How round is a protein? Exploring protein structures for globularity using conformal mapping.

We present a new algorithm that automatically computes a measure of the geometric difference between the surface of a protein and a round sphere. The algorithm takes as input two triangulated genus zero surfaces representing the protein and the round sphere, respectively, and constructs a discrete conformal map f between these surfaces. The conformal map is chosen to minimize a symmetric elastic energy E S (f) that measures the distance of f from an isometry. We illustrate our approach on a set of basic sample problems and then on a dataset of diverse protein structures. We show first that E S (f) is able to quantify the roundness of the Platonic solids and that for these surfaces it replicates well traditional measures of roundness such as the sphericity. We then demonstrate that the symmetric elastic energy E S (f) captures both global and local differences between two surfaces, showing that our method identifies the presence of protruding regions in protein structures and quantifies how these regions make the shape of a protein deviate from globularity. Based on these results, we show that E S (f) serves as a probe of the limits of the application of conformal mapping to parametrize protein shapes. We identify limitations of the method and discuss its extension to achieving automatic registration of protein structures based on their surface geometry

Maximization of Laplace-Beltrami eigenvalues on closed Riemannian surfaces

Let $(M,g)$ be a connected, closed, orientable Riemannian surface and denote by $\lambda_k(M,g)$ the $k$-th eigenvalue of the Laplace-Beltrami operator on $(M,g)$. In this paper, we consider the mapping $(M, g)\mapsto \lambda_k(M,g)$. We propose a computational method for finding the conformal spectrum $\Lambda^c_k(M,[g_0])$, which is defined by the eigenvalue optimization problem of maximizing $\lambda_k(M,g)$ for $k$ fixed as $g$ varies within a conformal class $[g_0]$ of fixed volume $textrm{vol}(M,g) = 1$. We also propose a computational method for the problem where $M$ is additionally allowed to vary over surfaces with fixed genus, $\gamma$. This is known as the topological spectrum for genus $\gamma$ and denoted by $\Lambda^t_k(\gamma)$. Our computations support a conjecture of N. Nadirashvili (2002) that $\Lambda^t_k(0) = 8 \pi k$, attained by a sequence of surfaces degenerating to a union of $k$ identical round spheres. Furthermore, based on our computations, we conjecture that $\Lambda^t_k(1) = \frac{8\pi^2}{\sqrt{3}} + 8\pi (k-1)$, attained by a sequence of surfaces degenerating into a union of an equilateral flat torus and $k-1$ identical round spheres. The values are compared to several surfaces where the Laplace-Beltrami eigenvalues are well-known, including spheres, flat tori, and embedded tori. In particular, we show that among flat tori of volume one, the $k$-th Laplace-Beltrami eigenvalue has a local maximum with value $\lambda_k = 4\pi^2 \left\lceil \frac{k}{2} \right\rceil^2 \left( \left\lceil \frac{k}{2} \right\rceil^2 - \frac{1}{4}\right)^{-\frac{1}{2}}$. Several properties are also studied computationally, including uniqueness, symmetry, and eigenvalue multiplicity.Comment: 43 pages, 18 figure

An Unstructured Mesh Convergent Reaction-Diffusion Master Equation for Reversible Reactions

The convergent reaction-diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction-diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction-diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle-particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model.Comment: 35 pages, 9 figures. Accepted, J. Comp. Phys. (2018

Beyond developable: computational design and fabrication with auxetic materials

We present a computational method for interactive 3D design and rationalization of surfaces via auxetic materials, i.e., flat flexible material that can stretch uniformly up to a certain extent. A key motivation for studying such material is that one can approximate doubly-curved surfaces (such as the sphere) using only flat pieces, making it attractive for fabrication. We physically realize surfaces by introducing cuts into approximately inextensible material such as sheet metal, plastic, or leather. The cutting pattern is modeled as a regular triangular linkage that yields hexagonal openings of spatially-varying radius when stretched. In the same way that isometry is fundamental to modeling developable surfaces, we leverage conformal geometry to understand auxetic design. In particular, we compute a global conformal map with bounded scale factor to initialize an otherwise intractable non-linear optimization. We demonstrate that this global approach can handle non-trivial topology and non-local dependencies inherent in auxetic material. Design studies and physical prototypes are used to illustrate a wide range of possible applications

An adaptive, hanging-node, discontinuous isogeometric analysis method for the first-order form of the neutron transport equation with discrete ordinate (SN) angular discretisation

In this paper a discontinuous, hanging-node, isogeometric analysis (IGA) method is developed and applied to the first-order form of the neutron transport equation with a discrete ordinate (SN) angular discretisation in two-dimensional space. The complexities involved in upwinding across curved element boundaries that contain hanging-nodes have been addressed to ensure that the scheme remains conservative. A robust algorithm for cycle-breaking has also been introduced in order to develop a unique sweep ordering of the elements for each discrete ordinates direction. The convergence rate of the scheme has been verified using the method of manufactured solutions (MMS) with a smooth solution. Heuristic error indicators have been used to drive an adaptive mesh refinement (AMR) algorithm to take advantage of the hanging-node discretisation. The effectiveness of this method is demonstrated for three test cases. The first is a homogeneous square in a vacuum with varying mean free path and a prescribed extraneous unit source. The second test case is a radiation shielding problem and the third is a 3×3 “supercell” featuring a burnable absorber. In the final test case, comparisons are made to the discontinuous Galerkin finite element method (DGFEM) using both straight-sided and curved quadratic finite elements