Collapsibility to a subcomplex of a given dimension is NP-complete

In this paper we extend the works of Tancer and of Malgouyres and Franc\'es, showing that $(d,k)$-collapsibility is NP-complete for $d\geq k+2$ except $(2,0)$. By $(d,k)$-collapsibility we mean the following problem: determine whether a given $d$-dimensional simplicial complex can be collapsed to some $k$-dimensional subcomplex. The question of establishing the complexity status of $(d,k)$-collapsibility was asked by Tancer, who proved NP-completeness of $(d,0)$ and $(d,1)$-collapsibility (for $d\geq 3$). Our extended result, together with the known polynomial-time algorithms for $(2,0)$ and $d=k+1$, answers the question completely

Discrete Morse theory for computing cellular sheaf cohomology

Sheaves and sheaf cohomology are powerful tools in computational topology, greatly generalizing persistent homology. We develop an algorithm for simplifying the computation of cellular sheaf cohomology via (discrete) Morse-theoretic techniques. As a consequence, we derive efficient techniques for distributed computation of (ordinary) cohomology of a cell complex.Comment: 19 pages, 1 Figure. Added Section 5.

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques