Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systematically explore the hierarchical structure of complex conformational space through the spectral analysis of the variance-covariance matrix of trajectory-mapped vectors. Non-degenerate ground state of the matrix directly predicts the ergodicity of simulation data. The ground state could be adopted as statistical weights of trajectories to correctly reconstruct the equilibrium properties, even though each trajectory only explores part of the conformational space. Otherwise, the degree of degeneracy simply gives the number of meta-stable states of the system under the time scale of individual trajectory. Manipulation on the eigenvectors leads to the classification of trajectories into non-transition ones within the states and transition ones between them. The transition states may also be predicted without a priori knowledge of the system. We demonstrate the application of the general method both to the system with a one-dimensional glassy potential and with the one of alanine dipeptide in explicit solvent.
Polyformer: a generative framework for thermodynamic modeling of polymeric molecules
PsiDagger；Department of Physics and Astronomy, University of Pittsburgh（物理与天文学系，匹兹堡大学）；Department of Chemistry and The PULSE Institute, Stanford University（化学系和PULSE研究所，斯坦福大学）；SLAC National Accelerator Laboratory（SLAC国家加速器实验室）
Learning conformational ensembles of proteins based on backbone geometry
Max Planck Institute for Polymer Research（马克斯·普朗克聚合物研究所）；Heidelberg Institute for Theoretical Studies（海德堡理论研究所）；IWR, Heidelberg University（海德堡大学IWR中心）；SciLifeLab and DBB at Stockholm University（斯德哥尔摩大学SciLifeLab和DBB中心）；Karlsruhe Institute of Technology（卡尔斯鲁厄技术大学）
Neural Thermodynamic Integration: Free Energies from Energy-based Diffusion Models
Institute for Theoretical Physics, Heidelberg University（海德堡大学理论物理研究所）；Department of Computer Science, University of Geneva（日内瓦大学计算机系）；Department of Physics, University of Geneva（日内瓦大学物理系）
