Markus J. Buehler

Rachel K. Luu, Markus J. Buehler

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

Markus J. Buehler

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Markus J. Buehler

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

Wei Lu, David L. Kaplan, Markus J. Buehler

Spider silks are remarkable materials characterized by superb mechanical properties such as strength, extensibility and lightweightedness. Yet, to date, limited models are available to fully explore sequence-property relationships for analysis and design. Here we propose a custom generative large-language model to enable design of novel spider silk protein sequences to meet complex combinations of target mechanical properties. The model, pretrained on a large set of protein sequences, is fine-tuned on ~1,000 major ampullate spidroin (MaSp) sequences for which associated fiber-level mechanical properties exist, to yield an end-to-end forward and inverse generative strategy. Performance is assessed through: (1), a novelty analysis and protein type classification for generated spidroin sequences through BLAST searches, (2) property evaluation and comparison with similar sequences, (3) comparison of molecular structures, as well as, and (4) a detailed sequence motif analyses. We generate silk sequences with property combinations that do not exist in nature, and develop a deep understanding the mechanistic roles of sequence patterns in achieving overarching key mechanical properties (elastic modulus, strength, toughness, failure strain). The model provides an efficient approach to expand the silkome dataset, facilitating further sequence-structure analyses of silks, and establishes a foundation for synthetic silk design and optimization.

Markus J. Buehler

Learning from nature has been a quest of humanity for millennia. While this has taken the form of humans assessing natural designs such as bones, butterfly wings, or spider webs, we can now achieve generating designs using advanced computational algorithms. In this paper we report novel biologically inspired designs of diatom structures, enabled using transformer neural networks, using natural language models to learn, process and transfer insights across manifestations. We illustrate a series of novel diatom-based designs and also report a manufactured specimen, created using additive manufacturing. The method applied here could be expanded to focus on other biological design cues, implement a systematic optimization to meet certain design targets, and include a hybrid set of material design sets.

Bo Ni, David L. Kaplan, Markus J. Buehler

Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pre-trained protein language model and maps mechanical unfolding responses to create novel proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are novel, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as target to enable the discovery of protein materials with superior mechanical properties.

Fiona Y. Wang, Markus J. Buehler

Scientific discovery is not only answer generation but revision of the representational regime in which evidence, artifacts, operations, and verifiers are typed. We develop a category-theoretic account of agentic discovery for materials science. In a fixed regime b with schema category S_b, the system state is a copresheaf I_t: S_b -> Set, and provenance is the category of elements \int_{S_b} I_t. Fixed-regime operation is an update on such states, endofunctorial only when provenance-preserving refinements are specified and preserved. Discovery is instead a verified regime transition u: S_b -> S_b': old artifacts are preserved, transported by the left Kan extension Lan_u I_t, and compared with the post-transition state to identify residual content beyond functorial transport. This separates retrieval, search, and discovery without subjective novelty. We instantiate the framework in two systems. In Builder/Breaker, a protein-mechanics world model is revised under a Minimum Description Length gate; the accepted law expresses within-chain flexibility as all-mode elastic compliance conditioned by slow collective-mode participation, or mode-conditioned compliance. In CategoryScienceClaw, typed skills, artifacts, open needs, workflow mutation, gates, stress tests, and public discourse become a proof-carrying knowledge-computation graph. A fiber-network example records candidate models, rejected alternatives, an AIC gate, perturbation tests, and an accepted orientation-tensor anisotropic stiffness surrogate over an isotropic fiber-count descriptor. Together, the cases show how category theory can be both a mathematical language for discovery and an engineering specification for self-revising AI discovery systems.

Wei Lu, Nic A. Lee, Markus J. Buehler

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

Wei Lu, Rachel K. Luu, Markus J. Buehler

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

Bo Ni, Markus J. Buehler

Solving mechanics problems using numerical methods requires comprehensive intelligent capability of retrieving relevant knowledge and theory, constructing and executing codes, analyzing the results, a task that has thus far mainly been reserved for humans. While emerging AI methods can provide effective approaches to solve end-to-end problems, for instance via the use of deep surrogate models or various data analytics strategies, they often lack physical intuition since knowledge is baked into the parametric complement through training, offering less flexibility when it comes to incorporating mathematical or physical insights. By leveraging diverse capabilities of multiple dynamically interacting large language models (LLMs), we can overcome the limitations of conventional approaches and develop a new class of physics-inspired generative machine learning platform, here referred to as MechAgents. A set of AI agents can solve mechanics tasks, here demonstrated for elasticity problems, via autonomous collaborations. A two-agent team can effectively write, execute and self-correct code, in order to apply finite element methods to solve classical elasticity problems in various flavors (different boundary conditions, domain geometries, meshes, small/finite deformation and linear/hyper-elastic constitutive laws, and others). For more complex tasks, we construct a larger group of agents with enhanced division of labor among planning, formulating, coding, executing and criticizing the process and results. The agents mutually correct each other to improve the overall team-work performance in understanding, formulating and validating the solution. Our framework shows the potential of synergizing the intelligence of language models, the reliability of physics-based modeling, and the dynamic collaborations among diverse agents, opening novel avenues for automation of solving engineering problems.

