相关论文: Large phenotype jumps in biomolecular evolution
A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…
The aim of this paper is to investigate the distribution of a continuous homopolymer in the presence of an attractive finitely supported potential. The most intricate behavior can be observed if we simultaneously vary two parameters: the…
In cancer, treatment failure and disease recurrence have been associated with small subpopulations of cancer cells with a stem-like phenotype. In this paper, we develop and investigate a phenotype-structured model of solid tumour growth in…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
Evolvability is defined as the ability of a population to generate heritable variation to facilitate its adaptation to new environments or selection pressures. In this article, we consider evolvability as a phenotypic trait subject to…
The distribution of fitness effects of adaptive mutations remains poorly understood, both empirically and theoretically. We study this distribution using a version of Fisher's geometrical model without pleiotropy, such that each mutation…
Understanding how stochastic and non-linear deterministic processes interact is a major challenge in population dynamics theory. After a short review, we introduce a stochastic individual-centered particle model to describe the evolution in…
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
By quantitative studies of statistics of polymer stretching in a random flow and of a flow field we demonstrate that the stretching of polymer molecules in a 3D random flow occurs rather sharply via the coil-stretch transition at the value…
Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species,…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the…
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform…
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…
Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states,…
We present a coherent Bayesian framework for selection of the most likely model from the five genetic models (genotypic, additive, dominant, co-dominant, and recessive) commonly used in genetic association studies. The approach uses a…
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…
Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…
Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The number of…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…