Related papers: Geometry of the Kimura 3-parameter model
By fixing all parameters in a phylogenetic likelihood model except for one branch length, one obtains a one-dimensional likelihood function. In this work, we introduce a mathematical framework to characterize the shapes of such…
We study 2-cocycle twists, or equivalently Zhang twists, of semigroup algebras over a field k. If the underlying semigroup is affine, that is abelian, cancellative and finitely generated, then Spec k[S] is an affine toric variety over k,…
We consider a class of area-preserving, piecewise affine maps on the 2-sphere. These maps encode degenerating families of K3 surface automorphisms and are profitably studied using techniques from tropical and Berkovich geometries.
We study Seiberg-Witten (SW) geometries for rank-two theories, encompassing 4D field theories as well as 5D and 6D Kaluza-Klein (KK) theories. The singular model for each SW geometry is derived from a one-parameter family of algebraic…
We propose a geometric theory of flavor based on the discrete group $(S_3)^3$, in the context of the minimal supersymmetric standard model. The group treats three objects symmetrically, while making fundamental distinctions between the…
We address the problem of studying the toric ideals of phylogenetic invariants for a general group-based model on an arbitrary claw tree. We focus on the group $\mathbb Z_2$ and choose a natural recursive approach that extends to other…
We study basic geometric properties of some group analogue of affine Springer fibers and compare with the classical Lie algebra affine Springer fibers. The main purpose is to formulate a conjecture that relates the number of irreducible…
The earlier approach is used for description of qubits and geometric phase parameters, the things critical in the area of topological quantum computing. The used tool, Geometric (Clifford) Algebra is the most convenient formalism for that…
Any ruled surface in Euclidean 3-space is described as a curve of unit dual vectors in the algebra of dual quaternions (=the even Clifford algebra of type (0,3,1)). Combining this classical framework and Singularity Theory, we characterize…
Group-based models arise in algebraic statistics while studying evolution processes. They are represented by embedded toric algebraic varieties. Both from the theoretical and applied point of view one is interested in determining the ideals…
We present an intriguing and precise interplay between algebraic geometry and the phenomenology of generations of particles. Using the electroweak sector of the MSSM as a testing ground, we compute the moduli space of vacua as an algebraic…
We provide a construction of examples of semistable degeneration via toric geometry. The applications include a higher dimensional generalization of classical degeneration of K3 surface into 4 rational components, an algebraic geometric…
In the last decades affine algebraic varieties and Stein manifolds with big (infinite-dimensional) automorphism groups have been intensively studied. Several notions expressing that the automorphisms group is big have been proposed. All of…
We develop a technique to study curves in a variety which has a degeneration into some union of varieties. The class of such varieties is very broad, but the theory becomes particularly useful when the variety has a degeneration into a…
This is an outline of work in progress concerning an algebro-geometric form of the Strominger-Yau-Zaslow conjecture. We introduce a limited type of degeneration of Calabi-Yau manifolds, which we call toric degenerations. For these, the…
To each symmetric algebra we associate a family of algebras that we call quantum affine wreath algebras. These can be viewed both as symmetric algebra deformations of affine Hecke algebras of type $A$ and as quantum deformations of affine…
This note presents two observations which have in common that they lie at the boundary of toric geometry. The first one because it concerns the deformation of affine toric varieties into non toric germs in order to understand how to avoid…
We study topological properties of automorphisms of 4-dimensional torus generated by integer symplectic matrices. The main classifying element is the structure of the topology of a foliation generated by unstable leaves of the automorphism.…
Framework materials and their deformations provide a compelling relation between materials science and algebraic geometry. Physical distance constraints within the material transform into polynomial constraints, making algebraic geometry…
This survey consists of two parts. Part 1 is devoted to amoebas. These are images of algebraic subvarieties in the complex torus under the logarithmic moment map. The amoebas have essentially piecewise-linear shape if viewed at large.…