402 research outputs found
"Going back to our roots": second generation biocomputing
Researchers in the field of biocomputing have, for many years, successfully
"harvested and exploited" the natural world for inspiration in developing
systems that are robust, adaptable and capable of generating novel and even
"creative" solutions to human-defined problems. However, in this position paper
we argue that the time has now come for a reassessment of how we exploit
biology to generate new computational systems. Previous solutions (the "first
generation" of biocomputing techniques), whilst reasonably effective, are crude
analogues of actual biological systems. We believe that a new, inherently
inter-disciplinary approach is needed for the development of the emerging
"second generation" of bio-inspired methods. This new modus operandi will
require much closer interaction between the engineering and life sciences
communities, as well as a bidirectional flow of concepts, applications and
expertise. We support our argument by examining, in this new light, three
existing areas of biocomputing (genetic programming, artificial immune systems
and evolvable hardware), as well as an emerging area (natural genetic
engineering) which may provide useful pointers as to the way forward.Comment: Submitted to the International Journal of Unconventional Computin
Models of natural computation : gene assembly and membrane systems
This thesis is concerned with two research areas in natural computing: the computational nature of gene assembly and membrane computing. Gene assembly is a process occurring in unicellular organisms called ciliates. During this process genes are transformed through cut-and-paste operations. We study this process from a theoretical point of view. More specifically, we relate the theory of gene assembly to sorting by reversal, which is another well-known theory of DNA transformation. In this way we obtain a novel graph-theoretical representation that provides new insights into the nature of gene assembly. Membrane computing is a computational model inspired by the functioning of membranes in cells. Membrane systems compute in a parallel fashion by moving objects, through membranes, between compartments. We study the computational power of various classes of membrane systems, and also relate them to other well-known models of computation.Netherlands Organisation for Scientific Research (NWO), Institute for Programming research and Algorithmics (IPA)UBL - phd migration 201
Two Refinements of the Template-Guided DNA Recombination Model of Ciliate Computing
To solve the mystery of the intricate gene unscrambling mechanism in ciliates, various theoretical models for this process have been proposed from the point of view of computation. Two main models are the reversible guided recombination system by Kari and Landweber and the template-guided recombination (TGR) system by Prescott, Ehrenfeucht and Rozenberg, based on two categories of DNA recombination: the pointer guided and the template directed recombination respectively. The latter model has been generalized by Daley and McQuillan. In this thesis, we propose a new approach to generate regular languages using the iterated TGR system with a finite initial language and a finite set of templates, that reduces the size of the template language and the alphabet compared to that of the Daley-McQuillan model. To achieve computational completeness using only finite components we also propose an extension of the contextual template-guided recombination system (CTGR system) by Daley and McQuillan, by adding an extra control called permitting contexts on the usage of templates. Then we prove that our proposed system, the CTGR system using permitting contexts, has the capability to characterize the family of recursively enumerable languages using a finite initial language and a finite set of templates. Lastly, we present a comparison and analysis of the computational power of the reversible guided recombination system and the TGR system. Keywords: ciliates, gene unscrambling, in vivo computing, DNA computing, cellular computing, reversible guided recombination, template-guided recombination
Further Open Problems in Membrane Computing
A series of open problems and research topics in membrane com-
puting are pointed out, most of them suggested by recent developments in this
area. Many of these problems have several facets and branchings, and further
facets and branchings can surely be found after addressing them in a more
careful manner
Chromosome Descrambling Order Analysis in ciliates
Ciliates are a type of unicellular eukaryotic organism that has two types of nuclei within each cell; one is called the macronucleus (MAC) and the other is known as the micronucleus (MIC). During mating, ciliates exchange their MIC, destroy their own MAC, and create a new MAC from the genetic material of their new MIC. The process of developing a new MAC from the exchanged new MIC is known as gene assembly in ciliates, and it consists of a massive amount of DNA excision from the micronucleus, and the rearrangement of the rest of the DNA sequences. During the gene assembly process, the DNA segments that get eliminated are known as internal eliminated segments (IESs), and the remaining DNA segments that are rearranged in an order that is correct for creating proteins, are called macronuclear destined segments (MDSs).
A topic of interest is to predict the correct order to descramble a gene or chromosomal segment. A prediction can be made based on the principle of parsimony, whereby the smallest sequence of operations is likely close to the actual number of operations that occurred. Interestingly, the order of MDSs in the newly assembled 22,354 Oxytricha trifallax MIC chromosome fragments provides evidence that multiple parallel recombinations occur, where the structure of the chromosomes allows for interleaving between two sections of the developing macronuclear chromosome in a manner that can be captured with a common string operation called the shuffle operation (the shuffle operation on two strings results in a new string by weaving together the first two, while preserving the order within each string). Thus, we studied four similar systems involving applications of shuffle to see how the minimum number of operations needed to assemble differs between the types. Two algorithms for each of the first two systems have been implemented that are both shown to be optimal. And, for the third and fourth systems, four and two heuristic algorithms, respectively, have been implemented. The results from these algorithms revealed that, in most cases, the third system gives the minimum number of applications of shuffle to descramble, but whether the best implemented algorithm for the third system is optimal or not remains an open question. The best implemented algorithm for the third system showed that 96.63% of the scrambled micronuclear chromosome fragments of Oxytricha trifallax can be descrambled by only 1 or 2 applications of shuffle. This small number of steps lends theoretical evidence that some structural component is enforcing an alignment of segments in a shuffle-like fashion, and then parallel recombination is taking place to enable MDS rearrangement and IES elimination.
Another problem of interest is to classify segments of the MIC into MDSs and IESs; this is the second topic of the thesis, and is a matter of determining the right "class label", i.e. MDS or IES, on each nucleotide. Thus, training data of labelled input sequences was used with hidden Markov models (HMMs), which is a well-known supervised machine learning classification algorithm. HMMs of first-, second-, third-, fourth-, and fifth-order have been implemented. The accuracy of the classification was verified through 10-fold cross validation. Results from this work show that an HMM is more likely to fail to accurately classify micronuclear chromosomes without having some additional knowledge
Formal Model and Simulation of the Gene Assembly Process in Ciliates
The construction process of the functional macronucleus in certain types of ciliates is known as the
ciliate gene assembly process. It consists of a massive amount of DNA excision from the micronucleus and the rearrangement of the rest of the DNA sequences (in the case of stichotrichous ciliates). While several computational models have tried to represent certain parts of the gene assembly process, the real process remains not completely understood. In this research, a new formal model called the Computational 2JLP model is introduced based on the recent biological 2JLP model.
For justifying the formal model, a simulation is created and tested with real data. Several parameters are
introduced in the model that are used to test ambiguities or edge cases of the biological model. Parameters are systematically tested from the simulation to try to find their optimal values. Interestingly, a negative correlation is found between a parameter (which is used to filter out scnRNAs that are similar to IES specific sequences from the macronucleus) and the outcome of the simulation. It indicates that if a scnRNA consists of both an MDS and IES, then from the perspective of maximizing the outcome of the simulation, it is desirable to filter out this scnRNA.
The simulator successfully performs the gene assembly process whether the inputs are scrambled or
unscrambled DNA sequences. It is desirable for this model to serve as a foundation for future computational and mathematical study, and to help inform and refine the biological model
Osztott modellek a molekuláris számĂtástudományban = Distributed models of molecular computation
A vizsgálĂłdások tárgyai olyan, biokĂ©miai folyamatokat modellezĹ‘ vagy biokĂ©miai folyamatok által inspirált működĂ©si elvű számĂtástudományi eszközök, számĂtási modellek voltak, melyek fĹ‘ jellemzĹ‘je az osztott Ă©s párhuzamos működĂ©s. A projekt cĂ©lja volt a molekuláris számĂtások termĂ©szetĂ©nek, a modellek sajátosságainak jobban megfelelĹ‘ szempontok figyelembe vĂ©tele, ezáltal esetleg a biokĂ©miai folyamatok jobb megĂ©rtĂ©se, illetve a formális nyelvek Ă©s automaták elmĂ©letĂ©nek továbbfejlesztĂ©se, eszköztárának bĹ‘vĂtĂ©se a biokĂ©miai folyamatok Ă©s az osztott modellek által inspirált irányba. VizsgálĂłdásaink kiterjedtek a DNS rekombináciĂł motiválta számĂtási eszközök mellett a membrán rendszerek terĂĽletĂ©re, kĂĽlönös tekintettel a membrán automatákra. A kutatás során vizsgáltuk Ăşj működĂ©si mĂłdok tulajdonságait Ă©s az ezekbĹ‘l levonhatĂł következtetĂ©seket, eredmĂ©nyeket Ă©rtĂĽnk el bizonyos modellek mĂ©ret-bonyolultságának vizsgálata illetve a formális nyelv fogalmának vĂ©gtelen ábĂ©cĂ©re valĂł kiterjesztĂ©se terĂ©n. | Our research concentrated on computational models which are not only based on or inspired by natural, mostly biochemical processes, but work in a distributed and parallel manner. The aim of the project was to investigate and identify those important aspects and special properties describing the nature of molecular computation which might not only help to better understand natural processes, but could also contribute to the extension of the theory of formal languages and automata by introducing new tools and techniques in a nature inspired, nature motivated way. Our investigations not only concerned computational models based on DNA recombination, but also membrane systems and membrane automata. We investigated new modes of operation of existing models, obtained results about the descriptional (size) complexity of certain devices, and about extending the notion of formal language to infinite alphabets
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