相关论文: Large phenotype jumps in biomolecular evolution
We analyze a (1+1)-dimension directed random walk model of a polymer dipped in a medium constituted by two immiscible solvents separated by a flat interface. The polymer chain is heterogeneous in the sense that a single monomer may…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…
Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based definition of phenotype as a partial steady state that is…
We present a model for evolving population which maintains genetic polymorphism. By introducing random mutation in the model population at a constant rate, we observe that the population does not become extinct but survives, keeping…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
A microscopic agent dynamical model for diploid age-structured populations is used to study evolution of polymorphism and sympatric speciation. The underlying ecology is represented by a unimodal distribution of resources of some width.…
Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state…
We are interested in the study of models describing the evolution of a polymorphic population with mutation and selection in the specific scales of the biological framework of adaptive dynamics. The population size is assumed to be large…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
Current molecular generative models primarily focus on improving drug-target binding affinity and specificity, often neglecting the system-level phenotypic effects elicited by compounds. Transcriptional profiles, as molecule-level readouts…
We model the growth, dispersal and mutation of two phenotypes of a species using reaction-diffusion equations, focusing on the biologically realistic case of small mutation rates. After verifying that the addition of a small linear mutation…
We consider populations structured by a phenotypic trait and a space variable, in a non-homogeneous environment. In the case of sex- ual populations, we are able to derive models close to existing mod- els in theoretical biology, from a…
We are interested in modeling Darwinian evolution resulting from the interplay of phenotypic variation and natural selection through ecological interactions. The population is modeled as a stochastic point process whose generator captures…
Living species, ranging from bacteria to animals, exist in environmental conditions that exhibit spatial and temporal heterogeneity which requires them to adapt. Risk-spreading through spontaneous phenotypic variations is a known concept in…
The growth dynamics of rigid biopolymers, consisting of $N$ parallel protofilaments, is investigated theoretically using simple approximate models. In our approach, the structure of a polymer's growing end and lateral interactions between…
Cellular phenotype is characterized by different components such as cell size, protein content and cell cycle time. These are global variables that are the outcome of multiple internal microscopic processes. Accordingly, they display some…
We consider the model for the distribution of a long homopolymer in a potential field. The typical shape of the polymer depends on the temperature parameter. We show that at a critical value of the temperature the transition occurs from a…
In the context of global warming, tree populations rely on two primary mechanisms of adaptation: phenotypic plasticity, which enables individuals to adjust their behavior in response to environmental stress, and genetic evolution, driven by…
In unicellular organisms such as bacteria and in most viruses, mutations mainly occur during reproduction. Thus, genotypes with a high birth rate should have a higher mutation rate. However, standard models of asexual adaptation such as the…