Persistent Homology in Sparse Regression and its Application to Brain Morphometry

Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region.Comment: submitted to IEEE Transactions on Medical Imagin

Persistent Magnetic Wreaths in a Rapidly Rotating Sun

When our Sun was young it rotated much more rapidly than now. Observations of young, rapidly rotating stars indicate that many possess substantial magnetic activity and strong axisymmetric magnetic fields. We conduct simulations of dynamo action in rapidly rotating suns with the 3-D MHD anelastic spherical harmonic (ASH) code to explore the complex coupling between rotation, convection and magnetism. Here we study dynamo action realized in the bulk of the convection zone for a system rotating at three times the current solar rotation rate. We find that substantial organized global-scale magnetic fields are achieved by dynamo action in this system. Striking wreaths of magnetism are built in the midst of the convection zone, coexisting with the turbulent convection. This is a surprise, for it has been widely believed that such magnetic structures should be disrupted by magnetic buoyancy or turbulent pumping. Thus, many solar dynamo theories have suggested that a tachocline of penetration and shear at the base of the convection zone is a crucial ingredient for organized dynamo action, whereas these simulations do not include such tachoclines. We examine how these persistent magnetic wreaths are maintained by dynamo processes and explore whether a classical mean-field $\alpha$-effect explains the regeneration of poloidal field.Comment: 17 pages, 9 figures, 1 appendix, emulateapj format; published version of sections 3-4, 7 and appendix from arXiv:0906.240

Self-organized dynamics and the transition to turbulence of confined active nematics

We study how confinement transforms the chaotic dynamics of bulk microtubule-based active nematics into regular spatiotemporal patterns. For weak confinements, multiple continuously nucleating and annihilating topological defects self-organize into persistent circular flows of either handedness. Increasing confinement strength leads to the emergence of distinct dynamics, in which the slow periodic nucleation of topological defects at the boundary is superimposed onto a fast procession of a pair of defects. A defect pair migrates towards the confinement core over multiple rotation cycles, while the associated nematic director field evolves from a distinct double spiral towards a nearly circularly symmetric configuration. The collapse of the defect orbits is punctuated by another boundary-localized nucleation event, that sets up long-term doubly-periodic dynamics. Comparing experimental data to a theoretical model of an active nematic, reveals that theory captures the fast procession of a pair of $+\frac{1}{2}$ defects, but not the slow spiral transformation nor the periodic nucleation of defect pairs. Theory also fails to predict the emergence of circular flows in the weak confinement regime. The developed confinement methods are generalized to more complex geometries, providing a robust microfluidic platform for rationally engineering two-dimensional autonomous flows