Atomistic simulations have the potential to elucidate the molecular basis of biological processes such as protein misfolding in Alzheimer’s disease or the conformational changes that drive...
Jan, 01, 2010
How Simbios' state-of-the-art software tools are contributing to high-impact biomedical research
Simbios began with a simple idea: that physics-based simulation of biological structures at all scales could benefit from a
unified tool-building effort.
At the same time, the thinking went,...
Oct, 01, 2009
Simulations illuminate the inner workings of blood at multiple levels
Understanding blood flow and coagulation is crucial to treating blood disorders such as hemophilia and thrombosis, and to dealing with diseases such as AIDS, malaria, and diabetes that have...
Jun, 07, 2012
How cell-centered models are adding fundamental insights into our understanding of cell behaviors
The cell is like our financial system: Even if you have a diagram of all the complex interactions going on, you still cannot intuit how the whole system will react when perturbed. Indeed, the cell...
Apr, 01, 2010
Advances in visualization changing work flows for understanding molecular dynamics, tracking cell movements, and designing interventional procedures
The pathway from raw data to valuable visualization of molecules, cells or organs being simulated over time involves several potentially painstaking steps. Typically, researchers must generate a set...
Sep, 02, 2011
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
Profiles in Computer Science Courage Part I: Reflections on the rewards of plunging into biomedicine
Interviews with Leonidas Guibas, Ron Shamir, Michael Black, David Haussler, Daphne Koller, Erin Halperin, Gene Myers, Paul Groth and Bruce Donald
To a computer scientist, the fields of biology and medicine can seem like the vast Pacific Ocean, says Leonidas Guibas, PhD, professor of computer science at Stanford University. “You go to the...
Apr, 01, 2011
The Human Genome Project has spurred extraordinary developments in our ability to characterize cellular systems in high-throughput fashion. Polymorphism, methylation, gene expression, and proteomics...
Apr, 01, 2008
A newly created molecular computer works in human cells and offers the flexibility of a general-purpose circuit. The advance, described in Nature Biotechnology in May, brings closer the eventual...
Oct, 01, 2007
Watching changes over time
These days, molecular biologists often gather data over a period of time—observing shifts as they occur inside groups of cells undergoing natural changes. The researchers then face the daunting...
Jun, 01, 2010