Related papers: Horizontal transfer between loose compartments sta…
In biological cells, DNA replication is carried out by the replisome, a protein complex encompassing multiple DNA polymerases. DNA replication is semi-discontinuous: a DNA polymerase synthesizes one (leading) strand of the DNA continuously,…
Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the…
The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA World, self-replicating RNAs have yet to be identified in a natural context, leaving a key…
A fundamental problem in protobiological dynamics is to understand how chemically generated polymers can form persistent sequence distributions before the emergence of replication. We study deterministic polymer growth in which each finite…
Through in-depth thinking and reasoning about the conditions required for cells to maintain unchanged material distribution, it is concluded that life metabolic reactions require high information content. However, the self-replication of a…
As a confined thin sheet crumples, it spontaneously segments into flat facets delimited by a network of ridges. Despite the apparent disorder of this process, statistical properties of crumpled sheets exhibit striking reproducibility.…
To double the cellular population of ribosomes, a fraction of the active ribosomes is allocated to synthesize ribosomal proteins. Subsequently, these ribosomal proteins enter the ribosome self-assembly process, synthesizing new ribosomes…
The emergence of self-replication and information transmission in life's origin remains unexplained despite extensive research on the topic. A hypothesis explaining the transition from a simple organic world to a complex RNA world is…
The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic…
An important transition after the origin of life was the first emergence of a Darwinian population, self-reproducing entities exhibiting differential reproduction, phenotypic variation, and inheritance of phenotypic traits. The simplest…
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…
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
The now classical replicator equation describes a wide variety of biological phenomena, including those in theoretical genetics, evolutionary game theory, or in the theories of the origin of life. Among other questions, the permanence of…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
A mechanism of the replication of proto-RNAs in oligomer world is proposed. The replication is carried out by a minimum cycle which is sustained by a ligase and a helicase. We expect that such a cycle actually worked in the primordial soup…
A self-replicating system where the elements belonging to a solution category can replicate themselves by copying their own informations, is considered. The information carried by each element is defined by an element of all the n multiple…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
Plasmids are autonomously replicating genetic elements in bacteria. At cell division plasmids are distributed among the two daughter cells. This gene transfer from one generation to the next is called vertical gene transfer. We study the…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells.…