Related papers: Large phenotype jumps in biomolecular evolution
Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce…
Understanding the relationship between genomic variation and variation in phenotypes for quantitative traits such as physiology, yield, fitness or behavior, will provide important insights for both predicting adaptive evolution and for…
We study the probabilistic evolution of a birth and death continuous time measure-valued process with mutations and ecological interactions. The individuals are characterized by (phenotypic) traits that take values in a compact metric…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
The presence of phenomena analogous to phase transition in Statistical Mechanics, has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
Biological functions are typically performed by groups of cells that express predominantly the same genes, yet display a continuum of phenotypes. While it is known how one genotype can generate such non-genetic diversity, it remains unclear…
In a physical system, changing parameters such as temperature can induce a phase transition: an abrupt change from one state of matter to another. Analogous phenomena have recently been observed in large language models. Typically, the task…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
By analyzing the real space nonequilibrium dynamics of polymers, we elucidate the physics of driven translocation and propose its dynamical scaling scenario analogous to that in the surface growth phenomena. We provide a detailed account of…
We consider a partial differential equation model for the growth of heterogeneous cell populations subdivided into multiple distinct discrete phenotypes. In this model, cells preferentially move towards regions where they feel less…
Many theoretical models have been formulated to better understand the coevolutionary patterns that emerge from antagonistic interactions. These models usually assume that the attacks by the exploiters are random, so the effect of victim…
The exploration of vast genotype spaces poses fundamental challenges for evolving populations. As the number of genotypes encoding viable phenotypes grows exponentially with genome length, populations can only explore a tiny fraction of…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
Reaction diffusion equations have been used to model a wide range of biological phenomenon related to population spread and proliferation from ecology to cancer. It is commonly assumed that individuals in a population have homogeneous…
By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation, and genetic drift. This requires us to track only four macroscopic variables,…
Identifying subtle phenotypic variations in cellular images is critical for advancing biological research and accelerating drug discovery. These variations are often masked by the inherent cellular heterogeneity, making it challenging to…
We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force $f>\fh \sim k_BT\xi_p/a^2$ the biopolymers behave as Freely Jointed…
In both population genetics and forensic genetics it is important to know how haplotypes are distributed in a population. Simulation of population dynamics helps facilitating research on the distribution of haplotypes. In forensic genetics,…