Biomolecular Computing Devices in Synthetic Biology

Biomolecular Computing Devices in Synthetic Biology

Jesús M. Miró (Universidad Politécnica de Madrid (UPM), Spain) and Alfonso Rodríguez-Patón (Universidad Politécnica de Madrid (UPM), Spain)
DOI: 10.4018/978-1-59904-996-0.ch014
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Abstract

Synthetic biology and biomolecular computation are disciplines that fuse when it comes to designing and building information processing devices. In this chapter, we study several devices that are representative of this fusion. These are three gene circuits implementing logic gates, a DNA nanodevice and a biomolecular automaton. The operation of these devices is based on gene expression regulation, the so-called competitive hybridization and the workings of certain biomolecules like restriction enzymes or regulatory proteins. Synthetic biology, biomolecular computation, systems biology and standard molecular biology concepts are also defined to give a better understanding of the chapter. The aim is to acquaint readers with these biomolecular devices born of the marriage between synthetic biology and biomolecular computation.
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Synthetic Biology, Biomolecular Computation And Systems Biology

The definition of synthetic biology is changing and the borders of this discipline are fuzzy. In the following, we will try to give a comprehensive definition that includes the most relevant research that is being developed and could be considered to be part of this field. We will also describe biomolecular computation and systems biology. Systems biology is also a relative new and emerging field that can help to move synthetic biology and biomolecular computation forward.

Synthetic biology: is a discipline half-way between science and engineering (Benner, 2005; De Lorenzo, 2006; ETC group, 2007). It is concerned with:

  • The design, construction and modification of biomolecular systems and organisms to perform specific functions.

  • To get a better understanding of biological mechanisms.

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Table of Contents
Foreword
Alfonso Araque Almendros
Acknowledgment
Ana B. Porto Pazos, Alejandro Pazos Sierra, Washington Buño Buceta
Chapter 1
Eduardo Malmierca, Nazareth P. Castellanos, Valeri A. Makarov, Angel Nuñez
It is well know the temporal structure of spike discharges is crucial to elicit different types of neuronal plasticity. Also, precise and... Sample PDF
Corticofugal Modulation of Tactile Responses of Neurons in the Spinal Trigeminal Nucleus: A Wavelet Coherence Study
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Chapter 2
Didier Le Ray, Morgane Le Bon-Jego, Daniel Cattaert
Computational neuroscience has a lot to gain from invertebrate research. In this chapter focusing on the sensory-motor network that controls leg... Sample PDF
Neural Mechanisms of Leg Motor Control in Crayfish: Insights for Neurobiologically-Inspired Autonomous Systems
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Chapter 3
Oscar Herreras, Julia Makarova, José Manuel Ibarz
Neurons send trains of action potentials to communicate each other. Different messages are issued according to varying inputs, but they can also mix... Sample PDF
Forward Dendritic Spikes: A Mechanism for Parallel Processing in Dendritic Subunits and Shifting Output Codes
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Chapter 4
Gheorghe Paun, Mario J. Perez-Jimenez
This chapter is a quick survey of spiking neural P systems, a branch of membrane computing which was recently introduced with motivation from neural... Sample PDF
Spiking Neural P Systems: An Overview
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Chapter 5
Juan Ramón Rabuñal Dopico, Javier Pereira Loureiro, Mónica Miguélez Rico
In this chapter, we state an evolution of the Recurrent ANN (RANN) to enforce the persistence of activations within the neurons to create activation... Sample PDF
Simulation of the Action Potential in the Neuron's Membrane in Artificial Neural Networks
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Chapter 6
Ana B. Porto Pazos, Alberto Alvarellos González, Alejandro Pazos Sierra
The Artificial NeuroGlial Networks, which try to imitate the neuroglial brain networks, appeared in order to process the information by means of... Sample PDF
Recent Methodology in Connectionist Systems
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Chapter 7
José A. Fernández-León, Gerardo G. Acosta, Miguel A. Mayosky, Oscar C. Ibáñez
This work is intended to give an overview of technologies, developed from an artificial intelligence standpoint, devised to face the different... Sample PDF
A Biologically Inspired Autonomous Robot Control Based on Behavioural Coordination in Evolutionary Robotics
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Chapter 8
Enrique Mérida-Casermeiro, Domingo López-Rodríguez, J.M. Ortiz-de-Lazcano-Lobato
In this chapter, two important issues concerning associative memory by neural networks are studied: a new model of hebbian learning, as well as the... Sample PDF
An Approach to Artificial Concept Learning Based on Human Concept Learning by Using Artificial Neural Networks
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Chapter 9
Enrique Fernández-Blanco, Julian Dorado, Nieves Pedreira
The artificial embryogeny term overlaps all the models that try to adapt cellular properties into artificial models. This chapter presents a new... Sample PDF
Artificial Cell Systems Based in Gene Expression Protein Effects
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Chapter 10
Computing vs. Genetics  (pages 165-181)
José M. Barreiro, Juan Pazos
This chapter first presents the interrelations between computing and genetics, which both are based on information and, particularly... Sample PDF
Computing vs. Genetics
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Chapter 11
Iara Moema Oberg Vilela
This chapter discusses guidelines and models of Mind from Cognitive Sciences in order to generate an integrated architecture for an artificial mind... Sample PDF
Artificial Mind for Virtual Characters
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Chapter 12
Zhijun Yang, Felipe M.G. França
As an engine of almost all life phenomena, the motor information generated by the central nervous system (CNS) plays a critical role in the... Sample PDF
A General Rhythmic Pattern Generation Architecture for Legged Locomotion
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Chapter 13
Marcos Gestal, José Manuel Vázquez Naya, Norberto Ezquerra
Traditionally, the Evolutionary Computation (EC) techniques, and more specifically the Genetic Algorithms (GAs), have proved to be efficient when... Sample PDF
Genetic Algorithms and Multimodal Search
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Chapter 14
Jesús M. Miró, Alfonso Rodríguez-Patón
Synthetic biology and biomolecular computation are disciplines that fuse when it comes to designing and building information processing devices. In... Sample PDF
Biomolecular Computing Devices in Synthetic Biology
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Chapter 15
Alejandro Rodríguez, Alexander Grushin, James A. Reggia
Drawing inspiration from social interactions in nature, swarm intelligence has presented a promising approach to the design of complex systems... Sample PDF
Guiding Self-Organization in Systems of Cooperative Mobile Agents
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Chapter 16
Agostino Forestiero, Carlo Mastroianni, Fausto Pupo, Giandomenico Spezzano
This chapter proposes a bio-inspired approach for the construction of a self-organizing Grid information system. A dissemination protocol exploits... Sample PDF
Evaluating a Bio-Inspired Approach for the Design of a Grid Information System: The SO-Grid Portal
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Chapter 17
Steven M. Corns, Daniel A. Ashlock, Kenneth Mark Bryden
This chapter presents Graph Based Evolutionary Algorithms. Graph Based Evolutionary Algorithms are a generic enhancement and diversity management... Sample PDF
Graph Based Evolutionary Algorithms
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Chapter 18
Daniela Danciu
Neural networks—both natural and artificial, are characterized by two kinds of dynamics. The first one is concerned with what we would call... Sample PDF
Dynamics of Neural Networks as Nonlinear Systems with Several Equilibria
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Chapter 19
Jianhua Yang, Evor L. Hines, Ian Guymer, Daciana D. Iliescu, Mark S. Leeson, Gregory P. King, XuQuin Li
In this chapter a novel method, the Genetic Neural Mathematical Method (GNMM), for the prediction of longitudinal dispersion coefficient is... Sample PDF
A Genetic Algorithm-Artificial Neural Network Method for the Prediction of Longitudinal Dispersion Coefficient in Rivers
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Chapter 20
Malcolm J. Beynon, Kirsty Park
This chapter employs the fuzzy decision tree classification technique in a series of biological based application problems. With its employment in a... Sample PDF
The Exposition of Fuzzy Decision Trees and Their Application in Biology
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About the Contributors