Materials
Anticipating the Selectivity of Intramolecular Cyclization Reaction Pathways with Neural Network Potentials
Casetti, Nicholas, Anstine, Dylan, Isayev, Olexandr, Coley, Connor W.
Reaction mechanism search tools have demonstrated the ability to provide insights into likely products and rate-limiting steps of reacting systems. However, reactions involving several concerted bond changes - as can be found in many key steps of natural product synthesis - can complicate the search process. To mitigate these complications, we present a mechanism search strategy particularly suited to help expedite exploration of an exemplary family of such complex reactions, cyclizations. We provide a cost-effective strategy for identifying relevant elementary reaction steps by combining graph-based enumeration schemes and machine learning techniques for intermediate filtering. Key to this approach is our use of a neural network potential (NNP), AIMNet2-rxn, for computational evaluation of each candidate reaction pathway. In this article, we evaluate the NNP's ability to estimate activation energies, demonstrate the correct anticipation of stereoselectivity, and recapitulate complex enabling steps in natural product synthesis.
MoRA: On-the-fly Molecule-aware Low-Rank Adaptation Framework for LLM-based Multi-Modal Molecular Assistant
Yin, Tao, Zhang, Xiaohong, Zhang, Jiacheng, Huang, Li, Zhang, Zhibin, Zeng, Yuansong, Xie, Jin, Yan, Meng
Effectively integrating molecular graph structures with Large Language Models (LLMs) is a key challenge in drug discovery. Most existing multi-modal alignment methods typically process these structures by fine-tuning the LLM or adding a static adapter simultaneously. However, these approaches have two main limitations: (1) it optimizes a shared parameter space across all molecular inputs, limiting the model's ability to capture instance-specific structural features; and (2) fine-tuning the LLM for molecular tasks can lead to catastrophic forgetting, undermining its general reasoning capabilities. In this paper, instead of static task-oriented adaptation, we propose an instance-specific parameter space alignment approach for each molecule on-the-fly. To this end, we introduce Molecule-aware Low-Rank Adaptation (MoRA) that produces a unique set of low-rank adaptation weights for each input molecular graph. These weights are then dynamically injected into a frozen LLM, allowing the model to adapt its reasoning to the structure of each molecular input, while preserving the LLM's core knowledge. Extensive experiments demonstrate that on key molecular tasks, such as chemical reaction prediction and molecular captioning, MoRA's instance-specific dynamic adaptation outperforms statically adapted baselines, including a 14.1% relative improvement in reaction prediction exact match and a 22% reduction in error for quantum property prediction. The code is available at https://github.com/jk-sounds/MoRA.
Tracing Multilingual Knowledge Acquisition Dynamics in Domain Adaptation: A Case Study of English-Japanese Biomedical Adaptation
Zhao, Xin, Yoshinaga, Naoki, Tsuta, Yuma, Aizawa, Akiko
Multilingual domain adaptation (ML-DA) is widely used to learn new domain knowledge across languages into large language models (LLMs). Although many methods have been proposed to improve domain adaptation, the mechanisms of multilingual knowledge acquisition, how domain knowledge is learned within a language and transferred across languages, remain underexplored. This gap leads to suboptimal performance, particularly in low-resource settings. This work examines the learning dynamics of LLMs during ML-DA. Because prior ML-DA studies often train and evaluate on datasets with mismatched knowledge coverage, we propose AdaXEval, an adaptive evaluation method that builds multiple-choice QA datasets from the same bilingual domain corpus used for training, thereby directly studying multilingual knowledge acquisition. Through continual training of LLMs with diverse data recipes, we track how LLMs acquire domain facts and pinpoint the mechanism behind the transformation process from domain training data to knowledge. Our experiments on a 13B English-Japanese bilingual LLM reveal that cross-lingual transfer remains challenging despite a high-quality bilingual corpus. The code has been released.
This Watch Brand Has Made a Completely New Kind of Strap Using Lasers
It looks like fabric, feels like metal, and is as light as rubber. Any watch fan looking to tick all of the above boxes would normally expect to be a dab hand with a spring bar removal tool to experience all the above individually, but a new strap developed by Malaysian independent brand Ming appears to now offer the best of all worlds. The one strap to rule them all has been dubbed the Polymesh, and is 3D-printed from grade five titanium, and comprises 1,693 interconnected pieces (including the buckle) held together without any pins or screws. The only additional parts requiring assembly are the quick-release spring bars at each end that attach it to the watch--the articulated pin buckle is also formed in the same process. Ming says that the strap, which is made up from rows of 15 equilateral triangles, meshed together and bookended by larger end pieces, "has more motion engineered into the radial axis than the lateral one," leading to a supple end result that drapes like fabric yet retains the strength of titanium.
Automating Structural Engineering Workflows with Large Language Model Agents
Liang, Haoran, Zhou, Yufa, Kalaleh, Mohammad Talebi, Mei, Qipei
We introduce $\textbf{MASSE}$, the first Multi-Agent System for Structural Engineering, effectively integrating large language model (LLM)-based agents with real-world engineering workflows. Structural engineering is a fundamental yet traditionally stagnant domain, with core workflows remaining largely unchanged for decades despite its substantial economic impact and global market size. Recent advancements in LLMs have significantly enhanced their ability to perform complex reasoning, long-horizon planning, and precise tool utilization -- capabilities well aligned with structural engineering tasks such as interpreting design codes, executing load calculations, and verifying structural capacities. We present a proof-of-concept showing that most real-world structural engineering workflows can be fully automated through a training-free LLM-based multi-agent system. MASSE enables immediate deployment in professional environments, and our comprehensive validation on real-world case studies demonstrates that it can reduce expert workload from approximately two hours to mere minutes, while enhancing both reliability and accuracy in practical engineering scenarios.
