Bacterial Foraging Optimization

Bacterial Foraging Optimization

Kevin M. Passino (The Ohio State University, USA)
Copyright: © 2012 |Pages: 16
DOI: 10.4018/978-1-4666-1592-2.ch013
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Abstract

The bacterial foraging optimization (BFO) algorithm mimics how bacteria forage over a landscape of nutrients to perform parallel nongradient optimization. In this article, the author provides a tutorial on BFO, including an overview of the biology of bacterial foraging and the pseudo-code that models this process. The algorithms features are briefly compared to those in genetic algorithms, other bio-inspired methods, and nongradient optimization. The applications and future directions of BFO are also presented.
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1 Introduction: Bacterial Foraging: E. Coli

The E. coli bacterium has a plasma membrane, cell wall, and capsule that contain, for instance, the cytoplasm and nucleoid. The pili (singular, pilus) are used for a type of gene transfer to other E. coli bacteria, and flagella (singular, flagellum) are used for locomotion. The cell is about in diameter, and in length. The E. coli cell only weighs about picogram, and is composed of about water. Salmonella typhimurium is a similar type of bacterium.

The E. coli bacterium is probably the best understood microorganism. Its entire genome has been sequenced; it contains 4,639,221 of the A, C, G, and T “letters”—adenosine, cytosine, guanine, and thymine—arranged into a total of 4,288 genes. When E. coli grows, it gets longer, then divides in the middle into two “daughters.” Given sufficient food and held at the temperature of the human gut (one place where they live) of deg. C, E. coli can synthesize and replicate everything it needs to make a copy of itself in about min.; hence, growth of a population of bacteria is exponential with a relatively short “time to double” the population size. For instance, following (Berg, 2000), if at noon today you start with one cell and sufficient food, by noon tomorrow there will be cells, which is enough to pack a cube meters on one side. (It should be clear that with enough food, at this reproduction rate, they could quickly cover the entire earth with a knee-deep layer!)

The E. coli bacterium has a control system that enables it to search for food and try to avoid noxious substances (the resulting motions are called “taxes”). For instance, it swims away from alkaline and acidic environments, and towards more neutral ones. To explain the motile behavior of E. coli bacteria, we will explain its actuator (the flagella), “decision-making,” sensors, and closed-loop behavior (i.e., how it moves in various environments—its “motile behavior”). You will see that E. coli perform a type of “saltatory search.”

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