We utilize the deformation theory of algebraic singularities to study charged matter in compactifications of M-theory, F-theory, and type IIa string theory on elliptically fibered Calabi-Yau manifolds. In F-theory, this description is more physical than that of resolution. We describe how two-cycles can be identified and systematically studied after deformation. For ADE singularities, we realize non-trivial ADE representations as sublattices of Z^N, where N is the multiplicity of the codimension one singularity before deformation. We give a method for the determination of Picard-Lefschetz vanishing cycles in this context and utilize this method for one-parameter smooth deformations of ADE singularities. We give a general map from junctions to weights and demonstrate that Freudenthal's recursion formula applied to junctions correctly reproduces the structure of high-dimensional ADE representations, including the 126 of SO(10) and the 43,758 of E_6. We identify the Weyl group action in some examples, and verify its order in others. We describe the codimension two localization of matter in F-theory in the case of heterotic duality or simple normal crossing and demonstrate the branching of adjoint representations. Finally, we demonstrate geometrically that deformations correctly reproduce the appearance of non-simply-laced algebras induced by monodromy around codimension two singularities, showing the reduction of D_4 to G_2 in an example. A companion mathematical paper will follow.
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