Chemical reaction-diffusion implementation of finding the shortest paths in a labyrinth.

An experimental technique for finding the shortest paths in a labyrinth is elaborated on based on chemical reaction-diffusion media. The system designed has hybrid architecture that combines an information-processing reaction-diffusion medium performing operations of high computational complexity with a digital computer carrying out supplementary operations. Two principal points are assumed as a basis for this design. They are the following: a light-sensitive Belousov-Zhabotinsky-type reagent chosen as a reaction-diffusion medium that offers the opportunity to simulate a labyrinth and spread wave evolution by its images stored in the medium; fast light-induced phase wave processes that spread through the labyrinth in seconds instead of the dozens of minutes typical of trigger waves inherent in reaction-diffusion media. Images of consecutive wave-spreading steps are stored in the memory of a digital computer. These images are used to determine the shortest paths based on the additional procedure of testing for the connectedness of labyrinth fragments.

Finding paths in a labyrinth based on reaction-diffusion media.

During the past few decades, many proposals were made on how to take an effective solution for finding a path in a labyrinth, one of the most well known problems of high computational complexity inherent in information processing by biomolecular and biological entities. In particular, attempts were made to use a technique attractive enough for solving this problem based on wave processes in reaction-diffusion media. Trigger waves in reaction diffusion systems spread simultaneously through all paths of the labyrinth in a highly parallel mode. Regretfully, the velocity of these waves is extremely low which gave no way for the practical implementation of this technique until now. An effective 'hardware' system was designed which was capable of finding a path in a labyrinth using fast phase waves. Three principal points were assumed as a basis for this design, i.e. (1) hybrid architecture that combined an information processing reaction-diffusion medium which performs operations of high computational complexity with a digital computer carrying out supplementary image processing operations; (2) light-sensitive information processing media of Belousov-Zhabotinsky type that enables the simulation of the labyrinth and spreading wave evolution by their images stored in the medium and reduces the problem to the image processing operations; (3) fast light-induced phase wave processes that spreads through the labyrinth in several seconds instead of hours which is typical for trigger waves inherent in reaction-diffusion media. These fundamentals along with the additional procedure of testing for labyrinth fragment connectness provided us with the opportunity to solve labyrinth problems.

Towards a biomolecular computer. Information processing capabilities of biomolecular nonlinear dynamic media.

The information processing capabilities of biomolecular excitable media based on nonlinear dynamic mechanisms are discussed. Given even the simplest medium geometry, dynamics and information processing features inherent in biomolecular excitable media proves to be diverse and sophisticated. For the case of pseudo two-dimensional versions these media can be described in terms of neural networks having lateral connections. The main responses of shunting on-center off-surround feedback neural networks and pseudo two-dimensional excitable systems to the external excitations are surprisingly similar. The excitable media are capable of short-time memory, of contour enhancement and quenching or amplifying small features depending on medium state. The analogies discussed reaffirm specific neural net characteristics of excitable media and give the opportunity to estimate more accurate excitable medium characteristics.

Biomolecular computer: roots and promises.

There are two basic issues inherent in contemporary molecular and biomolecular computing and urgent for its future development. They are: (i) fundamentals, that is general principles, starting points and correlation's between different approaches to design biomolecular information processing devices, (ii) working criteria, that is goals and principles for the choice of the device designing characteristics to achieve these goals. These issues are common to all major approaches of contemporary biomolecular computing. Increasing behavioral complexity of an information processing device seems to be a criterion for designing biomolecular means capable of solving problems of high computational complexity.

Practical approach to implementation of neural nets at the molecular level.

Potentialities for implementing simple neural net information processing devices based on chemical and biochemical dynamic media are discussed. This approach gives an opportunity to construct efficient systems capable of performing some primitive operations important for imaging processing.

Molecular neural network devices based on non-linear dynamic media: basic primitive information processing operations.

Basic primitive image-processing operations performed by molecular and biomolecular dynamic media functioning in the oscillating mode are discussed. These operations have rather high computational complexity and can be considered as simulations of human vision capabilities.

Molecular neural network devices based on non-linear dynamic media.

The importance of non-linear dynamic mechanisms for implementing neural network devices at a molecular level is discussed. Information processing devices based on these mechanisms proved to be capable of performing some primitive operations important for image processing.

Biomolecular computing: from the brain-machine disanalogy to the brain-machine analogy.

The analogy between the main information features of the brain and molecular non-discrete information processing devices based on non-linear dynamic mechanisms is considered. These information processing mechanisms predetermine the character of basic primitive operations of these devices, which seem to be capable of solving problems of a rather high computational complexity. Non-linear dynamic processing mechanisms open the way to elaboration of devices embodying, in a natural way, the fuzziness of information features that is typical of information processing inherent in soft 'humanistic' systems.

Non-discrete biomolecular computing: an approach to computational complexity.

General principles of information processing at the molecular level inherent in simple biological and biomolecular entities can be used to elaborate essentially new non-discrete information-processing devices. These principles are: giant parallelism of information processing; processing mechanisms based on complicated non-linear dynamics; high efficiency of information transformations; considerable behavioral complexity of computational (pseudoelementary) primitives; and the possibility of variation and evolution of the molecular components of information-processing devices, including the possibility of evolutionary learning. Problems of high computational complexity are currently of great practical importance. Non-discrete biomolecular information-processing devices seem to be able to solve effectively some classes of problems of high computational complexity.

Purple membrane multilayers: detailed structure and photoelectric characteristics of bacteriorhodopsin.

The structure of the Langmuir purple membrane (PM) monolayer was studied by scanning tunneling microscopy (STM). The topography of both the external and cytoplasmic sides of the monolayer was investigated. The thickness of the PM monolayer was determined to be about 4 nm. PM films include specific oval 'crater'-like structures of 50-60 nm in diameter.

Towards a biomolecular computer.

A new version of computing and information processing devices may result from major principles of information processing at molecular level. Non-discrete biomolecular computers based on these principles seems to be capable of solving problems of high computational complexity. One of the possible ways to implement these devices is based on biochemical non-linear dynamical systems. Means and ways to materialize biomolecular computers are discussed.