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At the onset of bio-complexity: microscopic devils, molecular bio-motors, and computing cells

  • Statistical thermodynamics and chemical kinetics
  • Published:
Rendiconti Lincei. Scienze Fisiche e Naturali Aims and scope Submit manuscript

Abstract

Nano scale motility, that is the hallmark of life, emerges when coordinated movements take over from molecular chaos. In biological world, at nanometric size, significant witnesses are present, starting from cellular traffic flows till the organized behaviors of complex molecular machines. Although their origins and evolution are still the objects of investigations, the understanding of physico-chemical mechanisms capable of extracting coordinated movements from the stochastic energy fluctuations of the surrounding liquid is improving. By accounting for the contribution due to the free energy supplied from the hydrolysis of ATP, information theory allows some meaningful in-deepments on processes and mechanisms that contribute to the increase in the complexity present in biological processes. The transfer of some engineering concepts to the biological cells shaped through a set of interacting components with functional, as well as structural relationships, evidences the presence of set-up similar to the ones conventional computers, in which the electronic circuits are able to manage logical expressions. The implications on the emergent synthetic biology are discussed, as well.

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(Taken from Benoit Perthame, ENS Paris)

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(Taken from: Cohen W, A Computer Scientist’s Guide to Cell Biology: Travelogue from a Stranger in a Strange Land)

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(Arranged from Gerd H. G. and Moe Berhens, “Biological Microprocessor, No. 7, April 2013)

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Abbreviations

a :

Molecular or particle diameter

\(D = (k_{{\text{B}}} T/3\pi \mu a)\) :

Diffusion coefficient

E :

Energy

Ex:

Exergy

F = U − TS :

Helmholtz free energy

G = H − TS :

Gibbs free energy

H :

Enthalpy

I :

Information

P :

Pressure

Pi:

Phosphoric acid

pi :

Probability

P(x,t):

Probability distribution function

S :

Entropy

t :

Time

T :

Temperature

u :

Fluid or particle velocity

U :

Internal energy, characteristic fluid velocity in Eq. (1)

V :

Potential energy

w(x n/x s):

Transition probability between the states n and s

\(\mu\) :

Viscosity

\(\rho\) :

Density

x,y,z :

Cartesian coordinates

\({\text{d}}r^{3} = {\text{d}}x{\text{d}}y{\text{d}}z\) :

Elementary volume in a Cartesian space

Re = ULρ/μ :

Reynolds number

δ(…):

Dirac delta function

\(\Phi\) :

Flux

\(\nabla\) :

Gradient

\(\nabla^{2} \equiv \nabla \cdot (\nabla )\) :

Laplacian

\(\beta = 1/k_{{\text{B}}} T\) :

Being kB the Boltzmann constant

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Authors and Affiliations

  1. Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Via Mancinelli 7, 20131, Milan, Italy

    Sergio Carrà

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  1. Sergio Carrà
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Correspondence to Sergio Carrà.

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This paper is the peer-reviewed version of a presentation.at the Conference Statistical thermodynamics and chemical kinetics: far away from equilibrium held at the Accademia Nazionale dei Lincei in Rome, 25–26 June 2019. Program and abstracts at the link Statistical Thermodynamics and Chemical—Manifestazione | Accademia Nazionale dei Lincei.

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Carrà, S. At the onset of bio-complexity: microscopic devils, molecular bio-motors, and computing cells. Rend. Fis. Acc. Lincei 32, 215–232 (2021). https://doi.org/10.1007/s12210-020-00971-1

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