On the Growth Rate of Non-Enzymatic Molecular Replicators

TL;DR

This paper investigates how various factors like temperature, strand length, and sequence composition influence the replication rate of non-enzymatic molecular replicators, combining thermodynamic analysis and Brownian dynamics simulations.

Contribution

It introduces a combined analytical and simulation approach to understand the dependence of replication rates on physical and chemical parameters.

Findings

Longer strands have a replication advantage at low temperatures.

Hybridization rates are significantly affected by temperature and strand length.

The combined model depicts a fitness landscape for molecular replicators.

Abstract

It is well known that non-enzymatic template directed molecular replicators X + nO ---> 2X exhibit parabolic growth d[X]/dt = k [X]^{1/2}. Here, we analyze the dependence of the effective replication rate constant k on hybridization energies, temperature, strand length, and sequence composition. First we derive analytical criteria for the replication rate k based on simple thermodynamic arguments. Second we present a Brownian dynamics model for oligonucleotides that allows us to simulate their diffusion and hybridization behavior. The simulation is used to generate and analyze the effect of strand length, temperature, and to some extent sequence composition, on the hybridization rates and the resulting optimal overall rate constant k. Combining the two approaches allows us to semi-analytically depict a fitness landscape for template directed replicators. The results indicate a clear replication advantage for longer strands at low temperatures.