ABSTRACT

BIO MOLECULAR COMPUTING

Biomolecular computing, computations performed by biomolecules, is challenging traditional approaches to computation both theoretically and technologically. Often placed within the wider context of natural or even unconventional computing, the study of natural and artificial molecular computations is adding to our understanding both of biology and computer science well beyond the framework of neuroscience. The papers in this special theme document only a part of an increasing involvement of Europe in this far reaching undertaking. In this introduction, I wish to outline the current scope of the field and assemble some basic arguments that biomolecular computation is of central importance to both computer science and biology. Readers will also find arguments for not dismissing DNA Computing as limited to exhaustive search and for a qualitatively distinctive advantage over all other types of computation including quantum computing.

The idea that molecular systems can perform computations is not new and was indeed more natural in the pre-transistor age. Most computer scientists know of von Neumanns discussions of self-reproducing automata in the late 1940s, some of which were framed in molecular terms. Here the basic issue was that of bootstrapping: can a machine construct a machine more complex than itself? Important was the idea, appearing less natural in the current age of dichotomy between hardware and software, that the computations of a device can alter the device itself. This vision is natural at the scale of molecular reactions, although it may appear utopic to those running huge chip production facilities. Alan Turing also looked beyond purely symbolic processing to natural bootstrapping mechanisms in his work on self-structuring in molecular and biological systems. Purely chemical computers have been proposed by Ross and Hjelmfelt extending this approach. In biology, the idea of molecular information processing took hold starting from the unraveling of the genetic code and translation machinery and extended to genetic regulation, cellular signaling, protein trafficking, morphogenesis and evolution - all of this independently of the development in the neurosciences. For example, because of the fundamental role of information processing in evolution, and the ability to address these issues on laboratory time scales at the molecular level, I founded the first multi-disciplinary Department of Molecular Information Processing in 1992. In 1994 came Adlemans key experiment demonstrating that the tools of laboratory molecular biology could be used to program computations with DNA in vitro. The huge information storage capacity of DNA and the low energy dissipation of DNA processing lead to an explosion of interest in massively parallel DNA Computing. For serious proponents of the field however, there really never was a question of brute search with DNA solving the problem of an exponential growth in the number of

alternative solutions indefinitely. In a new field, one starts with the simplest algorithms and proceeds from there: as a number of contributions and patents have shown, DNA Computing is not limited to simple algorithms or even, as we argue here, to a fixed hardware configuration. After 1994, universal computation and complexity results for DNA Computing rapidly ensued (recent examples of ongoing projects here are reported in this collection by Rozenberg, and Csuhaj-Varju). The laboratory procedures for manipulating populations of DNA were formalized and new sets of primitive operations proposed: the connection with recombination and so called splicing systems was particularly interesting as it strengthened the view of evolution as a computational process. Essentially, three classes of DNA Computing are now apparent: intramolecular, intermolecular and supramolecular. Cutting across this classification, DNA Computing approaches can be distinguished as either homogeneous (ie well stirred) or spatially structured (including multi-compartment or membrane systems, cellular DNA computing and dataflow like architectures using microstructured flow systems) and as either in vitro (purely chemical) or in vivo (ie inside cellular life forms). Approaches differ in the level of programmability, automation, generality and parallelism (eg SIMD vs MIMD) and whether the emphasis is on achieving new basic operations, new architectures, error tolerance, evolvability or scalability. The Japanese Project lead by Hagiya focuses on intramolecular DNA Computing, constructing programmable state machines in single DNA molecules which operate by means of intramolecular conformational transitions. Intermolecular DNA Computing, of which Adleman's experiment is an example, is still the dominant form, focusing on the hybridization between different DNA molecules as a basic step of computations and this is common to the three projects reported here having an experimental component

(McCaskill, Rozenberg and Amos). Beyond Europe, the group of Wisconsin are prominent in exploiting a surface based approach to intermolecular DNA Computing using DNA Chips. Finally, supramolecular DNA Computing, as pioneered by Eric Winfree, harnesses the process of self-assembly of rigid DNA molecules with different sequences to perform computations. The connection with nanomachines and nanosystems is then clear and will become more pervasive in the near future. In my view, DNA Computation is exciting and should be more substantially funded in Europe for the following reasons: it opens the possibility of a simultaneous bootstrapping solution of future computer design, construction and efficient computation It provides programmable access to nanosystems and the world of molecular biology, extending the reach of computation it admits complex, efficient and universal algorithms running on dynamically constructed dedicated molecular hardware it can contribute to our understanding of information flow in evolution and biological construction it is opening up new formal models of computation, extending our understanding of the limits of computation. The difference with Quantum Computing is dramatic. Quantum Computing involves high physical technology for the isolation of mixed quantum states necessary to implement (if this is scalable) efficient computations solving combinatorially complex problems such as factorization. DNA Computing operates in natural noisy environments, such as a glass of water. It involves an evolvable platform for computation in which the computer construction machinery

itself is embedded. Embedded computing is possible without electrical power in microscopic, error prone and real time environments, using mechanisms and technology compatible with our own make up. Because DNA Computing is linked to molecular construction, the computations may eventually also be employed to build three dimensional self-organizing partially electronic or more remotely even quantum computers. Moreover, DNA Computing opens computers to a wealth of applications in intelligent manufacturing systems, complex molecular diagnostics and molecular process control. The papers in this section primarily deal with Biomolecular Computing. The first contribution outlines the European initiative in coordinating Molecular Computing (EMCC). Three groups present their multidisciplinary projects involving joint theoretical and experimental work. Two papers are devoted to extending the range of formal models of computation. The collection concludes with a small sampler from the more established approach to biologically inspired computation using neural network models. It is interesting that one of these contributions addresses the application of neural modelling to symbolic information processing. However, the extent to which informational biomolecules play a specific role in long term memory and the structuring of the brain, uniting neural and molecular computation, still awaits clarification.

Bio-Molecular Computing Technology

Bio-Molecular uses DNA and other Biological materials as the blocks for planning of living computational machines to solve complex problems. Natural computations performed by bio molecules with this field to which electronics engineering, bio physics, chemistry, molecular biology, solid state physics and computer science contribute to extent. It has developed a bio logical computer, composed of DNA molecules and enzymes than can provide a biological phenomenon. Leonard Adleman is a Father of DNA Computing that possible by finding the best solution to following problems with a molecular computer. 1. A Real Problem 2. A Hamiltonian Path Problem 3. A Traveling Salesman Problem. Computation Process

The basic idea behind smart molecules is to develop massively distributed living machines. It is used to perform basic automated tasks. DNA system is a generic most advanced organic form of autonomous programmable computing devices. Bio-Molecules involve the encoding, manipulation and retrieve information at a macro molecular level. The bio logical systems have more facilities like self assembly, recognition, high speed processing, learning and self reproduction. Overall process of computation carried out the input molecules to provide a last step output in the form of dsDNA molecules.

Definition Molecular computing is an emerging field to which chemistry, biophysics, molecular biology, electronic engineering, solid state physics and computer science contribute to a large extent. It involves the encoding, manipulation and retrieval of information at a macromolecular level in contrast to the current techniques, which accomplish the above functions via IC miniaturization of bulk devices. The biological systems have unique abilities such as pattern recognition, learning, self-assembly and selfreproduction as well as high speed and parallel information processing. The aim of this article is to exploit these characteristics to build computing systems, which have many advantages over their inorganic (Si,Ge) counterparts.

DNA computing began in 1994 when Leonard Adleman proved thatDNA computing was possible by finding a solution to a real- problem, a Hamiltonian Path Problem, known to us as the Traveling Salesman Problem,with a molecular computer. In theoretical terms, some scientists say the actual beginnings of DNA computation should be attributed to Charles Bennett's work. Adleman, now considered the father of DNA computing, is a professor at the University of Southern California and spawned the field with his paper, "Molecular Computation of Solutions of Combinatorial Problems." Since then, Adleman has demonstrated how the massive parallelism of a trillion DNA strands can simultaneously attack different aspects of a computation to crack even the toughest combinatorial problems.

Adleman's Traveling Salesman Problem: The objective is to find a path from start to end going through all the points only once. This problem is difficult for conventional computers to solve because it is a "non-deterministic polynomial time problem" . These problems, when they involve large numbers, are intractable with conventional computers, but can be solved using massively parallel computers like DNA computers. The Hamiltonian Path problem was chosen by Adleman because it is known problem.

The following algorithm solves the Hamiltonian Path problem: 1.Generate random paths through the graph. 2.Keep only those paths that begin with the start city (A) and conclude with the end city (G). 3.If the graph has n cities, keep only those paths with n cities. (n=7) 4.Keep only those paths that enter all cities at least once. 5.Any remaining paths are solutions.

The key was using DNA to perform the five steps in the above algorithm. Adleman's first step was to synthesize DNA strands of known sequences, each strand 20 nucleotides long. He represented each of the six vertices of the path by a separate strand, and further represented each edge between two consecutive vertices, such as 1 to 2, by a DNA strand which consisted of the last ten nucleotides of the strand representing vertex 1 plus the first 10 nucleotides of the vertex 2 strand. Then, through the sheer amount of DNA molecules (3x1013 copies for each edge in this experiment!) joining together in all possible combinations, many random paths were generated. Adleman used well-established techniques of molecular biology to weed out the Hamiltonian path, the one that entered all vertices, starting at one and ending at six. After generating the numerous random paths in the first step, he used polymerase chain reaction (PCR) to amplify and keep only the paths that began on vertex 1 and ended at vertex 6. The next two steps kept only those strands that passed through six vertices, entering each vertex at least once. At this point, any paths that remained would code for a Hamiltonian path, thus solving the problem.

through Biocomputers 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. The term nanobiotechnology can be defined in multiple ways; in a more general sense, nanobiotechnology can be defined as any type of technology that uses both nano-scale materials, i.e. materials having characteristic dimensions of 1-100 nanometers, as well as biologically based materials. A more restrictive definition views nanobiotechnology more specifically as the design and engineering of proteins that can then be assembled into larger, functional structures (116117) (9).,1 The implementation of nanobiotechnology, as defined in this narrower sense, provides scientists with the ability to engineer biomolecular systems specifically so that they interact in a fashion that can ultimately result in the computational functionality of a computer. The promising field of biocomputer research uses the science behind nano-sized biomaterials to create various forms of computational devices, which may have many potential applications in the future. One day, biocomputers using nanobiotechnology may become the cheapest, most energyefficient, most powerful, and most economical of any commercially available computer. Already, scientists are making significant headway in the advancement of this science.

Scientific Background
Biocomputers use biologically derived materials to perform computational functions. A biocomputer consists of a pathway or series of metabolic pathways involving biological materials that are engineered to behave in a certain manner based upon the conditions (input) of the system. The resulting pathway of reactions that takes place constitutes an output, which is based on the engineering design of the biocomputer and can be interpreted as a form of computational analysis. Three distinguishable types of biocomputers include biochemical computers, biomechanical computers, and bioelectronic computers. Our task is to investigate how synthetic biochemical systems can be designed to carry out algorithms and compute; what models of computation arise from biochemical processes and how they can be programmed; and how to "compile" abstract descriptions of biomolecular algorithms down to specific synthetic DNA sequences that implement the desired computation in the laboratory. Like the carefully orchestrated molecular processes that occur within living cells, biomolecular computation can in principle occur autonomously, without the need for any external intervention during the computation. Being able to design and understand such systems is our ultimate goal. We are exploring several interconnected paradigms of biomolecular computation, based loosely on processes that are ubiquitous throughout living organisms. Algorithmic self-assembly of DNA tiles (inspired by crystals, microtubules, and virus capsids on the biological side, and by Wang tiles on the mathematical) encodes information in the geometric arrangement of tiles, and performs logical steps by the selective addition of tiles as geometrically compatible sites. Algorithmic self-assembly may be ideally suited for bottom-up self-fabrication of complex nanostructures. A major question concerns how to reduce error rates during assembly; we are investigating "proofreading" logic for error-resilient algorithmic growth, as well as methods to programmably control the nucleation of self-assembled structures. Both theoretical and experimental projects are ongoing.

In vitro RNA transcriptional circuits are a stripped-down, bare-bones version of genetic regulatory networks in the cell; signals are carried by the concentration of specific RNA transcripts; RNA polymerase and RNase regulate the production and degradation of RNA. In vitro RNA transcriptional circuits should allow dynamic control of biomolecular processes -- at the time scale of minutes. On the theory side, we have shown how these networks can function as biochemical neural networks; on the experimental side, we have demonstrated and characterized a two-node bistable circuit. Future research aims at spatial patterning in reaction-diffusion conditions, and at measuring stochastic behavior due to small copy numbers in small volumes.Biochemical circuits, such as cellular signal transduction cascades, are logically related to boolean circuits. For example, a given enzyme molecules may be either phosphorylated ("on") or not ("off"). Phosphorylation cascades are ideal for the study of reliable computation in the presence of thermal "noise". More generally, one may ask how to design formal chemical reaction networks to perform computation, and how stochastic noise is shaped by network activity. Experimentally, we are constructing DNA-based logic gates that can be "wired" into arbitrary circuits.

Chemical self-replication and evolution must have gotten started somehow, way back when. We are using algorithmic self-assembly to investigate a radical hypothesis of Graham Cairns-Smith, that life got started as clay crystals that reproduced patterns as they grew. On paper, at least, it appears that simple crystal growth mechanisms are sufficient for very complex Darwinian evolution. RNA and DNA hybridization and folding are essential processes for all DNA computing, and can perform complex logical operations in their own right. Realistic yet tractable models of nucleic acid interactions form the foundation for higher-level descriptions of DNA nanodevices, and allow for automated design of DNA sequences for DNA structures and devices. We are developing fast simulation algorithms for simulating folding at the secondary structure level.

x Deoxyribonucleic acid is present in all organisms. Whether it is mammal, bird or bacteria DNA is
responsible for a functioning organism. Looking at the two tables provided, there are some noticeable trends that could be identified, as well as conclusions that can be derived. The idea that more complex organism have more DNA mass per cell, that the mass of DNA in somatic cells is constant (there is a range but it is very slight) for any particular organism, that sperm cells are haploid cells and that all organisms have DNA present in their cells are ideas present from the tables provided. The fact that all of the organisms, whether it is mammal, bird or fungi have a mass of DNA present in their cells shows that DNA is present for a reason. If a mammal has an approximate DNA mass in each cell of 6pg and birds have an average DNA mass of 2pg per cell then this DNA has to have a specific function in the body, which explains its initial appearance in each cell. Also, because the organism has a DNA mass in each cell then DNA would have to be passed from the parents onto their offspring. The masses of DNA in the somatic cells of the chicken are all approximately the same. The DNA mass found in a heart cell of the chicken measured at 2.45 pg while the mass of the DNA in each kidney cell weighed at 2.50pg. This can be explained by the fact that when an egg is fertilized by a sperm cell, the fertilized egg eventually becomes the starting point for all the different cells. During the process of mitosis, the fertilized egg is duplicating to form a cluster of cells, while doing so the DNA is also being duplicated and eventually these cluster of cells will become specialized for different functions in different areas of the body. The small but notable variance in the value of masses of the somatic cells can be attributed to experimental error. More complex organisms have a higher DNA mass content per cell. Per cell a mammal has a DNA mass content per cell of 6 pg while a bird has an average DNA mass content of 2pg. The mass of DNA present in each of the cells is dependant on how complex the organism is, the higher the complexity the more DNA that is needed for the organism to function with its internal functions. Since there is more information for the organism itself, then the DNA mass will increase. From the tables provided the mass of the DNA found in sperm cells can be noted. While the mass of DNA seems to fall in the same range for all the different cells in the chickens body, the sperm cell is an odd case. With a mass of DNA of 1.26 pg the sperm cell holds the smallest number, as well as the number that does not fit in with the rest of the other values assigned as values for DNA in the different parts of the cells in the chickens body. This can be explained by the fact that the sperm cell is a haploid cell, and that it carries half the DNA that an organism will eventually obtain, the other half coming from the egg. If the sperm cell, with a DNA mass of 1.26 pg were to fertilize the egg (which has a DNA mass of 1.26 pg), the resulting organism will have a DNA mass of 2.52 pg. This value fits in with the rest of the values observed in the second chart. It can be noted that DNA is passed on from both the sperm and egg cell. The initial presence of the DNA in each of the organisms cells, the fact that the mass of DNA in each of the somatic cells of the chicken is approximately the same, that sperm cells carry half of the mass of DNA of an ordinary somatic cell, and that more complex organisms have a higher DNA mass content per cell than lower organism are ideas present in the tables. From these four points extracted from the tables DNA seems to be an important component for each organism responsible for carrying information.

ertices, entering each vertex at lea