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Date: 19 December 2014
New tool for biological systems  


Topic Name: New tool for biological systems
Category: Nanobiotechnology
    
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Research persons: Umberto Ravaioli

Location: 3255 Beckman Institute, MC-251,405 N. Mathews,Urbana, Illinois 61801, United States

Details

New tool for 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.”
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.
Additional images simulated from BioMOCA are featured on the

International Science Grid
.
About Researchers:
Umberto Ravaioli
Professor
3255 Beckman Institute, MC-251
405 N. Mathews
Urbana, Illinois 61801
217-333-2280
Ph.D. - Electrical Engineering, Arizona State University 1986

Research Interests:
Monte Carlo simulation of high speed electronic devices
Numerical methods for semiconductor device simulation
Quantum devices
Supercomputation and Visualization
Reliability of MOS Devices
Charge Transport in Biological Systems (Ionic Channels)
Properties of Carbon Nanotubes
 
Funded:
This work is funded by the National Science
Foundation
and the National Institutes of
Health.


In The Images-
Researchers Umberto Ravaioli & 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.


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