpretable microstructure modeling across the manufacturing landscape is discussed.

Reconciling Causality and Non-Equilibrium Thermodynamics with Hamiltonian Causal Models

Causal modeling of physical temporal phenomena must handle interventions that act along trajectories, nonstationary induced laws, path-dependent effects, and feedback mediated by dynamics, all challenging in standard causal models. We introduce Hamiltonian Causal Models (HCMs), a trajectory-level framework in which observed variables interact with local environments and interventions act as controls of Hamiltonian mechanisms. HCMs separate immutable equations of motion from intervenable mechanisms and define causal effects as discrepancies between interventional path laws. A key motivation for HCMs is their natural interface with non-equilibrium thermodynamics. Entropy production quantifies the irreversibility of a process and is a central causal observable: it is estimable from data and witnesses causal effects along the system's evolution that are invisible to endpoint and cumulative versions of the standard average treatment effect. As in physics, cause and effect are not primitives of the relation between two random variables but arise from the non-invertibility of the thermodynamic arrow. With this, our paper reconciles the language of statistical causal models and non-stationary thermodynamics, offering new tools to describe causality in a wide range of physical systems.

A Collective Variational Principle Unifying Bayesian Inference, Game Theory, and Thermodynamics

Collective intelligence emerges across biological, physical, and artificial systems without central coordination, yet a unifying principle governing such behaviour remains elusive. The Free Energy Principle explains how individual agents adapt through variational inference, while game theory formalises strategic interactions. Here we introduce the Game-Theoretic Free Energy Principle, a unified framework showing that multi-agent systems performing local free-energy minimisation implicitly implement a stochastic game. We prove that, under bounded rationality and local information constraints, stationary points of collective free energy correspond to approximate Nash equilibria of an induced game. Conversely, a broad class of cooperative games admits a variational representation in which equilibria arise as Gibbs distributions over coalitions, establishing a bridge between Bayesian inference and strategic interaction. To characterise higher-order effects, we introduce a free-energy formulation of the Harsanyi dividend, isolating irreducible multi-agent synergy. This yields a predictive theory of cooperation, including a falsifiable non-monotonic relationship between sensory precision and agent influence. We validate this prediction across neural, biological, and artificial multi-agent systems. These results identify a common variational principle underlying inference, thermodynamics, and game-theoretic equilibrium.

The Kerimov-Alekberli Model: An Information-Geometric Framework for Real-Time System Stability

This study introduces the Kerimov-Alekberli model, a novel information-geometric framework that redefines AI safety by formally linking non-equilibrium thermodynamics to stochastic control for the ethical alignment of autonomous systems. By establishing a formal isomorphism between non-equilibrium thermodynamics and stochastic control, we define systemic anomalies as deviations from a Riemannian manifold. The model utilizes the Kullback-Leibler divergence as the primary metric, governed by a dynamic threshold derived from the Fisher Information Metric. We further ground this framework in the Landauer Principle, proving that adversarial perturbations perform measurable physical work by increasing the system's informational entropy. Validation on the NSL-KDD dataset and unmanned aerial vehicle trajectory simulations demonstrated that our model achieves effective real-time detection via the FPT trigger, with strong performance metrics (e.g., high accuracy and low FPR) on benchmark datasets. This study provides a rigorous physical foundation for AI safety, transitioning from heuristic, rule-based ethical frameworks to a thermodynamics-based stability paradigm by grounding ethical violations in quantifiable physical work and entropic information.