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We investigate algebraic and topological signatures of networks of coupled oscillators. Translating dynamics into a system of algebraic equations enables us to identify classes of network topologies that exhibit unexpected behaviors. Many previous studies focus on synchronization of networks having high connectivity, or of a specific type (e.g. circulant networks). We introduce the Kuramoto ideal; an algebraic analysis of this ideal allows us to identify features beyond synchronization, such as positive dimensional components in the set of potential solutions (e.g. curves instead of points). We prove sufficient conditions on the network structure for such solutions to exist. The points lying on a positive dimensional component of the solution set can never correspond to a linearly stable state. We apply this framework to give a complete analysis of linear stability for all networks on at most eight vertices. Furthermore, we describe a construction of networks on an arbitrary number of vertices having linearly stable states that are not twisted stable states., Comment: v1: 22 pages, 6 figures, v2: 23 pages, 6 figures. Modified to reflect referee suggestions

We enumerate topologically-inequivalent compact Calabi-Yau threefold hypersurfaces. By computing arithmetic and algebraic invariants and the Gopakumar-Vafa invariants of curves, we prove that the number of distinct simply connected Calabi-Yau threefold hypersurfaces resulting from triangulations of four-dimensional reflexive polytopes is 4, 27, 183, 1,184 and 8,036 at $h^{1,1}$ = 1, 2, 3, 4, and 5, respectively. We also establish that there are ten equivalence classes of Wall data of non-simply connected Calabi-Yau threefolds from the Kreuzer-Skarke list. Finally, we give a provisional count of threefolds obtained by enumerating non-toric flops at $h^{1,1} =2$., Comment: 40 pages, 1 figure, 5 tables

We present a computational algebra solution to reverse engineering the network structure of discrete dynamical systems from data. We use monomial ideals to determine dependencies between variables that encode constraints on the possible wiring diagrams underlying the process generating the discrete-time, continuous-space data. Our work assumes that each variable is either monotone increasing or decreasing. We prove that with enough data, even in the presence of small noise, our method can reconstruct the correct unique wiring diagram., Comment: 19 pages, 5 figures

We study Euclidean D3-branes wrapping divisors $D$ in Calabi-Yau orientifold compactifications of type IIB string theory. Witten's counting of fermion zero modes in terms of the cohomology of the structure sheaf $\mathcal{O}_D$ applies when $D$ is smooth, but we argue that effective divisors of Calabi-Yau threefolds typically have singularities along rational curves. We generalize the counting of fermion zero modes to such singular divisors, in terms of the cohomology of the structure sheaf $\mathcal{O}_{\overline{D}}$ of the normalization $\overline{D}$ of $D$. We establish this by detailing compactifications in which the singularities can be unwound by passing through flop transitions, giving a physical incarnation of the normalization process. Analytically continuing the superpotential through the flops, we find that singular divisors whose normalizations are rigid can contribute to the superpotential: specifically, $h^{\bullet}_{+}(\mathcal{O}_{\overline{D}})=(1,0,0)$ and $h^{\bullet}_{-}(\mathcal{O}_{\overline{D}})=(0,0,0)$ give a sufficient condition for a contribution. The examples that we present feature infinitely many isomorphic geometric phases, with corresponding infinite-order monodromy groups $\Gamma$. We use the action of $\Gamma$ on effective divisors to determine the exact effective cones, which have infinitely many generators. The resulting nonperturbative superpotentials are Jacobi theta functions, whose modular symmetries suggest the existence of strong-weak coupling dualities involving inversion of divisor volumes., Comment: 31 pages, 4 figures