Haiqian Yang, Yuan Cao, Markus J. Buehler

World models have enabled interactive exploration of game environments and robotic manipulation, but physical engineering remains beyond their reach: real materials exhibit nonlinear constitutive laws, carry history-dependent internal state, undergo inertial dynamics, and may possess hierarchical structures spanning multiple length scales. We present LEIA (Learned Environment for Interactive Architected materials), a world model that lets engineers apply boundary conditions step by step and observe the resulting deformation and stress fields in real time. LEIA handles large three-dimensional unstructured meshes and generates autoregressive responses to user-specified loading. We introduce MicroPlate, a benchmark of architected plates spanning two regimes of microstructure modeling: architected lattices that resolve microstructure explicitly through three-dimensional geometry, and a homogeneous plate where microstructural change is modeled implicitly through internal degrees of freedom. MicroPlate is used to assess LEIA alongside four baseline methods across both regimes. Finally, we demonstrate that LEIA enables efficient candidate generation and ranking for fast surrogate-guided search for de novo designs of architected materials, with stress-accurate candidate ranking validated by finite element ground truth.

Alireza Ghafarollahi, Markus J. Buehler

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

Bianca Datta, Markus J. Buehler, Yvonne Chow et al.

Global food systems must deliver nutritious, sustainable foods while sharply reducing environmental impact. Yet, food innovation remains slow, empirical, and fragmented. Artificial intelligence (AI) offers a transformative path to link molecular composition to functional performance, connect chemical structure to sensory outcomes, and accelerate cross-disciplinary innovation across the production pipeline. While broadly applicable to food systems, we focus on sustainable proteins--plant-based, fermentation-derived, and cultivated--as a high-impact testbed for AI-driven closed-loop design. We review the applications, opportunities, and challenges of AI for Food as an emerging discipline that integrates ingredient design, formulation development, fermentation and production, texture analysis, sensory science, manufacturing, and recipe generation. We identify four priorities: advancing scientific machine learning with embedded domain priors, treating food as a programmable biomaterial, building self-driving laboratories for automated discovery, and developing deep reasoning models that integrate nutrition and sustainability. Integrating AI responsibly into the food innovation cycle can accelerate the transition to sustainable food systems and establish a predictive, design-driven science of food for human and planetary health.

Alireza Ghafarollahi, Markus J. Buehler

The design of alloys is a multi-scale problem that requires a holistic approach that involves retrieving relevant knowledge, applying advanced computational methods, conducting experimental validations, and analyzing the results, a process that is typically reserved for human experts. Machine learning (ML) can help accelerate this process, for instance, through the use of deep surrogate models that connect structural features to material properties, or vice versa. However, existing data-driven models often target specific material objectives, offering limited flexibility to integrate out-of-domain knowledge and cannot adapt to new, unforeseen challenges. Here, we overcome these limitations by leveraging the distinct capabilities of multiple AI agents that collaborate autonomously within a dynamic environment to solve complex materials design tasks. The proposed physics-aware generative AI platform, AtomAgents, synergizes the intelligence of large language models (LLM) the dynamic collaboration among AI agents with expertise in various domains, including knowledge retrieval, multi-modal data integration, physics-based simulations, and comprehensive results analysis across modalities that includes numerical data and images of physical simulation results. The concerted effort of the multi-agent system allows for addressing complex materials design problems, as demonstrated by examples that include autonomously designing metallic alloys with enhanced properties compared to their pure counterparts. Our results enable accurate prediction of key characteristics across alloys and highlight the crucial role of solid solution alloying to steer the development of advanced metallic alloys. Our framework enhances the efficiency of complex multi-objective design tasks and opens new avenues in fields such as biomedical materials engineering, renewable energy, and environmental sustainability.

Markus J. Buehler

Transformer neural networks show promising capabilities, in particular for uses in materials analysis, design and manufacturing, including their capacity to work effectively with both human language, symbols, code, and numerical data. Here we explore the use of large language models (LLMs) as a tool that can support engineering analysis of materials, applied to retrieving key information about subject areas, developing research hypotheses, discovery of mechanistic relationships across disparate areas of knowledge, and writing and executing simulation codes for active knowledge generation based on physical ground truths. When used as sets of AI agents with specific features, capabilities, and instructions, LLMs can provide powerful problem solution strategies for applications in analysis and design problems. Our experiments focus on using a fine-tuned model, MechGPT, developed based on training data in the mechanics of materials domain. We first affirm how finetuning endows LLMs with reasonable understanding of domain knowledge. However, when queried outside the context of learned matter, LLMs can have difficulty to recall correct information. We show how this can be addressed using retrieval-augmented Ontological Knowledge Graph strategies that discern how the model understands what concepts are important and how they are related. Illustrated for a use case of relating distinct areas of knowledge - here, music and proteins - such strategies can also provide an interpretable graph structure with rich information at the node, edge and subgraph level. We discuss nonlinear sampling strategies and agent-based modeling applied to complex question answering, code generation and execution in the context of automated force field development from actively learned Density Functional Theory (DFT) modeling, and data analysis.

