Fourth-order flows in surface modelling

This short article is a brief account of the usage of fourth-order curvature flow in surface modelling

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Spinor representation of surfaces and complex stresses on membranes and interfaces

Variational principles are developed within the framework of a spinor representation of the surface geometry to examine the equilibrium properties of a membrane or interface. This is a far-reaching generalization of the Weierstrass-Enneper representation for minimal surfaces, introduced by mathematicians in the nineties, permitting the relaxation of the vanishing mean curvature constraint. In this representation the surface geometry is described by a spinor field, satisfying a two-dimensional Dirac equation, coupled through a potential associated with the mean curvature. As an application, the mesoscopic model for a fluid membrane as a surface described by the Canham-Helfrich energy quadratic in the mean curvature is examined. An explicit construction is provided of the conserved complex-valued stress tensor characterizing this surface.Comment: 17 page

Minimal surfaces - variational theory and applications

Minimal surfaces are among the most natural objects in Differential Geometry, and have been studied for the past 250 years ever since the pioneering work of Lagrange. The subject is characterized by a profound beauty, but perhaps even more remarkably, minimal surfaces (or minimal submanifolds) have encountered striking applications in other fields, like three-dimensional topology, mathematical physics, conformal geometry, among others. Even though it has been the subject of intense activity, many basic open problems still remain. In this lecture we will survey recent advances in this area and discuss some future directions. We will give special emphasis to the variational aspects of the theory as well as to the applications to other fields.Comment: Proceedings of the ICM, Seoul 201

Second-order Shape Optimization for Geometric Inverse Problems in Vision

We develop a method for optimization in shape spaces, i.e., sets of surfaces modulo re-parametrization. Unlike previously proposed gradient flows, we achieve superlinear convergence rates through a subtle approximation of the shape Hessian, which is generally hard to compute and suffers from a series of degeneracies. Our analysis highlights the role of mean curvature motion in comparison with first-order schemes: instead of surface area, our approach penalizes deformation, either by its Dirichlet energy or total variation. Latter regularizer sparks the development of an alternating direction method of multipliers on triangular meshes. Therein, a conjugate-gradients solver enables us to bypass formation of the Gaussian normal equations appearing in the course of the overall optimization. We combine all of the aforementioned ideas in a versatile geometric variation-regularized Levenberg-Marquardt-type method applicable to a variety of shape functionals, depending on intrinsic properties of the surface such as normal field and curvature as well as its embedding into space. Promising experimental results are reported

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus