Actin quantum automata: Communication and computation in molecular networks

Siccardi, Stefano; Adamatzky, Andrew

doi:10.1016/j.nancom.2015.01.002

Cited by 34 publications

(36 citation statements)

References 39 publications

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“…We speculated that a computation in actin filaments could be implemented with travelling patterns of excitation. We implemented computing schemes in several families of actin filament models, from quantum automata to lattice with Morse potential 11–15 . The models proposed previously dealt with a coarse-grain computation on actin filaments, chains of F-actin units, where each monomer stored a single bit.…”

Section: Introductionmentioning

confidence: 99%

Logical gates in actin monomer

Adamatzky

2017

Sci Rep

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We evaluate information processing capacity of a single actin molecule by calculating distributions of logical gates implemented by the molecule via propagating patterns of excitation. We represent a filamentous actin molecule as an excitable automaton network (F-actin automaton). where every atom updates its state depending on states of atoms its connected to with chemical bonds (hard neighbours) and atoms being in physical proximity to the atom (soft neighbours). A resting atom excites if a sum of its excited hard neighbours and a weighted sum of its soft neighbours belong to some specified interval. We demonstrate that F-actin automata implement OR, AND, XOR and AND-NOT gates via interacting patterns of excitation. Gate AND is the most common gate and gate XOR is the rarest. Using the architectures of gates discovered we implement one bit half-adder and controlled-not circuits in the F-actin automata. Speed and space values of the F-actin molecular computers are discussed.

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Section: Introductionmentioning

confidence: 99%

Logical gates in actin monomer

Adamatzky

2017

Sci Rep

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“…They also can be used as organic electronic elements (Adamatzky 2015(Adamatzky , 2016. The structural machine might form a platform for developing Physarum programming languages, compilers and interface between human operators and the slime mould (Schumann et al 2014;Siccardi and Adamatzky 2015;Pancerz and Schumann 2016).…”

Section: Discussionmentioning

confidence: 99%

“…While designing experimental laboratory prototypes of computing devices from living slime mould P. polycephalum (Adamatzky 2015(Adamatzky , 2016, we found that actin networks might play a key role in distributed sensing, decentralized information processing and parallel decision-making in a living cell Adamatzky and Mayne 2015;Mayne, Adamatzky, and Jones 2015). The actin-automata exhibit a wide a range of mobile and stationary patterns, which were later used to design computational models of quantum (Siccardi and Adamatzky 2015) and Boolean (Siccardi, Tuszynski, and Adamatzky 2016) gates implementable on actin fibre, as well as realization of universal computation with cyclic tag systems (Martinez, Adamatzky, and Mclntosh 2015). The previously proposed model of an actin filament in a form of a finite-state machine, or automaton network, constitutes a very special case of studied in this paper structural machines, which provide much more powerful tools for exploration of possibilities of biologically based computation.…”

Section: Discussionmentioning

confidence: 99%

Structural machines and slime mould computation

Burgin¹,

Adamatzky

2017

International Journal of General Systems

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A Physarum machine is a programmable amorphous biological computer experimentally implemented in the vegetative state of true slime mould Physarum polycephalum. It comprises an amorphous yellowish mass with networks of protoplasmic veins, programmed by spatial configurations of attracting and repelling gradients. The goal of this paper to advance formalism of Physarum machines providing theoretical tools for exploration of possibilities of these machines and extension of their applications. To achieve this goal, we introduce structural machines and study their properties.

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“…More recently, some other molecules which are based on diboryl monoradical anions have been proposed [17]. Some research is also devoted to the study of molecular QCA devices based on the actin protein [18,19]. Unlike the metallic and the magnetic cases, only one experimental attempt has been carried out on a mixed-valence complex [20], measuring a charge transfer within molecules in a film.…”

Section: Background: Molecular Qcamentioning

confidence: 99%

Effectiveness of Molecules for Quantum Cellular Automata as Computing Devices

Ardesi

Pulimeno

Graziano

et al. 2018

JLPEA

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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 well-stated. Devices are typically analyzed with quantum physics-based approaches which are far from the electronic engineering world and make it difficult to design, simulate and fabricate molecular devices. In this work, we define new figures of merits to characterize the molecules, which are based on the post-processing of results obtained from ab initio simulations. We define the Aggregated Charge (AC), the electric-field generated at the receiver molecule (EFGR), the Vin-Vout and Vin-AC transcharacteristics (VVT and VACT), the Vout maps (VOM) and the MQCA cell working zones (CWZ). These quantities are compatible with an electronic engineering point of view and can be used to analyze the capability of molecules to propagate information. 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. The adopted methodology provides the quantitative characterization of the molecules necessary for digital designers, to design digital circuits, and for technologists, to the future fabrication of MQCA devices.

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Actin quantum automata: Communication and computation in molecular networks

Cited by 34 publications

References 39 publications

Logical gates in actin monomer

Logical gates in actin monomer

Structural machines and slime mould computation

Effectiveness of Molecules for Quantum Cellular Automata as Computing Devices

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