A space decomposition method for path planning of loop linkages

This paper introduces box approximations as a new tool for path planning of closed-loop linkages. Box approximations are finite collections of rectangloids that tightly envelop the robot's free space at a desired resolution. They play a similar role to that of approximate cell decompositions for open-chain robots - they capture the free-space connectivity in a multi-resolutive fashion and yield rectangloid channels enclosing collision-free paths - but have the additional property of enforcing the satisfaction of loop closure constraints frequently arising in articulated linkages. We present an efficient technique to compute such approximations and show how resolution-complete path planners can be devised using them. To the authors' knowledge, this is the first space-decomposition approach to closed-loop linkage path planning proposed in the literature.This work has been partially supported by the Spanish Ministryof Education and Science through the contract DPI2004-07358, by the“Comunitat de Treball dels Pirineus” under contract 2006ITT-10004, andby Ram ́on y Cajal and I3 programme funds.Peer ReviewedPostprint (author's final draft

A space decomposition method for path planning of loop linkages

This paper introduces box approximations as a new tool for path planning of closed-loop linkages. Box approximations are finite collections of rectangloids that tightly envelop the robot's free space at a desired resolution. They play a similar role to that of approximate cell decompositions for open-chain robots - they capture the free-space connectivity in a multi-resolutive fashion and yield rectangloid channels enclosing collision-free paths - but have the additional property of enforcing the satisfaction of loop closure constraints frequently arising in articulated linkages. We present an efficient technique to compute such approximations and show how resolution-complete path planners can be devised using them. To the authors' knowledge, this is the first space-decomposition approach to closed-loop linkage path planning proposed in the literature.Peer Reviewe

Complete Path Planning for Closed Kinematic Chains with Spherical Joints

We study the path planning problem, without obstacles, for closed kinematic chains with n links connected by spherical joints in space or revolute joints in the plane. The configuration space of such systems is a real algebraic variety whose structure is fully determined using techniques from algebraic geometry and differential topology. This structure is then exploited to design a complete path planning algorithm that produces a sequence of compliant moves, each of which monotonically increases the number of links in their goal configurations. The average running time of this algorithm is proportional to n³. While less efficient than the O(n) algorithm of Lenhart and Whitesides, our algorithm produces paths that are considerably smoother. More importantly, our analysis serves as a demonstration of how to apply advanced mathematical techniques to path planning problems. Theoretically

Implications of Motion Planning: Optimality and k-survivability

We study motion planning problems, finding trajectories that connect two configurations of a system, from two different perspectives: optimality and survivability. For the problem of finding optimal trajectories, we provide a model in which the existence of optimal trajectories is guaranteed, and design an algorithm to find approximately optimal trajectories for a kinematic planar robot within this model. We also design an algorithm to build data structures to represent the configuration space, supporting optimal trajectory queries for any given pair of configurations in an obstructed environment. We are also interested in planning paths for expendable robots moving in a threat environment. Since robots are expendable, our goal is to ensure a certain number of robots reaching the goal. We consider a new motion planning problem, maximum k-survivability: given two points in a stochastic threat environment, find n paths connecting two given points while maximizing the probability that at least k paths reach the goal. Intuitively, a good solution should be diverse to avoid several paths being blocked simultaneously, and paths should be short so that robots can quickly pass through dangerous areas. Finding sets of paths with maximum k-survivability is NP-hard. We design two algorithms: an algorithm that is guaranteed to find an optimal list of paths, and a set of heuristic methods that finds paths with high k-survivability

De Novo Protein Structure Modeling from Cryoem Data Through a Dynamic Programming Algorithm in the Secondary Structure Topology Graph

Proteins are the molecules carry out the vital functions and make more than the half of dry weight in every cell. Protein in nature folds into a unique and energetically favorable 3-Dimensional (3-D) structure which is critical and unique to its biological function. In contrast to other methods for protein structure determination, Electron Cryorricroscopy (CryoEM) is able to produce volumetric maps of proteins that are poorly soluble, large and hard to crystallize. Furthermore, it studies the proteins in their native environment. Unfortunately, the volumetric maps generated by current advances in CryoEM technique produces protein maps at medium resolution about (~5 to 10Å) in which it is hard to determine the atomic-structure of the protein. However, the resolution of the volumetric maps is improving steadily, and recent works could obtain atomic models at higher resolutions (~3Å). De novo protein modeling is the process of building the structure of the protein using its CryoEM volumetric map. Thereupon, the volumetric maps at medium resolution generated by CryoEM technique proposed a new challenge. At the medium resolution, the location and orientation of secondary structure elements (SSE) can be visually and computationally identified. However, the order and direction (called protein topology) of the SSEs detected from the CryoEM volumetric map are not visible. In order to determine the protein structure, the topology of the SSEs has to be figured out and then the backbone can be built. Consequently, the topology problem has become a bottle neck for protein modeling using CryoEM In this dissertation, we focus to establish an effective computational framework to derive the atomic structure of a protein from the medium resolution CryoEM volumetric maps. This framework includes a topology graph component to rank effectively the topologies of the SSEs and a model building component. In order to generate the small subset of candidate topologies, the problem is translated into a layered graph representation. We developed a dynamic programming algorithm (TopoDP) for the new representation to overcome the problem of large search space. Our approach shows the improved accuracy, speed and memory use when compared with existing methods. However, the generating of such set was infeasible using a brute force method. Therefore, the topology graph component effectively reduces the topological space using the geometrical features of the secondary structures through a constrained K-shortest paths method in our layered graph. The model building component involves the bending of a helix and the loop construction using skeleton of the volumetric map. The forward-backward CCD is applied to bend the helices and model the loops