'Noise' tunes logic circuit made from virus genes

November 08, 2011

In the world of engineering, "noise" - random fluctuations from environmental sources such as heat - is generally a bad thing. In electronic circuits, it is unavoidable, and as circuits get smaller and smaller, noise has a greater and more detrimental effect on a circuit's performance. Now some scientists are saying: if you can't beat it, use it. Engineers from Arizona State University in Tempe and the Space and Naval Warfare Systems Center (SPAWAR) in San Diego, Calif., are exploiting noise to control the basic element of a computer - a logic gate that can be switched back and forth between two different logic functions, such as AND\OR - using a genetically engineered system derived from virus DNA. In a paper accepted to the AIP's journal Chaos, the team has demonstrated, theoretically, that by exploiting sources of external noise, they can make the network switch between different logic functions in a stable and reliable way.

The scientists focused on a single-gene network in a bacteriophage λ (lamda). The gene they use regulates the production of a particular protein in the virus. Normally, there are biological reactions that regulate the creation and destruction of this protein; upsetting that balance results in a protein concentration that is either too high or too low. The scientists assigned a "1" to one concentration and a "0" to the other. By manipulating the protein concentration, the team could encode the logic gate input values and obtain the desired output values.

Researchers modeled the system as two potential energy "wells" separated by a hump, corresponding to an energy barrier. In the presence of too much noise, the system never relaxes into one of the two wells, making the output unpredictable. Too little noise, on the other hand, does not provide the boost necessary for the system to reach a high enough protein concentration to overcome the energy barrier; in this case, there is also a high probability that the biological logic gate will fail to achieve its predicted computation. But an optimal amount of noise stabilizes the circuit, causing the system to jump into the "correct well" - and stay there. This proof-of-concept work offers the possibility of exploiting noise in biologic circuits instead of regarding it as a laboratory curiosity or a nuisance, the researchers say.
-end-
Article: "Logical stochastic resonance with correlated internal and external noises in a synthetic biological logic block" is accepted for publication in Chaos: An Interdisciplinary Journal of Nonlinear Science.

Authors: Anna Dari (1), Behnam Kia (2), Adi R. Bulsara (3), and William L. Ditto (3).

(1) School of Biological and Health Systems Engineering, Arizona State University, Tempe
(2) School of Electrical, Computer, and Energy Engineering, Arizona State University, Tempe
(3) Space and Naval Warfare Systems Center Pacific (SPAWAR), San Diego, Calif.

American Institute of Physics

Related Protein Articles from Brightsurf:

The protein dress of a neuron
New method marks proteins and reveals the receptors in which neurons are dressed

Memory protein
When UC Santa Barbara materials scientist Omar Saleh and graduate student Ian Morgan sought to understand the mechanical behaviors of disordered proteins in the lab, they expected that after being stretched, one particular model protein would snap back instantaneously, like a rubber band.

Diets high in protein, particularly plant protein, linked to lower risk of death
Diets high in protein, particularly plant protein, are associated with a lower risk of death from any cause, finds an analysis of the latest evidence published by The BMJ today.

A new understanding of protein movement
A team of UD engineers has uncovered the role of surface diffusion in protein transport, which could aid biopharmaceutical processing.

A new biotinylation enzyme for analyzing protein-protein interactions
Proteins play roles by interacting with various other proteins. Therefore, interaction analysis is an indispensable technique for studying the function of proteins.

Substituting the next-best protein
Children born with Duchenne muscular dystrophy have a mutation in the X-chromosome gene that would normally code for dystrophin, a protein that provides structural integrity to skeletal muscles.

A direct protein-to-protein binding couples cell survival to cell proliferation
The regulators of apoptosis watch over cell replication and the decision to enter the cell cycle.

A protein that controls inflammation
A study by the research team of Prof. Geert van Loo (VIB-UGent Center for Inflammation Research) has unraveled a critical molecular mechanism behind autoimmune and inflammatory diseases such as rheumatoid arthritis, Crohn's disease, and psoriasis.

Resurrecting ancient protein partners reveals origin of protein regulation
After reconstructing the ancient forms of two cellular proteins, scientists discovered the earliest known instance of a complex form of protein regulation.

Sensing protein wellbeing
The folding state of the proteins in live cells often reflect the cell's general health.

Read More: Protein News and Protein Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.