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Strand Algebras for DNA Computing [chapter]

Luca Cardelli
2009 Lecture Notes in Computer Science  
We present a process algebra for DNA computing, discussing compilation of other formal systems into the algebra, and compilation of the algebra into DNA structures.  ...  Strand Algebras By a strand algebra we mean a process algebra [11] where the main components represent DNA strands, DNA gates, and their interactions.  ...  Strand algebra connects a simple but powerful class of DNA system to a rich set of techniques from process algebra for studying concurrent systems.  ... 
doi:10.1007/978-3-642-10604-0_2 fatcat:uiwjx3ujargrjeh2pstqgp7p4e

Strand algebras for DNA computing

Luca Cardelli
2010 Natural Computing  
We present a process algebra for DNA computing, discussing compilation of other formal systems into the algebra, and compilation of the algebra into DNA structures.  ...  Strand Algebras By a strand algebra we mean a process algebra [11] where the main components represent DNA strands, DNA gates, and their interactions.  ...  Strand algebra connects a simple but powerful class of DNA system to a rich set of techniques from process algebra for studying concurrent systems.  ... 
doi:10.1007/s11047-010-9236-7 fatcat:kundz7lkdnb37ghdoiart4wg3m

Gener: a minimal programming module for chemical controllers based on DNA strand displacement

Ozan Kahramanoğulları, Luca Cardelli
2015 Bioinformatics  
Gener is a development module for programming chemical controllers based on DNA strand displacement.  ...  two-domain strand displacement algebra, the minimal available so far.  ...  The double-stranded DNA strand displacement algebras perform computations as a result of the interactions between single and double-stranded DNA structures: the single-stranded structures act as signals  ... 
doi:10.1093/bioinformatics/btv286 pmid:25957353 pmcid:PMC4547617 fatcat:5nopj7ykhzathal3yzohbksqwe

Algebras and Languages for Molecular Programming [chapter]

Luca Cardelli
2010 Lecture Notes in Computer Science  
populations. n x m gates Compiling Strand Algebra to DNA Compiling Strand Algebra to DNA • compile(x) = • compile([x 1 ,..  ...  ,y m ] 0 is an inert solution o Theory of Concurrency • Signals (single stranded DNA) are prepared o Process Algebra as the "Boolean Algebra" of DNA Computing by (artificial) DNA synthesis Random Random  ... 
doi:10.1007/978-3-642-13523-1_2 fatcat:lrm4kdniw5ef5im3ca3smk7cti

Simplification of Boolean Algebra through DNA Computing

Sanchita Paul, Gadadhar Sahoo
2010 International Journal of Computer Applications  
In this paper we introduced a new DNA computing algorithm for reducing any Boolean expression to its simplest form by using DNA strands.  ...  DNA Computing utilizes the properties of DNA for performing the computations.  ...  In this paper we introduced a new DNA computing algorithm for reducing any Boolean expression to its simplest form by using DNA strands.  ... 
doi:10.5120/365-552 fatcat:7fyqvg2rrvegvjmv4egzulcx64

Review on DNA Strand Algebra and its Application [article]

Mandrita Mondal, Kumar S. Ray
2020 arXiv   pre-print
In this paper we have reviewed the algebraic explanation of concurrent DNA processes using DNA strand algebra, process calculus and DNA strand graph.  ...  Finally, we have presented DNA cryptography as one of the prominent areas for the future scope of research work where DNA strand algebra can be used as formal modelling tool to authenticate the security  ...  DNA 3 strand algebra is essentially dependent on process algebra. We will also focus on process calculus in the context of DNA computation and DNA strand graph.  ... 
arXiv:1903.04260v2 fatcat:i55emh5uq5be7ibczufkr44kwe

Logical Inference by DNA Strand Algebra [article]

Kumar Sankar Ray, Mandrita Mondal
2015 arXiv   pre-print
Based on the concept of DNA strand displacement and DNA strand algebra we have developed a method for logical inference which is not based on silicon based computing.  ...  Thus, the present approach to logical inference based on DNA strand algebra is basically an attempt to develop expert system design in the domain of DNA computing.  ...  Conclusion We have successfully developed one method for logical inference based on DNA strand algebra.  ... 
arXiv:1506.04923v1 fatcat:dbtvhjvwtrebdpanudreipo3au

A Formal Model for Databases in DNA [chapter]

