Computing airflow dynamics
We can’t see them, but tiny particles—dust, pollen, microbes, and the like—swirl around us in complicated, turbulent pathways. New numerical simulations suggest that, at least in...
Jun, 01, 2010
AMOEBA's polarizable force field now integrated with OpenMM
Many have long hoped that molecular dynamics calculations—the computation of how molecules move and interact with other molecules—would revolutionize the world of synthetic chemistry,...
Sep, 01, 2011
While science educators actively debate the relative merits of teaching natural science in an integrated fashion, some authors are writing texts that will make it happen. Philip Nelson’s book,...
Jun, 01, 2005
Cancer proteins highly interactive
New research suggests that cancer proteins, like influential people, have the most connections. These results, from an extensive study of how human proteins interact with one another, could help...
Jan, 01, 2007
Helping newcomers understand the lay of the land
As a program manager in biomedical computing and computational biology at the National Institutes of Health, I field many questions, particularly from new investigators. They ask questions like:...
Apr, 01, 2010
New approaches extend multiscale models to represent cellular mesoscales and bridge from molecular to cellular models
In an era of increasingly comprehensive molecular characterizations of living systems, computation has emerged as a key technology to facilitate integrative understanding of biological mechanisms....
Feb, 19, 2013
Biologists have long taken gas exchange for granted, assuming that gases simply seep through the cell’s lipid membrane. Since 1998, however, evidence has been building that gases might also be...
Jul, 01, 2007
The antiviral drugs Tamiflu and Relenza target a key flu protein—neuraminidase—preventing it from doing its job of releasing virus particles from infected cells into the body. The type of...
Jul, 01, 2009
Now, with just a few mouse clicks, anyone with a computer and an Internet connection can create graphic images of RNA molecules (using ToRNADo) or generate the ion environments that surround these...
Jan, 01, 2007
Affinity propagation clusters lots of different kinds of data better and faster than other methods
Starting in preschool we all learn how to get organized. Typically, we start with pre-determined categories (dolls, trains, blocks); pre-set ideas about what belongs in each category (Barbie: doll;...
Jul, 01, 2007