John E. Stone, M.S.
John E. Stone, M.S. is
Senior Research Programmer at the
Theoretical and Computational
Biophysics Group at the
Beckman Institute for Advanced Science and
Technology at the University of Illinois.
He is also cofounder of the
University of Missouri-Rolla
Solar Car Team.
John authored Random Numbers, Efficiency, and Other Things, Real-Time GPU Spheres, and The Ups and Downs of Multithreaded Ray Tracing and Optimization, and coauthored A System for Interactive Molecular Dynamics Simulation and Accelerating Software-based MPEG Encoding Using the VIS Instruction Set.
John is the lead developer of VMD, a high performance molecular visualization tool used by biophysicists and structural biologists all over the world. VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
He is also working on a Tachyon Parallel / Multiprocessor Ray Tracing System. He’s been developing a parallel ray tracing library named Tachyon, for use on distributed memory parallel computers, shared memory computers, and clusters of workstations. Tachyon supports MPI for distributed memory parallel computers, threads for shared memory machines, and can support both simultaneously for clusters of shared memory machines. Tachyon has been selected for inclusion in the SPEC MPI2007 benchmark suite. Tachyon supports the typical ray tracer features, most of the common geometric primitives, shading and texturing modes, etc. It also supports less common features such as HDR image output, ambient occlusion lighting, and support for various triangle mesh and volumetric texture formats beneficial for molecular visualization (e.g. rendering VMD scenes).
John earned his Bachelor of Science in Computer Science and his Master of Science at the University of Missouri-Rolla.