Fiona Y. Wong, Markus J. Buehler

Scientific evidence often spans instruments, databases, and disciplines, so no single source records the full phenomenon. This makes it difficult to determine when coordinated AI agents add value over simpler scientific workflows. We evaluate this question with a cross-domain benchmark spanning four scientific tasks: mapping molecular structure into musical representations, detecting historical paradigm shifts in science, identifying vector-borne disease emergence, and vetting transiting-exoplanet candidates. Each case uses a frozen evaluation panel, predefined scoring protocols, explicit baselines, ablations or null controls, and stated limitations. The results define three operating regimes. When different disciplines each capture only part of the phenomenon, cross-channel composites improve over single-channel baselines: climate-vector emergence reaches AUROC 0.944 and exoplanet vetting reaches AUROC 0.955. However, the exoplanet workflow is effectively tied with a strong combined-summary baseline, showing that decomposition does not always improve top-line performance. When one signal dominates, as in paradigm-shift detection, coordination mainly improves interpretation and traceability. For molecular sonification, the gain is representational rather than predictive. ScienceClaw x Infinite provides the auditable artifact and provenance layer for this evaluation. The benchmark therefore assigns value to coordination only when the corresponding performance, provenance, or representation claim is supported by explicit comparators.

Fiona Y. Wang, Lee Marom, Subhadeep Pal et al.

We present ScienceClaw + Infinite, a framework for autonomous scientific investigation in which independent agents conduct research without central coordination, and any contributor can deploy new agents into a shared ecosystem. The system is built around three components: an extensible registry of over 300 interoperable scientific skills, an artifact layer that preserves full computational lineage as a directed acyclic graph (DAG), and a structured platform for agent-based scientific discourse with provenance-aware governance. Agents select and chain tools based on their scientific profiles, produce immutable artifacts with typed metadata and parent lineage, and broadcast unsatisfied information needs to a shared global index. The ArtifactReactor enables plannerless coordination: peer agents discover and fulfill open needs through pressure-based scoring, while schema-overlap matching triggers multi-parent synthesis across independent analyses. An autonomous mutation layer actively prunes the expanding artifact DAG to resolve conflicting or redundant workflows, while persistent memory allows agents to continuously build upon complex epistemic states across multiple cycles. Infinite converts these outputs into auditable scientific records through structured posts, provenance views, and machine-readable discourse relations, with community feedback steering subsequent investigation cycles. Across four autonomous investigations, peptide design for the somatostatin receptor SSTR2, lightweight impact-resistant ceramic screening, cross-domain resonance bridging biology, materials, and music, and formal analogy construction between urban morphology and grain-boundary evolution, the framework demonstrates heterogeneous tool chaining, emergent convergence among independently operating agents, and traceable reasoning from raw computation to published finding.

Jaime A. Berkovich, Markus J. Buehler

Conway's Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer (GPT) model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

Haiqian Yang, Anh Q. Nguyen, Dapeng Bi et al.

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how every single cell decides to position itself relative to its neighboring cells. Despite its importance, it remains a major challenge to understand and predict the behavior of every cell within the living tissue over time during such intricate processes. To tackle this question, we propose a geometric deep learning model that can predict multicellular folding and embryogenesis, accurately capturing the highly convoluted spatial interactions among cells. We demonstrate that multicellular data can be represented with both granular and foam-like physical pictures through a unified graph data structure, considering both cellular interactions and cell junction networks. We successfully use our model to achieve two important tasks, interpretable 4-D morphological sequence alignment, and predicting local cell rearrangements before they occur at single-cell resolution. Furthermore, using an activation map and ablation studies, we demonstrate that cell geometries and cell junction networks together regulate local cell rearrangement which is critical for embryo morphogenesis. This approach provides a novel paradigm to study morphogenesis, highlighting a unified data structure and harnessing the power of geometric deep learning to accurately model the mechanisms and behaviors of cells during development. It offers a pathway toward creating a unified dynamic morphological atlas for a variety of developmental processes such as embryogenesis.

Dat Quoc Ha, Md Ferdous Alam, Markus J. Buehler et al.

