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, we propose a gating strategy that 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 of adaptations are established to solve specific 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, adaptable and changeable models with strong domain knowledge and the capability to integrate across areas of knowledge. With the X-LoRA model featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, and protein mechanics we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, and adversarial agentic modeling including ontological knowledge graphs. The model is capable not only of making quantitative predictions …

Fungal mycelium, a living network of filamentous threads, thrives on lignocellulosic waste and exhibits rapid growth, hydrophobicity, and intrinsic regeneration, offering a potential means to create next-generation sustainable and functional composites. However, existing hybrid-living mycelium composites (myco-composites) are tremendously constrained by conventional mold-based manufacturing processes, which are only compatible with simple geometries and coarse biomass substrates that enable gas exchange. Here we introduce a class of structural myco-composites manufactured with a novel platform that harnesses high-resolution biocomposite additive manufacturing and robust mycelium colonization with indirect inoculation. We leverage principles of hierarchical composite design and selective nutritional provision to create a robust myco-composite that is scalable, tunable, and compatible with complex …

Nature has severely outpaced humans in developing multifunctional, hierarchical materials that access impressive material properties, all the while being fully degradable and part of native ecosystems. But how can we effectively model the intricate time and length scales in biological systems to translate design principles to meet engineering demands? We postulate that generative artificial intelligence (AI) can play a crucial role in solving this interdisciplinary challenge, translating insights across disparate knowledge domains and forming the basis for a new sustainable materials economy. Techniques like generative adversarial networks, transformer neural networks, and diffusion denoising modeling have been used to solve complex bio-inspired design challenges. Emerging tools such as multimodal large language models provide robust foundations with reasoning abilities that can be multiplied if connected into multi-agent systems with access to first principles (e.g., Density Functional Theory, molecular dynamics, coarse-grained simulations) or physical experiments (e.g., autonomous manufacturing, universal material/mechanical testing). Through this approach, generative AI can not only address complex forward and inverse tasks but also develop ontological knowledge that offers interpretability using graph theory, facilitating the translation of knowledge across diverse scientific domains. This approach empowers critical thinking essential for addressing contemporary global environmental challenges. The emerging next generation of AI systems surpasses limitations imposed by original training data, actively exploring new understanding …

Sewage sludge, a biosolid product of wastewater processing, is an often-overlooked source of rich organic waste. Hydrothermal processing (HTP), which uses heat and pressure to convert biomass into various solid, liquid, and gaseous products, has shown promise in converting sewage sludge into new materials with potential application in biofuels, asphalt binders, and bioplastics. In this study we focus on hydrochar, the carbonaceous HTP solid phase, and investigate its use as a bio-based filler in additive manufacturing technologies. We explore the impact of HTP and subsequent thermal activation on chemical and structural properties of sewage sludge and discuss the role of atypical metallic and metalloid dopants in organic material processing. In additive manufacturing composites, although the addition of hydrochar generally decreases mechanical performance, we show that toughness and strain can be recovered with hierarchical microstructures, much like biological materials that achieve outstanding properties by architecting relatively weak building blocks.

The inference of multicellular self-assembly is the central quest of understanding morphogenesis, including embryos, organoids, tumors, and many others. However, it has been tremendously difficult to identify structural features that can indicate multicellular dynamics. Here we propose to harness the predictive power of graph-based deep neural networks (GNN) to discover important graph features that can predict dynamics. To demonstrate, we apply a physically informed GNN (piGNN) to predict the motility of multicellular collectives from a snapshot of their positions both in experiments and simulations. We demonstrate that piGNN is capable of navigating through complex graph features of multicellular living systems, which otherwise can not be achieved by classical mechanistic models. With increasing amounts of multicellular data, we propose that collaborative efforts can be made to create a multicellular data bank (MDB) from which it is possible to construct a large multicellular graph model (LMGM) for general-purposed predictions of multicellular organization.

