Euclidean distance geometry and applications

Euclidean distance geometry is the study of Euclidean geometry based on the concept of distance. This is useful in several applications where the input data consists of an incomplete set of distances, and the output is a set of points in Euclidean space that realizes the given distances. We survey some of the theory of Euclidean distance geometry and some of the most important applications: molecular conformation, localization of sensor networks and statics.Comment: 64 pages, 21 figure

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

International audienceBackground: The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only. Results: In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations. Conclusions: We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides

Stabilization of cascaded nonlinear systems under sampling and delays

Over the last decades, the methodologies of dynamical systems and control theory have been playing an increasingly relevant role in a lot of situations of practical interest. Though, a lot of theoretical problem still remain unsolved. Among all, the ones concerning stability and stabilization are of paramount importance. In order to stabilize a physical (or not) system, it is necessary to acquire and interpret heterogeneous information on its behavior in order to correctly intervene on it. In general, those information are not available through a continuous flow but are provided in a synchronous or asynchronous way. This issue has to be unavoidably taken into account for the design of the control action. In a very natural way, all those heterogeneities define an hybrid system characterized by both continuous and discrete dynamics. This thesis is contextualized in this framework and aimed at proposing new methodologies for the stabilization of sampled-data nonlinear systems with focus toward the stabilization of cascade dynamics. In doing so, we shall propose a small number of tools for constructing sampled-data feedback laws stabilizing the origin of sampled-data nonlinear systems admitting cascade interconnection representations. To this end, we shall investigate on the effect of sampling on the properties of the continuous-time system while enhancing design procedures requiring no extra assumptions over the sampled-data equivalent model. Finally, we shall show the way sampling positively affects nonlinear retarded dynamics affected by a fixed and known time-delay over the input signal by enforcing on the implicit cascade representation the sampling process induces onto the retarded system

Optimal Partial Discretization Orders for Discretizable Distance Geometry

International audienceThe Distance Geometry Problem (DGP) asks whether a simple weighted undirected graph G = (V,E,d) can be embedded in a given space so that the weights of the edges of G, when available, are the same as the distances between pairs of embedded vertices. The DGP can be discretized when some particular assumptions are satisfied, which are strongly dependent on the vertex ordering assigned to G. In this work, we focus on the problem of identifying optimal partial discretization orders for the DGP. The solutions to this problem are in fact vertex orders that allow for the discretization of the DGP. Moreover, these partial orders are optimal in the sense that they optimize, at each rank, a given set of objectives aimed to improve the structure of the search space after the discretization. This ordering problem is tackled from a theoretical point of view, and some practical experiences on sets of artificially generated instances, as well as on real-life instances, are provided