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From Rules to Reasoning: A Survey of Large Language Model-Based Approaches to Scientific Hypothesis and Idea Generation

Scientific hypothesis generation represents a fundamental challenge in contemporary research due to exponentially expanding literature volumes and increasing disciplinary specialization. Large language models (LLMs) have emerged as transformative tools for automated scientific discovery, moving beyond traditional rule-based and literature-mining approaches. Four paradigmatic approaches define current LLM-driven hypothesis generation: direct prompting and fine-tuning methods, knowledge-enhanced frameworks integrating retrieval-augmented generation (RAG), multi-agent collaborative systems simulating research teams, and reasoning-focused approaches implementing cognitive architectures. Domain-specific applications demonstrate statistical equivalence to human expert performance in social psychology, experimental validation in biomedical research, and near-expert quality in astronomy. Evaluation methodologies encompass human expert assessment, LLM-as-judge frameworks, and comprehensive benchmarking systems. Technical challenges include hallucination management, knowledge integration limitations, and balancing novelty with feasibility. Future directions emphasize hybrid neural-symbolic architectures and sophisticated human-AI collaboration models for responsible scientific discovery acceleration.

AI-driven discovery

Stabilizer Scars

Quantum many-body scars are eigenstates in nonintegrable isolated quantum systems that defy typical thermalization paradigms, violating the eigenstate thermalization hypothesis and quantum ergodicity. Here, we identify exact analytic scar solutions in a 2+1 dimensional lattice gauge theory in a quasi-1D limit as zero-magic resource stabilizer states. Our results also highlight the importance of magic resources for gauge theory thermalization, revealing a connection between computational complexity and quantum ergodicity.

eigenstate thermalization

The Origin of Palimpsests

Palimpsests are the most enigmatic impact features observed on icy worlds of the Solar System. Palimpsests are large impact features which are bright, old, mostly flat, and roughly circular. They range from >150 to ~350 km in diameter and sometimes exhibit recognizable associated radial secondary ejecta crater strings beyond their rims. Curiously, among all the Solar System's icy worlds, palimpsests are exclusively seen on the icy Galilean moons. Palimpsests are obviously different than similarly sized impact features seen on other icy satellites. For example, Evander, a 350 km diameter peak-ring impact basin on Saturn’s moon Dione, has a very low depth/diameter ratio of 0.008, indicating significant viscous relaxation. Nevertheless, it still retains short wavelength topography including a prominent central peak, peak ring, and a continuous rim, none of which are seen at palimpsests. Palimpsests display an approximately circular, and dominating, expanse of undulating plains, which is level with surrounding terrain and shows no recognizable rim. At the center of palimpsests are smooth central plains that are enclosed by a low scarp. Central plains material superposes the surrounding undulating plains and is littered with small blocks reminiscent of “small chaos” on Europa. Palimpsests have yet to be explored using modern impact simulation tools. We have begun to investigate two competing hypotheses: (A) Palimpsests form on targets which have a preexisting near-subsurface layer that is liquid or solid but very weak, and is excavated as proximal ejecta; or (B) They form in a solid ice target underlain by a steep thermal gradient that strongly influences the resulting impact feature, including the production of impact-induced melting at depth that is then a major component of proximal ejecta. Our results will have profound implications for the early thermal history of the icy Galilean satellites. We will test our two hypotheses for the formation of palimpsests on Ganymede (where they are both best observed and preserved) by means of 2D iSALE hydrodynamic simulations of impacts into ice targets that will be structured according to the scenarios for each hypothesis, with select runs in 3D. We have already conducted a pilot study using 2D iSALE that has yielded promising results, which we will report out at the meeting.

palimpsests

32 examples of LLM applications in materials science and chemistry: towards automation, assistants, agents, and accelerated scientific discovery

Abstract Large language models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 32 total projects developed during the second annual LLM hackathon for applications in materials science and chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

Computer Science

The glass-ceiling convective regime and the origin and diversity of coronae on Venus

Venus and Earth are rocky planets of roughly the same size and bulk density, yet their surface volcanic and tectonic features appear substantially different. On Venus, the coexistence of large volcanic highlands—interpreted as the surface expression of long-lived mantle plumes—alongside coronae, smaller features thought to be caused by transient thermal diapirs, remains enigmatic. Using two-dimensional numerical models of mantle convection with sharp and broad mineral phase transitions for pyrolite, we show that both scales of upwellings can be generated in a stagnant lid planet with an interior temperature 250 to 400 K warmer than Earth’s. The smaller plumes originate from a ~600 km deep internal layer that exists as a consequence of the different sequence of mineral phase transitions that occur in warmer mantles less processed and differentiated by partial melting and volcanism. Future models that include melting will provide further tests of our hypothesis.

Science & Technology - Other Topics

Entanglement properties of SU(2) gauge theory

Understanding how isolated quantum systems thermalize is central to both fundamental physics and the development of quantum technologies. In this Perspective, we present recent and new results on thermalization in nonabelian gauge theory from exact real-time simulations of two-dimensional lattice models. We discuss tests of the eigenstate thermalization hypothesis, entanglement entropy dynamics, the absence of persistent non-thermal states, spectral signatures, and measures of quantum complexity. Our new results include a two-step thermalization process in localized regions and the role of higher gauge field representations. These findings suggest that thermalization in gauge theories may offer a test case for quantum advantage.

information theory and computation

Automatic battery formation cycler and controller

Automatic battery formation cycler and controller to determine charge capacity and to perform charge-discharge operations for electrochemical cells intended for satellite power sources

CHARGE DISTRIBUTION

Remote Guidance of a Mothership-Daughtership Formation for Asteroid Exploration

This work presents an application of Model Predictive Control to maintain long-term stability for a three-satellite formation around the asteroid Apophis via remote guidance. The mothership and two daughterships perform tomographic characterization with a bistatic radar. The mothership estimates the states of all three spacecraft and determines the necessary control to maintain the desired antipodal daughtership states. An Extended Kalman Filter estimates the mothership states. A Batch Least Squares algorithm estimates the daughtership states and performs maneuver reconstruction for the mothership-administered thrust commands under thruster and gravitational uncertainty. The formulation maintains the antipodal angle with growing instability amidst these uncertainties.