Inverse design tools such as Topology Optimization (TO) can achieve new levels of improvement for high-performance engineered structures. However, widespread use is hindered by high computational times and a black-box nature that inhibits user interaction. Human-in-the-loop TO approaches are emerging that integrate human intuition into the design generation process. However, these rely on the time-consuming bottleneck of iterative region selection for design modifications. To reduce the number of iterative trials, this contribution presents an AI co-pilot that uses machine learning to predict the user's preferred regions. The prediction model is configured as an image segmentation task with a U-Net architecture. It is trained on synthetic datasets where human preferences either identify the longest topological member or the most complex structural connection. The model successfully predicts plausible regions for modification and presents them to the user as AI recommendations. The human preference model demonstrates generalization across diverse and non-standard TO problems and exhibits emergent behavior outside the single-region selection training data. Demonstration examples show that the new human-in-the-loop TO approach that integrates the AI co-pilot can improve manufacturability or improve the linear buckling load by 39% while only increasing the total design time by 15 sec compared to conventional simplistic TO.

Markus J. Buehler

We introduce materiomusic as a generative framework linking the hierarchical structures of matter with the compositional logic of music. Across proteins, spider webs and flame dynamics, vibrational and architectural principles recur as tonal hierarchies, harmonic progressions, and long-range musical form. Using reversible mappings, from molecular spectra to musical tones and from three-dimensional networks to playable instruments, we show how sound functions as a scientific probe, an epistemic inversion where listening becomes a mode of seeing and musical composition becomes a blueprint for matter. These mappings excavate deep time: patterns originating in femtosecond molecular vibrations or billion-year evolutionary histories become audible. We posit that novelty in science and art emerges when constraints cannot be satisfied within existing degrees of freedom, forcing expansion of the space of viable configurations. Selective imperfection provides the mechanism restoring balance between coherence and adaptability. Quantitative support comes from exhaustive enumeration of all 2^12 musical scales, revealing that culturally significant systems cluster in a mid-entropy, mid-defect corridor, directly paralleling the Hall-Petch optimum where intermediate defect densities maximize material strength. Iterating these mappings creates productive collisions between human creativity and physics, generating new information as musical structures encounter evolutionary constraints. We show how swarm-based AI models compose music exhibiting human-like structural signatures such as small-world connectivity, modular integration, long-range coherence, suggesting a route beyond interpolation toward invention. We show that science and art are generative acts of world-building under constraint, with vibration as a shared grammar organizing structure across scales.

Eric L. Buehler, Markus J. Buehler

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, our gating strategy uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create never-before-used deep layer-wise combinations to solve tasks. The design is inspired by the biological principles of universality and diversity, where neural network building blocks are reused in different hierarchical manifestations. Hence, the X-LoRA model can be easily implemented for any existing large language model (LLM) without a need for modifications of the underlying structure. We develop a tailored X-LoRA model that offers scientific capabilities including forward/inverse analysis tasks and enhanced reasoning capability, focused on biomaterial analysis, protein mechanics and design. The impact of this work include access to readily expandable and adaptable models with strong domain knowledge and the capability to integrate across areas of knowledge. Featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, protein biophysics, mechanics and quantum-mechanics based molecular properties, we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, adversarial agentic modeling including ontological knowledge graph construction, as well as molecular design. The model is capable not only of making quantitative predictions of nanomechanical properties of proteins or quantum mechanical molecular properties, but also reasons over the results and correctly predicts likely mechanisms that explain distinct molecular behaviors.

Markus J. Buehler

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Tarjei Paule Hage, Markus J. Buehler

Can reinforcement learning with hard, verifiable rewards teach a compact language model to reason about physics, or does it primarily learn to pattern-match toward correct answers? We study this question by training a 1.5B-parameter reasoning model on beam statics, a classic engineering problem, using parameter-efficient RLVR with binary correctness rewards from symbolic solvers, without teacher-generated reasoning traces. The best BeamPERL checkpoint achieves a 66.7% improvement in Pass@1 over the base model. However, the learned competence is anisotropic: the model generalizes compositionally (more loads) but fails under topological shifts (moved supports) that require the same equilibrium equations. Intermediate checkpoints yield the strongest reasoning, while continued optimization degrades robustness while maintaining reward. These findings reveal a key limitation of outcome-level alignment: reinforcement learning with exact physics rewards induces procedural solution templates rather than internalization of governing equations. The precision of the reward signal - even when analytically exact - does not by itself guarantee transferable physical reasoning. Our results suggest that verifiable rewards may need to be paired with structured reasoning scaffolding to move beyond template matching toward robust scientific reasoning.

Xiyuan Yang, Jiaru Zou, Rui Pan et al.

