Representation choice shapes the interpretation of protein conformational dynamics

Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single representation. Here, we show that representation choice is not neutral: it fundamentally shapes the conformational organization, similarity relationships, and apparent transitions inferred from identical simulation data. To complement existing representations, we introduce Orientation features, a geometrically grounded, rotation-aware encoding of protein backbone. We compare it against common descriptions across three dynamical regimes: fast-folding proteins, large-scale domain motions, and protein-protein association. Across these systems, we find that different representations emphasize complementary aspects of conformational space, and that no single representation provides a complete picture of the underlying dynamics. To facilitate systematic comparison, we developed ManiProt, a library for efficient computation and analysis of multiple protein representations. Our results motivate a comparative, representation-aware framework for the interpretation of molecular dynamics simulations.

Field-Assisted Molecular Communication: Girsanov-Based Channel Modeling and Dynamic Waveform Optimization

Analytical modeling of field-assisted molecular communication under dynamic electric fields is fundamentally challenging due to the coupling between stochastic transport and complex boundary geometries, which renders conventional partial differential equation (PDE) approaches intractable. In this work, we introduce an effective stochastic modeling approach to address this challenge. By leveraging trajectory-reweighting techniques, we derive analytically tractable channel impulse response (CIR) expressions for both fully-absorbing and passive spherical receivers, where the latter serves as an exact theoretical baseline to validate our modeling accuracy. Building upon these models, we establish a dynamic waveform design framework for system optimization. Under a maximum \textit{a posteriori} decision-feedback equalizer (MAP-DFE) framework, we show that the first-slot received probability serves as the primary determinant of the bit error probability (BEP), while inter-symbol interference manifests as higher-order corrections. Exploiting the monotonic response of the fully-absorbing architecture and using the limitations of the passive model to justify this strategic focus, we reformulate BEP minimization into a distance-based optimization problem. We propose a unified, low-complexity Maximize Received Probability (MRP) algorithm, encompassing the Maximize Hitting Probability (MHP) and Maximize Sensing Probability (MSP) methods, to dynamically enhance desired signals and suppress inter-symbol interference. Numerical results validate the accuracy of the proposed modeling approach and demonstrate near-optimal detection performance.

Cost-Penalized Fitness in FMA-Orchestrated Mixture of Experts: Experimental Evidence for Molecular Memory in Domain Adaptation

We present experimental results from seven controlled runs of nanoFMT, a Free-Market Algorithm (FMA) orchestrated transformer with dynamic Mixture-of-Experts (MoE) management. The experiments address a fundamental question for advanced LLM development: how should an MoE system manage its expert pool when operating at full capacity under changing data distributions? We demonstrate that cost-penalized fitness metrics, combined with a linear grace period for newborn experts, produce a system that accumulates domain expertise through diversification rather than replacement. The central result is a round-trip domain shift experiment showing 9-11x faster recovery when returning to a previously learned domain, with zero expert births or replacements required. This "molecular memory" effect -- where dormant experts survive and reactivate when their domain returns -- has no analogue in current MoE management approaches. A preliminary cost analysis estimates annual savings of $39.1M and 27.1 GWh energy reduction for an OpenAI-scale provider under a moderate scenario.

BloClaw: An Omniscient, Multi-Modal Agentic Workspace for Next-Generation Scientific Discovery

The integration of Large Language Models (LLMs) into life sciences has catalyzed the development of "AI Scientists." However, translating these theoretical capabilities into deployment-ready research environments exposes profound infrastructural vulnerabilities. Current frameworks are bottlenecked by fragile JSON-based tool-calling protocols, easily disrupted execution sandboxes that lose graphical outputs, and rigid conversational interfaces inherently ill-suited for high-dimensional scientific data.We introduce BloClaw, a unified, multi-modal operating system designed for Artificial Intelligence for Science (AI4S). BloClaw reconstructs the Agent-Computer Interaction (ACI) paradigm through three architectural innovations: (1) An XML-Regex Dual-Track Routing Protocol that statistically eliminates serialization failures (0.2% error rate vs. 17.6% in JSON); (2) A Runtime State Interception Sandbox that utilizes Python monkey-patching to autonomously capture and compile dynamic data visualizations (Plotly/Matplotlib), circumventing browser CORS policies; and (3) A State-Driven Dynamic Viewport UI that morphs seamlessly between a minimalist command deck and an interactive spatial rendering engine. We comprehensively benchmark BloClaw across cheminformatics (RDKit), de novo 3D protein folding via ESMFold, molecular docking, and autonomous Retrieval-Augmented Generation (RAG), establishing a highly robust, self-evolving paradigm for computational research assistants. The open-source repository is available at https://github.com/qinheming/BloClaw.

Universal and efficient graph neural networks with dynamic attention for machine learning interatomic potentials

The core of molecular dynamics simulation fundamentally lies in the interatomic potential. Traditional empirical potentials lack accuracy, while first-principles methods are computationally prohibitive. Machine learning interatomic potentials (MLIPs) promise near-quantum accuracy at linear cost, but existing models still face challenges in efficiency and stability. We presents Machine Learning Advances Neural Network (MLANet), an efficient and robust graph neural network framework. MLANet introduces a dual-path dynamic attention mechanism for geometry-aware message passing and a multi-perspective pooling strategy to construct comprehensive system representations. This design enables highly accurate modeling of atomic environments while achieving exceptional computational efficiency, making high-fidelity simulations more accessible. Tested across a wide range of datasets spanning diverse systems, including organic molecules (e.g., QM7, MD17), periodic inorganic materials (e.g., Li-containing crystals), two-dimensional materials (e.g., bilayer graphene, black phosphorus), surface catalytic reactions (e.g., formate decomposition), and charged systems, MLANet maintains competitive prediction accuracy while its computational cost is markedly lower than mainstream equivariant models, and it enables stable long-time molecular dynamics simulations. MLANet provides an efficient and practical tool for large-scale, high-accuracy atomic simulations.

