We study a class of structured optimal control problems in which the main diagonal of the dynamic matrix is a linear function of the design variable. While such problems are in general challenging and nonconvex, for positive systems we prove convexity of the H2 and H∞ optimal control formulations which allow for arbitrary convex constraints and regularization of the control input. Moreover, we establish differentiability of the H∞ norm when the graph associated with the dynamical generator is weakly connected and develop a customized algorithm for computing the optimal solution even in the absence of differentiability. We apply our results to the problems of leader selection in directed consensus networks and combination drug therapy for HIV treatment. In the context of leader selection, we address the combinatorial challenge by deriving upper and lower bounds on optimal performance. For combination drug therapy, we develop a customized subgradient method for efficient treatment of diseases whose mutation patterns are not connected.(A ≥ 0) if A has positive (nonnegative) entries and A 0 (A 0) if A is symmetric and positive (semi)-definite. We define the sparsity pattern of a vector u, sp (u), as the set of indices for which u i is nonzero, u 1 := i |u i | is the 1 norm, and K † : R n×n → R m is the adjoint of a linear operator K: R m → R n×n if it satisfies, X, K(u) = K † (X), u for all u ∈ R m and X ∈ R n×n .Definition 1 (Graph associated with a matrix): G(A) = (V, E) is the graph associated with a matrix A ∈ R n×n , with the set of nodes (vertices) V := {1, . . . , n} and the set of edges E := {(i, j)| A ij = 0}, where (i, j) denotes an edge pointing from node j to node i.Definition 2 (Strongly connected graph): A graph (V, E) is strongly connected if there is a directed path between any two distinct nodes in V.Definition 3 (Weakly connected graph): A graph (V, E) is weakly connected if replacing its edges with undirected edges results in a strongly connected graph.Definition 4 (Balanced graph): A graph (V, E) is balanced if, for every node i ∈ V, the sum of edge weights on the edges pointing to node i is equal to the sum of edge weights on the edges pointing from node i.Definition 5: A dynamical system is positive if, for any nonnegative initial condition and any nonnegative input, the output is nonnegative for all time. A linear time-invariant system,