Bacteria Modeled Machines

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Running Head: BACTERIA BASED NANOMACHINES 1

Bacteria Based NanomachinesNano Report: Nanomachines

Richard A. Sitterley

Excelsior CollegeIntroduction to Nanotechnology


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Abstract

This report explores the development of nanomachines that are based on the anatomy of bacteria.

Specific advantages of using the bacterial model are addressed, as well as specific challenges faced by

bacteria-sized objects in the human body. The primary focus of this papers is on bacteria based

nanomachines designed to function inside the human body. Brownian motion is explained, from a

basic standpoint, in its relevance to nanosized objects in an aqueous environment. The flagellum

propulsion system used by bacteria such as E. Coli is also covered, describing its basic components and

their natural bottom-up assembly. A top-down approach to designing Artificial Bacterial Flagella

(ABFs) is introduced as well, noting similarities and differences of these devices to real bacteria.


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Introduction

One approach to designing nanoscale machines is to model their design based on bacterial anatomy.

An initial question that one may ask, considering all of the existing methods of mechanical and robotic

engineering that have developed over time, is Why model nanomachines from bacteria? As an

example of this thought process, one may consider that modern technology has some very effective

designs for submarines. Considering this, one may ask why we do not simply miniaturize this machine

to micron sized proportions. From a basic standpoint, this initially may seem like a good strategy for

building a nanomachine. However, the existing model of a normal submarine simply could not

function at a microscopic size, even if all of its nanosized components were properly designed and

functional. We will return to the submarine comparison later in this report, but for now it will suffice to

say that nanomachines are affected by different forces and principles than larger machines that we are

familiar with. The bacterial model for nanomachines makes sense because, from a certain perspective,

bacteria are basically a functional nanomachine created through natural processes. Bacteria, which

were among the first living oranisms to inhabit the earth, have evolved for millions of years. As such,

they have developed effective means of propulsion, reproduction, and cross communication that has

proven effective for objects of their size. This paper will focus on bacteria-based nanomachines

intended to operate inside the human body.

The Bacteria-Based Approach

Advances in microbiology over the years has allowed a rather thorough understanding of many types

of bacteria. Scientists now have a firm grasp on certain mechanisms used by bacteria to navigate


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through their environment and perform their unique functions. Some common bacteria, such as E.

Coli, are very well understood and documented through extensive research conducted on them for

many years (Jones, 2008). Health related concerns with E. Coli have driven further research on this

bacteria so that we can better prevent and treat E. Coli bacteria infection in humans. However, these

efforts have also provided information that is useful to scientists for designing nanomachines modeled

after these bacteriia. Just as the wagon wheel helped inspire the use of wheels for automobiles, bacteria

are a source of inspiration for designing nanomachines.

To some, it may seem odd to design a machine that will operate within the human body, and model this

machine from bacteria which are generally considered harmful and infectious to humans. To many

scientists, it is the efficiency at which bacteria are able to invade our bodies that makes them the ideal

model for a nanomachine. Although bacteria often serve a harmful purpose in the body, this purpose

can be modified to help us. It is relevant to mention that bacteria are already being used for helpful

purposes in water treatment, solar cells, fuel production, and medicine. Within our own bodies,

bacteria also aid in the digestive process, breaking down minerals, and making essential vitamins. As

nanotechnology continues to advance, scientists hope to design nanomachines that can perform a

variety of helpful functions from inside our bodies.

Identified Challenges

From a nanoscale perspective, oil, water, and other water based fluids should not be considered free-

flowing, as nanoparticles encounter a great deal of high impact collisions and mass obstructions while

immersed in fluids (Jones, 2008). Inside the human body, and more precisely the fluids that flow

through it, is an environment that is dominated by high viscosity. Viscosity of the surrounding medium


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plays a much bigger role for smaller particles than for larger ones, which is also the case for any

conceptual nanomachine we may try to build. Nanoscale objects exhibit a type of constant vibratory

motion, which is considered random in nature, due to the multitude of forces that influence objects of

such small mass and size (Jones). This is commonly known as Brownian motion, and to a nanoparticle,

Brownian motion is every bit as significant as gravity is to larger objects. Brownian motion is

complex, influenced by heat, viscosity, van der Waals forces, and other factors. For the scope of this

report, it is sufficient to state that Brownian motion affects the motion of small particles through

constant random collisions with other particles that make up the surrounding medium (Jones, 2008).

