Fast Blending Scheme for Molecular Surface Representation

Representation of molecular surfaces is a well established way to study the interaction of molecules. The state-of-theart molecular representation is the SES model, which provides a detailed surface visualization. Nevertheless, it is computationally expensive, so the less accurate Gaussian model is traditionally preferred. We introduce a novel surface representation that resembles the SES and approaches the rendering performance of the Gaussian model. Our technique is based on the iterative blending of implicit functions and avoids any pre-computation. Additionally, we propose a GPU-based ray-casting algorithm that efficiently visualize our molecular representation. A qualitative and quantitative comparison of our model with respect to the Gaussian and SES models is presented. As showcased in the paper, our technique is a valid and appealing alternative to the Gaussian representation. This is especially relevant in all the applications where the cost of the SES is prohibitive.

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

[2]  Hans Hagen,et al.  Fast Ray Tracing of Arbitrary Implicit Surfaces with Interval and Affine Arithmetic , 2009, Comput. Graph. Forum.

[3]  László Szécsi,et al.  Real-Time Metaball Ray Casting with Fragment Lists , 2012, Eurographics.

[4]  B. Bush,et al.  Macromolecular shape and surface maps by solvent exclusion. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Marc Baaden,et al.  Complex molecular assemblies at hand via interactive simulations , 2009, J. Comput. Chem..

[6]  Loïc Barthe,et al.  Extrusion of 1D Implicit Profiles: Theory and First Application , 2001, Int. J. Shape Model..

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

[8]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[9]  Deok-Soo Kim,et al.  Triangulation of molecular surfaces , 2009, Comput. Aided Des..

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

[11]  Frederick P. Brooks,et al.  Computing smooth molecular surfaces , 1994, IEEE Computer Graphics and Applications.

[12]  Thomas Ertl,et al.  Hardware-Accelerated Glyphs for Mono- and Dipoles in Molecular Dynamics Visualization , 2005, EuroVis.

[13]  Loren C. Carpenter,et al.  The A -buffer, an antialiased hidden surface method , 1984, SIGGRAPH.

[14]  Timo Ropinski,et al.  Seamless Visual Abstraction of Molecular Surfaces , 2013, SCCG.

[15]  Ivan Viola,et al.  Implicit representation of molecular surfaces , 2012, 2012 IEEE Pacific Visualization Symposium.

[16]  Ivan Viola,et al.  Implicit surfaces for interactive graph based cavity analysis of molecular simulations , 2012, 2012 IEEE Symposium on Biological Data Visualization (BioVis).

[17]  TariniMarco,et al.  Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization , 2006 .

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

[19]  Roman Durikovic,et al.  Implicit Surfaces for Dynamic Growth of Digestive System , 2002, Shape Modeling International.

[20]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

[21]  Alexander A. Pasko,et al.  SARDF: Signed Approximate Real Distance Functions in Heterogeneous Objects Modeling , 2008, Heterogeneous Objects Modelling and Applications.

[22]  Oliver Deussen,et al.  Image enhancement by unsharp masking the depth buffer , 2006, ACM Trans. Graph..

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

[24]  Ronald Fedkiw,et al.  Level set methods and dynamic implicit surfaces , 2002, Applied mathematical sciences.

[25]  Ross T. Whitaker,et al.  Curvature-based transfer functions for direct volume rendering: methods and applications , 2003, IEEE Visualization, 2003. VIS 2003..

[26]  Thomas Ertl,et al.  Interactive Visualization of Molecular Surface Dynamics , 2009, IEEE Transactions on Visualization and Computer Graphics.

[27]  Tim Weyrich,et al.  Eurographics Symposium on Point-based Graphics (2006) Gpu-based Ray-casting of Quadratic Surfaces , 2022 .

[28]  P. J. Narayanan,et al.  Real-Time Ray Tracing of Implicit Surfaces on the GPU , 2010, IEEE Transactions on Visualization and Computer Graphics.

[29]  Shan Zhao,et al.  Minimal molecular surfaces and their applications , 2008, J. Comput. Chem..

[30]  John C. Hart,et al.  Sphere tracing: a geometric method for the antialiased ray tracing of implicit surfaces , 1996, The Visual Computer.

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

[32]  Andrei Sherstyuk,et al.  Kernel functions in convolution surfaces: a comparative analysis , 1999, The Visual Computer.

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

[34]  Barak A. Pearlmutter Fast Exact Multiplication by the Hessian , 1994, Neural Computation.

[35]  Justin Hensley,et al.  Real‐Time Concurrent Linked List Construction on the GPU , 2010, Comput. Graph. Forum.

[36]  Daniel Baum,et al.  Accelerated Visualization of Dynamic Molecular Surfaces , 2010, Comput. Graph. Forum.

[37]  Alexei Sourin,et al.  Function representation in geometric modeling: concepts, implementation and applications , 1995, The Visual Computer.

[38]  Charles T. Loop,et al.  Real-time GPU rendering of piecewise algebraic surfaces , 2006, ACM Trans. Graph..

[39]  Pat Hanrahan,et al.  Ray tracing algebraic surfaces , 1983, SIGGRAPH.

[40]  Klaus Schulten,et al.  Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories , 2012, EuroVis.

[41]  Brian Wyvill,et al.  A Gradient-Based Implicit Blend , 2012 .

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

[43]  Rodrigo de Toledo,et al.  Extending the graphic pipeline with new GPU-accelerated primitives , 2005 .