Spontaneous emergence of autocatalytic information-coding polymers

Tkachenko, Alexei V.; Maslov, Sergei

doi:10.1063/1.4922545

Cited by 37 publications

(40 citation statements)

References 19 publications

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“…In particular, the model by Hordijk et al [22] makes a connection between the classical Kauffman model of autocatalytic sets [12] and polymer systems capable of template-assisted ligation (see also [23] for further development of that approach). Recently, we theoretically established [26] that a cyclically-driven system of this type is capable of producing long, mutually-catalyzing chains starting from a primordial soup dominated by monomers.…”

Section: Template-assisted Ligationmentioning

confidence: 99%

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Onset of natural selection in auto-catalytic heteropolymers

Tkachenko

Maslov

2017

Preprint

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(AVT) and maslov@illinois.edu (SM)Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life. To elucidate this transition, we study a theoretical model of informationstoring heteropolymers capable of template-assisted ligation and subjected to cyclic non-equilibrium driving forces. We discover that this simple physical system undergoes a spontaneous reduction of the information entropy due to the competition of chains for constituent monomers. This natural-selectionlike process ultimately results in the survival of a limited subset of polymer sequences. Importantly, the number of surviving sequences remains exponentially large, thus opening up the possibility of further increase in complexity due to Darwinian evolution. We also propose potential experimental implementations of our model using either biopolymers or artificial nano-structures.

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Section: Template-assisted Ligationmentioning

confidence: 99%

“…Here we further develop the model introduced in Ref. [26]. It describes the emergence of heteropolymers out of the "primordial soup" of monomers by virtue of template-assisted ligation.…”

Section: Modelmentioning

confidence: 99%

Onset of natural selection in auto-catalytic heteropolymers

Tkachenko

Maslov

2017

Preprint

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“…The only special aspect of the system studied here is that we have a complete characterization of the energy landscape of the colloidal particles, and therefore are able to easily make the design choices for a templated catalytic reaction to emerge. However, we see no reason why similar phenomena could not emerge from other soft-matter systems, in particular, polymers or gels (31). As but one example, it is interesting to contemplate whether a system of RNA strands might be designed to lead to an exponential catalytic cycle.…”

Section: Discussionmentioning

confidence: 99%

“…We believe that the dissociation from the template could be induced by the very process of bonding among attached monomers (33) and/or by weakening in time of the monomer-template bonds (19), both of which require consumption of energy. The weakening and breaking of monomer-template bonds might be controlled by an externally imposed (i.e., day-night) cycle for these bonds (31,34,35), which could set the disassociation timescale. A first step toward time-dependent interactions has been realized between nanoparticles by using complex strand-displacement reactions that rely on a DNA fuel source (20,36).…”

Section: Discussionmentioning

confidence: 99%

Spontaneous emergence of catalytic cycles with colloidal spheres

Zeravcic

Brenner

2017

Proc. Natl. Acad. Sci. U.S.A.

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Colloidal particles endowed with specific time-dependent interactions are a promising route for realizing artificial materials that have the properties of living ones. Previous work has demonstrated how this system can give rise to self-replication. Here, we introduce the process of colloidal catalysis, in which clusters of particles catalyze the creation of other clusters through templating reactions. Surprisingly, we find that simple templating rules generically lead to the production of huge numbers of clusters. The templating reactions among this sea of clusters give rise to an exponentially growing catalytic cycle, a specific realization of Dyson's notion of an exponentially growing metabolism. We demonstrate this behavior with a fixed set of interactions between particles chosen to allow a catalysis of a specific sixparticle cluster from a specific seven-particle cluster, yet giving rise to the catalytic production of a sea of clusters of sizes between 2 and 11 particles. The fact that an exponentially growing cycle emerges naturally from such a simple scheme demonstrates that the emergence of exponentially growing metabolisms could be simpler than previously imagined.catalytic cycles | DNA-coated colloids | metabolism | templating T he origin of life is usually associated with self-replication, the ability of an entity to create copies of itself (1). Thus inspired, there have been many efforts in recent years aimed at creating artificial systems with self-replicative capacity. These are typically inspired by the linear chain mechanism of DNA. However, living systems are more than individual entities that can replicate themselves. Dyson (2) and Oparin (3) argued that a more critical aspect of living systems is the creation of a metabolism, a complex cascade of chemical reactions that together are able to accomplish more than any single chemical reaction can do on its own. Using a simple mathematical model, the so-called "garbage bag model," Dyson presented a scenario through which such a complex metabolism could arise spontaneously. His idea is that a random set of catalysts will catalyze arbitrary chemical reactions in a nonsynergistic fashion. However, if each catalyst is more likely to function when there are others that are synergistic with it, then there is a critical amount of cooperativity above which metabolic cycles spontaneously emerge. This idea has been explored through abstract simulations (4). In a similar spirit, Kauffman and coworkers have shown that if the probability of one species catalyzing the formation of another is above a threshold, then catalytic cycles naturally emerge (5-7).Whether this scenario can naturally occur in practice remains obscure. The fundamental question is to determine how likely it is for a soup of interacting catalysts to self-organize into an exponentially growing catalytic cycle. How special do the interactions between the different components need to be for spontaneous exponentially growing catalytic cycles to emerge? In this work, we present an explicit demon...

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“…Many possibilities exist concerning (ii), whereby a time dependent forcing in the bulk rate constants or in boundary conditions can affect the kinetics of polymerization such as in day-night models of polymerization 40 . Concerning (iii), one way to describe the coupling of a system to an environment is to introduce chemostats which impose that the concentration of certain polymers be fixed.…”

Section: Discussionmentioning

confidence: 99%

Length and sequence relaxation of copolymers under recombination reactions

Blokhuis

Lacoste

2017

The Journal of Chemical Physics

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We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law describes the infinite size limit, while the second one, based on the chemical master equation, describes systems of finite size. We compare the predictions of both approaches for the relaxation of thermodynamic quantities towards equilibrium. We find that for some choice of initial conditions, the entropy of the sequence distribution can be lowered at the expense of increasing the entropy of the length distribution. We consider mainly energetically neutral reactions, except for one simple case of non-neutral reactions.

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Spontaneous emergence of autocatalytic information-coding polymers

Cited by 37 publications

References 19 publications

Onset of natural selection in auto-catalytic heteropolymers

Onset of natural selection in auto-catalytic heteropolymers

Spontaneous emergence of catalytic cycles with colloidal spheres

Length and sequence relaxation of copolymers under recombination reactions

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