On discovering functions in actin filament automata

We simulate an actin filament as an automaton network. Every atom takes two or three states and updates its state, in discrete time, depending on a ratio of its neighbours in some selected state. All atoms/automata simultaneously update their states by the same rule. Two state transition rules are considered. In semi-totalistic Game of Life like actin filament automaton atoms take binary states ‘0’ and ‘1’ and update their states depending on a ratio of neighbours in the state ‘1’. In excitable actin filament automaton atoms take three states: resting, excited and refractory. A resting atom excites if a ratio of its excited neighbours belong to some specified interval; transitions from excited state to refractory state and from refractory state to resting state are unconditional. In computational experiments, we implement mappings of an 8-bit input string to an 8-bit output string via dynamics of perturbation/excitation on actin filament automata. We assign eight domains in an actin filament as I/O ports. To write True to a port, we perturb/excite a certain percentage of the nodes in the domain corresponding to the port. We read outputs at the ports after some time interval. A port is considered to be in a state True if a number of excited nodes in the port's domain exceed a certain threshold. A range of eight-argument Boolean functions is uncovered in a series of computational trials when all possible configurations of eight-elements binary strings were mapped onto excitation outputs of the I/O domains.

[1]  Jack A. Tuszynski,et al.  Ferroelectric behavior in microtubule dipole lattices: Implications for information processing, signaling and assembly/disassembly* , 1995 .

[2]  Steen Rasmussen,et al.  Information Processing in Microtubules: Biomolecular Automata and Nanocomputers , 1989 .

[3]  Yuichiro Maéda,et al.  The nature of the globular- to fibrous-actin transition , 2009, Nature.

[4]  E. Korn,et al.  Actin polymerization and its regulation by proteins from nonmuscle cells. , 1982, Physiological reviews.

[5]  M. Cifra,et al.  Electrical Vibrations of Yeast Cell Membrane , 2007 .

[6]  J. Pokorný,et al.  Excitation of vibrations in microtubules in living cells. , 2004, Bioelectrochemistry.

[7]  Y. Goda,et al.  Actin in action: the interplay between the actin cytoskeleton and synaptic efficacy , 2008, Nature Reviews Neuroscience.

[8]  R. Holzwarth,et al.  Attosecond control of electronic processes by intense light fields , 2003, Nature.

[9]  Jack A. Tuszynski,et al.  Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules , 2005, Math. Comput. Model..

[10]  J. A. Pérez-Hernández,et al.  Attosecond physics at the nanoscale , 2016, Reports on progress in physics. Physical Society.

[11]  A. Szent-Györgyi,et al.  The Early History of the Biochemistry of Muscle Contraction , 2004, The Journal of general physiology.

[12]  Julian Francis Miller,et al.  Evolution In Materio: Evolving Logic Gates in Liquid Crystal , 2007, Int. J. Unconv. Comput..

[14]  J. Tuszynski,et al.  Results of Molecular Dynamics Computations of the Structural and Electrostatic Properties of Tubulin and Their Consequences for Microtubules , 2004 .

[15]  M. Zivanov,et al.  Solitonic Ionic Currents Along Microtubules , 2010 .

[16]  Jack A. Tuszynski,et al.  The Dendritic Cytoskeleton as a Computational Device: An Hypothesis , 2006 .

[17]  H. Cantiello,et al.  Ionic wave propagation along actin filaments. , 2004, Biophysical journal.

[18]  Andrew Adamatzky,et al.  Boolean gates on actin filaments , 2015, ArXiv.

[19]  Jürgen Schmidhuber,et al.  Discovering Boolean Gates in Slime Mould , 2016, ArXiv.

[20]  L. Kavitha,et al.  Localized discrete breather modes in neuronal microtubules , 2017 .

[21]  M. Sataric,et al.  Ionic Pulses along Cytoskeletal Protophilaments , 2011 .

[22]  Stéphanie Portet,et al.  Nonlinear assembly kinetics and mechanical properties of biopolymers , 2005 .

[23]  Y. Goda,et al.  The actin cytoskeleton: integrating form and function at the synapse. , 2005, Annual review of neuroscience.

[24]  S. Hastings,et al.  Spatial Patterns for Discrete Models of Diffusion in Excitable Media , 1978 .

[25]  A. Priel,et al.  A nonlinear cable-like model of amplified ionic wave propagation along microtubules , 2008 .

[26]  Andrew Adamatzky,et al.  Models of Computing on Actin Filaments , 2017 .

[27]  Andrew Adamatzky,et al.  Logical gates in actin monomer , 2017, Scientific Reports.

[28]  Steen Rasmussen,et al.  Computational connectionism within neurons: a model of cytoskeletal automata subserving neural networks , 1990 .

[29]  Andrew Adamatzky,et al.  Actin quantum automata: Communication and computation in molecular networks , 2015, Nano Commun. Networks.

[30]  M. Cifra,et al.  Measurement of Electrical Oscillations and Mechanical Vibrations of Yeast Cells Membrane Around 1 kHz , 2009, Electromagnetic biology and medicine.

[31]  I. Lamprecht,et al.  Vibrations in Microtubules , 1997, Journal of biological physics.

[32]  John H. Conway,et al.  The game of life. , 1996, The Hastings Center report.

[33]  Katsumi Midorikawa,et al.  Probing attosecond dynamics of molecules by an intense a-few-pulse attosecond pulse train , 2017, International Congress on High-Speed Imaging and Photonics.

[34]  Andrew Adamatzky,et al.  Quantum Actin Automata and Three-Valued Logics , 2016, IEEE Journal on Emerging and Selected Topics in Circuits and Systems.

[35]  Andrew Adamatzky,et al.  Logical Gates Implemented by Solitons at the Junctions Between One-Dimensional Lattices , 2016, Int. J. Bifurc. Chaos.

[36]  A. Davydov,et al.  Solitons, bioenergetics, and the mechanism of muscle contraction , 1979 .

[37]  John E. Lisman,et al.  A Role of Actin Filament in Synaptic Transmission and Long-Term Potentiation , 1999, The Journal of Neuroscience.

[38]  E. Fifková,et al.  Cytoplasmic actin in neuronal processes as a possible mediator of synaptic plasticity , 1982, The Journal of cell biology.

[39]  Gunnar F Schröder,et al.  Near-atomic resolution for one state of F-actin. , 2015, Structure.

[40]  M. Sataric,et al.  ACTIN FILAMENTS AS NONLINEAR RLC TRANSMISSION LINES , 2009 .

[41]  Hilla Peretz,et al.  The , 1966 .

[42]  U. Kleineberg,et al.  Single-Cycle Nonlinear Optics , 2008, Science.

[43]  Julian Francis Miller,et al.  Evolution-in-materio: evolving computation in materials , 2014, Evolutionary Intelligence.

[44]  J. Tuszynski,et al.  Nonlinear ionic pulses along microtubules , 2011, The European physical journal. E, Soft matter.

[45]  Andrew Adamatzky,et al.  Game of Life Cellular Automata , 2010 .

[46]  Michal Cifra,et al.  Vibrations of microtubules: Physics that has not met biology yet , 2017 .

[47]  Andrew Adamatzky,et al.  On the Dynamics of Excitation and Information Processing in F-actin: Automaton Model , 2017, Complex Syst..