I'd like to pay homage to James Burke and his inspiring PBS show Connections by taking you on my own short journey of connected ideas.
The timeless game of chess has long been a grand challenge for artificial intelligence, with the number of possible games being much greater than the number of atoms in the universe. Baron...
Jan, 01, 2006
A new application automates MSM visualization
An unfolded protein can move through thousands of intermediate structures (conformations) before finding its properly folded state. One approach to understanding this process involves simulating a...
Feb, 19, 2013
Exploring the current state of connectomics--in the midst of hype
Connectomics is having a moment. Following on the heels of genomics, proteomics, transcriptomics, metabolomics, and microbiomics, the latest “omic” to seize the spotlight is generating...
Jun, 20, 2013
Having developed detailed and sophisticated models of both E. Coli and human metabolism, researchers can begin to build toward a whole cell model that will be useful for the study of human health and disease.
If biologists really understood the functioning of the genome, they could in principle recreate it in silico. Instead of a choreographed swirl of molecules inside a living cell, electrons...
Oct, 01, 2008
Simulating molecular movement gives a more accurate view of binding sites.
If a picture’s worth a thousand words, then a motion picture, such as that provided by molecular dynamics (MD) simulations, must contain a wealth of information. It’s this potential...
Oct, 01, 2008
In March, Simbios released version 1.0 of the SimTK Simulation toolkit. A cornerstone of this release is Simbody, a new piece of the open-source SimTK Core toolkit for physics-based simulation....
Apr, 01, 2008
A unique opportunity to build both flexibility and high performance into a piece of software.
OpenCL is a cross-platform language for doing general purpose computation on graphics processing units (GPUs) and other massively parallel architectures. One of its most interesting features is the...
Apr, 01, 2010
In the world of molecular dynamics (MD), researchers often need to analyze and extract meaningful results from millions of conformations. Existing software for accomplishing this task focuses on...
Oct, 01, 2009
OpenMM provides a common interface for doing MD simulations on GPUs
Over the last three years, the lab of Vijay Pande, PhD, at Stanford University has optimized their molecular dynamics (MD) algorithms to take advantage of the fast computing that’s possible...
Jul, 01, 2008
Simbody introduces the concept of a “mobilizer,” which directly expresses a part’s movement, however complex, purely in relation to another part
Typically, researchers who simulate life in motion—from particles to people—start by describing the motion of each part of an object independently of the other parts. Additional equations...
Jan, 01, 2008
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