Related papers: Kinetic Selection of Template Polymer with Complex…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
Template directed replication of nucleic acids is at the essence of all living beings and a major milestone for any origin of life scenario. We here present an idealized model of prebiotic sequence replication, where binary polymers act as…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
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.…
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins of biochemical life still remain an open question. Since…
The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
The production of sequence-specific copolymers using copolymer templates is fundamental to the synthesis of complex biological molecules and is a promising framework for the synthesis of synthetic chemical complexes. Unlike the…
An important issue for the origins of life is ensuring the accurate maintenance of information in replicating polymers in the face of inevitable errors. Here, we investigated how this maintenance depends on reaction kinetics by…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
Non-equilibrium selection pressures were proposed for the formation of oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask…
The dynamical behavior of two types of non-equilibrium systems is discussed: $(a)$ two-dimensional cellular structures, and $(b)$ living polymers. Simple models governing their evolution are introduced and steady state distributions (cell…
A biological system consists of a variety of polymers that are synthesized from monomers, by catalysis that exists only for some long polymers. It is important to elucidate the emergence and sustenance of such autocatalytic polymerization.…
Each living species carries a complex DNA sequence that determines their unique features and functionalities. It is generally assumed that life started from a random pool of oligonucleotides sequences, generated by a prebiotic…
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these…
We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
We present a novel mechanism for resolving the mechanical rigidity of nanoscopic circular polymers that flow in a complex environment. The emergence of a regime of negative differential mobility induced by topological interactions between…
Analysis of molecular scale interactions and chemical structure offers an enormous opportunity to tune material properties for targeted applications. However, designing materials from molecular scale is a grand challenge owing to the…