超高次元分子構造空間における衝突回避ポアソン運動計画
Collision-Free Poisson Motion Planning in Ultra High-Dimensional Molecular Conformation Spaces
生体分子の超高次元構造空間で衝突を避けつつ多様な立体配座を効率的にサンプリングするため、近接リンク間の一時的制約とポアソンディスク運動計画を超高次元に拡張した手法を提案した。
著者: Rasmus Fonseca, Dominik Budday, Henry van den Bedem
分類: cs.RO
原文アブストラクト
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute joints and non-covalent interactions as holonomic constraints, can accurately characterize these native ensembles. However, sampling biomolecules remains challenging owing to their ultra-high dimensional configuration spaces, and the requirement to avoid (self-) collisions, which results in low acceptance rates. Here, we present two novel mechanisms to overcome these limitations. First, we introduced temporary constraints between near-colliding links. The resulting constraint varieties instantaneously redirect the search for collision-free conformations, and couple motions between distant parts of the linkage. Second, we adapted a randomized Poisson-disk motion planner, which prevents local oversampling and widens the search, to ultra-high dimensions. We evaluated our algorithm on several model systems. Our contributions apply to general high-dimensional motion planning problems in static and dynamic environments with obstacles.
