What can open-source software do for biomedical research? Based on our experience at the National Alliance for Medical Image Computing (NA-MIC), we believe that open source software can be used very...
Mar, 01, 2009
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
In science, there is a need to balance research in domain sciences and the infrastructure to support that research. Basic research mediated through peer review is understood to produce useful...
Jan, 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
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
To understand biology—and provide appropriate medical care—scientists need to understand interactions across multiple scales. Hence the Physiome.
This is the reality of human biology: events span a 109 range in lengthscale (molecular to organismal) and a 1014 range in timescale (molecular movement to years). To understand this biology—...
Jun, 01, 2010
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
A computational model of alpha-synuclein as it aggregates
Under a microscope, the curious protein clumps that dot the brains of Parkinson’s patients stick out like the culprits they are. But no one has yet caught the protein—alpha-synuclein...
Jul, 01, 2007
Like humans, cells are affected by their physical environment, their neighbors, the context in which they exist. Much research has focused on the chemical signals that control cell behavior. But...
Sep, 01, 2011
Despite their identical genomes, cells in the body develop distinct personalities—become neurons or liver cells, for instance—due to differences in gene expression. The mechanism that...
Apr, 01, 2009
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