Guidance

The Effects of Gravity on Combustion and Structure Formation During Combustion Synthesis in Gasless Systems

There have been relatively few publications examining the role of gravity during combustion synthesis (CS), mostly involving thermite systems. The main goal of this research was to study the influence of gravity on the combustion characteristics of heterogeneous gasless systems. In addition, some aspects of microstructure formation processes which occur during gasless CS were also studied. Four directions for experimental investigation have been explored: (1) the influence of gravity force on the characteristic features of heterogeneous combustion wave propagation (average velocity, instantaneous velocities, shape of combustion front); (2) the combustion of highly porous mixtures (with porosity greater than that for loose powders), which cannot be obtained in normal gravity; (3) the effect of gravity on sample expansion during combustion, in order to produce highly porous materials under microgravity conditions; and (4) the effect of gravity on the structure formation mechanism during the combustion synthesis of poreless composite materials.

Arvind Varma

Time-History Statistics of Soot Formation in A Model Gas Turbine Combustor

Soot formation is a complex dynamic and intermittent process determined by properties of the fuel, combustor design, and combustor operation. Although the major steps in soot formation (i.e., formation of precursors, inception, growth and evolution) are similar for a variety of carbonaceous fuels, applications, and operating conditions, it remains unclear when the temporal transition between these steps occurs. An engineering prediction tool coupled with computational fluid physics (CFD), therefore needs to accurately model all these complex steps. To develop such a model, we propose the time-history concept for understanding the time dependency of soot formation as a function of local properties (i.e., temperature, velocity, local fuel air ratio, etc.). We continue our previous work with modeling the DLR aero-combustor [1] with our updated in-house CFD code, Open National Combustion Code (OpenNCC), that now includes a Multiple Time-Scale Flamelet Progress Variable approach and a the semi-empirical two-equation soot model. We injected massless tracer particles upstream of the injector region of the combustor to collect time-history statistics of the solution variables. The correlations between the collected statistics with respect to the experimental soot volume fraction data showed that time-history effect of certain flow variables, including turbulent kinetic energy (TKE), and multiple species is indeed important for soot formation. We then conducted a time-history based correlation analysis to determine the key species and the concentration ranges critical for soot formation (C6H5-based nucleation, acetylene-based surface growth, and oxidation with OH and O2). Based on the time-history correlation coefficient (THCC) analysis, we propose possible modifications to improve the current two-equation model.

LES

A Case Study of AI-assisted Creation of a Thermodynamics Model of Precipitation Formation During Rapid Depressurization of a Vented Container

Precipitation may form in humid containers undergoing rapid depressurization. This precipitation may be liquid, i.e. fog, if the dewpoint is crossed above the freezing point of water, or direct snow crystallization if the dewpoint is crossed below the freezing point. Accurate modeling of this effect is potentially important for rapidly ascending vented containers in aircraft, spacecraft, and launch vehicles, as well as rapidly depressurizing vacuum chambers. A transient thermodynamics model of precipitation formation during the rapid depressurization of a container was developed in python. The model is written for a generic container and includes an optional water pool and water vapor source. Details of the model and results from several example cases spanning the full capabilities of the model, including a validation case, will be presented. Although the model is not novel, in contrast to prior works, this one was treated as a case study of the assistance of AI Large Language Models (LLMs) to create physical models. Impressions, performance, time, and cost of using AI for this task will be discussed.

precipitation

NOx mediated formation of ε – UO 3 during thermal decomposition of uranyl nitrate hexahydrate under static air conditions

The thermal decomposition of uranyl nitrate hexahydrate in air at temperatures of 650 – 800 °C is expected to yield α – U 3 O 8 through intermediate UO 3 phases. Here, n this study, Raman spectroscopy complimented by powder X-ray diffraction revealed the unexpected formation of ε – UO 3 as an accompanying phase during thermal decomposition of UNH at 700 °C under static air conditions. Experiments demonstrated that ε – UO 3 does not form during the initial ramp up stage nor during the high temperature heating period; but instead forms during the cooling stage between 250 – 400 °C. Additional experiments revealed that UNH initially decomposes through an amorphous UO 3 intermediate prior to α – U 3 O 8 formation. Attempts to bypass the U 3 O 8 precursor in the formation of ε – UO 3 were unsuccessful, supporting the necessity of U 3 O 8 (α – U 3 O 8 in this study) in the formation of ε – UO 3 . The observed phase evolution is proposed to result from the NOx species generated during UNH thermal decomposition, which create localized oxidizing conditions within the furnace under static air conditions. Furthermore, a predominantly phase pure ε – UO 3 was synthesized under static air conditions through the addition of an extra plateau at 250 °C during the cooling step. These findings demonstrate the importance of gas-phase chemistry and cooling conditions in uranium oxide phase evolution and provide additional insight into ε – UO 3 formation pathways.

Epsilon uranium trioxide