Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories

We present an efficient algorithm for computation of surface representations enabling interactive visualization of large dynamic particle data sets. Our method is based on a GPU-accelerated data-parallel algorithm for computing a volumetric density map from Gaussian weighted particles. The algorithm extracts an isovalue surface from the computed density map, using fast GPU-accelerated Marching Cubes. This approach enables interactive frame rates for molecular dynamics simulations consisting of millions of atoms. The user can interactively adjust the display of structural detail on a continuous scale, ranging from atomic detail for in-depth analysis, to reduced detail visual representations suitable for viewing the overall architecture of molecular complexes. The extracted surface is useful for interactive visualization, and provides a basis for structure analysis methods.

[1]  Thomas Ertl,et al.  Parallel Contour-Buildup algorithm for the molecular surface , 2011, 2011 IEEE Symposium on Biological Data Visualization (BioVis)..

[2]  Hans-Peter Seidel,et al.  GPU point list generation through histogram pyramids , 2006 .

[3]  J. A. Grant,et al.  A Gaussian Description of Molecular Shape , 1995 .

[4]  Abel J. P. Gomes,et al.  Graphics processing unit‐based triangulations of Blinn molecular surfaces , 2011, Concurr. Comput. Pract. Exp..

[5]  Martin Falk,et al.  3D visualization of concentrations from stochastic agent-based signal transduction simulations , 2010, 2010 IEEE International Symposium on Biomedical Imaging: From Nano to Macro.

[6]  Tomoyuki Nishita,et al.  GPU‐based Fast Ray Casting for a Large Number of Metaballs , 2008, Comput. Graph. Forum.

[7]  Rüdiger Westermann,et al.  Efficient High-Quality Volume Rendering of SPH Data , 2010, IEEE Transactions on Visualization and Computer Graphics.

[8]  William E. Lorensen,et al.  Marching cubes: A high resolution 3D surface construction algorithm , 1987, SIGGRAPH.

[9]  James F. Blinn,et al.  A Generalization of Algebraic Surface Drawing , 1982, TOGS.

[10]  Amitabh Varshney,et al.  Parallel, stochastic measurement of molecular surface area. , 2008, Journal of molecular graphics & modelling.

[11]  Klaus Schulten,et al.  GPU acceleration of cutoff pair potentials for molecular modeling applications , 2008, CF '08.

[12]  Martin Falk,et al.  Interactive Exploration of Protein Cavities , 2011, Comput. Graph. Forum.

[13]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[14]  Daniel Baum,et al.  Eurographics/ Ieee-vgtc Symposium on Visualization 2010 Accelerated Visualization of Dynamic Molecular Surfaces , 2022 .

[15]  Thomas Ertl,et al.  Image-Space GPU Metaballs for Time-Dependent Particle Data Sets , 2007, VMV.

[16]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[17]  J. A. Grant,et al.  A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape , 1996, J. Comput. Chem..

[18]  Frederick P. Brooks,et al.  Linearly Scalable Computation of Smooth Molecular Surfaces , 1997 .

[19]  Hans-Peter Seidel,et al.  High‐speed Marching Cubes using HistoPyramids , 2008, Comput. Graph. Forum.

[20]  R Abagyan,et al.  The contour-buildup algorithm to calculate the analytical molecular surface. , 1996, Journal of structural biology.

[21]  Klaus Schulten,et al.  Accelerating Molecular Modeling Applications with GPU Computing , 2009 .

[22]  M. L. Connolly Analytical molecular surface calculation , 1983 .