MATTERIX: toward a digital twin for robotics-assisted chemistry laboratory automation

Accelerated materials discovery is critical for addressing global challenges. However, developing new laboratory workflows relies heavily on real-world experimental trials, and this can hinder scalability because of the need for numerous physical make-and-test iterations. Here we present MATTERIX, a multiscale, graphics processing unit-accelerated robotic simulation framework designed to create high-fidelity digital twins of chemistry laboratories, thus accelerating workflow development. This multiscale digital twin simulates robotic physical manipulation, powder and liquid dynamics, device functionalities, heat transfer and basic chemical reaction kinetics. This is enabled by integrating realistic physics simulation and photorealistic rendering with a modular graphics processing unit-accelerated semantics engine, which models logical states and continuous behaviors to simulate chemistry workflows across different levels of abstraction. MATTERIX streamlines the creation of digital twin environments through open-source asset libraries and interfaces, while enabling flexible workflow design via hierarchical plan definition and a modular skill library that incorporates learning-based methods. Our approach demonstrates sim-to-real transfer in robotic chemistry setups, reducing reliance on costly real-world experiments and enabling the testing of hypothetical automated workflows in silico. The project website is available at https://accelerationconsortium.github.io/Matterix/ .

TreeWriter: AI-Assisted Hierarchical Planning and Writing for Long-Form Documents

Long documents pose many challenges to current intelligent writing systems. These include maintaining consistency across sections, sustaining efficient planning and writing as documents become more complex, and effectively providing and integrating AI assistance to the user. Existing AI co-writing tools offer either inline suggestions or limited structured planning, but rarely support the entire writing process that begins with high-level ideas and ends with polished prose, in which many layers of planning and outlining are needed. Here, we introduce TreeWriter, a hierarchical writing system that represents documents as trees and integrates contextual AI support. TreeWriter allows authors to create, save, and refine document outlines at multiple levels, facilitating drafting, understanding, and iterative editing of long documents. A built-in AI agent can dynamically load relevant content, navigate the document hierarchy, and provide context-aware editing suggestions. A within-subject study (N=12) comparing TreeWriter with Google Docs + Gemini on long-document editing and creative writing tasks shows that TreeWriter improves idea exploration/development, AI helpfulness, and perceived authorial control. A two-month field deployment (N=8) further demonstrated that hierarchical organization supports collaborative writing. Our findings highlight the potential of hierarchical, tree-structured editors with integrated AI support and provide design guidelines for future AI-assisted writing tools that balance automation with user agency.

Discrete Feynman-Kac Correctors

Discrete diffusion models have recently emerged as a promising alternative to the autoregressive approach for generating discrete sequences. Sample generation via gradual denoising or demasking processes allows them to capture hierarchical non-sequential interdependencies in the data. These custom processes, however, do not assume a flexible control over the distribution of generated samples. We propose Discrete Feynman-Kac Correctors, a framework that allows for controlling the generated distribution of discrete masked diffusion models at inference time. We derive Sequential Monte Carlo (SMC) algorithms that, given a trained discrete diffusion model, control the temperature of the sampled distribution (i.e. perform annealing), sample from the product of marginals of several diffusion processes (e.g. differently conditioned processes), and sample from the product of the marginal with an external reward function, producing likely samples from the target distribution that also have high reward. Notably, our framework does not require any training of additional models or fine-tuning of the original model. We illustrate the utility of our framework in several applications including: efficient sampling from the annealed Boltzmann distribution of the Ising model, improving the performance of language models for code generation and amortized learning, as well as reward-tilted protein sequence generation.

Informing Acquisition Functions via Foundation Models for Molecular Discovery

Bayesian Optimization (BO) is a key methodology for accelerating molecular discovery by estimating the mapping from molecules to their properties while seeking the optimal candidate. Typically, BO iteratively updates a probabilistic surrogate model of this mapping and optimizes acquisition functions derived from the model to guide molecule selection. However, its performance is limited in low-data regimes with insufficient prior knowledge and vast candidate spaces. Large language models (LLMs) and chemistry foundation models offer rich priors to enhance BO, but high-dimensional features, costly in-context learning, and the computational burden of deep Bayesian surrogates hinder their full utilization. To address these challenges, we propose a likelihood-free BO method that bypasses explicit surrogate modeling and directly leverages priors from general LLMs and chemistry-specific foundation models to inform acquisition functions. Our method also learns a tree-structured partition of the molecular search space with local acquisition functions, enabling efficient candidate selection via Monte Carlo Tree Search. By further incorporating coarse-grained LLM-based clustering, it substantially improves scalability to large candidate sets by restricting acquisition function evaluations to clusters with statistically higher property values. We show through extensive experiments and ablations that the proposed method substantially improves scalability, robustness, and sample efficiency in LLM-guided BO for molecular discovery.

