Molecular Electronics
Enma 465
May 14, 2003
By
Charles Brooks
Mark Hanna
Chen Kung
Jia Ni
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Introduction
Molecular electronics is a field emerging around the premise that is a possible to
build individual molecules that can perform functions identical to those of the key
components of today’s microcircuits. Current technologies used in microelectronics are
approaching a limit to become smaller. Thus researchers are trying to develop more
sophisticated forms of microelectronics or maybe “nano”-electronics.
The areas of
interest overlap with biotechnology, which includes DNA and cellular computing.
Why are people so fascinated with molecular electronics and why do researchers
want to develop this form of technology when the modern technology of a siliconintegrated circuit can double its computing speed every 18 to 24 months? Why form
molecular electronics when engineers can now put on a sliver of silicon of just a few
square centimeters some 100 million transistors? The reason behind forming molecular
electronics is because the world has a demand for smaller, faster, and just plain better
technologies than we have. These several million transistors on centimeter square silicon
are still far larger than molecular-scale devices would be. “To put the size differential in
perspective, if the conventional transistor were scaled up so that it occupied the printed
page you are reading, a molecular device would be the period at the end of this sentence.”
(6). Researchers believe in a dozen years, when industry projections suggest that silicon
transistors will have shrunk to about 120 nanometers in length, they will still be more
than 60,000 times larger in area than molecular electronic devices (6).
The most
important aspect of developing molecular electronics is because at some point, chip-
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fabrication specialists will find it economically infeasible to continue scaling down
microelectronics. The phenomena such as stray signals on the chip, the need to dissipate
the heat from so many closely packed devices, and the difficulty of creating the devices
in the first place will halt or severely slow progress when even more transistors are
packed onto a chip. Therefore molecular electronics promises a more economically
feasible way to more capable microelectronics.
Many researchers around the world have started to combine biology and
electronics in the formation of molecular electronics. Recent studies have shown that
individual molecules can conduct and switch electric current and store information. In
July of 1999 an electronic switch consisting of a layer of several million molecules of an
organic substance called rotaxane was developed by researches of Hewlett Packard and
the University of California at Los Angeles. Another major breakthrough is in June
2002, Fuji Xerox biotechnology made a prototype transistor of DNA from salmon sperm.
Researchers successfully passed an electric current through the DNA-transistor (7). This
demonstrates that the chain behaves in a similar fashion to semiconductors. The current
is created by attaching three thin electrodes; two to the ends and the third to the middle of
the DNA chain. During the test runs, the voltage of the middle electrode was altered to
switch OFF and ON the transmission function of the DNA chain. The length of the
transistor is just 10 nm, about one 10,000th the thickness of a human hair (7).
Researchers of Fuji Xerox claims that within 10 years a commercialized super small chip
made with DNA transistors will be developed and a super computer will be built small
enough to fit into the palm of the hand.
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Self-assembly is the autonomous organization of components into patterns or
structures without human intervention. Self-assembling processes are common
throughout nature and technology. They involve components from the molecular scale
(crystals) to the planetary (weather systems) scale and many different kinds of
interactions. The concept of self-assembly is used increasingly in many disciplines, with
a different emphasis in each.
Living cells self assemble. The cell offers countless examples of functional selfassembly that stimulate the design of non-living systems. Self-assembly is one of the few
practical strategies for making ensembles of nanostructures. It will therefore be an
essential part of nanotechnology.
Manufacturing electronics will benefit from
applications of self-assembly. (4)
DNA in molecular electronics is a promising area because researchers believe that
it can achieve super-high density memory and high sensitive detection technology. DNA
has be studied and tested for decades within biology, thus researchers have past
experience to aid in understanding the behavior of DNA’s structure and performance in
new applications and environments.
Cellular computing is another promising area for the future of microelectronics.
Researchers know well that cells have much, with respect to function, in common with
machines and computers while also being very compact and self-assembling. If the
ability to harness the computing power of cells is gained, this also may have the potential
to break the barrier of making smaller computing technologies.
