Using computational models, researchers are gaining traction toward understanding what makes a stem cell a stem cell; how gene expression drives stem cell differentiation; why studying stem cell heterogeneity is important; and, ultimately, how stem cells control their fate.
To the casual observer, stem cells offer the almost magical promise of—Voila!—turning into exactly the kind of cell needed to repair an injured spinal cord or replace a damaged organ. And...
Apr, 01, 2010
CompuCell-3D models behaviors rather than genes
Researchers have successfully simulated how growing blood vessels affect the sizes and shapes of tumors using a 3-D model based solely on how cells behave—without reference to intracellular...
Jan, 01, 2010
A virtual lab rat; simulated DNA; an artificial pancreas; & integrating mental health data
Several biomedical computing projects received multi-million dollar funding in the fall of 2011, including efforts to: simulate the cardiac physiology of the rat; build a state-of-the-art DNA...
Jan, 02, 2012
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
Researchers can now create musculoskeletal models and simulations on an open source platform. In August, Simbios researchers released OpenSim 1.0. This freely available software can, in about 20...
Oct, 01, 2007
Filling a gap in single molecule experimental work
Scientists sometimes find themselves up to their elbows in Styrofoam balls, pipe cleaners, and metal rods as they try to build models of the molecules they are studying. Now, they can exchange all...
Apr, 01, 2010
Hidden Markov models estimate DNA loop kinetics
The hidden Markov model—a statistical model used for decades in fields as diverse as speech recognition and climatology—has received an update and a new application. Researchers at the...
Apr, 01, 2007
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 the past, many biomechanical models of gait have omitted the arms. But as such models strive for greater realism, it has become more important to account for secondary movement by the arms.
Most people swing their arms when they walk. Indeed, like several characters in a classic Seinfeld episode, we’re surprised when they don’t. Yet we don’t really need to swing our...
Jul, 01, 2008
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