Recursive or looped language models have recently emerged as a new scaling axis by iteratively refining the same model computation over latent states to deepen reasoning. We extend such scaling principle from a single model to multi-agent systems, and ask: Can agent collaboration itself be scaled through recursion? To this end, we introduce RecursiveMAS, a recursive multi-agent framework that casts the entire system as a unified latent-space recursive computation. RecursiveMAS connects heterogeneous agents as a collaboration loop through the lightweight RecursiveLink module, enabling in-distribution latent thoughts generation and cross-agent latent state transfer. To optimize our framework, we develop an inner-outer loop learning algorithm for iterative whole-system co-optimization through shared gradient-based credit assignment across recursion rounds. Theoretical analyses of runtime complexity and learning dynamics establish that RecursiveMAS is more efficient than standard text-based MAS and maintains stable gradients during recursive training. Empirically, we instantiate RecursiveMAS under 4 representative agent collaboration patterns and evaluate across 9 benchmarks spanning mathematics, science, medicine, search, and code generation. In comparison with advanced single/multi-agent and recursive computation baselines, RecursiveMAS consistently delivers an average accuracy improvement of 8.3%, together with 1.2$\times$-2.4$\times$ end-to-end inference speedup, and 34.6%-75.6% token usage reduction. Code and Data are provided in https://recursivemas.github.io.

Lee Marom, Skylar Tibbits, Gioele Zardini et al.

Natural materials achieve adaptive behavior through hierarchical organization and coupled mechanisms across scales. Their translation into engineering, however, remains largely heuristic. What is missing is a formal translation framework that carries biological design logic into engineered realization while preserving physical consistency across levels of abstraction. Here we present a category theoretic compositional framework for verified nature-derived design. The framework defines a category of stimulus response dynamical systems with natural and artificial subcategories. It introduces a structure preserving implementation functor from biological mechanics to engineered systems. It also formalizes a machine agnostic specification layer that links behavioral intent to executable fabrication programs. We instantiate the framework on the hygromorphic pinecone hierarchy as a representative biological case. We implement the full pipeline in Grasshopper, where formal specifications are translated into modular parametric scripts that preserve the compositional structure of the model. The resulting designs are fabricated by fused filament fabrication, evaluated experimentally, and tested against model predictions derived from the pipeline. The current implementation generates four actuator classes spanning two stimulus types and two kinematic responses. One actuator arises purely through composition from previously validated components, without additional manual derivation. The results show that compositionality can function not just as a descriptive language, but as a generative and system level verifiable method for mechanical material design. More broadly, the work provides a concrete route for embedding formal multiscale reasoning within increasingly computational, generative, and physics-driven design workflows.

Isabella A. Stewart, Markus J. Buehler

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

Markus J. Buehler

PRefLexOR (Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning) combines preference optimization with concepts from Reinforcement Learning to enable models to self-teach through iterative reasoning improvements. We propose a recursive learning approach that engages the model in multi-step reasoning, revisiting, and refining intermediate steps before producing a final output in training and inference phases. Through multiple training stages, the model first learns to align its reasoning with accurate decision paths by optimizing the log odds between preferred and non-preferred responses. During this process, PRefLexOR builds a dynamic knowledge graph by generating questions from random text chunks and retrieval-augmentation to contextualize relevant details from the entire training corpus. In the second stage, preference optimization enhances model performance by using rejection sampling to fine-tune reasoning quality by continually producing in-situ training data while masking the reasoning steps. Recursive optimization within a thinking token framework introduces iterative feedback loops, where the model refines reasoning, achieving deeper coherence, consistency, and adaptability. Implemented in small language models with only 3 billion parameters, we should that even tiny models can iteratively teach themselves to reason with greater depth and reflectivity. Our implementation is straightforward and can be incorporated into any existing pretrained LLM. We focus our examples on applications in biological materials science and demonstrate the method in a variety of case studies that range from in-domain to cross-domain applications. Using reasoning strategies that include thinking and reflection modalities we build a multi-agent recursive self-improving inference approach to successively improve responses via repeated sampling in inference time.

Markus J. Buehler

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

Zhenze Yang, Sarah K. Yorke, Tuomas P. J. Knowles et al.

Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external environmental stimuli on the self-assembly behaviour of these systems. However, there is yet to be a systematic study that gathers this rich literature data and collectively examines these experimental factors to provide a global picture of the fundamental rules that govern protein self-assembly behavior. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and literature mining facilitated by a large language model. As a result, we collect more than 1,000 experimental data entries with information about peptide sequence, experimental conditions and corresponding self-assembly phases. Utilizing the collected data, ML models are trained and evaluated, demonstrating excellent accuracy (>80\%) and efficiency in peptide assembly phase classification. Moreover, we fine-tune our GPT model for peptide literature mining with the developed dataset, which exhibits markedly superior performance in extracting information from academic publications relative to the pre-trained model. We find that this workflow can substantially improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the mechanisms governing peptide self-assembly. In doing so, novel structures can be accessed for a range of applications including sensing, catalysis and biomaterials.

