Related papers: Sequence selection by dynamical symmetry breaking …
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
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.…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…
The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…
We study a Brownian particle passively driven by a field obeying the noisy Burgers equation. We demonstrate that the system exhibits replica symmetry breaking in the path ensemble with the initial position of the particle being fixed. The…
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…
Selection is central to biological evolution, yet there has been no general experimental framework for quantifying selection in chemical systems before life. Here we demonstrate that selection in a prebiological chemical system can be…
A general and basic model of primordial evolution--a soup of reacting finitary and discrete processes--is employed to identify and analyze fundamental mechanisms that generate and maintain complex structures in prebiotic systems. The…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
Spontaneous self-replication in cellular automata has long been considered rare, with most known examples requiring careful design or artificial initialization. In this paper, we present formal, causal evidence that such replication can…
We review models of biological evolution in which the population frequency changes deterministically with time. If the population is self-replicating, although the equations for simple prototypes can be linearised, nonlinear equations arise…
Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others.…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
Bacteria regulate their motility through a variety of mechanisms, including quorum sensing (QS) and other density-dependent responses mediated by diffusible signals. While nonlinear density-dependent motility is well known in active-matter…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
We perform a Bayesian analysis on abundance data for ten species of North American duck, using the results to investigate the evidence in favour of biologically motivated hypotheses about the causes and mechanisms of density dependence in…
We propose an alternative to the prevailing two origin of life narratives, one based on a replicator first hypothesis, and one based on a metabolism first hypothesis. Both hypotheses have known difficulties: All known evolvable molecular…