Latest work on Molecular Computing

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Latest work on Molecular Computing

INTRODUCTION :

·         ORIGIN :

·         The origin of molecular computing was as early as 1961. Which was conceived by Feynman In 1994 .Adleman  give idea about  a DNA molecular biological calculation method based on the Hamilton graph and successfully achieved molecular computing in DNA solution for the first time in 2019.

Reference:

Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266(5187), 1021–1024 (1994).

What is Molecular Computing?

Molecular computing is the science of using individual molecules to build computer programs. Scientists in the field of nanocomputing are investigating several different possibilities, including the use of biological molecules.

Molecular computer is biomolecule information processing machine .

Autonomous control of chemical reactions.

Encoded in molecules themselves • Nanoscale, low energy • Massive parallelism • Physical and chemical functions of molecules • Objectives of molecular computing

Scientific investigation of computational power of molecules and their reactions.

Engineering realization of new computational paradigms based on molecular reactions.

References:

M. Hagiya, T. Yokomori: DNA Computer, Baifukan, 2001. –M. Hagiya: Present and Future of Molecular Computer Progress towards Molecular Programming, Saiensu-sha, 2004

·        Introduction to Molecular Computing Table of Contents:

• Analysis of computational power of molecular reactions.

 Computational models ・ Computability ・ Complexity

• Computational aspects of molecular systems design. Design of molecules ・ Design of molecular reactions

• Application of computational power of molecular reactions .Intelligent molecular sensing  Self-assembly. Molecular machines.• New computational paradigms based on molecular reactions. Membrane computing ・ Amorphous computing .Association with optical and quantum .Association with molecular electronics.

 Objectives of Molecular Computing

1) Analysis of computational power of molecular reactions and Applications.

2) Molecular sensors using molecular computation .

3) Application to biotechnology .

4) Programmed self-assembly and molecular machines.

5) Application to nanotechnology .

6) Evolutionary computation by molecules .

7) Application to molecular evolution .

8) New computational paradigms based on molecular reactions.

• References:

 M. Hagiya, T. Yokomori: DNA Computer, Baifukan, 2001. – M. Hagiya: Present and Future of Molecular Computer --- Progress towards Molecular Programming, Saiensu-sha, 2004.

Types of Molecular Computer.

There are three main types of Molecular Computer:

1)Biochemical computer 

2) Bio Mechanical Computer 

3) Bio Electronic Computer

·         Biochemical Computer:

 Bio computers use systems of biologically derived molecules such as DNA and proteins to perform computational calculations involving storing, retrieving, and processing data.

The development of biocomputers has been made possible by the expanding new science of nanobiotechnology.Unusual concepts are biochemical computers, such as the DNA computer, and the quantum-mechanical computer. The following presents both of these concepts although their realizations are still far away. Both examples show that it is important to enlarge the scope beyond the nanoelectronics implemented in solid-state materials. In this challenging case we have to consider all possible ways that lead to an efficient parallel processing .

·        Biomechanical Computer:

Biomechanical computers are similar to biochemical computers in that they both perform a specific operation that can be interpreted as a functional computation based upon specific initial conditions which serve as input. They differ, however, in what exactly serves as the output signal. In biochemical computers, the presence or concentration of certain chemicals serves as the output signal. In biomechanical computers, however, the mechanical shape of a specific molecule or set of molecules under a set of initial conditions serves as the output. Biomechanical computers rely on the nature of specific molecules to adopt certain physical configurations under certain chemical

conditions. The mechanical, three-dimensional structure of the product of the biomechanical computer is detected and interpreted appropriately as a calculated output.

·        Bioelectronic computers:

Biocomputers can also be constructed in order to perform electronic computing. Again, like both biomechanical and biochemical computers, computations are performed by interpreting a specific output that is based upon an initial set of conditions that serve as input. In bioelectronic computers, the measured output is the nature of the electrical conductivity that is observed in the bioelectronic computer. This output comprises specifically designed biomolecules that conduct electricity in highly specific manners based upon the initial conditions that serve as the input of the bioelectronic system.

References:

1.      Wispelway. June. "Nanobiotechnology: The Integration of Nanoengineering and Biotechnology to the Benefit of Both." Society for Biological Engineering (Special Section): Nanobiotechnology, p. 34

2.     ^ Ratner. Daniel and Mark. Nanotechnology: A Gentle Introduction to the Next Big Idea. Pearson Education. Inc: 2003, p. 116-7

3.     ^ Gary Stix. "Little Big Science." Understanding Nanotechnology (p6-16). Scientific American. Inc. and Byron Preiss Visual Publications. Inc: 2002, p. 9

4.     ^ Jump up to:^a b c d Freitas. Robert A. Nanomedicine Volume I: Basic Capabilities. Austin. Texas: Landes Bioscience. 1999.^:349–51

Theory of Molecular Computation:

Yokomori's group obtained numerous theoretical results based on the new computation paradigms such as splicing system and self-organization.

Especially, the group proposed a new schema of computation called "computation = self assembly + transformation", which clarified the inherent computational power of molecules.

References:

Yuhui Lu, Craig S Lent. A metric for characterizing the bistability of molecular quantum-dot cellular automata. Nanotechnology 2008, 19 (15),155703. DOI: 10.1088/0957-4484/19/15/155703

Analysis of Molecular Computation and its Design Strategy:

In order to assist the experimental design of molecular algorithms and reaction systems, Hagiya, Nishikawa, Arita and Rose studied simulation, computational complexity, reaction mechanism, and sequence design of molecular computation. Especially, a new simulator called VNA(Virtual Nucleic Acid) was developed for reproducing molecular computation in a computer. Moreover, criteria for the sequence design was actively studied too.

