k-Color Multi-Robot Motion Planning

We present a simple and natural extension of the multi-robot motion planning problem where the robots are partitioned into groups (colors), such that in each group the robots are interchangeable. Every robot is no longer required to move to a specific target, but rather to some target placement that is assigned to its group. We call this problem k-color multi-robot motion planning and provide a sampling-based algorithm specifically designed for solving it. At the heart of the algorithm is a novel technique where the k-color problem is reduced to several discrete multi-robot motion planning problems. These reductions amplify basic samples into massive collections of free placements and paths for the robots. We demonstrate the performance of the algorithm by an implementation for the case of disc robots and polygonal robots translating in the plane. We show that the algorithm successfully and efficiently copes with a variety of challenging scenarios, involving many robots, while a simplified version of this algorithm, that can be viewed as an extension of a prevalent sampling-based algorithm for the k-color case, fails even on simple scenarios. Interestingly, our algorithm outperforms a well established implementation of PRM for the standard multi-robot problem, in which each robot has a distinct color.Comment: 2

Algorithms for detecting dependencies and rigid subsystems for CAD

Geometric constraint systems underly popular Computer Aided Design soft- ware. Automated approaches for detecting dependencies in a design are critical for developing robust solvers and providing informative user feedback, and we provide algorithms for two types of dependencies. First, we give a pebble game algorithm for detecting generic dependencies. Then, we focus on identifying the "special positions" of a design in which generically independent constraints become dependent. We present combinatorial algorithms for identifying subgraphs associated to factors of a particular polynomial, whose vanishing indicates a special position and resulting dependency. Further factoring in the Grassmann- Cayley algebra may allow a geometric interpretation giving conditions (e.g., "these two lines being parallel cause a dependency") determining the special position.Comment: 37 pages, 14 figures (v2 is an expanded version of an AGD'14 abstract based on v1

Motioning connected subgraphs into a graph

In this paper we study connected subgraphs and how to motion them inside a connected graph preserving the connectivity. We determine completely the group of movements.Comment: 17 pages, 18 figure

Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion

Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have contributed significantly to insights into protein molecular mechanisms and function. However, despite a shared purpose of these approaches, the topological nature of rigidity analysis, and thereby the absence of motion modes, has impeded a direct comparison. Here, we present an alternative, kinematic approach to rigidity analysis, which circumvents these drawbacks. We introduce a novel protein hydrogen bond network spectral decomposition, which provides an orthonormal basis for collective motions modulated by non-covalent interactions, analogous to the eigenspectrum of normal modes, and decomposes proteins into rigid clusters identical to those from topological rigidity. Our kinematic flexibility analysis bridges topological rigidity theory and ENM, and enables a detailed analysis of motion modes obtained from both approaches. Our analysis reveals that collectivity of protein motions, reported by the Shannon entropy, is significantly lower for rigidity theory versus normal mode approaches. Strikingly, kinematic flexibility analysis suggests that the hydrogen bonding network encodes a protein-fold specific, spatial hierarchy of motions, which goes nearly undetected in ENM. This hierarchy reveals distinct motion regimes that rationalize protein stiffness changes observed from experiment and molecular dynamics simulations. A formal expression for changes in free energy derived from the spectral decomposition indicates that motions across nearly 40% of modes obey enthalpy-entropy compensation. Taken together, our analysis suggests that hydrogen bond networks have evolved to modulate protein structure and dynamics