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Simulating Crowded Cytoplasm

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...
May, 31, 2010
Computing Has Changed Biology Forever

And people are starting to notice

In 1991, a prescient editorial in Nature by Harvard’s Walter Gilbert, PhD, (“Towards a paradigm shift in biology”) included these observations on the utility and impact of computing...
Mar, 31, 2006
Unlocking the Genetics of Complex Diseases: GWAS and Beyond

Building upon the clues provided by GWAS to gain new insights

Some diseases, such as cystic fibrosis, have a beautiful simplicity: A genetic misspelling cripples a protein, which profoundly and predictably alters the body. Find the faulty gene for these so-...
Jan, 12, 2015
Where Tuberculosis Meets Computation: 10 Points of Intersection

Computation offers a window into a disease often described as a black box

The growing threats of multi-drug resistant (MDR) and extensively drug resistant (XDR) tuberculosis (TB) are spurring worldwide interest in faster and more innovative research approaches, such as...
Jun, 05, 2012
Watching Blood Vessels Grow and Shrink

2-D simulation shows angiogenesis as it happens

Microscopic capillaries grow on demand, snaking toward hungry cells needing their blood supply. Understanding how to control this process could help scientists promote wound healing or halt cancer in...
Dec, 31, 2006
Modeling A Gene Therapy Delivery Vehicle
Gene therapy to correct inherited illnesses hinges on successful delivery of DNA into a person’s cells. Most gene therapists work with viruses to ferry their DNA cargo. Yet the body tends to...
Sep, 30, 2009
Big Data Analytics In Biomedical Research

Can the complexities of biology be boiled down to Amazon.com-style recommendations?  The examples here suggest possible pathways to an intelligent healthcare system with big data at its core.

“We have recommendations for you,” announces the website Amazon.com each time a customer signs in.   This mega-retailer analyzes billions of customers’ purchases—nearly $...
Jan, 01, 2012
A Boost for MD Sampling

Simbios researchers meld a powerful combo of tools

In 2011, Simbios researchers reported achieving greater speed and accuracy in molecular dynamics simulations by tying the polarizable force fields from AMOEBA (Atomic Multipole Optimized Energetics...
Mar, 01, 2014
Putting Exacycles and Markov State Models to Work on GPCRs

The yield: an unprecedented and insightful millisecond simulation

Despite being well-studied, much remains unknown about the dynamics of G-protein coupled receptors (GPCRs), molecules that are prominent drug targets. Recent work published in the journal Nature...
aMD, AMOEBA, Markov State Models, OpenMM
Mar, 01, 2014
LIFE IS CROWDED: Modeling the Cell's Interior

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...
crowding, macromolecule, molecular dynamics
Mar, 31, 2011
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