Data Curation for Machine Learning Interatomic Potentials by Determinantal Point Processes

The development of machine learning interatomic potentials faces a critical computational bottleneck with the generation and labeling of useful training datasets. We present a novel application of determinantal point processes (DPPs) to the task of selecting informative subsets of atomic configurations to label with reference energies and forces from costly quantum mechanical methods. Through experiments with hafnium oxide data, we show that DPPs are competitive with existing approaches to constructing compact but diverse training sets by utilizing kernels of molecular descriptors, leading to improved accuracy and robustness in machine learning representations of molecular systems. Our work identifies promising directions to employ DPPs for unsupervised training data curation with heterogeneous or multimodal data, or in online active learning schemes for iterative data augmentation during molecular dynamics simulation.

Markov State--Space Modeling and Channel Characterization for DNA-Based Molecular Communication

In this paper, we study DNA-based molecular communication with microarray-style reception under reversible hybridization, where the bound-state observation exhibits both inter-symbol interference and colored counting noise. To capture these effects in a communication-oriented form, we develop a Markov state-space framework based on a voxelized reaction--diffusion model, in which a block-structured transition matrix describes molecular transport and binding/unbinding dynamics. For the microarray specialization, this representation yields the channel impulse response, the equilibrium gain, and a settling-time-based characterization of the effective channel memory. Building on the resulting symbol-rate observation model for on--off keying, we derive a grouped-binomial counting model and obtain a closed-form expression for the covariance of the counting noise. Based on these statistics, we further develop a differential-threshold detector and a finite-memory decision-feedback equalizer. Numerical results validate the theoretical correlation behavior and show that the relative performance of the proposed receivers depends strongly on the channel-memory regime.

SIGMA: Structure-Invariant Generative Molecular Alignment for Chemical Language Models via Autoregressive Contrastive Learning

Linearized string representations serve as the foundation of scalable autoregressive molecular generation; however, they introduce a fundamental modality mismatch where a single molecular graph maps to multiple distinct sequences. This ambiguity leads to \textit{trajectory divergence}, where the latent representations of structurally equivalent partial graphs drift apart due to differences in linearization history. To resolve this without abandoning the efficient string formulation, we propose Structure-Invariant Generative Molecular Alignment (SIGMA). Rather than altering the linear representation, SIGMA enables the model to strictly recognize geometric symmetries via a token-level contrastive objective, which explicitly aligns the latent states of prefixes that share identical suffixes. Furthermore, we introduce Isomorphic Beam Search (IsoBeam) to eliminate isomorphic redundancy during inference by dynamically pruning equivalent paths. Empirical evaluations on standard benchmarks demonstrate that SIGMA bridges the gap between sequence scalability and graph fidelity, yielding superior sample efficiency and structural diversity in multi-parameter optimization compared to strong baselines.

MolQuest: A Benchmark for Agentic Evaluation of Abductive Reasoning in Chemical Structure Elucidation

Large language models (LLMs) hold considerable potential for advancing scientific discovery, yet systematic assessment of their dynamic reasoning in real-world research remains limited. Current scientific evaluation benchmarks predominantly rely on static, single-turn Question Answering (QA) formats, which are inadequate for measuring model performance in complex scientific tasks that require multi-step iteration and experimental interaction. To address this gap, we introduce MolQuest, a novel agent-based evaluation framework for molecular structure elucidation built upon authentic chemical experimental data. Unlike existing datasets, MolQuest formalizes molecular structure elucidation as a multi-turn interactive task, requiring models to proactively plan experimental steps, integrate heterogeneous spectral sources (e.g., NMR, MS), and iteratively refine structural hypotheses. This framework systematically evaluates LLMs' abductive reasoning and strategic decision-making abilities within a vast and complex chemical space. Empirical results reveal that contemporary frontier models exhibit significant limitations in authentic scientific scenarios: notably, even state-of-the-art (SOTA) models achieve an accuracy of only approximately 50%, while the performance of most other models remains below the 30% threshold. This work provides a reproducible and extensible framework for science-oriented LLM evaluation, our findings highlight the critical gap in current LLMs' strategic scientific reasoning, setting a clear direction for future research toward AI that can actively participate in the scientific process.

Data-driven construction of machine-learning-based interatomic potentials for gas-surface scattering dynamics: the case of NO on graphite

Accurate atomistic simulations of gas-surface scattering require potential energy surfaces that remain reliable over broad configurational and energetic ranges while retaining the efficiency needed for extensive trajectory sampling. Here, we develop a data-driven workflow for constructing a machine-learning interatomic potential (MLIP) tailored to gas-surface scattering dynamics, using nitric oxide (NO) scattering from highly oriented pyrolytic graphite (HOPG) as a benchmark system. Starting from an initial ab initio molecular dynamics (AIMD) dataset, local atomic environments are described by SOAP descriptors and analyzed in a reduced feature space obtained through principal component analysis. Farthest point sampling is then used to build a compact training set, and the resulting Deep Potential model is refined through a query-by-committee active-learning strategy using additional configurations extracted from molecular dynamics simulations over extended ranges of incident energies and surface temperatures. The final MLIP reproduces reference energies and forces with high fidelity and enables large-scale molecular dynamics simulations of NO scattering from graphite at a computational cost far below that of AIMD. The simulations provide detailed insight into adsorption energetics, trapping versus direct scattering probabilities, translational energy loss, angular distributions, and rotational excitation. Overall, the results reproduce the main experimental trends and demonstrate that descriptor-guided sampling combined with active learning offers an efficient and transferable strategy for constructing MLIPs for gas-surface interactions.