Joris J. M. Gillis, Jan Van den Bussche
2012 Lecture Notes in Computer Science  
DNAQL stands to general DNA computing as the standard relational algebra for relational databases stands to general-purpose conventional computing.  ...  Our goal is to better understand, at a theoretical level, the database aspects of DNA computing.  ...  If the DNA strand for symbol a ∈ Σ is w, then the DNA strand for the complementary symbolā, is, naturally, the Watson-Crick complementary strand to w.  ... 
doi:10.1007/978-3-642-28067-2_2 fatcat:3hw4cxxmqzcefds2tdeyr2d4xi

The DNA query language DNAQL

Robert Brijder, Joris J. M. Gillis, Jan Van den Bussche
2013 Proceedings of the 16th International Conference on Database Theory - ICDT '13  
This paper presents an exposition of the authors' past and present work on the query language DNAQL for querying databases in DNA. In DNA computing, data is represented and stored in DNA molecules.  ...  Next, a set of formal operations on DNA complexes is defined, much in the spirit of the operations of the relational algebra in the relational data model.  ...  (Tony) Bonner for getting him interested in DNA, a long, long time ago. Tony suggested Jan to read The Cartoon Guide to Genetics [19] which Jan still highly recommends to all interested readers.  ... 
doi:10.1145/2448496.2448497 dblp:conf/icdt/BrijderGB13 fatcat:5pra6uwlnjdvrmhcwv2ni2gapa

Combinatorial Strand Algebra in Insertion Modeling System

Dmitriy M. Klionov
2012 International Conference on Information and Communication Technologies in Education, Research, and Industrial Applications  
Letichevsky in 1987. and on the way of implementation of strand algebras -a process algebra for DNA computing devised by Luca Cardelli in order to compile other formal systems into the algebra, and compilation  ...  of this algebra into DNA structures.  ...  Algebra Strand algebra is a process algebra [18] where the main components represent DNA strands, DNA gates, and their interactions.  ... 
dblp:conf/icteri/Klionov12 fatcat:l5xhot75cja6lfeqsdcvrtxemy

Page 4861 of Mathematical Reviews Vol. , Issue 2004f [page]

2004 Mathematical Reviews  
Therefore, DNA computing is not viable for 3-SAT.” 2004f:68039 68Q17 14P25 52B05 Biirgisser, Peter (D-PDRB; Paderborn) Lower bounds and real algebraic geometry.  ...  The separate (or extract) operation, which is a key manipulation of DNA computing, only extracts some of the required DNA strands.  ... 

Page 2571 of Mathematical Reviews Vol. , Issue 97D [page]

1997 Mathematical Reviews  
Many restriction enzymes cut the two strands of double-stranded DNA at different positions leaving overhangs of single-stranded DNA.  ...  Different algo- rithmic algebras are proposed which are adequate for well-known constructing methods. A criterion of functional completeness for the Dijkstra algebra is also established.  ... 

Page 8277 of Mathematical Reviews Vol. , Issue 2001K [page]

2001 Mathematical Reviews  
The yes-tube contains DNA strands from T that have a given sub- sequence S and the no-tube contains DNA strands from T that do not have S as a subsequence.  ...  Completeness criteria are stated for Dijkstra meta-algebras for the case in which logical constants are absent.  ... 

Article for analog vector algebra computation

Allen P Mills, Bernard Yurke, Philip M Platzman
1999 Biosystems (Amsterdam. Print)  
This new type of DNA computing has the advantage that it should be fault tolerant and thus more immune to DNA hybridization errors than a Boolean DNA computer.  ...  We introduce the concept of an analog neural network represented by chemical operations performed on strands of DNA.  ...  Introduction The various chemical operations that can be performed on strands of DNA form an algebra that can be used to make artificial structures solely from DNA (Chen and Seeman, 1991; Zhang and Seeman  ... 
doi:10.1016/s0303-2647(99)00044-1 pmid:10636042 fatcat:kfb2ivrsuvh3vbjrncgmh5makm

Page 8881 of Mathematical Reviews Vol. , Issue 2000m [page]

2000 Mathematical Reviews  
The basic idea behind this model is the use of several possible shapes of partially double-stranded DNA mole- cules which have single-stranded DNA segments, so-called “sticky ends”.  ...  ISBN 3-540-64196-3 This is a great book for those interested in formal language theory and its connections to the new ideas of DNA based computing.  ... 
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