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Self-Assembly in Electronics
Self-assembly is the autonomous organization of components into patterns or
structures without human intervention. Self-assembling processes are common
throughout nature and technology. They involve components from the molecular scale
(crystals) to the planetary (weather systems) scale and many different kinds of
interactions. The concept of self-assembly is used increasingly in many disciplines, with
a different emphasis in each.
Living cells self assemble. The cell offers countless examples of functional selfassembly that stimulate the design of non-living systems. Self-assembly is one of the few
practical strategies for making ensembles of nanostructures. It will therefore be an
essential part of nanotechnology.
Manufacturing electronics will benefit from
applications of self assembly. (4)
Types of Self-Assembly
There are different kinds of self assembly: static and dynamic. Static selfassembly involves systems that are at global or local equilibrium and do not dissipate
energy. For example, molecular crystals are formed by static self-assembly; so are most
folded, globular proteins. In static self-assembly, formation of the ordered structure may
require energy but once it is formed, it is stable.
In dynamic self-assembly the interactions responsible for the formation of
structures or patterns between components only occur if the system is dissipating energy.
The patterns formed by competition between reaction and diffusion in oscillating
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chemical reactions are simple examples; biological cells are much more complex ones.
The study of dynamic self-assembly is in its infancy.
Although much of current understanding of self-assembly comes from the
examination of static systems, the greatest challenges, and opportunities, lie in studying
dynamic systems. (4)
Present and Future Applications
Self-assembly is already a widely applied strategy in synthesis and fabrication.
Can one predict areas where self assembly will be used in the future? Perhaps, these are
possibilities:

Crystallization at All Scales. The formation of regular, crystalline lattices is a
fundamental process in self-assembly, and is a method to convert ;100-nm
particles into photonic materials; using micrometer-scale components may lead to
new routes to microelectronic devices (6).

Robotics and Manufacturing. Robots are indispensable to current systems for
manufacturing.
As components become smaller, following the trend in
miniaturization through microfabrication to nanofabrication, conventional robotic
methods will fail because of the difficulty in building robots that can
economically manipulate component only micrometers in size. Self-assembly
offers a new approach to the assembly of parts with nano and micrometer
dimensions.

Nanoscience and Technology. There are two approaches to the fabrication of
nanosystems: bottom-up and top-down. Chemical synthesis is developing a range
of methods for making nanostructures—colloids, nanotubes, and wires—to use in
bottom-up approaches. Self-assembly offers a route for assembling these
components into larger, functional ensembles.

Microelectronics. The fabrication of microelectronic devices is based almost
entirely on photolithography, an intrinsically two-dimensional technology.
Another computer of great interest—the brain—is three-dimensional. There are
no clear strategic paths from two-dimensional to three-dimensional technology
(and, of course, no absolute certainty that three-dimensional microelectronic
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devices will be useful, al-though the brain is certainly a three-dimensional system,
and three dimensionality offers, in principle, the advantages of short interconnects
and efficient use of volume). Self-assembly offers a possible route to threedimensional microsystems. (4)
Forming 3-D Electrical Networks by Self Assembly
In one study, self-assembly of millimeter-scale polyhedra, with surfaces patterned
with solder dots, wires, and light-emitting diodes, generated electrically functional, threedimensional networks. The patterns of dots and wires controlled the structure of the
networks formed; both parallel and serial connections were generated.
Most fabrication of microelectronic devices is carried out by photolithography
and is intrinsically two-dimensional (2D). The 3D interconnections required in current
devices are fabricated by the superposition of stacked, parallel planes and by their
connection using perpendicular vias. This group demonstrates self-assembly as a strategy
to form interconnections between electronic devices and prefabricated circuits, and to
form 3D electrical circuits.
