Noé Demange

Noé Demange, Yann Strozecki, Sandrine Vial

In this paper, we propose a method to build molecular cages designed to capture a specific substrate. We model a cage as a graph of atoms with coordinates in space, and several constraints on their edges (degree, length and angle). We use a simple method to place binding patterns which are able to interact with certain parts of the substrate. We then propose an algorithm which considers all possible ways of connecting these binding patterns and try to construct the smallest possible molecular paths realizing these connections. We investigate many variants of our method in order to obtain the most efficient algorithm, able to build cages of more than a hundred atoms.

Noé Demange, Yann Strozecki

We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a spanning tree. Motivated by applications in chemoinformatics, we investigate the decision, counting, and enumeration variants of this problem. We show that the decision problem is $NP$-complete. Nevertheless, it becomes tractable in several structured settings: it is fixed-parameter tractable in the number of parts, and admits polynomial or linear-time algorithms on complete, quasi-complete, and $t$-quasi-complete multipartite graphs. We also study enumeration, for which we design efficient flashlight-search based algorithms with optimal delay for complete multipartite graphs, and a weight-guided heuristic that prioritizes low-weight solutions and performs well in practice.