Alireza Ghafarollahi, Markus J. Buehler

A multi-agent AI model is used to automate the discovery of new metallic alloys, integrating multimodal data and external knowledge including insights from physics via atomistic simulations. Our multi-agent system features three key components: (a) a suite of LLMs responsible for tasks such as reasoning and planning, (b) a group of AI agents with distinct roles and expertise that dynamically collaborate, and (c) a newly developed graph neural network (GNN) model for rapid retrieval of key physical properties. A set of LLM-driven AI agents collaborate to automate the exploration of the vast design space of MPEAs, guided by predictions from the GNN. We focus on the NbMoTa family of body-centered cubic (bcc) alloys, modeled using an ML-based interatomic potential, and target two key properties: the Peierls barrier and solute/screw dislocation interaction energy. Our GNN model accurately predicts these atomic-scale properties, providing a faster alternative to costly brute-force calculations and reducing the computational burden on multi-agent systems for physics retrieval. This AI system revolutionizes materials discovery by reducing reliance on human expertise and overcoming the limitations of direct all-atom simulations. By synergizing the predictive power of GNNs with the dynamic collaboration of LLM-based agents, the system autonomously navigates vast alloy design spaces, identifying trends in atomic-scale material properties and predicting macro-scale mechanical strength, as demonstrated by several computational experiments. This approach accelerates the discovery of advanced alloys and holds promise for broader applications in other complex systems, marking a significant step forward in automated materials design.

Alireza Ghafarollahi, Markus J. Buehler

Advances in artificial intelligence (AI) promise autonomous discovery, yet most systems still resurface knowledge latent in their training data. We present Sparks, a multi-modal multi-agent AI model that executes the entire discovery cycle that includes hypothesis generation, experiment design and iterative refinement to develop generalizable principles and a report without human intervention. Applied to protein science, Sparks uncovered two previously unknown phenomena: (i) a length-dependent mechanical crossover whereby beta-sheet-biased peptides surpass alpha-helical ones in unfolding force beyond ~80 residues, establishing a new design principle for peptide mechanics; and (ii) a chain-length/secondary-structure stability map revealing unexpectedly robust beta-sheet-rich architectures and a "frustration zone" of high variance in mixed alpha/beta folds. These findings emerged from fully self-directed reasoning cycles that combined generative sequence design, high-accuracy structure prediction and physics-aware property models, with paired generation-and-reflection agents enforcing self-correction and reproducibility. The key result is that Sparks can independently conduct rigorous scientific inquiry and identify previously unknown scientific principles.

Markus J. Buehler

The pursuit of automated scientific discovery has fueled progress from symbolic logic to modern AI, forging new frontiers in reasoning and pattern recognition. Transformers function as potential systems, where every possible relationship remains latent potentiality until tasks impose constraints, akin to measurement. Yet, refining their sampling requires more than probabilistic selection: solutions must conform to specific structures or rules, ensuring consistency and the invocation of general principles. We present Graph-PReFLexOR (Graph-based Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning), a framework that combines graph reasoning with symbolic abstraction to dynamically expand domain knowledge. Inspired by reinforcement learning, Graph-PReFLexOR defines reasoning as a structured mapping, where tasks yield knowledge graphs, abstract patterns, and ultimately, final answers. Inspired by category theory, it encodes concepts as nodes and their relationships as edges, supporting hierarchical inference and adaptive learning through isomorphic representations. Demonstrations include hypothesis generation, materials design, and creative reasoning, such as discovering relationships between mythological concepts like 'thin places' with materials science. We propose a 'knowledge garden growth' strategy that integrates insights across domains, promoting interdisciplinary connections. Results with a 3-billion-parameter Graph-PReFLexOR model show superior reasoning depth and adaptability, underscoring the potential for transparent, multidisciplinary AI-driven discovery. It lays the groundwork for general autonomous reasoning solutions.

Markus J. Buehler

We present an approach to modifying Transformer architectures by integrating graph-aware relational reasoning into the attention mechanism, merging concepts from graph neural networks and language modeling. Building on the inherent connection between attention and graph theory, we reformulate the Transformer's attention mechanism as a graph operation and propose Graph-Aware Isomorphic Attention. This method leverages advanced graph modeling strategies, including Graph Isomorphism Networks (GIN) and Principal Neighborhood Aggregation (PNA), to enrich the representation of relational structures. Our approach captures complex dependencies and generalizes across tasks, as evidenced by a reduced generalization gap and improved learning performance. Additionally, we expand the concept of graph-aware attention to introduce Sparse GIN-Attention, a fine-tuning approach that employs sparse GINs. By interpreting attention matrices as sparse adjacency graphs, this technique enhances the adaptability of pre-trained foundational models with minimal computational overhead, endowing them with graph-aware capabilities. Sparse GIN-Attention fine-tuning achieves improved training dynamics and better generalization compared to alternative methods like low-rank adaption (LoRA). We discuss latent graph-like structures within traditional attention mechanisms, offering a new lens through which Transformers can be understood. By evolving Transformers as hierarchical GIN models for relational reasoning. This perspective suggests profound implications for foundational model development, enabling the design of architectures that dynamically adapt to both local and global dependencies. Applications in bioinformatics, materials science, language modeling, and beyond could benefit from this synthesis of relational and sequential data modeling, setting the stage for interpretable and generalizable modeling strategies.

