12,851 research outputs found
Formal models of the extension activity of DNA polymerase enzymes
The study of formal language operations inspired by enzymatic actions on DNA is part of ongoing efforts to provide a formal framework and rigorous treatment of DNA-based information and DNA-based computation. Other studies along these lines include theoretical explorations of splicing systems, insertion-deletion systems, substitution, hairpin extension, hairpin reduction, superposition, overlapping concatenation, conditional concatenation, contextual intra- and intermolecular recombinations, as well as template-guided recombination.
First, a formal language operation is proposed and investigated, inspired by the naturally occurring phenomenon of DNA primer extension by a DNA-template-directed DNA polymerase enzyme. Given two DNA strings u and v, where the shorter string v (called the primer) is Watson-Crick complementary and can thus bind to a substring of the longer string u (called the template) the result of the primer extension is a DNA string that is complementary to a suffix of the template which starts at the binding position of the primer. The operation of DNA primer extension can be abstracted as a binary operation on two formal languages: a template language L1 and a primer language L2. This language operation is called L1-directed extension of L2 and the closure properties of various language classes, including the classes in the Chomsky hierarchy, are studied under directed extension. Furthermore, the question of finding necessary and sufficient conditions for a given language of target strings to be generated from a given template language when the primer language is unknown is answered. The canonic inverse of directed extension is used in order to obtain the optimal solution (the minimal primer language) to this question.
The second research project investigates properties of the binary string and language operation overlap assembly as defined by Csuhaj-Varju, Petre and Vaszil as a formal model of the linear self-assembly of DNA strands: The overlap assembly of two strings, xy and yz, which share an overlap y, results in the string xyz. In this context, we investigate overlap assembly and its properties: closure properties of various language families under this operation, and related decision problems. A theoretical analysis of the possible use of iterated overlap assembly to generate combinatorial DNA libraries is also given.
The third research project continues the exploration of the properties of the overlap assembly operation by investigating closure properties of various language classes under iterated overlap assembly, and the decidability of the completeness of a language. The problem of deciding whether a given string is terminal with respect to a language, and the problem of deciding if a given language can be generated by an overlap assembly operation of two other given languages are also investigated
A study of systems implementation languages for the POCCNET system
The results are presented of a study of systems implementation languages for the Payload Operations Control Center Network (POCCNET). Criteria are developed for evaluating the languages, and fifteen existing languages are evaluated on the basis of these criteria
The Parallelism Motifs of Genomic Data Analysis
Genomic data sets are growing dramatically as the cost of sequencing
continues to decline and small sequencing devices become available. Enormous
community databases store and share this data with the research community, but
some of these genomic data analysis problems require large scale computational
platforms to meet both the memory and computational requirements. These
applications differ from scientific simulations that dominate the workload on
high end parallel systems today and place different requirements on programming
support, software libraries, and parallel architectural design. For example,
they involve irregular communication patterns such as asynchronous updates to
shared data structures. We consider several problems in high performance
genomics analysis, including alignment, profiling, clustering, and assembly for
both single genomes and metagenomes. We identify some of the common
computational patterns or motifs that help inform parallelization strategies
and compare our motifs to some of the established lists, arguing that at least
two key patterns, sorting and hashing, are missing
Site-Directed Insertion: Decision Problems, Maximality and Minimality
Site-directed insertion is an overlapping insertion operation that can be
viewed as analogous to the overlap assembly or chop operations that concatenate
strings by overlapping a suffix and a prefix of the argument strings. We
consider decision problems and language equations involving site-directed
insertion. By relying on the tools provided by semantic shuffle on trajectories
we show that one variable equations involving site-directed insertion and
regular constants can be solved. We consider also maximal and minimal variants
of the site-directed insertion operation
Coding-theorem Like Behaviour and Emergence of the Universal Distribution from Resource-bounded Algorithmic Probability
Previously referred to as `miraculous' in the scientific literature because
of its powerful properties and its wide application as optimal solution to the
problem of induction/inference, (approximations to) Algorithmic Probability
(AP) and the associated Universal Distribution are (or should be) of the
greatest importance in science. Here we investigate the emergence, the rates of
emergence and convergence, and the Coding-theorem like behaviour of AP in
Turing-subuniversal models of computation. We investigate empirical
distributions of computing models in the Chomsky hierarchy. We introduce
measures of algorithmic probability and algorithmic complexity based upon
resource-bounded computation, in contrast to previously thoroughly investigated
distributions produced from the output distribution of Turing machines. This
approach allows for numerical approximations to algorithmic
(Kolmogorov-Chaitin) complexity-based estimations at each of the levels of a
computational hierarchy. We demonstrate that all these estimations are
correlated in rank and that they converge both in rank and values as a function
of computational power, despite fundamental differences between computational
models. In the context of natural processes that operate below the Turing
universal level because of finite resources and physical degradation, the
investigation of natural biases stemming from algorithmic rules may shed light
on the distribution of outcomes. We show that up to 60\% of the
simplicity/complexity bias in distributions produced even by the weakest of the
computational models can be accounted for by Algorithmic Probability in its
approximation to the Universal Distribution.Comment: 27 pages main text, 39 pages including supplement. Online complexity
calculator: http://complexitycalculator.com
The Complexity of Fixed-Height Patterned Tile Self-Assembly
We characterize the complexity of the PATS problem for patterns of fixed
height and color count in variants of the model where seed glues are either
chosen or fixed and identical (so-called non-uniform and uniform variants). We
prove that both variants are NP-complete for patterns of height 2 or more and
admit O(n)-time algorithms for patterns of height 1. We also prove that if the
height and number of colors in the pattern is fixed, the non-uniform variant
admits a O(n)-time algorithm while the uniform variant remains NP-complete. The
NP-completeness results use a new reduction from a constrained version of a
problem on finite state transducers.Comment: An abstract version appears in the proceedings of CIAA 201
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