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Molecules as Automata [chapter]

Luca Cardelli
2009 Lecture Notes in Computer Science  
a and once as !  ...  γ·[X] : 1 = total number of X molecules (rounded to an integer).  ...  a pairs in E) v i is the state change caused by interaction i (as a difference) a i (r) = r i ⋅h i (r) is the propensity of interaction i in state r, defined by a base rate of interaction and a state-dependent  ... 
doi:10.1007/978-3-642-03429-9_2 fatcat:5oidbxabmjhkdkfo4w6kmzuply

Effectiveness of Molecules for Quantum Cellular Automata as Computing Devices

Yuri Ardesi, Azzurra Pulimeno, Mariagrazia Graziano, Fabrizio Riente, Gianluca Piccinini
2018 Journal of Low Power Electronics and Applications  
Notwithstanding the increasing interest in Molecular Quantum-Dot Cellular Automata (MQCA) as emerging devices for computation, a characterization of their behavior from an electronic standpoint is not  ...  We apply and verify the methodology to three molecules already proposed in the literature for MQCA and we state to which extent these molecules can be effective for computation.  ...  Conclusions and Future Works The molecular implementation of Field-Coupled Nanocomputing, known as Molecular Quantum-dot Cellular Automata, has been assessed as a possible technology to overcome the issues  ... 
doi:10.3390/jlpea8030024 fatcat:ribssrhzlbc2fgbxr2zfih5uvq

Molecules as Automata [chapter]

Luca Cardelli
Lecture Notes in Computer Science  
Macromolecules, in particular, are seen as stateful concurrent agents that interact with each other through a dynamic interface.  ...  A macromolecule, therefore, is qualitatively different from the small molecules of inorganic chemistry.  ...  Our main criterion is that, as in finite-state automata, we should be able to easily and separately draw the individual automata, both as a visual aid to design and analysis, and to emulate the illustration-based  ... 
doi:10.1007/978-3-540-87531-4_4 fatcat:5vbro7gxajalhpq2by5ufk2mbm

Molecular Implementations of Cellular Automata [chapter]

Satyajit Sahu, Hiroshi Oono, Subrata Ghosh, Anirban Bandyopadhyay, Daisuke Fujita, Ferdinand Peper, Teijiro Isokawa, Ranjit Pati
2010 Lecture Notes in Computer Science  
Molecular realizations of Cellular Automata that exhibit computational behavior have been the holy grail of nanocomputer architectures.  ...  We find that the interaction rules in molecular Cellular Automata tend to be of a mixed variety, ranging from those with long-distance interactions to the more conventional direct-neighborhood type of  ...  As a result, electrons from negatively charged molecules will tunnel to neighboring molecules in the direction of a PPC.  ... 
doi:10.1007/978-3-642-15979-4_73 fatcat:qh4irtcxzrehjieg36zv6zjytq

Quadra-Quantum Dots and Related Patterns of Quantum Dot Molecules: Basic Nanostructures for Quantum Dot Cellular Automata Application [chapter]

Somsak Panyakeow
2011 Cellular Automata - Innovative Modelling for Science and Engineering  
automata principle (M.  ...  Quantum Dot Cellular Automata Application  ...  Quadra-Quantum Dots and Related Patterns of Quantum Dot Molecules: Basic Nanostructures for Quantum Dot Cellular Automata Application, Cellular Automata -Innovative Modelling for Science and Engineering  ... 
doi:10.5772/15990 fatcat:nb3ljj4ifvazrhnbtirimugavm

Biomolecular Implementation of Computing Devices with Unbounded Memory [chapter]

Matteo Cavaliere, Nataša Jonoska, Sivan Yogev, Ron Piran, Ehud Keinan, Nadrian C. Seeman
2005 Lecture Notes in Computer Science  
In particular, we show a procedure to implement automata with unbounded stack memory, push-down automata, using circular DNA molecules and a class IIs restriction enzyme.  ...  The same ideas are extended to show a way to implement push-down automata with two stacks (i.e, universal computing devices) using two circular molecules glued with a DX molecule and a class IIs restriction  ...  Implementing 2PDA's Using DX Molecules In a similar way as presented in Section 2 we can implement 2PDA's i.e., push down automata with two stacks.  ... 
doi:10.1007/11493785_4 fatcat:iktbzimnxbc4xdlpfjrn74nyli

Quadra-Quantum Dots and Related Patterns of Quantum Dot Molecules: Basic Nanostructures for Quantum Dot Cellular Automata Application

Somsak Panyakeow
2010 Engineering Journal  
automata principle (M.  ...  Quantum Dot Cellular Automata Application  ...  Quadra-Quantum Dots and Related Patterns of Quantum Dot Molecules: Basic Nanostructures for Quantum Dot Cellular Automata Application, Cellular Automata -Innovative Modelling for Science and Engineering  ... 
doi:10.4186/ej.2010.14.4.41 fatcat:bxhdlvjhnbcttjconoo72awreq

Finding and defining the natural automata acting in living plants: Toward the synthetic biology for robotics and informatics in vivo

Tomonori Kawano, François Bouteau, Stefano Mancuso
2012 Communicative & Integrative Biology  
as natural sequential machines (namely, the Mealy machines or Moore machines) or finite state automata.  ...  In the present review article, as the chemical and biological basis for natural computing or informatics, some plants, plant cells or plant-derived molecules involved in signaling are listed and classified  ...  as automata.  ... 
doi:10.4161/cib.21805 pmid:23336016 pmcid:PMC3541313 fatcat:7z3h25wilneb3ftfybavrujkse

An autonomous DNA model for finite state automata

Israel M. Martinez Perez, Karl Heinz Zimmermann, Zoya Ignatova
2009 International Journal of Bioinformatics Research and Applications  
This model is called sticker automata model as the transition rules and input data are encoded by single stranded DNA molecules (stickers).  ...  This model called sticker automata model is based on the hybridization of single stranded DNA molecules (stickers) encoding transition rules and input data.  ...  Discussion At this moment, we are implementing in laboratory 2-state and 4-state automata using the sticker automata model. As soon as we have the first results, it will be included in the paper.  ... 
doi:10.1504/ijbra.2009.022465 pmid:19136366 fatcat:udohgrjbqvcpdjrlc46l3mn7um

Architectural Design of Quantum Cellular Automata to Implement Logical Computation [chapter]

Alejandro Leon
2011 Cellular Automata - Innovative Modelling for Science and Engineering  
The energy separation between the states AS and FS is usually referred in the cellular automata literature as "kink energy" E K .  ...  The cells that make up the architecture of the automata correspond to the molecules and to sections of the nanoribbon.  ...  The main attractive feature of cellular automata is that, in spite of their conceptual simplicity which allows an easiness of implementation for computer simulation, as a detailed and complete mathematical  ... 
doi:10.5772/16156 fatcat:pflvnatcnff3vgikck7rqfr4ji

Predictive landscapes hidden beneath biological cellular automata [article]

Lars Koopmans, Hyun Youk
2021 arXiv   pre-print
Another modeling approach uses cellular automata to represent living systems as discrete dynamical systems with binary variables.  ...  One cannot measure many intracellular parameters or can only measure them as snapshots in time.  ...  We later generalized the multicellular entropy to secreteand-sense automata involving any number of cell types and any number of secreted molecules (e.g., three types of cells with two molecules whereby  ... 
arXiv:2105.01999v2 fatcat:ua5pciwv2nczrbhjfhvsiyewqq

The computational power of Benenson automata

David Soloveichik, Erik Winfree
2005 Theoretical Computer Science  
By exhibiting a way to simulate arbitrary circuits, we show that these "Benenson automata" are capable of computing arbitrary Boolean functions.  ...  is cut repeatedly by a restriction enzyme in a manner dependent upon the presence of particular short DNA "rule molecules."  ...  Our definition of Benenson automata (as well as the biochemical implementation) allows for conflicting cutting rules.  ... 
doi:10.1016/j.tcs.2005.07.027 fatcat:zqh3ofvcwbasxl734njmur3zsu

Open-ended evolution in cellular automata worlds

Peter Andras
2017 Proceedings of the 14th European Conference on Artificial Life ECAL 2017  
We consider biological and social systems as a flux of interacting components that transiently participate in interactions with other system components as part of these systems.  ...  Here we provide an implementation of a such model of evolving systems using a cellular automata world.  ...  The number of kinds of molecules involved in cells is also similarly infinite, given the possible variations of molecules (e.g. consider the huge DNA molecules).  ... 
doi:10.7551/ecal_a_073 dblp:conf/ecal/Andras17 fatcat:nnptyfiwkvdbzng22px2d5ntiu

Biomolecular computers with multiple restriction enzymes

Sebastian Sakowski, Tadeusz Krasinski, Jacek Waldmajer, Joanna Sarnik, Janusz Blasiak, Tomasz Poplawski
2017 Genetics and Molecular Biology  
We use this method to construct multistate, biomolecular, nondeterministic finite automata with four commercially available restriction enzymes as hardware.  ...  The idea of a DNA computer proposed by Ehud Shapiro's group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software  ...  Conventionally, finite automata (finite state machines) are used as controllers for electromechanical devices such as automatic doors and supermarket entrances (Sipser, 2006) , as well as for many household  ... 
doi:10.1590/1678-4685-gmb-2016-0132 pmid:29064510 pmcid:PMC5738618 fatcat:u7iof2pgvrgp7fmnxfaxhmraji

More powerful biomolecular computers [article]

Janusz Blasiak, Tadeusz Krasinski, Tomasz Poplawski, Sebastian Sakowski
2011 arXiv   pre-print
This creates an opportunity to implement in laboratories of more complex finite automata and other theoretical models of computers: pushdown automata, Turing machines.  ...  Reaction tube contained a set of DNA fragments representing input and transitions molecules, 1u BbvI and AcuI as well as 7 chloroform and izoamyl alcohol (25:24:1) and sorted by 8% polyacrylamide  ...  The DNA codes of the transitions of such automata, an input word ab (accepted by this automaton) and an additional molecule indicating the final state are presented inFigure 3.  ... 
arXiv:1109.5893v1 fatcat:4zuo4yn5ezf2xpksx3qe4cuony
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