Bo Ni, Markus J. Buehler

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

Haiqian Yang, Florian Meyer, Shaoxun Huang et al.

Multicellular self-assembly into functional structures is a dynamic process that is critical in the development and diseases, including embryo development, organ formation, tumor invasion, and others. Being able to infer collective cell migratory dynamics from their static configuration is valuable for both understanding and predicting these complex processes. However, the identification of structural features that can indicate multicellular motion has been difficult, and existing metrics largely rely on physical instincts. Here we show that using a graph neural network (GNN), the motion of multicellular collectives can be inferred from a static snapshot of cell positions, in both experimental and synthetic datasets.

Jaime A. Berkovich, Noah S. David, Markus J. Buehler

Cellular automata (CA) provide a minimal formalism for investigating how simple local interactions generate rich spatiotemporal behavior in domains as diverse as traffic flow, ecology, tissue morphogenesis and crystal growth. However, automatically discovering the local update rules for a given phenomenon and using them for quantitative prediction remains challenging. Here we present AutomataGPT, a decoder-only transformer pretrained on around 1 million simulated trajectories that span 100 distinct two-dimensional binary deterministic CA rules on toroidal grids. When evaluated on previously unseen rules drawn from the same CA family, AutomataGPT attains 98.5% perfect one-step forecasts and reconstructs the governing update rule with up to 96% functional (application) accuracy and 82% exact rule-matrix match. These results demonstrate that large-scale pretraining over wider regions of rule space yields substantial generalization in both the forward (state forecasting) and inverse (rule inference) problems, without hand-crafted priors. By showing that transformer models can faithfully infer and execute CA dynamics from data alone, our work lays the groundwork for abstracting real-world dynamical phenomena into data-efficient CA surrogates, opening avenues in biology, tissue engineering, physics and AI-driven scientific discovery.

Rachel K. Luu, Markus J. Buehler

Generative AI has made rapid progress in text, image, and video synthesis, yet text-to-3D modeling for scientific design remains particularly challenging due to limited controllability and high computational cost. Most existing 3D generative methods rely on meshes, voxels, or point clouds which can be costly to train and difficult to control. We introduce Bioinspired123D, a lightweight and modular code-as-geometry pipeline that generates fabricable 3D structures directly through parametric programs rather than dense visual representations. At the core of Bioinspired123D is Bioinspired3D, a compact language model finetuned to translate natural language design cues into Blender Python scripts encoding smooth, biologically inspired geometries. We curate a domain-specific dataset of over 4,000 bioinspired and geometric design scripts spanning helical, cellular, and tubular motifs with parametric variability. The dataset is expanded and validated through an automated LLM-driven, Blender-based quality control pipeline. Bioinspired3D is then embedded in a graph-based agentic framework that integrates multimodal retrieval-augmented generation and a vision-language model critic to iteratively evaluate, critique, and repair generated scripts. We evaluate performance on a new benchmark for 3D geometry script generation and show that Bioinspired123D demonstrates a near fourfold improvement over its non-finetuned base model, while also outperforming substantially larger state-of-the-art language models despite using far fewer parameters and compute. By prioritizing code-as-geometry representations, Bioinspired123D enables compute-efficient, controllable, and interpretable text-to-3D generation, lowering barriers to AI driven scientific discovery in materials and structural design.

Fiona Y. Wang, Di Sheng Lee, David L. Kaplan et al.

Designing proteins de novo with tailored structural, physicochemical, and functional properties remains a grand challenge in biotechnology, medicine, and materials science, due to the vastness of sequence space and the complex coupling between sequence, structure, and function. Current state-of-the-art generative methods, such as protein language models (PLMs) and diffusion-based architectures, often require extensive fine-tuning, task-specific data, or model reconfiguration to support objective-directed design, thereby limiting their flexibility and scalability. To overcome these limitations, we present a decentralized, agent-based framework inspired by swarm intelligence for de novo protein design. In this approach, multiple large language model (LLM) agents operate in parallel, each assigned to a specific residue position. These agents iteratively propose context-aware mutations by integrating design objectives, local neighborhood interactions, and memory and feedback from previous iterations. This position-wise, decentralized coordination enables emergent design of diverse, well-defined sequences without reliance on motif scaffolds or multiple sequence alignments, validated with experiments on proteins with alpha helix and coil structures. Through analyses of residue conservation, structure-based metrics, and sequence convergence and embeddings, we demonstrate that the framework exhibits emergent behaviors and effective navigation of the protein fitness landscape. Our method achieves efficient, objective-directed designs within a few GPU-hours and operates entirely without fine-tuning or specialized training, offering a generalizable and adaptable solution for protein design. Beyond proteins, the approach lays the groundwork for collective LLM-driven design across biomolecular systems and other scientific discovery tasks.