Reference:

 Adamatzky, A., Costello, B.D.L., Asai, T.: Reaction-Diffusion Computers. Elsevier Science, Amsterdam/Boston (2005)Google Scholar

Molecular implementation of Autonomous DNA Computation : Sakamoto and Hagiya's group realized the implementation of automata using hairpin-formed DNA molecules, and its computational model became known worldwide as whiplash PCR. They used the hairpin-formed DNA to solve the satisfiability problem of a boolean formula, and succeeded in the sample experiment (Fig.2), whose detail can be seen on Science journal Sakamoto00Science.The above results demonstrated the new potential of molecular computation. A computation by the autonomous assembly of molecular structures.

References:

Machluf, M., Orsola, A., Atala, A.: Controlled release of therapeutic agents: slow delivery and cell encapsulation. World J. Urol. 18, 80–83 (2000)Google Scholar

Automated DNA Computation in Solid-Phase:

Suyama's group invented a solid-phase method which drastically reduces the number of DNA molecules required for molecular computation. The group constructed a DNA computer based on this technology and is leading the world in the experimental scale of molecular computation. Suyama also studied the application of the DNA computer to biotechnology such as gene.

 Molecular Memory: Yamamura, together with T. Head at Binghamton University, proposed the implementation of a write-once memory and its application and named it `aqueous computing.The write-once memory is represented by a double-stranded circular DNA (plasmid). This plasmid contains multiple regions whose terminals are flanked by restriction sites. The write operation is implemented by removing a particular region using a specific restriction enzyme. Head and Yamamura also proposed the molecular solution with write-once memory for NP complete problems such as max-clique. Yamamura studied the use of PNA for molecular memory too.

Reference:

DIMACS Workshop, pp. 191–213. American Mathematical Society, Providence (1996).

DNA  nano-technology:

After transferring to Osaka Junior College of Electro Communication. Nishikawa, the former post doctoral fellow of the project started the study of DNA nano-technology on solid-phase in cooperation with Prof. Iwasaki's group at Institute of Scientific and Industrial Research, Osaka University. Prof. Iwasaki is famous in nano-technology on solid-phase and its applications, and presented his work on DNA hybridization at the international meeting on DNA computation.

Future of Molecular Computation:

It is no longer believed that DNA computers will solve NP-complete problems faster than traditional digital computers; modern computers can solve the satisfiability problem of more than several hundred variables without errors. To match their speed DNA computers would undergo incredible amount of breakthrough for their algorithms and for their implementation.Researchers are now acknowledging that it is a bad idea to make molecular computers compete with digital computers on the same problem domain. According to their opinion, it is better to regard NP-complete problems as mere benchmarks to evaluate molecular computers.Thus, it is an outdated idea to compare molecular computers with digital computers. Molecular computation should grow into a comprehensive study from basics to applications aiming at the information processing on molecular scale. Applications to biotechnology and nano-technology have been already started. In particular, the application to biotechnology is about to be realized, mainly because molecular computation uses biological molecules.For example, Suyama's group tries to use their DNA computer for the analysis with DNA chips. The DNA chip of Suyama's group is called `universal chip', which is designed not to directly measure raw genetic information from cells, but to indirectly measure designed sequences, DNA Coded Number, translated from the raw information. DNA Coded Number is designed with techniques in DNA computation so that their interaction to one another is minimal, and that their amplification rate in PCR is uniform. Suyama and Sakakibara further proposed "intelligent DNA chip", which can perform logical reasoning and learning by using DNA computation on DNA Coded Number. This is a typical application of molecular computation to biotechnology. Recently, biotechnology using molecular computation is called computationally inspired biotechnology.

Nano-technology, including molecular electronics, is an important application area too. DNA tile by E. Winfree is one such nano-technology with DNA (DNA nano-technology). A DNA tile can contain variable sequences at its single-stranded terminals, thus possessing combinatorial complexity. These tiles can self-assemble not only to a regular pattern but to a structure designated by a specific algorithm implemented in their single-stranded terminals. Self-assembly of this type is called algorithmic assembly. Algorithmic assembly can be used to design a template for placing molecular logic gates in molecular electronics.

Finally, let us mention one dreamlike perspective: medical application. Molecular computation has been studying an autonomous computation, such as whiplash PCR, which can change its state according to its environment. If we can realize a molecular machine which can measure its environmental factors and process information accordingly, then such a cellular machine opens a way to the medical application. Perhaps an elaborate E.coli engineered with molecular computation would diagnose our body by processing information on molecular scale, and would synthesize and exude appropriate medicines autonomously.

Reference:

 de Silva, A., Sandanayake, K.R.A.S.: Fluorescent pet (photoinduced electron transfer) sensors for alkali cations: optimization of sensor action by variation of structure and solvent. Tetrahedron Lett. 32(3), 421–424 (1991)

CONCULUSSION:

Molecular Computation Project  is an attempt to harness the computational power of molecules for information processing. In other words, it is a trial to develop a general-purpose computer with molecules The idea of computing with molecules had not been truly realized until 1994, when L. Adleman published a breakthrough for making a general-purpose computer with biological molecules. Since then, the word `DNA computation' became widespread for the meaning of computation with DNA molecules.Information processing on the molecular scale has been sought in several ways other than Adleman's, but the DNA computation is inherently different from other previous approaches: it aims the construction of a general-purpose computer based on the theory of universal computation. This goal seems to be hinted by the nature of DNA molecules, that is, an arbitrary concatenation of four natural bases forms one DNA sequence. We call this character of DNA as `combinatorial complexity'. Because of this complexity, DNA sequences can hold information of arbitral complexity by freely chaining four natural bases. Similarly, biological molecules such as RNA and proteins are appropriate for molecular computation, because they share this combinatorial complexity. It is worth mentioning that the combinatorial complexity underlies the complexity of life.