arXiv:2605.24002v1 Announce Type: cross Abstract: Computational materials science and chemistry span vast knowledge domains and fractured software ecosystems. Although large language models (LLMs) have demonstrated research capabilities, scaling monolithic agents to manage the rigor and complexity of atomistic research remains a challenge. Here, we introduce AtomisticSkills, an open-source harness framework that empowers general-purpose AI coding agents to conduct atomistic research across materials science, chemistry, and drug discovery. By hierarchically decomposing scientific workflows into agent skills and tools, AtomisticSkills provides agents with modular, extensible, and plug-and-play research capabilities. The framework integrates more than 100 human-curated multidisciplinary skills, including database access, thermodynamics and kinetics modeling, and diverse simulation engines employing machine learning interatomic potentials (MLIPs) and density functional theory (DFT). We validate its functional coverage against scientific literature and demonstrate robust orchestration capabilities across diverse scientific campaigns: generative design of Li-ion solid-state electrolytes, high-throughput screening of metal-organic frameworks for CO2 capture, autonomous MLIP benchmarking and fine-tuning, multi-stage structure-based virtual screening for drug design, multimodal X-ray diffraction pattern analysis, and screening of Fe-oxide catalysts for oxygen evolution reaction. AtomisticSkills provides a critical agent infrastructure towards building fully autonomous AI scientists.

arXiv:2603.07472v1 Announce Type: cross Abstract: In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure, we formulate genome reconstruction as a conditional generative modeling problem that samples heterogeneous conformations whose ensemble-averaged contacts are consistent with the input Hi-C data. A synthetic dataset is constructed using coarse-grained molecular dynamics simulations to generate chromatin ensembles and corresponding Hi-C maps under circular topology. Our models operate in a latent diffusion setting with a variational autoencoder that preserves per-bin alignment and supports replication-aware representations. Hi-C information is injected through a transformer-based encoder and cross-attention, enforcing a physically interpretable one-way constraint from Hi-C to structure. The model is trained using a flow-matching objective for stable optimization. On held-out ensembles, generated structures reproduce the input Hi-C distance-decay and structural correlation metrics while maintaining substantial conformational diversity, demonstrating the effectiveness of diffusion-based generative modeling for ensemble-level 3D genome reconstruction.

Cell Death Discovery, Published online: 09 March 2026; doi:10.1038/s41420-026-02950-1

Ferroptosis of smooth muscle cells in vascular diseases: from basic principles to clinical translation

arXiv:2602.23616v2 Announce Type: replace-cross Abstract: Diffractive optical neural networks (DONNs) have demonstrated unparalleled energy efficiency and parallelism by processing information directly in the optical domain. However, their computational expressivity is constrained by static, passive diffractive phase masks that lack efficient nonlinear responses and reprogrammability. To address these limitations, we introduce the Recurrent Diffractive Optical Neural Processor (ReDON), a novel architecture featuring reconfigurable, recurrent self-modulated nonlinearity. This mechanism enables dynamic, input-dependent optical transmission through in-situ electro-optic self-modulation, providing a highly efficient and reprogrammable approach to optical computation. Inspired by the gated linear unit (GLU) used in large language models, ReDON senses a fraction of the propagating optical field and modulates its phase or intensity via a lightweight parametric function, enabling effective nonlinearity with minimal inference overhead. As a non-von Neumann architecture in which the primary weighting elements (metasurfaces) remain fixed, ReDON substantially extends the nonlinear representational capacity and task adaptability of conventional DONNs through recurrent optical hardware reuse and dynamically tunable nonlinearity. We systematically investigate various self-modulation configurations to characterize the trade-offs between hardware efficiency and computational expressivity. On image recognition and segmentation benchmarks, ReDON improves test accuracy and mean intersection-over-union (mIoU) by up to 20% compared with prior DONNs employing either optical or digital nonlinearities at comparable model complexity and negligible additional power consumption. This work establishes a new paradigm for reconfigurable nonlinear optical computing, uniting recurrence and self-modulation within non-von Neumann analog processors.

arXiv:2504.04717v5 Announce Type: replace-cross Abstract: Recent advances in large language models (LLMs) have substantially improved single-turn task performance, yet real-world applications increasingly demand sophisticated multi-turn interactions. This survey provides a comprehensive review of recent progress in evaluating and enhancing multi-turn LLM interactions. Centered on a task-oriented taxonomy-spanning instruction following in domains such as mathematics and coding, and conversational engagement in role-playing, healthcare, education, and adversarial jailbreak settings-we systematically examine the challenges of maintaining context, coherence, fairness, and responsiveness across prolonged dialogues. We organize existing benchmarks and datasets into coherent categories reflecting the evolving landscape of multi-turn dialogue evaluation, and review a broad spectrum of enhancement methodologies, including model-centric strategies (in-context learning, supervised fine-tuning, reinforcement learning, and architectural innovations), external integration approaches (memory augmentation, retrieval-based methods, and knowledge graphs), and agent-based techniques for collaborative interaction. Finally, we identify open challenges and promising directions for future research to further improve the robustness and effectiveness of multi-turn LLM interactions.