Previous uses of self-assembly to fabricate electronic devices include shapedirected fluidic self-assembly of light-emitting diodes (LEDs) on silicon substrates and
coplanar integration of segmented integrated circuit (IC) devices into 2D “superchips”
using capillary forces at the surface of a flotation liquid. This group demonstrates the
formation of two classes of 3D electrical networks—parallel and serial— by selfassembly, as an early step toward a strategy for fabricating 3D microelectronic devices.
The basic unit in these assemblies is a polyhedron [a truncated
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octahedron ( TO)], on whose faces electrical circuits are printed. In the present
demonstrations, these circuits include LEDs to demonstrate electrical connectivity and
trace the networks; in the future, they will include devices with more complex
functionality (e.g., processors). The LEDs are wired to patterns of solder dots on adjacent
faces of the polyhedron. The TOs are suspended in an approximately isodense liquid at a
temperature above the melting point of the solder (m.p. ; 47°C), and allowed to tumble
gently into contact with one another. The drops of molten solder fuse, and the
minimization of their interfacial free energy generates the forces that assemble the TOs
into regular structures. Processes based on capillary interactions between solder drops
have been used previously to assemble electronic and patterned polyhedra. Their selfassembly into 3D structures include electrical networks (5).
Although self-assembly originated in the study of molecules, it is a strategy that
is, in principle, applicable at all scales. We believe that some of the self-assembling
systems that are most amenable to fundamental study, and that are also most readily
applied, may involve components that are larger than molecules, interacting by forces
that have not commonly been used in synthesis or fabrication.
Self-assembly thus
provides one solution to the fabrication of ordered aggregates from components with
sizes from nanometers to micrometers; these components fall awkwardly between the
sizes that can be manipulated by chemistry and those that can be manipulated by
conventional manufacturing. This range of sizes will be important for the development of
nanotechnology (and the expansion of microtechnology into areas other than
microelectronics). It will also be an area in which understanding biological structures and
processes is very important.
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DNA
Because of its well-known behavior and its electrical properties, DNA is a perfect
candidate to be used in molecular electronics. DNA has been the object of intense
research mainly due to its importance in biology. It is absolutely critical to the majority
of known life forms. It has very specific self-assembly properties and may be highly
selectively processed. DNA also functions at room temperatures and is highly stable.
Furthermore, the processing of DNA has been occurring excessively through the
biological sciences for many years. More recently, the electrical properties of DNA have
been studied to determine ways to fashion circuit element from it.
Deoxyribonucleic acid, referred to as DNA, is composed of two chains of
nucleotides.
These chains exist in a double helical structure with hydrogen bonds
connecting the nucleotides of one strand to the other. There are four base pairs that make
up the nucleotides. These four are adenine, thymine, cytosine, and guanine. Each base
has its compliment. Adenine is compliment to thymine as is cytosine to guanine. These
nucleotides are able to be in any sequence. This gives DNA the ability to store data, such
as hereditary information.
So far DNA as been the most successful biomimetic component used for selfassembly (1). DNA is an extremely fine model for self-assembly. Complimentary DNA
chains have a very strong affinity to each other and for a predictable structure when
associated (2).
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There exists the possibility of using the electrical properties of the chemical bonds
in DNA to use the molecule as a single electron transistor. Phosphorus bridges connect
the nucleotides along a chain. These phosphorus bridges form tunnel junctions for a net
charge. The single electron in the π bond that forms between the neighboring oxygens
and the phosphorus resembles an electron in a double well potential. When another
electron approaches this situation, it is unable to occupy the same lowest energy level due
to the Pauli exclusion principle. This electron is able to tunnel through the junction
because the energy barrier is low and narrow (3).
Figure 1: Schematic of two DNA nucleotides connected with a phosphorus
bridge. Dark circles are carbon atoms, white oxygen atoms (3).
It is also possible to selectively process DNA with the use of enzymes.
Restriction enzymes are able to mask specific segments of DNA. Researchers possess
the ability to coat DNA strands with metal. DNA bridges were constructed between two
gold electrodes spaced about 15 micrometers apart.
Specific sequences of DNA were
prepared with disulfide ends to attach to the gold electrodes. The DNA was processed
(including hybridization) using enzymes (T4 polynucleotide kinse and T4 ligase) and
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various chemicals. After the formation of the DNA bridge, the bridge is coated in silver
ions by ion exchange in a silver nitrate solution (8).
In order to form a single electron tunneling transistor two strands of DNA must be
used, a main strand and a gate strand. The end base of the gate strand is attached to its
compliment in the middle of the main strand. They are coated in metal except for the
connection between the main strand and gate strand and the neighboring phosphorus
bridges. The metallic coated end of the gate strand should be attached to a gate electrode
and the ends of the main strand should be connected to two other electrodes (3). The
creation of the interconnects pose a major challenge. This proposed DNA structure could
function as a single electron tunneling transistor. Figure 2 shows a schematic diagram of
the DNA transistor and its traditional equivalent.
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Figure 2: Schematic of DNA Set and equivalent circuit. The shaded rectangles
represent single stranded DNA. The Ps are bridging phosphorus bonds and the
white square is a base paired to its compliment through the H bond. Vg is gate
voltage in both situations (3).
The primary challenge faced by the completed design and mass production of the
DNA transistor is how to place the DNA transistors on a chip and connect all the proper
electrodes. This is one of the major limiting factors in the example mentioned earlier
with the DNA transistor created by Fuji Xerox (7).
The challenge of connecting the electrodes to the DNA chains may be overcome
by using the selectivity in the DNA chains and DNA-functionalized nanoparticles. Other
researchers have self assembled gold nanometer-sized particles by coating the particles
with specific DNA sequences (9). Figure 3 shows a larger gold particle connected to
many smaller gold particles using DNA as the connector.
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Figure 3: 8 and 31 nm gold nanoparticles connected using DNA (9)
Perhaps it is possible to use this technique to connect DNA transistors to each
other in desired arrangements creating a precise 3-d arrangement of transistors and
connectors.
Cellular Computing
One of the important divisions of molecular electronics is cellular computing.
Research into cellular computing is driven by the need for computer technology to
continue to get smaller. This research attempts to find an answer to the problem of what
happens when we reach the minimum size attainable with silicon technology. As with all
aspects of molecular electronics, cellular computing looks to biology to try and find some
of the answers about fabricating nanometer scale components.
Interest in cellular computing began in 1994, when Adleman demonstrated that
DNA molecules could be manipulated to perform a specific kind of mathematical
computation. This breakthrough stimulated interest in the possibility of fabricating a
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DNA based molecular computer. The challenge is to use the cells computing power to do
what we want it to do, instead of what it does naturally.
There are two types of molecular computers, true molecular computers, and
quasi-molecular computers. True molecular computers have completely self-contained
processes.
All of their computational operations, such as inputs, outputs, and state
transitions, are controlled by internally driven chemical reactions and molecular motors.
These true molecular computers can carry out their operations with no external support.
The only known example of a true molecular computer is the DNA based living cell (10).
Living cells can be thought of as true molecular computers because they have all
the components that make up this type of computer. Cells have inputs provided by
receptors, which recognize specific molecular ligands and input their information. The
internal state of the cell is determined by Intercellular Dissipative Structures, or IDS’s
(11). Examples of IDS’s are phosphoproteins, gradients of metabolite concentrations,
and mechanical stresses inside the cell. All of these entities contribute to determine the
internal state of the cell.
The primary goal of cellular computing is to use artificial true molecular
computers as the basis for a new computer technology. This is very difficult, because
true molecular computers do what they are programmed to do by their DNA. They are
not easily manipulated into producing a different output. On the other hand, the quasimolecular computer is much easier to manipulate, and serves as a better basis for
research. The quasi-molecular computer depends on getting most of its input and output
operations, and its state transitions from an outside source (10). In this case, the outside
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source would be a human, or robot, which helps the quasi-molecular computer do the
things it, can’t do on its own.
Adleman’s DNA based computing system is an example of a quasi-molecular
computer. In his experiment, he manipulated about 1014 molecules of 20-mer DNA to get
it to perform the mathematical calculation (12).
This system is a quasi-molecular
computer because he had to synthesize the 20-mer DNA sequences himself. He also ran
splicing reactions, and separated and purified the DNA products using conventional
molecular biological techniques. Without Adleman’s contribution to this process, the
quasi-molecular computer would not function at all. This introduces the secondary goal
of cellular computing; to fabricate more efficient quasi-molecular computers that can
carry out a major part of the computation with a minimal amount of assistance.
The idea of cellular computing depends on using biological components to
replace the function of similar man made ones. To understand how this can be done, it is
important to understand the biology of a cell, and how it functions as a molecular
computer. Furthermore, it is important to find which connections can be made between
molecular components and modern computers.
Cells carry current in the form of
electrons, in chemicals, while human-made computers use wires and electron fluxes for
this purpose. Cells use enzymes to turn on and off chemical reactions, as human made
computers use transistors to switch on or off the flow of electrons.
Chemicals also provide the energy source for cells, similar to the external power
supply for human-made computers. For information storage, cells use both sequence
patterns of biopolymers, and dissipative concentration gradients, or IDS’s (10), while
human-made computers use capacitors. Computational programs are stored in DNA in
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cells, in the form of lexical, syntactic and semantic genes, compared to the human-made
computer’s software.
Te fact that cells and human-made computers have these components that do the
same functions shows that they are fairly similar. It is these similarities that cause cells
to be considered true molecular computers.
Ji proposes three characteristics that
characterize the cell as a true molecular computer. The first, Molecularity, means that all
of the parts of the cell responsible for input, output, and state transitions are thermally
fluctuating molecules.
These processes within the cell are dependent on thermal
fluctuations to drive them (10).
The second is the existence of an internal energy source. All of the molecular
motors within the cell are driven by the energy stored within the motors themselves in the
form of conformons. Conformons are conformational strains in chains of DNA, which
cause the chains charge balance to be upset, and a small voltage to be developed. The
cell uses this relationship between mechanical and electrical energy as a form of energy
storage. Conformons have been shown to store 500 – 2500 Kcal/mol of energy in DNA,
as well as 40- 200 bits of information (13).
The third characteristic is computability. This is the capacity of the cell to
process input information and perform computations based on the information. In cells
this information usually comes from a set of instructions stored in the DNA. These three
characteristics of true molecular computers depend on the existence of three other things
to function. Intracellular Dissipative Structures, or IDS’s are necessary to connect the
information stored in biopolymers to the cell. Conformons are necessary to store the
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energy that drives the cells molecular motors. Finally, the cell needs a language to allow
cells to communicate with each other and make computations as a group (10).
One of the hardest things for humans to emulate using computers is the precision
of biological processes. This makes progress in cellular computing extremely difficult.
If this goal can be achieved, and we learn how to fabricate and use cells as true cellular
computers, a whole new dimension of computing is possible. Even though progress in
this field is slow, the potential is there for this research to lead to the development of an
entirely new computer technology.
Molecular electronics are the focus point of researchers today on a better and
smaller microelectronics.
DNA and cellular computing are capable of performing
functions identical to those of the key components of today’s microcircuits. The major
obstacle to overcome by researchers is how to assemble DNA and cells to perform the
functions needed in circuits.
Self-assembly is a major key to DNA production in
microelectronics and researchers have to figure out how to make use of the different
types of self-assembly to further develop a better microelectronics. Cellular computing is
another form of future microelectronics to make circuits smaller and contains more
transistors. Therefore the key to future applications of microelectronics is molecular
electronics.
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Adleman, L.M. “Molecular Computation of Solutions to Combinatorial
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