  Non-perturbative D-brane instanton effects in 4d N = 1 string
compactifications can be geometrized in terms of a backreacted generalized
geometry. We extend earlier results to setups in which the D-brane instanton is
charged under the 4d gauge symmetries, and show that the backreacted topology
yields the correct charged field theory operators in the 4d effective action.
In type IIA models with D6-branes, the backreaction of D2-brane instantons
forces the recombination of D6-branes, such that the 4d charged field theory
operators arise from basic worldsheet instantons in the backreacted geometry.
We provide large classes of examples of D2-brane instanton effects on
intersecting D6-brane systems in local models mirror to D3-branes at
singularities. The backreacted geometry and the field theory operators are
easily encoded in terms of simple operation in the graphs arising from the
underlying dimer diagrams. This description agrees, in the appropriate cases,
with the complex deformations triggered by certain fractional branes at the
bottom of duality cascades.
