In this paper, we introduce a path embedding problem inspired by the well-known hydrophobic-polar (HP) model of protein folding. A graph is said bicolored if each vertex is assigned a label in the set {red, blue}. For a given bicolored path P and a given bicolored graph G, our problem asks whether we can embed P into G in such a way as to match the colors of the vertices. In our model, G represents a protein's “blueprint,” and P is an amino acid sequence that has to be folded to form (part of) G. We first show that the bicolored path embedding problem is NP-complete even if G is a rectangular grid (a typical scenario in protein folding models) and P and G have the same number of vertices. By contrast, we prove that the problem becomes tractable if the height of the rectangular grid G is constant, even if the length of P is independent of G. Our proof is constructive: we give a polynomial-time algorithm that computes an embedding (or reports that no embedding exists), which implies that the problem is in XP when parameterized according to the height of G. Additionally, we show that the problem of embedding P into a rectangular grid G in such a way as to maximize the number of red-red contacts is NP-hard. (This problem is directly inspired by the HP model of protein folding; it was previously known to be NP-hard if G is not given, and P can be embedded in any way on a grid.) Finally, we show that, given a bicolored graph G, the problem of constructing a path P that embeds in G maximizing red-red contacts is Poly-APX-hard.

We study the computational complexity of the puzzle game Critter Crunch, where the player has to rearrange Critters on a board in order to eliminate them all. Smaller Critters can be fed to larger Critters, and Critters will explode if they eat too much. Critters come in several different types, sizes, and colors. We prove the NP-hardness of levels that contain Blocker Critters, as well as levels where the player must clear the board in a given number of moves (i.e., “puzzle mode”). We also characterize the complexity of the game, as a function of the number of columns on the board, in two settings: (i) the setting where Critters may have several different colors, but only two possible sizes, and (ii) the setting where Critters come in all three sizes, but with no color variations. In both settings, the game is NP-hard for levels with exactly two columns, and solvable in linear time for levels with only one column or more than two columns.