Actin Computation: Unlocking the Potential of Actin Filaments for Revolutionary Computing Systems

Contents
Preface
About the Editor
1. Actin
2. Actin Automata: Phenomenology and Localisations
	2.1 Introduction
	2.2 Automaton model
	2.3 Global characteristics
	2.4 Localisations
		2.4.1 Travelling localisations
		2.4.2 Stationary localisations
		2.4.3 Rules supporting both stationary and travelling localisations
	2.5 Discussion
3. Patterns and Dynamics of Rule 22 Cellular Automaton
	3.1 Introduction
		3.1.1 Rule 22: History
		3.1.2 Rule 22: Definition
		3.1.3 Rule 22 as an actin automaton
		3.1.4 Patterns and dynamics in Rule 22
	3.2 Mean field theory
		3.2.1 Mean field in the Game of Life
		3.2.2 Mean field in ECA Rule 22
		3.2.3 Mean field behaviour of Rule 22
	3.3 Chaos or determinism?
	3.4 Attractors
		3.4.1 Basins of attraction
		3.4.2 Longest paths and representative cycles
	3.5 de Bruijn diagrams
		3.5.1 Basic de Bruijn diagram
		3.5.2 Extended de Bruijn diagram
	3.6 Garden of Eden
	3.7 Fractals
		3.7.1 Iterated functions in Rule 22
		3.7.2 Rule 18, mutations, gaskets, and seashells
	3.8 Memory leads to complexity
		3.8.1 Rareness and unpredictability
4. Actin Automata with Memory
	4.1 Automata with memory
	4.2 Actin automata with memory
	4.3 Global characteristics
	4.4 Localisations
	4.5 Discussion
5. Dynamics of Excitation in F-actin: Automaton Model
	5.1 Introduction
	5.2 Model
	5.3 Dynamics of A0
		5.3.1 Single node stimulation
		5.3.2 (+)-stimulation
		5.3.3 (+−)-stimulation
	5.4 Dynamics of A1
		5.4.1 Single node stimulation
		5.4.2 (+)-stimulation
		5.4.3 (+−)-stimulation
	5.5 Stability of the dynamics
	5.6 Implementation of memory
	5.7 Discussion
6. Actin Networks Voltage Circuits
	6.1 Introduction
	6.2 The model
	6.3 Extension to bundle networks
	6.4 The network
	6.5 Preliminary results
	6.6 Results
		6.6.1 Ideal electrodes
			6.6.1.1 Boolean gates
			6.6.1.2 Time estimates
		6.6.2 Realistic electrodes
			6.6.2.1 Boolean gates
	6.7 Finite state machine
		6.7.1 Using two values of k = 4 and k = 6
	6.8 Discussion
7. Logical Gates Implemented by Solitons at the Junctions
	7.1 Introduction
	7.2 Model
	7.3 AND gate
	7.4 OR gate
	7.5 NOT gate
	7.6 Cascading gates
	7.7 Signal immunity to noise
	7.8 Discussion
8. Boolean Gates on Actin Filaments
	8.1 Background
	8.2 Actin filaments as nonlinear RLC transmission lines
	8.3 Evolution of pulses
	8.4 Gates with unforced pulses
	8.5 Gates with forced pulses
	8.6 Conclusion
9. Quantum Actin Automata
	9.1 Quantum Cellular Automata
	9.2 Application to actin-like structures
	9.3 Implementation
		9.3.1 Unitarity
		9.3.2 Evolution
	9.4 Gates
	9.5 Adders
10. Multi-valued Logic in Quantum Actin Automata
	10.1 Introduction
	10.2 Reading automata output, concatenating automata, and interpreting superposition
	10.3 Realisations of logic operators
		10.3.1 Lukasiewicz operators
		10.3.2 The G¨odel operators
		10.3.3 Lukasiewicz operators again
	10.4 Discussion
11. Logical Gates in Actin Monomer
	11.1 Introduction
	11.2 The model
	11.3 Dynamics of excitation
	11.4 Boolean gates
	11.5 One-bit half adder
	11.6 Controlled NOT gate
	11.7 Discussion
12. Discovering Functions in Actin Filament Automata
	12.1 Introduction
	12.2 Actin filament automata
	12.3 Discovering functions
	12.4 Discussion
13. Computing on Actin Bundles Network
	13.1 Introduction
	13.2 Model
	13.3 Results
		13.3.1 Structural gates
		13.3.2 Frequency-based gates
		13.3.3 Overall level of activity
		13.3.4 Spiking gates
	13.4 Discussion
14. Actin Droplet Machine
	14.1 Introduction
	14.2 Methods
		14.2.1 Three-dimensional actin network
		14.2.2 Automaton model
		14.2.3 Interfacing with the network
		14.2.4 Selecting excitation threshold and refractory delay to maximise a number of logical gates
	14.3 Actin droplet machine
	14.4 Discussion
References
Index