Related papers: Fold or die: experimental evolution in vitro
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
This paper presents Coralai, a framework for exploring diverse ecosystems of Neural Cellular Automata (NCA). Organisms in Coralai utilize modular, GPU-accelerated Taichi kernels to interact, enact environmental changes, and evolve through…
DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules,…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
A simple analytical framework to study the molecular quasispecies evolution of finite populations is proposed, in which the population is assumed to be a random combination of the constiyuent molecules in each generation,i.e., linkage…
We consider atomistic systems consisting of interacting particles arranged in atomic lattices whose quasi-static evolution is driven by time-dependent boundary conditions. The interaction of the particles is modeled by classical interaction…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
We introduce a model of molecular evolution in which the fitness of an individual depends both on its own and on the parent's genotype. The model can be solved by means of a nonlinear mapping onto the standard quasispecies model. The…
The fuel-driven process of replication in living systems generates distributions of copied entities with varying degrees of copying accuracy. Here we introduce a thermodynamically consistent ensemble for investigating universal population…
The elastic properties of the double-stranded DNA handles used in optical tweezers experiments on biomolecules are customarily modeled by an extensible worm-like chain model. Fitting such model to experimental data however is no trivial…
Systems of "living" polymers are ubiquitous in industry and are traditionally realised using surfactants. Here I review the state-of-the-art of living polymers and discuss non-equilibrium extensions that may be realised with advanced…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
Inspired by biological and cultural evolution, there have been many attempts to explore and elucidate the necessary conditions for open-endedness in artificial intelligence and artificial life. Using a continuous cellular automata called…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Prions are misfolded proteins that transmit their structural arrangement to neighboring proteins. In biological systems, prion dynamics can produce a variety of complex functional outcomes. Yet, an understanding of prionic causes has been…
Simple MCBR models of chemical evolution are extended to the limit of dominant gas inflow or outflow with respect to gas locked up into long-lived stars and remnants. For an assigned empirical differential oxygen abundance distribution,…
Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which…
In most biological studies and processes, cell proliferation and population dynamics play an essential role. Due to this ubiquity, a multitude of mathematical models has been developed to describe these processes. While the simplest models…
We are interested in the evolving genealogy of a birth and death process with trait structure and ecological interactions. Traits are hereditarily transmitted from a parent to its offspring unless a mutation occurs. The dynamics may depend…