MD-LLM-2: A Transferable Language Model of Molecular Dynamics with Physical Conditioning and Explicit Path Probabilities

arXiv:2610.10879 · q-bio.BM · Submitted 2026-10-07 · Read on arXiv

q-bio.BM

Submitted: 2026-10-07

Updated: 2026-10-07

Terminology

• Alignment — 11× in this paper · explained in 1 episode
• Core — 9× in this paper · explained in 2 episodes
• Calibration — 6× in this paper · explained in 7 episodes
• Embeddings — 4× in this paper · explained in 2 episodes
• Adam — 2× in this paper · explained in 2 episodes
• Exposure Bias — 2× in this paper · explained in 2 episodes
• Generative Model — 2× in this paper · explained in 2 episodes
• Perplexity — 2× in this paper · explained in 3 episodes
• Ab Initio — 1× in this paper · explained in 1 episode
• Adaptation — 1× in this paper · explained in 1 episode
• Aggregation — 1× in this paper · explained in 1 episode
• Generalization — 1× in this paper · explained in 13 episodes
• Generative Models — 1× in this paper · explained in 2 episodes
• Large Language Model (LLM) — 1× in this paper · explained in 3 episodes
• Regularization — 1× in this paper · explained in 3 episodes
• Representation Learning — 1× in this paper · explained in 2 episodes
• Robustness — 1× in this paper · explained in 5 episodes

Sources

• MD-LLM-1: A Large Language Model for Molecular Dynamics
• Qwen2.5 Technical Report

Related papers

• Speak to a Protein: An Interactive Multimodal Co-Scientist
• Learning Topological Representations of Protein Structure and Dynamics
• p2smi: A Python Toolkit for Peptide FASTA-to-SMILES Conversion and Molecular Property Analysis
• UNAAGI: Atom-Level Diffusion for Generating Non-Canonical Amino Acid Substitutions
• Co-folding with a Soup of Representations
• Non-Markovain Quantum State Diffusion for the Tunneling in SARS-COVID-19 virus