If we are to succeed at creating a machine that is the size of a bacterium, we must understand the

primary forces that affect bacteria and influence their design. In the human body, the fluid mechanics

affecting the propulsion of microbes is extremely different from fluid mechanics that influence the

design of boats, submarines, and other watercraft. If scientists could somehow shrink a submarine and

all of its working components down to the size of a bacterium, it would have no ability to steer or

propel itself through the human body as bacteria can. The body's fluids are generally water-based, and

as such their viscosity is relatively close to that of water. The reason our miniature submarine could

not propel itself is because, at normal scale, the primary force resisting the motion of a submarine is

inertia, while at the microscopic and nanoscopic scale, this primary impeding force is the viscosity of

water (Jones, 2008). Common water propulsion systems like those used to propel a submarine are not

designed to overcome such a highly viscous environment, which is comparable to moving through a

surrounding medium that is thicker than cold honey. The viscosity of the water does not truly change,

of course, but it is important for us to understand that water feels a million times more viscous to

bacteria than it does to us. Over time, bacteria have developed propulsion systems that allow them to

affectively travel through fluids. Careful study of bacteria have helped scientists discover that twisting


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rotary mechanisms are one of the more effective means of propulsion for nanosized objects in

environments of high viscosity (Jones).

Ideal Propulsion System

Scientists have a good understanding of E. Coli, and it is well understood that E. Coli use a type of

rotary motor to propel themselves through fluids (Jones, 2008). This motor, embedded in the cell wall,

is driven by energy obtained from hydrogen ions (Jones). This biochemical rotary motor turns a long,

whip like structure in a spiraling motion that propels the bacteria through fluids (Whitesides, 2001).

This structure, known as a flagellum, is made up of various self-assembled proteins called flagellin

(Applegate, 2010). This entire biochemical motor's structure, consisting of over forty basic

components is, in fact, constructed via self-assembly (Applegate). This is an inspiration to many

scientists in the field, as it demonstrates the potential of self-assembly in creating complex machines.

The most basic components of a flagellum propulsion system, starting at its base, are the stator, rotor,

hook, junction, and filament (Applegate). Although the flagellum structure is quite complex,

understanding these primary components serves as a good starting point when attempting to build a

similar nanoscale device. If scientists can master the basic design of this mechanism, future

developments may lead to even more advanced features based on the bacterial structure. For example,

if the flagellum of a bacterium breaks, it can be regenerated through self assembly of proteins

continuously moving through the central channel of the flagellum (Applegate). As we gain a better

understanding of nanomaterials and self-assembly, we may one day have the ability to design nanoscale

machines with this level of complexity.


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These ABFs are designed with biomedical applications in mind. Although ABFs are at a very early

stage in development, researchers hope to use them in the future to deliver drugs to specific places in

the body, clean plaque from arteries, and manipulate cellular structures in ways that would otherwise be

inaccessible or require dangerously invasive surgery to access. Despite the recent accomplishments in

ABF technology, researchers have a long way to go if they hope to produce nanomachines that are as

sophisticated as E. Coli. First of all, these existing ABFs only consist of two components, compared to

forty or so components that make up a true flagellum propulsion structure. Secondly, the ABF is rigid,

which limits its efficiency. Bacterial flagella are flexible, composed of self assembled proteins with

regenerative capability. Furthermore, bacterial flagella are self-propelled and do not require external

forces to guide them to a target. Perhaps the biggest limitation to producing ABFs that are comparable

to real bacteria is that ABFs are made using top-down methods, while nature creates bacteria through

bottom-up assembly. Improvements in bottom-up nanoscale production methods could pave the way

for more advanced ABFs.

Conclusion

In conclusion, the bacteria provide an effective model for designing nanomachines with an intended

function inside the human body. However, many functions and structural details of bacteria are still

unknown, and as we learn more about bacteria we can also gain useful information that may aid the

design of more functional nanomachines. Top-down production methods are a limiting factor in

producing bacteria based nanomachines. As bottom-up production methods develop, we can expect to

see nanomachines with more complexity on a smaller scale. Even with existing production methods, it

appears that we are very close to seeing nanomachines playing an active role in biomedical

applications, which may dramatically change how we diagnose and treat many diseases.


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Bibliography

Jones, R. (2008). Soft Machines: Nanotechnology and Life. New York, NY: Oxford University Press.

Whitesides, G. (2001). The Once and Future Nanomachine. Scientific American, September 16, 2001.

Retrieved from

http://www.ruf.rice.edu/~rau/phys600/whitesides.htm

Turco, G. (2010). Nanobots Are Coming! Nanobots Are Here! Depth of Processing

Retrieved from

http://depthofprocessing.blogspot.com/2010/09/nanobots-are-coming-nanobots-are-here.html

ETH Zurich (2009). Medical Micro-robots Made As Small As Bacteria. ScienceDaily.

Retrieved from

http://www.sciencedaily.com/releases/2009/04/090418085333.htm

Applegate, K. (2010). Self-Assembly of the Bacterial Flagellum: No Intelligence Required. The

Biologos Forum.

Retrieved from

http://biologos.org/blog/self-assembly-of-the-bacterial-flagellum-no-intelligence-required
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Bacteria Modeled Machines

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