Markus J. Buehler

We show that coherent, long-form musical composition can emerge from a decentralized swarm of identical, frozen foundation models that coordinate via stigmergic, peer-to-peer signals, without any weight updates. We compare a centralized multi-agent system with a global critic to a fully decentralized swarm in which bar-wise agents sense and deposit harmonic, rhythmic, and structural cues, adapt short-term memory, and reach consensus. Across symbolic, audio, and graph-theoretic analyses, the swarm yields superior quality while delivering greater diversity and structural variety and leads across creativity metrics. The dynamics contract toward a stable configuration of complementary roles, and self-similarity networks reveal a small-world architecture with efficient long-range connectivity and specialized bridging motifs, clarifying how local novelties consolidate into global musical form. By shifting specialization from parameter updates to interaction rules, shared memory, and dynamic consensus, MusicSwarm provides a compute- and data-efficient route to long-horizon creative structure that is immediately transferable beyond music to collaborative writing, design, and scientific discovery.

Rachel K. Luu, Jingyu Deng, Mohammed Shahrudin Ibrahim et al.

Large language models (LLMs) have reshaped the research landscape by enabling new approaches to knowledge retrieval and creative ideation. Yet their application in discipline-specific experimental science, particularly in highly multi-disciplinary domains like materials science, remains limited. We present a first-of-its-kind framework that integrates generative AI with literature from hitherto-unconnected fields such as plant science, biomimetics, and materials engineering to extract insights and design experiments for materials. We focus on humidity-responsive systems such as pollen-based materials and Rhapis excelsa (broadleaf lady palm) leaves, which exhibit self-actuation and adaptive performance. Using a suite of AI tools, including a fine-tuned model (BioinspiredLLM), Retrieval-Augmented Generation (RAG), agentic systems, and a Hierarchical Sampling strategy, we extract structure-property relationships and translate them into new classes of bioinspired materials. Structured inference protocols generate and evaluate hundreds of hypotheses from a single query, surfacing novel and experimentally tractable ideas. We validate our approach through real-world implementation: LLM-generated procedures, materials designs, and mechanical predictions were tested in the laboratory, culminating in the fabrication of a novel pollen-based adhesive with tunable morphology and measured shear strength, establishing a foundation for future plant-derived adhesive design. This work demonstrates how AI-assisted ideation can drive real-world materials design and enable effective human-AI collaboration.

Alireza Ghafarollahi, Markus J. Buehler

Conventional machine learning approaches accelerate inorganic materials design via accurate property prediction and targeted material generation, yet they operate as single-shot models limited by the latent knowledge baked into their training data. A central challenge lies in creating an intelligent system capable of autonomously executing the full inorganic materials discovery cycle, from ideation and planning to experimentation and iterative refinement. We introduce SparksMatter, a multi-agent AI model for automated inorganic materials design that addresses user queries by generating ideas, designing and executing experimental workflows, continuously evaluating and refining results, and ultimately proposing candidate materials that meet the target objectives. SparksMatter also critiques and improves its own responses, identifies research gaps and limitations, and suggests rigorous follow-up validation steps, including DFT calculations and experimental synthesis and characterization, embedded in a well-structured final report. The model's performance is evaluated across case studies in thermoelectrics, semiconductors, and perovskite oxides materials design. The results demonstrate the capacity of SparksMatter to generate novel stable inorganic structures that target the user's needs. Benchmarking against frontier models reveals that SparksMatter consistently achieves higher scores in relevance, novelty, and scientific rigor, with a significant improvement in novelty across multiple real-world design tasks as assessed by a blinded evaluator. These results demonstrate SparksMatter's unique capacity to generate chemically valid, physically meaningful, and creative inorganic materials hypotheses beyond existing materials knowledge.

Markus J. Buehler

We report fundamental insights into how agentic graph reasoning systems spontaneously evolve toward a critical state that sustains continuous semantic discovery. By rigorously analyzing structural (Von Neumann graph entropy) and semantic (embedding) entropy, we identify a subtle yet robust regime in which semantic entropy persistently dominates over structural entropy. This interplay is quantified by a dimensionless Critical Discovery Parameter that stabilizes at a small negative value, indicating a consistent excess of semantic entropy. Empirically, we observe a stable fraction (12%) of "surprising" edges, links between semantically distant concepts, providing evidence of long-range or cross-domain connections that drive continuous innovation. Concomitantly, the system exhibits scale-free and small-world topological features, alongside a negative cross-correlation between structural and semantic measures, reinforcing the analogy to self-organized criticality. These results establish clear parallels with critical phenomena in physical, biological, and cognitive complex systems, revealing an entropy-based principle governing adaptability and continuous innovation. Crucially, semantic richness emerges as the underlying driver of sustained exploration, despite not being explicitly used by the reasoning process. Our findings provide interdisciplinary insights and practical strategies for engineering intelligent systems with intrinsic capacities for long-term discovery and adaptation, and offer insights into how model training strategies can be developed that reinforce critical discovery.

Markus J. Buehler

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters that define the nature of the physical system at hand) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.