The Spine of the Cosmic Web

We present the SpineWeb framework for the topological analysis of the Cosmic Web and the identification of its walls, filaments and cluster nodes. Based on the watershed segmentation of the cosmic density field, the SpineWeb method invokes the local adjacency properties of the boundaries between the watershed basins to trace the critical points in the density field and the separatrices defined by them. The separatrices are classified into walls and the spine, the network of filaments and nodes in the matter distribution. Testing the method with a heuristic Voronoi model yields outstanding results. Following the discussion of the test results, we apply the SpineWeb method to a set of cosmological N-body simulations. The latter illustrates the potential for studying the structure and dynamics of the Cosmic Web.Comment: Accepted for publication HIGH-RES version: http://skysrv.pha.jhu.edu/~miguel/SpineWeb

Exploring power behaviors and trade-offs of in-situ data analytics

pre-printAs scientific applications target exascale, challenges related to data and energy are becoming dominating concerns. For example, coupled simulation workflows are increasingly adopting in-situ data processing and analysis techniques to address costs and overheads due to data movement and I/O. However it is also critical to understand these overheads and associated trade-offs from an energy perspective. The goal of this paper is exploring data-related energy/performance trade-offs for end-to-end simulation workflows running at scale on current high-end computing systems. Specifically, this paper presents: (1) an analysis of the data-related behaviors of a combustion simulation workflow with an in-situ data analytics pipeline, running on the Titan system at ORNL; (2) a power model based on system power and data exchange patterns, which is empirically validated; and (3) the use of the model to characterize the energy behavior of the workflow and to explore energy/performance tradeoffs on current as well as emerging systems

A Material Point Method for Elastoplasticity with Ductile Fracture and Frictional Contact

Simulating physical materials with dynamic movements to photo-realistic resolution has always been one of the most crucial and challenging topics in Computer Graphics. This dissertation considers large-strain elastoplasticity theory applied to the low-to-medium stiffness regime, with topological changes and codimensional objects incorporated. We introduce improvements to the Material Point Method (MPM) for two particular objectives, simulating fracturing ductile materials and incorporation of MPM and Lagrangian Finite Element Method (FEM).Our first contribution, simulating ductile fracture, utilizes traditional particle-based MPM [SSC13, SCS94] as well as the Lagrangian energy formulation of [JSS15] which uses a tetrahedron mesh, rather than particle-based estimation of the deformation gradient and potential energy. We model failure and fracture via elastoplasticity with damage. The material is elastic until its deformation exceeds a Rankine or von Mises yield condition. At that point, we use a softening model that shrinks the yield surface until it reaches the damage thresh- old. Once damaged, the material Lam ́e coefficients are modified to represent failed material. This approach to simulating ductile fracture with MPM is successful, as MPM naturally captures the topological changes coming from the fracture. However, rendering the crack surfaces can be challenging. We design a novel visualization technique dedicated to rendering the material’s boundary and its intersection with the evolving crack surfaces. Our approach uses a simple and efficient element splitting strategy for tetrahedron meshes to create crack surfaces. It employs an extrapolation technique based on the MPM simulation. For traditional particle-based MPM, we use an initial Delaunay tetrahedralization to connect randomly sampled MPM particles. Our visualization technique is a post-process and can run after the MPM simulation for efficiency. We demonstrate our method with several challenging simulations of ductile failure with considerable and persistent self-contact and applications with thermomechanical models for baking and cooking.Our second contribution, hybrid MPM–Lagrangian-FEM, aims to simulate elastic objects like hair, rubber, and soft tissues. It utilizes a Lagrangian mesh for internal force computation and a Eulerian grid for self-collision, as well as coupling with external materials. While recent MPM techniques allow for natural simulation of hyperelastic materials represented with Lagrangian meshes, they utilize an updated Lagrangian discretization and use the Eulerian grid degrees of freedom to take variations of the potential energy. It often coarsens the degrees of freedom of the Lagrangian mesh and can lead to artifacts. We develop a hybrid approach that retains Lagrangian degrees of freedom while still allowing for natural coupling with other materials simulated with traditional MPM, e.g., sand, snow, etc. Furthermore, while recent MPM advances allow for resolution of frictional contact with codimensional simulation of hyperelasticity, they do not generalize to the case of volumetric materials. We show that our hybrid approach resolves these issues. We demonstrate the efficacy of our technique with examples that involve elastic soft tissues coupled with kinematic skeletons, extreme deformation, and coupling with various elastoplastic materials. Our approach also naturally allows for two-way rigid body coupling

NMR Insights into Folding and Self-Association of Plasmodium falciparum P2

The eukaryotic 60S-ribosomal stalk is composed of acidic ribosomal proteins (P1 and P2) and neutral protein P0, which are thought to be associated as a pentameric structure, [2P1, 2P2, P0]. Plasmodium falciparum P2 (PfP2) appears to play additional non-ribosomal functions associated with its tendency for homo-oligomerization. Recombinant bacterially expressed PfP2 protein also undergoes self-association, as shown by SDS-PAGE analysis and light scattering studies. Secondary structure prediction algorithms predict the native PfP2 protein to be largely helical and this is corroborated by circular dichroism investigation. The 1H-15N HSQC spectrum of native P2 showed only 43 cross peaks compared to the expected 138. The observed peaks were found to belong to the C-terminal region, suggesting that this segment is flexible and solvent exposed. In 9 M urea denaturing conditions the chain exhibited mostly non-native β structural propensity. 15N Relaxation data for the denatured state indicated substantial variation in ms-µs time scale motion along the chain. Average area buried upon folding (AABUF) calculations on the monomer enabled identification of hydrophobic patches along the sequence. Interestingly, the segments of slower motion in the denatured state coincided with these hydrophobic patches, suggesting that in the denatured state the monomeric chain undergoes transient hydrophobic collapse. The implications of these results for the folding mechanism and self-association of PfP2 are discussed