Monika Sturm

An Object Oriented Simulation of Real Occurring Molecular Biological Processes for DNA Computing and Its Experimental Verification

We present a simulation tool for frequently used DNA operations on the molecular level including side effects based on a probabilistic approach. The specification of the considered operations is directly adapted from detailed observations of molecular biological processes in laboratory studies. Bridging the gap between formal models of DNA computing, we use process description methods from biochemistry and show the closeness of the simulation to the reality.

DNA-Computing – ein funktionales Modell im laborpraktischen Experiment

Zusammenfassung. Im Zentrum der Betrachtungen zum DNA-Computing steht die Frage nach den Chancen und Grenzen dieses neuen Berechnungsmodells, nachdem in den letzten Jahren eine rasante Entwicklung auf das Thema aufmerksam machte. Neben beachtlichen theoretischen Untersuchungen zum “Rechnen im Reagenzglas” werden auch laborpraktische Implementierungen favorisiert. An der TU Dresden wurde in interdisziplinärer Arbeit ein Integer-Rucksackproblem mittels eines DNA-Algorithmus im Labor gelöst und dabei eine Vielzahl molekularbiologischer Operationen analysiert. Mit Hilfe dieses Satzes von Operationen gelang eine universelle und labornahe Modellierung des DNA-Computing. Hierbei angewandte Techniken und Methoden werden vorgestellt und bewertet. Die Beschreibung des DNA-Algorithmus zeigt, wie sich Einzeloperationen vorteilhaft zu Operationsfolgen zusammensetzen lassen und gemeinsam mit einer geeigneten DNA-Kodierung der Eingangsdaten zur Lösung des Problems im Labor führen. Erstmalig wurden hierbei natürliche Zahlen verarbeitet. Die Arbeitsgemeinschaft DNA-Computing Dresden konzentriert sich auf Aufgabenstellungen, die formale Modelle des DNA-Computing mit überzeugenden Laborimplementierungen verbinden.Abstract. DNA computing as a new model for computation is worldwide considered with respect to its chances and limits. During the last years a huge progress in this field of research could be observed. Both remarkable theoretical studies about “Calculating inside the reaction tube” and lab-practical implementations are focussed. An instance of the integer knapsack problem was solved at Dresden University of Technology in an interdisciplinary manner. In this context, a multiplicity of molecular biological operations was analyzed. Using the applicable set of operations it was possible to model a universal description of DNA computing close to the laboratory. The methods and techniques the description is based on are introduced and evaluated. The specification of the DNA algorithm shows a way how single operations can be combined advantageously to a sequence of operations. This aspect and an appropriate DNA encoding of input data led to a successful solution in the laboratory. For the first time natural numbers were processed. The Dresden DNA Computation Group concentrates on objectives that connect formal models of DNA computing with convincing implementations in the laboratory.

Solving a PSPACE-complete problem by gene assembly

Gene assembly is a natural process of genome re-arrangement that occurs during sexual reproduction of unicellular organisms called ciliates. Two computational models adapting this process of gene assembly have been proposed: the intramolecular, e.g. (Ehrenfeucht et al., 2004, Computation in Living Cells: Gene Assembly in Ciliates), and the intermolecular model, e.g. (Landweber and Kari, 2001, Evolution as Computation). A context sensitive version of the intramolecular model introduced by Ishdorj and Petre (2007, Proceedings of the 6th International Conference on Unconventional Computation) was shown to be computationally universal and efficient for solving NP-complete problems. In this article we show that within this model PSPACE-complete problems can also be solved in linear time.