Anton: A computer dedicated to molecular dynamics simulations.
In biology, many exciting events happen on the millisecond timescale—proteins fold, channels open and close, and enzymes act on their substrates. Atomic-level simulations of this duration are...
Oct, 01, 2008
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
Bridging the gap between surgical simulation and surgical practice
When a knife cuts into an organ, forces push back in ways that mechanical engineers can, to some extent, predict. But other factors are also at play: Ions shift in solution within cells, causing...
Jan, 01, 2010
A model of chromatin explores how it folds and unfolds
To fit an organism’s DNA into a single cell, it has to be tightly compacted, first wound around proteins to form chromatin fibers, then further coiled into chromosomes. Computer simulations by...
Sep, 01, 2005
Modelers are using recent gains in computational power to consider the complex interactions of hundreds or thousands of macromolecules at once--a necessary first step toward whole cell simulation
Molecules in cells behave like people in crowded subway cars. Because they can barely budge or stretch out without bumping into a neighbor, they move more slowly, smush themselves into more compact...
Apr, 01, 2011
Where simulation and theory converge
For decades, scientists have believed that DNA of short lengths (150 base pairs or fewer) behaves as a relatively stiff rod—able to quiver a bit, but rarely forming a circle or tight angle...
Apr, 01, 2007
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
Katherine Holzbaur of Wake Forest University Medical School simulates the biomechanics of the upper limb.
from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Katherine Holzbaur, PhD, assistant professor of biomedical engineering at Wake Forest...
Oct, 01, 2009
Computer simulations suggest both existing theories of membrane fusion are valid
Cell membranes fuse with other membranes to allow material in and out. If incoming material includes invading viruses, that can be bad news for the cells. Until recently, the process of membrane...
Jan, 01, 2007
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