Discrete Differential Geometry of Triangles and Escher-Style Trick Art

This paper shows the usefulness of discrete differential geometry in global analysis. Using the discrete differential geometry of triangles, we could consider the global structure of closed trajectories (of triangles) on a triangular mesh consisting of congruent isosceles triangles. As an example, we perform global analysis of an Escher-style trick art, i.e., a simpler version of “Ascending and Descending”. After defining the local structure on the trick art, we analyze its global structure and attribute its paradox to a singular point (i.e., a singular triangle) at the center. Then, the endless “Penrose stairs” is described as a closed trajectory around the isolated singular point. The approach fits well with graphical projection and gives a simple and intuitive example of the interaction between global and local structures. We could deal with higher dimensional objects as well by considering n-simplices (n > 2) instead of triangles.

Discrete Exterior Calculus of Proteins and Their Cohomology

This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an important role in their functions. In our mathematical toy models, proteins are represented as a loop of triangles (2D model) or tetrahedra (3D model), where their interactions are defined as fusion of loops. The purpose of this paper is to describe the conditions for loop fusion using the language of cohomology. In particular, this paper uses cohomology to describe the conditions for “allosteric regulation”, which has been attracted attention in safer drug discovery. I hope that this paper will provide a new perspective on the mechanism of allosteric regulation. Advantages of the model include its topological nature. That is, we can deform the shape of loops by deforming the shape of triangles (or tetrahedra) as long as their folded structures are preserved. Another advantage is the simplicity of the “allosteric regulation” mechanism of the model. Furthermore, the effect of the “post-translational modification” can be understood as a resolution of singularities of a flow of triangles (or tetrahedra). No prior knowledge of either protein science, exterior calculus, or cohomology theory is required. The author hopes that this paper will facilitate the interaction between mathematics and protein science.

A Novel Design Method for Protein-Like Molecules from the Perspective of Sheaf Theory

Proteins perform a variety of functions in living organisms and their functions are largely determined by their shape. In this paper, we propose a novel mathematical method for designing protein-like molecules of a given shape. In the mathematical model, molecules are represented as loops of n-simplices (2-simplices are triangles and 3-simplices are tetrahedra). We design a new molecule of a given shape by patching together a set of smaller molecules that cover the shape. The covering set of small molecules is defined using a binary relation between sets of molecules. A new molecule is then obtained as a sum of the smaller molecules, where addition of molecules is defined using transformations acting on a set of (n + 1)-dimensional cones. Due to page limitations, only the two-dimensional case (i.e., loops of triangles) is considered. No prior knowledge of Sheaf Theory, Category Theory, or Protein Science is required. The author hopes that this paper will encourage further collaboration between Mathematics and Protein Science.