This master's thesis deals with the topic of cellular automata and their utilization in the research of self-replication, especially with the focus on self-replicating loops. It also shows several possible approaches how to optimize the replication process. The first part is focused on theoretical aspects of cellular automata. It acquaints the readers with the questions of self-replication in the cellular automata and present some of the existing self-replicating loops, starting with the widely known Langton's loop. The second part presents the optimization of the replication process considering two selected variants of self-repricating loops - Byl's loop and Chou-Reggia loop. Two approaches are introduced together with their possible combination. The first approach is based on multiple self-replication. The second one is based on the reduction of the number of steps of the cellular automaton needed to create a copy of the loop.

Molecular recognition plays an essential role in the self-assembly and self-organisation of biological and chemical systems alike—allowing individual components to form complex interconnected networks. Within these systems, the nature of the recognition and reactive processes determines their functional and structural properties, and even small changes in their identity or orientation can exert a dramatic effect on the observed properties. The rapidly developing field of systems chemistry aims to move away from the established paradigm in which molecules are studied in isolation, towards the study of networks of molecules that interact and react with each other. Taking inspiration from complex natural systems, where recognition processes never operate in isolation, systems chemistry aims to study chemical networks with the view to examining the system-level properties that arise from the interactions and reactions between the components within these systems. The work presented in this thesis aims to advance the nascent field of systems chemistry by bringing together small organic molecules that can react and interact together to form interconnected networks, exhibiting complex behaviour, such as self-replication, as a result. Three simple building blocks are used to construct a network of two structurally similar replicators and their kinetic behaviour is probed through a comprehensive kinetic analysis. The selectivity for one of the recognition-mediated reactive processes over another is examined within the network in isolation as well as in a scenario where the network is embedded within a pool of exchanging components. The interconnected, two-replicator network is examined under far-from-equilibrium reaction-diffusion conditions, showing that chemical replicating networks can exhibit signs of selective replication—a complex phenomenon normally associated with biological systems. Finally, a design of a well-characterised replicator is exploited for the construction of a network integrating self-replication with a another recognition-directed process, leading to the formation of a mechanically-interlocked architecture—a [2]rotaxane.

Evolución dirigida de proteínas: La evolución dirigida es una técnica que nos permite explorar funciones enzimáticas que no son requeridas en el ambiente natural. Esta técnica, simula procesos genéticos naturales y de selección. Esta estrategia se utiliza cuando un diseño racional es muy complicado. Consiste en una repetición de ciclos de diversificación y selección que llevan a la acumulación de mutaciones benéficas. Aquí se presenta dos ejemplos de evolución dirigida con los cuales se ha trabajado directamente: la ADN polimerasa del organismo  Thermus aquaticus usada comúnmente en PCR, y la proteína LacI que regula la expresión de genes usados para el metabolismo de lactosa en E. Coli. / Directed evolution allows us to explore protein functionalities not required in the natural environment. It mimics natural genetic processes and selective pressures. This approach is used when the molecular basis is not completely understood and rational design is a difficult task. This approach consists of serial cycles of consecutive diversification and selection which eventually lead to the accumulation of beneficial mutations. Here are presented two cases where directed evolution is used to modify two different proteins: Taq polymerase, enzyme used for DNA extension in PCR, and the LacI repressor protein which regulates gene expression on E.coli.

Numerous organisms produce ornately detailed inorganic structures (often known as shells) with features on length scales from 50 nm to several centimeters. One class of such organisms are the diatoms; microscopic algae that form silica frustules. Another group of algae, the coccolithophorids, produce similar calcium carbonate structures. Over 100,000 species comprise these two classes of algae, every one of which is endowed with a unique cytoskeleton structure. Using various types of displacement reactions, the chemistry of the original structure can be modified to produce a new material. Magnesium vapor has been found to displace the silicon in diatom frustules to yield an MgO structure. The conversion has been reported at temperatures from 650°C to 900°C. In the current work, the conversion and processing of silica frustules to MgO was examined in depth. The effect of reaction temperature on grain size and extent of conversion was evaluated. With the goal of obtaining high purity MgO structures, various methods for removing the silicon products of reaction were investigated. Wet chemistry and high temperature vapor etches were evaluated. The MgO reaction served as an intermediate step in the production of magnesium tungstate diatoms, which were imbued with photoluminescent properties. Reactions were identified to allow the conversion of calcium carbonate (calcite) structures to alternative chemistries. Calcite sand-dollars were converted to calcium tungstate or calcium molybdate by aqueous solution chemistry. In this process, sand dollar tests (shells) and coccolithophore frustules were reacted with ammonium para-molybdate or ammonium para-tungstate. The reactions were evaluated for shape preservation, phase purity, and photoluminescence of the structures.

This thesis deals with cellular systems and their applications to self - replication data structures. The sector cellular automats is a very interesting and inspiring area which seems now as a very suitable environment for the simulation of various phenomen. One of these phenomen may be, for example, artificial life or self- replication the structure, which transmits some useful information or carry out the necessary calculations. In this thesis is detailed subscribe cellular automats and their division. It focuses on Langtons loop, Codds automata, Byls loop, Chou-Reggia loop, Tempesti loop, Perrier loop, SDSR loop, Evoloop and Sexyloop. Part of the work is to accelerate replication Byls loops through change to the rules of cellular automat and the addition of functionality to the ability to release space to the completion of replication loops. At thesis, I also dealt with the evolutionary design of the rules of cellular automata.