Applying mesh conformation on shape analysis with missing data

A mesh conformation approach that makes use of deformable generic meshes has been applied to establishing correspondences between 3D shapes with missing data. Given a group of shapes with correspondences, we can build up a statistical shape model by applying principal component analysis (PCA). The conformation at first globally maps the generic mesh to the 3D shape based on manually located corresponding landmarks, and then locally deforms the generic mesh to clone the 3D shape. The local deformation is constrained by minimizing the energy of an elastic model. An algorithm was also embedded in the conformation process to fill missing surface data of the shapes. Using synthetic data, we demonstrate that the conformation preserves the configuration of the generic mesh and hence it helps to establish good correspondences for shape analysis. Case studies of the principal component analysis of shapes were presented to illustrate the successes and advantages of our approach

A numerical stabilization framework for viscoelastic fluid flow using the finite volume method on general unstructured meshes

A robust finite volume method for viscoelastic flow analysis on general unstructured meshes is developed. It is built upon a general-purpose stabilization framework for high Weissenberg number flows. The numerical framework provides full combinatorial flexibility between different kinds of rheological models on the one hand, and effective stabilization methods on the other hand. A special emphasis is put on the velocity-stress-coupling on co-located computational grids. Using special face interpolation techniques, a semi-implicit stress interpolation correction is proposed to correct the cell-face interpolation of the stress in the divergence operator of the momentum balance. Investigating the entry-flow problem of the 4:1 contraction benchmark, we demonstrate that the numerical methods are robust over a wide range of Weissenberg numbers and significantly alleviate the high Weissenberg number problem. The accuracy of the results is evaluated in a detailed mesh convergence study

The fully-implicit log-conformation formulation and its application to three-dimensional flows

The stable and efficient numerical simulation of viscoelastic flows has been a constant struggle due to the High Weissenberg Number Problem. While the stability for macroscopic descriptions could be greatly enhanced by the log-conformation method as proposed by Fattal and Kupferman, the application of the efficient Newton-Raphson algorithm to the full monolithic system of governing equations, consisting of the log-conformation equations and the Navier-Stokes equations, has always posed a problem. In particular, it is the formulation of the constitutive equations by means of the spectral decomposition that hinders the application of further analytical tools. Therefore, up to now, a fully monolithic approach could only be achieved in two dimensions, as, e.g., recently shown in [P. Knechtges, M. Behr, S. Elgeti, Fully-implicit log-conformation formulation of constitutive laws, J. Non-Newtonian Fluid Mech. 214 (2014) 78-87]. The aim of this paper is to find a generalization of the previously made considerations to three dimensions, such that a monolithic Newton-Raphson solver based on the log-conformation formulation can be implemented also in this case. The underlying idea is analogous to the two-dimensional case, to replace the eigenvalue decomposition in the constitutive equation by an analytically more "well-behaved" term and to rely on the eigenvalue decomposition only for the actual computation. Furthermore, in order to demonstrate the practicality of the proposed method, numerical results of the newly derived formulation are presented in the case of the sedimenting sphere and ellipsoid benchmarks for the Oldroyd-B and Giesekus models. It is found that the expected quadratic convergence of Newton's method can be achieved.Comment: 21 pages, 9 figure

Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through to change the DNA topology. Despite the central importance of this gate-opening event to Top2 function, the DNA-gate in all reported structures of Top2-DNA complexes is in the closed state. Here we present the crystal structure of a human Top2 DNA-gate in an open conformation, which not only reveals structural characteristics of its DNA-conducting path, but also uncovers unexpected yet functionally significant conformational changes associated with gate-opening. This structure further implicates Top2's preference for a left-handed DNA braid and allows the construction of a model representing the initial entry of another DNA duplex into the DNA-gate. Steered molecular dynamics calculations suggests the Top2-catalyzed DNA passage may be achieved by a rocker-switch-type movement of the DNA-gate

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme