Molecular electronics
For quantum mechanical study of the electrondistribution in a molecule, see stereoelectronics.
Molecular electronics is the study and application of molecular building blocks for the fabrication of electronic components. It is an interdisciplinary area that spans physics,chemistry, and materials science. The unifying feature is use of molecular building blocks to fabricate electronic components. Due to the prospect of size reduction in electronics offered by molecular-level control of properties, molecular electronics has generated much excitement. It provides a potential means to extend Moore's Lawbeyond the foreseen limits of small-scale conventional silicon integrated circuits.[1]
Molecular scale electronics
Molecular scale electronics, also called single molecule electronics, is a branch ofnanotechnology that uses single molecules, or nanoscale collections of single molecules, as electronic components. Because single molecules constitute the smallest stable structures possible, this miniaturization is the ultimate goal for shrinking electrical circuits.
Conventional electronic devices are traditionally made from bulk materials. Bulk methods have inherent limits, and are growing increasingly demanding and costly. Thus, the idea was born that the components could instead be built up atom by atom in a chemistry lab (bottom up) as opposed to carving them out of bulk material (top down). In single molecule electronics, the bulk material is replaced by single molecules. That is, instead of creating structures by removing or applying material after a pattern scaffold, the atoms are put together in a chemistry lab. The molecules used have properties that resemble traditional electronic components such as a wire, transistor, or rectifier.
Single molecule electronics is an emerging field, and entire electronic circuits consisting exclusively of molecular sized compounds are still very far from being realized. However, the continuous demand for more computing power, together with the inherent limits of the present day lithographic methods make the transition seem unavoidable. Currently, the focus is on discovering molecules with interesting properties and on finding ways to obtain reliable and reproducible contacts between the molecular components and the bulk material of the electrodes.
Molecular electronics operates in thequantum realm of distances less than 100 nanometers. Miniaturization down to single molecules brings the scale down to a regime where quantum mechanics effects are important. In contrast to the case in conventional electronic components, whereelectrons can be filled in or drawn out more or less like a continuous flow of electric charge, the transfer of a single electron alters the system significantly. The significant amount of energy due to charging has to be taken into account when making calculations about the electronic properties of the setup and is highly sensitive to distances to conducting surfaces nearby.
Graphical representation of a rotaxane, useful as a molecular switch.
One of the biggest problems with measuring on single molecules is to establish reproducible electrical contact with only one molecule and doing so without shortcutting the electrodes. Because the currentphotolithographic technology is unable to produce electrode gaps small enough to contact both ends of the molecules tested (in the order of nanometers) alternative strategies are put into use. These include molecular-sized gaps called break junctions, in which a thin electrode is stretched until it breaks. Another method is to use the tip of ascanning tunneling microscope (STM) to contact molecules adhered at the other end to a metal substrate.[2] Another popular way to anchor molecules to the electrodes is to make use of sulfur's high chemical affinity togold; though useful, the anchoring is non-specific and thus anchors the molecules randomly to all gold surfaces, and the contact resistance is highly dependent on the precise atomic geometry around the site of anchoring and thereby inherently compromises the reproducibility of the connection. To circumvent the latter issue, experiments have shown that fullerenes could be a good candidate for use instead of sulfur because of the large conjugated π-system that can electrically contact many more atoms at once than a single atom of sulfur.[3] The shift from metal electrodes to semiconductor electrodes allows for more tailored properties and thus for more interesting applications. There are some concepts for contacting organic molecules using semiconductor-only electrodes, for example by using indium arsenide nanowires with an embedded segment of the wider bandgap materialindium phosphide used as an electronic barrier to be bridged by molecules.[4]
One of the biggest hindrances for single molecule electronics to be commercially exploited is the lack of means to connect a molecular sized circuit to bulk electrodes in a way that gives reproducible results. Also problematic is that some measurements on single molecules are done at cryogenic temperatures, near absolute zero, which is very energy consuming.
Molecular materials for electronics
Further information: Conductive polymer and Organic electronics
Chemical structures of some conductive polymers. From top left clockwise: polyacetylene; polyphenylene vinylene; polypyrrole (X = NH) and polythiophene (X = S); and polyaniline (X = NH/N) and polyphenylene sulfide (X = S).
The biggest advantage of conductive polymers is their processability, mainly bydispersion. Conductive polymers are notplastics, i.e., they are not thermoformable, yet they are organic polymers, like (insulating) polymers. They can offer high electrical conductivity but have different mechanical properties than other commercially used polymers. The electrical properties can be fine-tuned using the methods of organic synthesis[5] and of advanced dispersion.[6]
The linear-backbone polymers such aspolyacetylene, polypyrrole, and polyaniline are the main classes of conductive polymers. Poly(3-alkylthiophenes) are the archetypical materials for solar cells and transistors.[5]
Conducting polymers have backbones of contiguous sp2 hybridized carbon centers. One valence electron on each center resides in a pz orbital, which is orthogonal to the other three sigma-bonds. The electrons in these delocalized orbitals have high mobility when the material is doped by oxidation, which removes some of these delocalized electrons. Thus the conjugated p-orbitals form a one-dimensional electronic band, and the electrons within this band become mobile when it is emptied partly. Despite intensive research, the relationship between morphology, chain structure, and conductivity is poorly understood yet.[7]
Due to their poor processability, conductive polymers have few large-scale applications. They have some promise in antistatic materials[5] and have been built into commercial displays and batteries, but have had limits due to the production costs, material inconsistencies, toxicity, poor solubility in solvents, and inability to directly melt process. Nevertheless, conducting polymers are rapidly gaining attraction in new uses with increasingly processable materials with better electrical and physical properties and lower costs. With the availability of stable and reproducible dispersions, poly(3,4-ethylenedioxythiophene) (PEDOT) andpolyaniline have gained some large scale applications. While PEDOT is mainly used in antistatic applications and as a transparent conductive layer in the form of PEDOT andpolystyrene sulfonic acid (PSS, mixed form: PEDOT:PSS) dispersions, polyaniline is widely used to make printed circuit boards, in the final finish, to protect copper from corrosion and preventing its solderability.[6] Newer nanostructured forms of conducting polymers provide fresh impetus to this field, with their higher surface area and better dispersability.
Human biocomputer
The term human biocomputer, coined byJohn C. Lilly, refers to the "hardware" of thehuman anatomy. This would include thebrain, internal organs, and other human organ systems such as cardiovascular, digestive,endocrine, immune, integumentary,lymphatic, muscular, nervous, reproductive,respiratory, skeletal, and urinary systems. The biocomputer has stored program properties, and self-metaprogramming properties, with limits determinable and to be determined.[1]
Parts
The functional organization of the human biocomputer is:[2]
Level
Description
Parts
11
Above and in biocomputer
unknown
10
Beyond metaprogramming
supra-species-metaprograms
9
To be metaprogrammed
supra-self-metaprograms
8
To metaprogram
self-metaprogram
awareness
7
To program sets of programs
metaprograms
metaprogram storage
6
Detailed instructions
programs
program storage
5
Details of instructions
subroutines
subroutine storage
4
Signs of activity
biochemical activity
neural activity
glial activity
vascular activity
3
Brain
biochemical brain
neural brain
glial brain
vascular brain
2
Body
biochemical body
sensory body
motor body
vascular body
1
External reality
biochemical
chemical
physical
General clarification
The levels of the human biocomputer are explained thus: Levels from one to two are the boundaries between external reality and the body. Certain energies and materials (heat, light, sound, food, and secretions) pass through this boundary in special places. Levels two to three are the boundaries of body and brain, in which special structures such as blood vessels, nerve fibers, and cerebrospinal fluid pass. Levels four through eleven are in the brain circuitry, and is the software inside the biocomputer. Levels after ten are termed unknown. This is to allow an openeness for future scientific research, and discoveries. This is also to illustrate the unwillingness to subscribe to any dogmatic belief, to encourage creative, courageous and imaginative investigation, to emphasize the necessity for unknown factors on all levels, and to point out the heuristic nature of this schema.[3]
Definitions
Mind
Mind, which is defined as the sum total of all the programs and metaprograms (and even supraself metaprograms) of a human biocomputer.[4] This is the software and is looked at as the opposite of the hardware.
Brain
The brain is defined as the visible, palpable living set of structures to be included in the human biocomputer.[5]
Stored programs
A stored program is defined as a set of instructions which are placed in memory storage of the biocomputer, and which control the biocomputer when orders are given for that program to be activated.[6]These programs can be activated by the same biocomputer, another biocomputer, or a situation outside of the biocomputer.
Metaprogramming
Metaprogramming is defined as a set of instructions, descriptions, and implementations of related thoughts and actions(programs).[7] Self metaprogramming involves the creation, revision, and reorganization of programs and metaprograms.[7]
DNA computing
  (Redirected from DNA computer)
DNA computing is a branch of computingwhich uses DNA, biochemistry, and molecular biology hardware, instead of the traditional silicon-based computer technologies. Research and development in this area concerns theory, experiments, and applications of DNA computing. The term "molectronics" has sometimes been used, but this term had already been used for an earlier technology, a then-unsuccessful rival of the first integrated circuits;[1] this term has also been used more generally, for molecular-scale electronic technology.[2]
History
Leonard Adleman, the inventor of DNA computing
This field was initially developed by Leonard Adleman of the University of Southern California, in 1994.[3] Adleman demonstrated a proof-of-concept use of DNA as a form of computation which solved the seven-pointHamiltonian path problem. Since the initial Adleman experiments, advances have been made and various Turing machines have been proven to be constructible.[4][5]
While the initial interest was in using this novel approach to tackle NP-hard problems, it was soon realized that they may not be best suited for this type of computation, and several proposals have been made to find a "killer application" for this approach. In 1997, computer scientist Mitsunori Ogihara working with biologist Animesh Ray suggested one to be the evaluation of Boolean circuits and described an implementation.[6][7]
In 2002, researchers from the Weizmann Institute of Science in Rehovot, Israel, unveiled a programmable molecular computing machine composed of enzymes and DNA molecules instead of silicon microchips.[8] On April 28, 2004, Ehud Shapiro, Yaakov Benenson, Binyamin Gil, Uri Ben-Dor, and Rivka Adar at the Weizmann Institute announced in the journal Nature that they had constructed a DNA computer coupled with an input and output module which would theoretically be capable of diagnosing cancerous activity within a cell, and releasing an anti-cancer drug upon diagnosis.[9]
In January 2013, researchers were able to store a JPEG photograph, a set of Shakespearean sonnets, and an audio file ofMartin Luther King, Jr.'s speech I Have a Dream on DNA digital data storage.[10]
In March 2013, researchers created atranscriptor (a biological transistor).[11]
In August 2016, researchers used the CRISPR gene-editing system to insert a GIF of a galloping horse and rider into the DNA of living bacteria.[12]
Idea
The organisation and complexity of all living beings is based on a coding system functioning with four key components of theDNA-molecule. Because of this, the DNA is very suited as a medium for data processing.[13] According to different calculations a DNA-computer with one liter of fluid containing six grams of DNA could potentially have a memory capacity of 3072 exabytes. The theoretical maximum data transfer speed would also be enormous due to the massiveparallelism of the calculations. Therefore, about 1000 petaFLOPS could be reached, while today's most powerful computers do not go above a few dozen (99 petaFLOPS being the current record).[citation needed]
Pros and cons
The slow processing speed of a DNA-computer (the response time is measured in minutes, hours or days, rather than milliseconds) is compensated by its potential to make a high amount of multiple parallel computations. This allows the system to take a similar amount of time for a complex calculation as for a simple one. This is achieved by the fact that millions or billions of molecules interact with each other simultaneously. However, it is much harder to analyze the answers given by a DNA-Computer than by a digital one.
Examples/Prototypes
In 1994 Leonard Adleman presented the first prototype of a DNA-Computer. The TT-100was a test tube filled with 100 microliters of a DNA-solution. He managed to solve for example an instance of the directed Hamiltonian path problem.[14]
In another experiment a simple version of the “travelling salesman problem” was “solved”. For this purpose, different DNA-fragments were created, each one of them representing a city that had to be visited. Every one of these fragments is capable of a linkage with the other fragments created. These DNA-fragments were produced and mixed in a test tube. Within seconds, the small fragments form bigger ones, representing the different travel routes. Through a chemical reaction (that lasts a few days), the DNA-fragments representing the longer routes were eliminated. The remains are the solution to the problem. However, current technical limitations prevent evaluation of the results. Therefore, the experiment isn’t suitable for application, but it is nevertheless a proof of concept.
Combinatorial problems
First results to these problems were obtained by Leonard Adleman (NASA JPL)
Tic-tac-toe game
In 2002, J. Macdonald, D. Stefanovic and Mr. Stojanovic created a DNA computer able to play tic-tac-toe against a human player.[15]The calculator consists of nine bins corresponding to the nine squares of the game. Each bin contains a substrate and various combinations of DNA enzymes. The substrate itself is composed of a DNA strand onto which was grafted a fluorescent chemical group at one end, and the other end, a repressor group. Fluorescence is only active if the molecules of the substrate are halved. The DNA enzyme simulate logical functions. For example, such a DNA will unfold if two specific types of DNA strand are introduced to reproduce the logic function AND.
By default, the computer is supposed to play first in the central square. The human player has then as a starter eight different types of DNA strands assigned to each of eight boxes that may be played. To indicate that box nr. i is being ticked, the human player pours into all bins the strands corresponding to input #i. These strands bind to certain DNA enzymes present in the bins, resulting in one of these two bins in the deformation of the DNA enzymes which binds to the substrate and cuts it. The corresponding bin becomes fluorescent, indicating which box is being played by the DNA computer. The various DNA enzymes are divided into various bins in such a way to ensure the victory of the DNA computer against the human player.
Capabilities
DNA computing is a form of parallel computing in that it takes advantage of the many different molecules of DNA to try many different possibilities at once.[16] For certain specialized problems, DNA computers are faster and smaller than any other computer built so far. Furthermore, particular mathematical computations have been demonstrated to work on a DNA computer. As an example, DNA molecules have been utilized to tackle the assignment problem.[17]
Jian-Jun Shu and colleagues built a DNAGPS[18] system and also conduct an experiment to show that magnetic fields can enhance charge transport through DNA[19] (or protein), which may allow organisms to sense magnetic fields.
Aran Nayebi[20] has provided a general implementation of Strassen's matrix multiplication algorithm on a DNA computer, although there are problems with scaling. In addition, Caltech researchers have created a circuit made from 130 unique DNA strands, which is able to calculate the square root of numbers up to 15.[21] Recently, Salehi et al. showed that with a new coding referred to as "fractional coding", chemical reactions in general and DNA reactions in particular, can compute polynomials. In the fractional coding two DNA molecules are used to represent each variable.[22]
DNA computing does not provide any new capabilities from the standpoint ofcomputability theory, the study of which problems are computationally solvable using different models of computation. For example, if the space required for the solution of a problem grows exponentially with the size of the problem (EXPSPACE problems) onvon Neumann machines, it still grows exponentially with the size of the problem on DNA machines. For very large EXPSPACE problems, the amount of DNA required is too large to be practical.
Methods
There are multiple methods for building a computing device based on DNA, each with its own advantages and disadvantages. Most of these build the basic logic gates (AND, OR,NOT) associated with digital logic from a DNA basis. Some of the different bases include DNAzymes, deoxyoligonucleotides, enzymes, toehold exchange.
DNAzymes
Catalytic DNA (deoxyribozyme or DNAzyme) catalyze a reaction when interacting with the appropriate input, such as a matchingoligonucleotide. These DNAzymes are used to build logic gates analogous to digital logic in silicon; however, DNAzymes are limited to 1-, 2-, and 3-input gates with no current implementation for evaluating statements in series.
The DNAzyme logic gate changes its structure when it binds to a matching oligonucleotide and the fluorogenic substrate it is bonded to is cleaved free. While other materials can be used, most models use a fluorescence-based substrate because it is very easy to detect, even at the single molecule limit.[23] The amount of fluorescence can then be measured to tell whether or not a reaction took place. The DNAzyme that changes is then “used,” and cannot initiate any more reactions. Because of this, these reactions take place in a device such as a continuous stirred-tank reactor, where old product is removed and new molecules added.
Two commonly used DNAzymes are named E6 and 8-17. These are popular because they allow cleaving of a substrate in any arbitrary location.[24] Stojanovic and MacDonald have used the E6 DNAzymes to build the MAYA I[25] and MAYA II[26] machines, respectively; Stojanovic has also demonstrated logic gates using the 8-17 DNAzyme.[27] While these DNAzymes have been demonstrated to be useful for constructing logic gates, they are limited by the need for a metal cofactor to function, such as Zn2+ or Mn2+, and thus are not useful in vivo.[23][28]
A design called a stem loop, consisting of a single strand of DNA which has a loop at an end, are a dynamic structure that opens and closes when a piece of DNA bonds to the loop part. This effect has been exploited to create several logic gates. These logic gates have been used to create the computers MAYA I and MAYA II which can play tic-tac-toe to some extent.[29]
Enzymes
Enzyme based DNA computers are usually of the form of a simple Turing machine; there is analogous hardware, in the form of an enzyme, and software, in the form of DNA.[30]
Benenson, Shapiro and colleagues have demonstrated a DNA computer using the FokIenzyme[31] and expanded on their work by going on to show automata that diagnose and react to prostate cancer: under expression of the genes PPAP2B and GSTP1and an over expression of PIM1 and HPN.[9]Their automata evaluated the expression of each gene, one gene at a time, and on positive diagnosis then released a single strand DNA molecule (ssDNA) that is an antisense for MDM2. MDM2 is a repressor ofprotein 53, which itself is a tumor suppressor.[32] On negative diagnosis it was decided to release a suppressor of the positive diagnosis drug instead of doing nothing. A limitation of this implementation is that two separate automata are required, one to administer each drug. The entire process of evaluation until drug release took around an hour to complete. This method also requires transition molecules as well as the FokI enzyme to be present. The requirement for the FokI enzyme limits application in vivo, at least for use in "cells of higher organisms".[33]It should also be pointed out that the 'software' molecules can be reused in this case.
Toehold exchange
DNA computers have also been constructed using the concept of toehold exchange. In this system, an input DNA strand binds to asticky end, or toehold, on another DNA molecule, which allows it to displace another strand segment from the molecule. This allows the creation of modular logic components such as AND, OR, and NOT gates and signal amplifiers, which can be linked into arbitrarily large computers. This class of DNA computers does not require enzymes or any chemical capability of the DNA.[34]
Algorithmic self-assembly
DNA arrays that display a representation of theSierpinski gasket on their surfaces. Click the image for further details. Image from Rothemund et al., 2004.[35]
DNA nanotechnology has been applied to the related field of DNA computing. DNA tiles can be designed to contain multiple sticky ends with sequences chosen so that they act asWang tiles. A DX array has been demonstrated whose assembly encodes anXOR operation; this allows the DNA array to implement a cellular automaton which generates a fractal called the Sierpinski gasket. This shows that computation can be incorporated into the assembly of DNA arrays, increasing its scope beyond simple periodic arrays.[35]