Projects
- Biological Codes in the Light of Coding Theory Biological (organic) codes like th egenetic code establish a mapping between different sets of molecules, or more generally components or processes, of different kinds by means of adaptors. A good example is given by the genetic code (mapping codons to amino acids utilizing transfer RNAs as adaptors). Recent years have shown a rapid increase in the number of published codes throughout the life sciences, especially in the biological sciences, with a focus on molecular biology and cognition. It turned out that there are many different definitions and concepts of codes as until today various disciplines independently developed their own working models of how codes in their respective area function. However, only a few attempts have been made to classify organic codes by mathematical terminology or to apply techniques from coding theory or information theory to organic codes. In our project we follow two ideas: At first it is the intention to see if and how construction and classification methods from classical information theory and coding theory can be transferred to certain organic codes. In the same line we will also investigate how general mappings as postulated in organic codes can be used to define new classes of codes in mathematics. In particular, we will try to understand the concept of adaptor that exists and is essential in organic codes, and see how a parallel tool could be used in the theory of classical codes to construct new or improve known codes with respect to their error detecting and correcting properties. The project is being conducted by Professors Dr. Elena Fimmel, Dr. Markus Gumbel and Dr. Lutz Strüngmann in cooperation with an international team from different countries. The team has applied for funding with the DFG and the project is supposed to start in May 2024.
DYNALIFE - Information, Coding, and Biological Function: the Dynamics of Life In the mid-twentieth century two new scientific disciplines emerged forcefully: molecular biology and information-communication theory. At the beginning cross-fertilisation was so deep that the term genetic code was universally accepted for describing the meaning of triplets of mRNA (codons) as amino acids.However, today, such synergy has not take advantage of the vertiginous advances in the two disciplines and presents more challenges than answers. These challenges are not only of great theoretical relevance but also represent unavoidable milestones for next generation biology: from personalized genetic therapy and diagnosis, to artificial life, to the production of biologically active proteins. Moreover, the matter is intimately connected to a paradigm shift needed in theoretical biology, pioneered long time ago in Europe, and that requires combined contributions from disciplines well outside the biological realm. The use of information as a conceptual metaphor needs to be turned into quantitative and predictive models that can be tested empirically and integrated in a unified view. The successful achievement of these tasks requires a wide multidisciplinary approach, and Europe is uniquely placed to construct a world leading network to address such an endeavour. The aim of this Action is to connect involved research groups throughout Europe into a strong network that promotes innovative and high-impact multi and interdisciplinary research and, at the same time, to develop a strong dissemination activity aimed at breaking the communication barriers between disciplines, at forming young researchers, and at bringing the field closer to a broad general audience. The project is being conducted by Professor Dr. Elena Fimmel and Prof. Dr. Lutz Strüngmann who are secondary proposers and memebers of the managing committee and core group of the European COST Action CA21169 - DYNALIFE. The action lasts 4 years and started October 2022.
- Is Quantum Information Approach Suitable For Modelling Genetic Code?
Since the early 1950s, marked by the revolutionary discovery of the double helix structure of DNA by F. Crick and J. Watson, Biology has probably been developing most intensively compared to other natural sciences. A lot of empirical data have already been revealed using increasingly sophisticated methods. In spite of a remarkable progress made during the last century, Theoretical Foundations of Biology still remain in a nascent state, which can be compared with the state of Theoretical Physics before Newton. This is the reason why it is necessary to search for a reliable theoretical basis especially in the modelling of the genetic code. This project aims to show the possibilities of modelling the information content carried by quantum mechanical DNA-molecules by means of the formalism used in quantum informatics. Such modelling would open new options to reveal nature’s information patents and to use them, for instance, in quantum computing and artificial intelligence (A.I.) Moreover, it would give an opportunity to understand the ways of managing information in living organisms. As an empirical base, the open accessible data from GenBank which contains hundreds of millions of long DNA texts collected from thousands of organisms can be used.
The project is being conducted by Professor Dr. Elena Fimmel in cooperation with the Laboratory of biomechanical systems of the Mechanical Engineering Research Institute of the Russian Academy of Sciences, Moscow, and funded by the German Research Foundation (DFG) for six months starting in September 2021.
- Uncrackable encryption from other universes of set theory Project funded by the Vector Foundation
Ordinary cryptographic methods to encrypt data are usually based on the limitations of memory, speed and capacity of modern computers. For instance, the RSA method uses the product of two large prime numbers and for decrypting the message the unique prime factor decomposition of the product is needed which takes even the best super computers inefficiently long. However, in theory it is possible to crack this kind of codes. The search for provably uncrackable encryption is therefore of greatest importance.
In the project Professor Dr. Lutz Strüngmann will combine cryptography and set theory which is a novel attempt to produce a new method for encryption. More explicitly, it is the idea to use the method of forcing which is well-known in set theory and turn it into an encryption algorithm. If this works theoretically we will also implement the algorithm and produce a corresponding software.
The project is funded by the Vector Foundation within the MINT program for one year and starts in January 2018. We would like to thank the Vector foundation for their kind support. - NeoTrie – a project on virtual reality, schools and the genetic information
Professor Dr. Lutz Strüngmann has recently started a collaboration with the University of Almeria and VIRTUALDOR (see http://www.virtualdor.com/) on a new software project related to virtual reality: NeoTrie (see http://virtualdor.com/NeoTrie-VR/). Originally designed for helping pupils in school to better understand geometry it is the idea of this collaboration to firstly incorporate the software in courses on mathematics taught at Mannheim University of Applied Sciences and secondly to further develop the software for a possible use in research activities of the competence center, e.g. in visualizing and investigating the genetic information. A first very successful workshop took place in Almeria in September 2018 (see https://sites.google.com/ual.es/imneo-vr) where the first steps of the project were discussed. - Concerning DNA as information
Members of the competence center have an ongoing collaboration with two research groups from the Universities of Bologna and Strasbourg concerning DNA as information. In particular the theory of circular codes is developed.