Logical gates in actin monomer

Abstract

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.

Actin droplet machine

“…We implemented several concrete implementations of logical gates and functions on a single actin filament [48] and on an intersection of several actin filaments [49] via collisions between solitons. We also used a reservoir-computing-like approach to discover functions on a single actin unit [50] and royalsocietypublishing.org/journal/rsos R. Soc. open sci.…”

Logics in fungal mycelium networks

“…The distribution demonstrates frequencies of discoveries of the fourinput-one-output logical gates and could be used for characterisation of a computational power of the fungal substrates. This is accompanied by distributions of gates discovered in experimental laboratory reservoir computing with slime mould Physarum polycephalum [18], succulent plant [8] and numerical modelling experiments on computing with protein verotoxin [3], actin bundles network [9], and actin monomer [4]. The distributions of gates discovered in natural systems are alike to each other in the hierarchies of the gates frequencies.…”

“…Figure 6. Comparative ratios of Boolean gates discovered in mycelium network analysed in present paper, black disc and solid line; slime mould Physarum polycephalum[18], black circle and dotted line; succulent plant[8], red snowflake and dashed line; single molecule of protein verotoxin[3], light blue '+' and dash-dot line; actin bundles network[9], green triangle pointing right and dash-dot-dot line; actin monomer[4], magenta triangle pointing left and dashed line. Area of xor gate is magnified in the insert.…”

Computing on actin bundles network

“…Computational studies discussed the feasibility of implementing Boolean gates on a single actin filament 31 and on an intersection of several actin filaments 32 via collisions between solitons. Further studies applied a reservoir-computing-like approach to discover functions on a single actin unit 33 as well as filament 34 . In 2016, for instance, we demonstrated that it is possible to implement logical circuits by linking the protein chains 32 .…”