DEQuify your force field: More efficient simulations using deep equilibrium models

Machine learning force fields show great promise in enabling more accurate molecular dynamics simulations compared to manually derived ones. Much of the progress in recent years was driven by exploiting prior knowledge about physical systems, in particular symmetries under rotation, translation, and reflections. In this paper, we argue that there is another important piece of prior information that, thus fa,r hasn't been explored: Simulating a molecular system is necessarily continuous, and successive states are therefore extremely similar. Our contribution is to show that we can exploit this information by recasting a state-of-the-art equivariant base model as a deep equilibrium model. This allows us to recycle intermediate neural network features from previous time steps, enabling us to improve both accuracy and speed by $10\%-20\%$ on the MD17, MD22, and OC20 200k datasets, compared to the non-DEQ base model. The training is also much more memory efficient, allowing us to train more expressive models on larger systems.

Learning with springs and sticks

Learning is a physical process. Here, we aim to study a simple dynamical system composed of springs and sticks capable of arbitrarily approximating any continuous function. The main idea of our work is to use the sticks to mimic a piecewise-linear approximation of the given function, use the potential energy of springs to encode a desired mean squared error loss function, and converge to a minimum-energy configuration via dissipation. We apply the proposed simulation system to regression tasks and show that its performance is comparable to that of multi-layer perceptrons. In addition, we study the thermodynamic properties of the system and find a relation between the free energy change of the system and its ability to learn an underlying data distribution. We empirically find a \emph{thermodynamic learning barrier} for the system caused by the fluctuations of the environment, whereby the system cannot learn if its change in free energy hits such a barrier. We believe this simple model can help us better understand learning systems from a physical point of view.

RoboCulture: A Robotics Platform for Automated Biological Experimentation

Automating biological experimentation remains challenging due to the need for millimeter-scale precision, long and multi-step experiments, and the dynamic nature of living systems. Current liquid handlers only partially automate workflows, requiring human intervention for plate loading, tip replacement, and calibration. Industrial solutions offer more automation but are costly and lack the flexibility needed in research settings. Meanwhile, research in autonomous robotics has yet to bridge the gap for long-duration, failure-sensitive biological experiments. We introduce RoboCulture, a cost-effective and flexible platform that uses a general-purpose robotic manipulator to automate key biological tasks. RoboCulture performs liquid handling, interacts with lab equipment, and leverages computer vision for real-time decisions using optical density-based growth monitoring. We demonstrate a fully autonomous 15-hour yeast culture experiment where RoboCulture uses vision and force feedback and a modular behavior tree framework to robustly execute, monitor, and manage experiments.

Scalable Autoregressive 3D Molecule Generation

Generative models of 3D molecular structure play a rapidly growing role in the design and simulation of molecules. Diffusion models currently dominate the space of 3D molecule generation, while autoregressive models have trailed behind. In this work, we present Quetzal, a simple but scalable autoregressive model that builds molecules atom-by-atom in 3D. Treating each molecule as an ordered sequence of atoms, Quetzal combines a causal transformer that predicts the next atom's discrete type with a smaller Diffusion MLP that models the continuous next-position distribution. Compared to existing autoregressive baselines, Quetzal achieves substantial improvements in generation quality and is competitive with the performance of state-of-the-art diffusion models. In addition, by reducing the number of expensive forward passes through a dense transformer, Quetzal enables significantly faster generation speed, as well as exact divergence-based likelihood computation. Finally, without any architectural changes, Quetzal natively handles variable-size tasks like hydrogen decoration and scaffold completion. We hope that our work motivates a perspective on scalability and generality for generative modelling of 3D molecules.

El Agente: An Autonomous Agent for Quantum Chemistry

Computational chemistry tools are widely used to study the behaviour of chemical phenomena. Yet, the complexity of these tools can make them inaccessible to non-specialists and challenging even for experts. In this work, we introduce El Agente Q, an LLM-based multi-agent system that dynamically generates and executes quantum chemistry workflows from natural language user prompts. The system is built on a novel cognitive architecture featuring a hierarchical memory framework that enables flexible task decomposition, adaptive tool selection, post-analysis, and autonomous file handling and submission. El Agente Q is benchmarked on six university-level course exercises and two case studies, demonstrating robust problem-solving performance (averaging >87% task success) and adaptive error handling through in situ debugging. It also supports longer-term, multi-step task execution for more complex workflows, while maintaining transparency through detailed action trace logs. Together, these capabilities lay the foundation for increasingly autonomous and accessible quantum chemistry.

ELECTRA: A Symmetry-breaking Cartesian Network for Charge Density Prediction with Floating Orbitals

We present the Electronic Tensor Reconstruction Algorithm (ELECTRA) - an equivariant model for predicting electronic charge densities using "floating" orbitals. Floating orbitals are a long-standing idea in the quantum chemistry community that promises more compact and accurate representations by placing orbitals freely in space, as opposed to centering all orbitals at the position of atoms. Finding ideal placements of these orbitals requires extensive domain knowledge though, which thus far has prevented widespread adoption. We solve this in a data-driven manner by training a Cartesian tensor network to predict orbital positions along with orbital coefficients. This is made possible through a symmetry-breaking mechanism that is used to learn position displacements with lower symmetry than the input molecule while preserving the rotation equivariance of the charge density itself. Inspired by recent successes of Gaussian Splatting in representing densities in space, we are using Gaussians as our orbitals and predict their weights and covariance matrices. Our method achieves a state-of-the-art balance between computational efficiency and predictive accuracy on established benchmarks.