New tool helps scientists understand biological systems
A new computational tool in nanotechnology research has been developed at the University of Illinois for simulating ion transfers in artificial membranes, decreasing time requirements for certain computations from years, in some cases, to days.
ECE Professor Umberto Ravaioli and his students with the Computational Multiscale Nanosystems group at the Beckman Institute for Advanced Science and Technology, have cultivated the technology called BioMOCA. This 3-D coarse-grained ion channel simulator is based on the Boltzmann Transport Monte Carlo methodology.
“Over the last few years, we’ve been more and more interested in the role that biology can play in technology,” Ravaioli said. “We realized that techniques used to solve problems in semiconductor devices could be adapted for biological systems as well.”
Normally, engineers investigate systems from an input-output point of view. That’s what intrigued Ravaioli. “We can look at a biological system and see that it behaves like a device. It may be a protein tube filled with water in a membrane, but to me, it’s no different than a piece of silicon in a semiconductor with electrodes attached to it, as far as charge conduction is concerned. It’s the same type of function, but it’s alive.”
These BioMOCA simulations are an example of the cumulative volume occupied by the trajectories of positively charged potassium (green) and negatively charged chlorine (gray) ions. Due to the strong pore charge the ions follow well separated paths with a corkscrew shape, which is consistent with molecular dynamics results.
Currently, the BioMOCA technology is available free for online computation to researchers and students at www.nanoHUB.org, a Web-based initiative headed by the Network for Computational Nanotechnology (NCN).
“It’s one of our missions to create an infrastructure for computational tools available online,” Ravaioli said. “The BioMOCA code is the flagship for nano-biotechnology efforts. It’s a good prototype to showcase all the different capabilities we’re developing at NCN—to do online computation and online visualization.”
Ravaioli hopes that in the future, tools like this will create an online community for scientists. “We benefit from having different groups interacting with each other,” he said. “If emerging fields are to get into computation and have to wait 10, 20, 30 years to develop their own capabilities from scratch, their development will be much slower. So what we hope to do besides providing new tools for our discipline is to provide a paradigm for new disciplines to evolve.”
Through collaboration with the National Center for Design of Biomimetic Nanoconductors at the Beckman Institute, the ultimate goal is to use BioMOCA as a tool in the hierarchy of several simulation approaches of varying complexity necessary to study nanomedical systems involved with the detection and cure of diseases. This research may one day reach the computational sophistication necessary to simulate in detail the calcium channels that send electrical signals to keep the heart pumping, the membrane channels carrying water to maintain kidney function, or the epithelial mechanisms responsible for cystic fibrosis.
This work is funded by the National Science Foundation and the National Institutes of Health.
Additional images simulated from BioMOCA are featured on the International Science Grid.