Computing using time steps -- a necessary approximation
Time flows like a continuous, steady river. And it moves forward—never back. These facts create inherent challenges for computer simulations of biological molecules in motion.
It would...
Jun, 19, 2013
Watching changes over time
These days, molecular biologists often gather data over a period of time—observing shifts as they occur inside groups of cells undergoing natural changes. The researchers then face the daunting...
Jun, 01, 2010
The availability of free and open access data, models, and software indisputably accelerates scientific progress. Unfortunately, dissemination necessitates organization, documentation, and quality...
Jan, 01, 2010
Diabetes, breast cancer, multiple sclerosis, Alzheimer’s disease. All are associated with several genes’ alleles interacting in complex ways with one another and the environment. Now,...
Jul, 01, 2007
During the one-hour drama that is human cell division, many genes enter and exit the stage. Until now, researchers did not know the identities of many of these actors, nor understand their various...
Apr, 01, 2011
The Human Genome Project has spurred extraordinary developments in our ability to characterize cellular systems in high-throughput fashion. Polymorphism, methylation, gene expression, and proteomics...
Apr, 01, 2008
The edict that academics must “publish or perish” serves not merely to advance careers, but also to stress the importance of transmitting knowledge from scientist to scientist and...
Jan, 01, 2006
Set objectives and follow through
Having engineered several scientific software applications for public consumption, the authors know from experience that the process offers unique challenges. Typically, the algorithms being...
Oct, 22, 2012
Getting the molecular dynamics car out of the garage
For those who are not practitioners of dynamical simulation methods, such as molecular dynamics (MD), one of the biggest misconceptions relates to time. Specifically, the mismatch between the...
Jun, 19, 2013
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
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