Rise of the Robochemist
Zhu, Jihong, Huang, Kefeng, Pipe, Jonathon, Horbaczewsky, Chris, Tyrrell, Andy, Fairlamb, Ian J. S.
Abstract--Chemistry, a long-standing discipline, has historically relied on manual and often time-consuming processes. While some automation exists, the field is now on the cusp of a significant evolution driven by the integration of robotics and artificial intelligence (AI), giving rise to the concept of the robochemist: a new paradigm where autonomous systems assist in designing, executing, and analyzing experiments. Robo-chemists integrate mobile manipulators, advanced perception, teleoperation, and data-driven protocols to execute experiments with greater adaptability, reproducibility, and safety. Rather than a fully automated replacement for human chemists, we envisioned the robochemist as a complementary partner that works collaboratively to enhance discovery, enabling a more efficient exploration of chemical space and accelerating innovation in pharmaceuticals, materials science, and sustainable manufacturing. This article traces the technologies, applications, and challenges that define this transformation, highlighting both the opportunities and the responsibilities that accompany the emergence of the robochemist. Ultimately, the future of chemistry is argued to lie in a symbiotic partnership where human intuition and expertise is amplified by robotic precision and AI-driven insight. The field of chemistry, a cornerstone of modern science and industry, has long been characterized by a blend of theoretical insight and practical, hands-on experimentation.
Generative Models for Helmholtz Equation Solutions: A Dataset of Acoustic Materials
Gramaccioni, Riccardo Fosco, Marinoni, Christian, Frezza, Fabrizio, Uncini, Aurelio, Comminiello, Danilo
Accurate simulation of wave propagation in complex acoustic materials is crucial for applications in sound design, noise control, and material engineering. Traditional numerical solvers, such as finite element methods, are computationally expensive, especially when dealing with large-scale or real-time scenarios. In this work, we introduce a dataset of 31,000 acoustic materials, named HA30K, designed and simulated solving the Helmholtz equations. For each material, we provide the geometric configuration and the corresponding pressure field solution, enabling data-driven approaches to learn Helmholtz equation solutions. As a baseline, we explore a deep learning approach based on Stable Diffusion with ControlNet, a state-of-the-art model for image generation. Unlike classical solvers, our approach leverages GPU parallelization to process multiple simulations simultaneously, drastically reducing computation time. By representing solutions as images, we bypass the need for complex simulation software and explicit equation-solving. Additionally, the number of diffusion steps can be adjusted at inference time, balancing speed and quality. We aim to demonstrate that deep learning-based methods are particularly useful in early-stage research, where rapid exploration is more critical than absolute accuracy.
oMeBench: Towards Robust Benchmarking of LLMs in Organic Mechanism Elucidation and Reasoning
Xu, Ruiling, Zhang, Yifan, Wang, Qingyun, Edwards, Carl, Ji, Heng
Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.
Getting Your Indices in a Row: Full-Text Search for LLM Training Data for Real World
Marinas, Ines Altemir, Kucherenko, Anastasiia, Sternfeld, Alexander, Kucharavy, Andrei
The performance of Large Language Models (LLMs) is determined by their training data. Despite the proliferation of open-weight LLMs, access to LLM training data has remained limited. Even for fully open LLMs, the scale of the data makes it all but inscrutable to the general scientific community, despite potentially containing critical data scraped from the internet. In this paper, we present the full-text indexing pipeline for the Apertus LLM training data. Leveraging Elasticsearch parallel indices and the Alps infrastructure, a state-of-the-art, highly energy-efficient arm64 supercluster, we were able to index 8.6T tokens out of 15.2T used to train the Apertus LLM family, creating both a critical LLM safety tool and effectively an offline, curated, open web search engine. Our contribution is threefold. First, we demonstrate that Elasticsearch can be successfully ported onto next-generation arm64-based infrastructure. Second, we demonstrate that full-text indexing at the scale of modern LLM training datasets and the entire open web is feasible and accessible. Finally, we demonstrate that such indices can be used to ensure previously inaccessible jailbreak-agnostic LLM safety. We hope that our findings will be useful to other teams attempting large-scale data indexing and facilitate the general transition towards greener computation.
Machine Learning Detection of Lithium Plating in Lithium-ion Cells: A Gaussian Process Approach
Patnaik, Ayush, Fogelquist, Jackson, Zufall, Adam B, Robinson, Stephen K, Lin, Xinfan
Lithium plating during fast charging is a critical degradation mechanism that accelerates capacity fade and can trigger catastrophic safety failures. Recent work has identified a distinctive dQ/dV peak above 4.0 V as a reliable signature of plating onset; however, conventional methods for computing dQ/dV rely on finite differencing with filtering, which amplifies sensor noise and introduces bias in peak location. In this paper, we propose a Gaussian Process (GP) framework for lithium plating detection by directly modeling the charge-voltage relationship Q(V) as a stochastic process with calibrated uncertainty. Leveraging the property that derivatives of GPs remain GPs, we infer dQ/dV analytically and probabilistically from the posterior, enabling robust detection without ad hoc smoothing. The framework provides three key benefits: (i) noise-aware inference with hyperparameters learned from data, (ii) closed-form derivatives with credible intervals for uncertainty quantification, and (iii) scalability to online variants suitable for embedded BMS. Experimental validation on Li-ion coin cells across a range of C-rates (0.2C-1C) and temperatures (0-40°C) demonstrates that the GP-based method reliably detects plating peaks under low-temperature, high-rate charging, while correctly reporting no peaks in baseline cases. The concurrence of GP-identified differential peaks, reduced charge throughput, and capacity fade measured via reference performance tests confirms the method's accuracy and robustness, establishing a practical pathway for real-time lithium plating detection.