AgentCell is the first simulation program to model a biochemical network at the molecular, single cell, and population levels simultaneously.
When a bacterium swims toward food, it follows a chaotic path, alternating between spinning randomly and driving forward, or ‘tumbling’ and ‘running.’ Computer scientists at...
Sep, 01, 2005
For a bacterium to admit certain large nutrients, a steady tug from inside might do the trick, according to computer simulations recently published in Biophysical Journal.
Bacterial membranes...
Oct, 01, 2007
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
The structure of RNA is an important key to its function—including its role in disease. However, the structure of most RNAs is unknown because their extreme flexibility and high charge...
Mar, 01, 2009
Understanding how actin produces force by pushing rather than squeezing
Rocketing within and between human gut cells, Listeria monocytogenes—a motile, foodborne bacterium—leaves a comet-like tail of actin protein behind it and makes us sick. Scientists have...
Jan, 01, 2010
Model fits experimental evidence
In biology textbooks, the carefully rendered cross-section of an E. coli cell often resembles a well-organized and spacious apartment, with everything in its place and ample room for movement. But a...
Jun, 01, 2010
Simulating how cells form patterns.
Normal zebrafish have stripes, but mutant forms may display spots, blotches, or labyrinthine patterns. It’s a scenario that Rudyard Kipling might turn into a wonderful “just-so”...
Jul, 01, 2008
Defining biomedical computation
Looking back at some of the intellectual achievements of the last half century, it is clear that humankind has made tremendous progress in many areas, but arguably none more so than in the two areas...
Jun, 01, 2005
Mouse hair development patterns follow Turing's predictions
In the 1950s, computer science pioneer Alan Turing suggested an elegantly simple mechanism for how biological patterns such as scales, feathers, and hair might form. Now, more than fifty years later...
Apr, 01, 2007
Hi-C technique looks at chromosomes at unprecedented level of resolution
Try taking a human hair as long as Manhattan and cramming it—unsnarled—inside a marble. This is the challenge faced by a 2-meter-long strand of DNA as it folds into its compact array of...
Jan, 01, 2010