Particlization in hybrid models

In hybrid models, which combine hydrodynamical and transport approaches to describe different stages of heavy-ion collisions, conversion of fluid to individual particles, particlization, is a non-trivial technical problem. We describe in detail how to find the particlization hypersurface in a 3+1 dimensional model, and how to sample the particle distributions evaluated using the Cooper-Frye procedure to create an ensemble of particles as an initial state for the transport stage. We also discuss the role and magnitude of the negative contributions in the Cooper-Frye procedure.Comment: 18 pages, 28 figures, EPJA: Topical issue on "Relativistic Hydro- and Thermodynamics"; version accepted for publication, typos and error in Eq.(1) corrected, the purpose of sampling and change from UrQMD to fluid clarified, added discussion why attempts to cancel negative contributions of Cooper-Frye are not applicable her

Visual cavity analysis in molecular simulations

Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied

Phong normal interpolation revisited

Phong shading is one of the best known, and at the same time simplest techniques to arrive at realistic images when rendering 3D geometric models. However, despite (or maybe due to) its success and its widespread use, some aspects remain to be clarified with respect to its validity and robustness. This might be caused by the fact that the Phong method is based on geometric arguments, illumination models, and clever heuristics. In this article we address some of the fundamentals that underlie Phong shading, such as the computation of vertex normals for nonmanifold models and the adequacy of linear interpolation and we apply a new interpolation technique to achieve an efficient and qualitatively improved result

SUBDIVISION SURFACES FOR FAST APPROXIMATE IMPLICIT POLYGONIZATION

We propose a fast method of generating an approximate polygonal mesh from an implicit surface. Current workstations are still not capable of producing polygon meshes fast enough for the interactive modeling of complex implicit models. We propose a hybrid method that combines current implicit polygonization techniques with the faster sub-division surface technique applied as a post-process to smooth the implicit mesh. In an interactive environment the smooth mesh points can be migrated to the implicit surface, in idle moments when the user is not interacting with the model. The technique can be further enhanced by providing tools for the user to indicate areas of interest that can be preferentially smoothed.We are currently acquiring citations for the work deposited into this collection. We recognize the distribution rights of this item may have been assigned to another entity, other than the author(s) of the work.If you can provide the citation for this work or you think you own the distribution rights to this work please contact the Institutional Repository Administrator at [email protected]

Hi-speed, Hi-fi, Hi-lights : a fast algorithm for the specular term in the Phong illumination model

The computational effort to render images with light sources and camera at infinity is less than with light sources at finite distance from the illuminated surface. On the other hand, in the case of an infinitely remote light source and camera, planar polygons don’t receive highlights. In this paper, a method is suggested to use the (relatively cheap) infinite-distance model instead of the expensive finite-distance model for the computation of highlights. It works by replacing a light source at finite distance by a light source at infinite distance, and at the same time adjusting the normal vectors in such a way that the resulting illumination pattern stays the same. With these modifications, a simple table look-up comes in the place of an expensive computation to obtain the specular term in the standard illumination model

Shrinkwrap : an adaptive algorithm for polygonizing an implicit surface

An algorithm is presented which generates a triangular mesh to approximate an equi-potential surface. The algorithm is adaptive in the sense that the lengths of the sides of the triangles in the mesh vary with the local curvature of the underlying surface. A quantitative analysis of the accuracy of the algorithm is given along with an empirical comparison with earlier algorithms.We are currently acquiring citations for the work deposited into this collection. We recognize the distribution rights of this item may have been assigned to another entity, other than the author(s) of the work.If you can provide the citation for this work or you think you own the distribution rights to this work please contact the Institutional Repository Administrator at [email protected]

Polygon inflation for animated models: a method for the extrusion of arbitrary polygon meshes

A method for the extrusion of arbitrary polygon meshes is introduced. This method can be applied to model a large class of complex 3-D closed surfaces. It consists of defining a (typically small) set of connected polygons in 3-D that form a skeleton of the final object, and assigning extrusion distances to all polygons. The two sides of a polygon may have different extrusion distances. An automatic extrusion algorithm constructs a closed 3-D polygon mesh around the skeleton, making use of the indicated extrusion distances. We call this process inflating the polygons of the skeleton. Unlike traditional extrusion, the method works for non-planar skeleton configurations, and it also supports branching skeleton structures (i.e. edges with more than two incident polygons). © 1997 by John Wiley & Sons, Ltd