Using generative Artificial Intelligence (AI), we transformed a set of 1,000 scientific papers in the area of biological materials into detailed ontological knowledge graphs, revealing their inherently scale-free nature. Using graph traversal path detection between dissimilar concepts based on combinatorial ranking of node similarity and betweenness centrality, we reveal deep insights into unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, and propose never-before-seen material designs and their behaviors. One comparison revealed detailed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. The algorithm further created an innovative hierarchical mycelium-based composite that incorporates joint synthesis of graph sampling with principles extracted from Kandinsky's Composition VII painting, where the resulting composite reflects a balance of chaos and order, with features like adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across physical, biological, and artistic spheres, revealing a nuanced ontology of immanence and material flux that resonates with postmodern philosophy, and positions these interconnections within a heterarchical framework. Our findings reveal the dynamic, context-dependent interplay of entities beyond traditional hierarchical paradigms, emphasizing the significant role of individual components and their fluctuative relationships within the system. Our predictions achieve a far higher …

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 …

Impact articles, ranging across a variety of topics and article types. Notable trends include a focus on the deep integration of simulation, experiment, and theory; data-driven analysis and design; and creative uses of multilevel materials structuring. These themes cut across the articles in this issue and showcase the importance of multidisciplinary research in the advancement of materials function through materiomic approaches. Thereby, advances are not only achieved by developing better models or synthesis methods, but especially through integrating a set of advances that includes new instrumentation and in situ characterization methods, synthesis approaches, data collection methods, as well as strategic developments to make data from across disparate sources, studies, and materials more integrable. Wu, Li et al. 1 report several ways to enhance mechanical performance, including wear resistance, of Co-free …

Reversible crosslinkers can enable several desirable mechanical properties, such as improved toughness and self-healing, when incorporated in polymer networks for bioengineering and structural applications. In this work, we performed coarse-grained molecular dynamics to investigate the effect of the energy landscape of reversible crosslinkers on the dynamic mechanical properties of crosslinked polymer network hydrogels. We report that, for an ideal network, the energy potential of the crosslinker interaction drives the viscosity of the network, where a stronger potential results in a higher viscosity. Additional topographical analyses reveal a mechanistic understanding of the structural rearrangement of the network as it deforms and indicate that as the number of defects increases in the network, the viscosity of the network increases. As an important validation for the relationship between the energy landscape of …

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 took 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 …

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 pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers …

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 a custom generative large‐language model is proposed to enable the 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 approach that is aplied in a multi‐agent strategy. Performance is assessed through: 1) a novelty analysis and protein type classification for generated spidroin sequences through Basic Local Alignment Search Tool (BLAST) searches, 2 …

This chapter focuses on the use of advanced imaging-based techniques to assess the complex mechanical patterns of hard tissue, with a specific focus on bone and tooth. Hard tissues are complex hierarchical materials, requiring constant technological advancement to capture their structure-function relationship at different dimensional levels. Experimental techniques such as digital volume correlation, mainly based on X-ray tomography, greatly contributed to deepen understanding of hard tissues local deformation with investigations ranging from clinical computed tomography (CT) to nanoCT. In recent years, the advent of artificial intelligence proposed novel methodologies encompassing image classification and imaging-based mechanical predictions, which have the potential to revolutionize the field of hard tissue mechanics. These approaches and their integration are illustrated with various examples.

Whether on a hike, in a remote disaster zone or in your own home, access to clean water is critical. Filtration of freshwater to remove ultrafine particles like micro/nanoplastics, pathogens or other toxic components is unfortunately usually quite expensive, unportable and environmentally unfriendly.

Metal-coordination bonds, a highly tunable class of dynamic noncovalent interactions, are pivotal to the function of a variety of protein-based natural materials and have emerged as binding motifs to produce strong, tough, and self-healing bioinspired materials. While natural proteins use clusters of metal-coordination bonds, synthetic materials frequently employ individual bonds, resulting in mechanically weak materials. To overcome this current limitation, we rationally designed a series of elastin-like polypeptide templates with the capability of forming an increasing number of intermolecular histidine–Ni2+ metal-coordination bonds. Using single-molecule force spectroscopy and steered molecular dynamics simulations, we show that templates with three histidine residues exhibit heterogeneous rupture pathways, including the simultaneous rupture of at least two bonds with more-than-additive rupture forces. The …

The study of biological materials and bio‐inspired materials science is well established; however, surprisingly little knowledge is 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 is 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 strengthened with enhanced reasoning ability, as well as with Retrieval‐Augmented Generation (RAG) to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect …

We report the use of a multimodal generative artificial intelligence framework, the X-LoRA-Gemma large language model (LLM), to analyze, design and test molecular design. The X-LoRA-Gemma model, inspired by biological principles and featuring ~7 billion parameters, dynamically reconfigures its structure through a dual-pass inference strategy to enhance its problem-solving abilities across diverse scientific domains. The model is used to first identify molecular engineering targets through a systematic human-AI and AI-AI self-driving multi-agent approach to elucidate key targets for molecular optimization to improve interactions between molecules. Next, a multi-agent generative design process is used that includes rational steps, reasoning and autonomous knowledge extraction. Target properties of the molecule are identified either using a Principal Component Analysis (PCA) of key molecular properties or sampling from the distribution of known molecular properties. The model is then used to generate a large set of candidate molecules, which are analyzed via their molecular structure, charge distribution, and other features. We validate that as predicted, increased dipole moment and polarizability is indeed achieved in the designed molecules. We anticipate an increasing integration of these techniques into the molecular engineering workflow, ultimately enabling the development of innovative solutions to address a wide range of societal challenges. We conclude with a critical discussion of challenges and opportunities of the use of multimodal generative AI for molecular engineering, analysis and design.

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate models that address end-to-end problems by linking protein structure to material properties or vice versa. However, these models frequently focus on specific material objectives or structural properties, limiting their flexibility when incorporating out-of-domain knowledge into the design process or comprehensive data analysis is required. In this study, we introduce ProtAgents, a platform for de novo protein design based on Large Language Models (LLMs), where multiple AI agents with distinct capabilities collaboratively address complex tasks within a dynamic environment. The versatility in agent development allows for expertise in diverse domains, including knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis. The dynamic collaboration between agents, empowered by LLMs, provides a versatile approach to tackling protein design and analysis problems, as demonstrated through diverse examples in this study. The problems of interest encompass designing new proteins, analyzing protein structures and obtaining new first-principles data -- natural vibrational frequencies -- via physics simulations. The concerted effort of the system allows for powerful automated and synergistic design of de novo proteins with targeted mechanical properties. The flexibility in designing the agents, on one hand, and their capacity in autonomous collaboration through the dynamic LLM …

Inspired by natural materials, hierarchical architected materials can achieve enhanced properties including achieving tailored mechanical responses. However, the design space for such materials is often exceedingly large, and both predicting mechanical properties of complex hierarchically organized materials and designing such materials for specific target properties can be extremely difficult. In this paper we report a deep learning approach using an attention-based diffusion model, capable of providing both, forward predictions of nonlinear mechanical properties as a function of the hierarchical material structure as well as solving inverse design problems in order to discover hierarchical microstructure candidates for a specified nonlinear mechanical response. We exemplify the method for a system of compressively loaded four-hierarchy level materials derived from a family of honeycomb structures, where …

The dynamics of material failure is a critical phenomenon relevant to a range of scientific and engineering fields, from healthcare to structural materials. We propose a specially designed deep neural network, DyFraNet, which can predict dynamic fracture behaviors by identifying a complete history of fracture propagation—from the onset of cracking, as a crack grows through the material, modeled as a series of frames evolving over time and dependent on each other. Furthermore, the model can not only forecast future fracture processes but also backcast to elucidate past fracture histories. In this scenario, once provided with the outcome of a fracture event, the model will reveal past events that led to this state and can also predict future evolutions of the failure process. By comparing the predicted results with atomistic-level simulations and theory, we show that DyFraNet can capture dynamic fracture mechanics by …