相关论文: Viral RNA replication modes: evolutionary and dyna…
Polymerization of RNA from a template DNA is carried out by a molecular machine called RNA polymerase (RNAP). It also uses the template as a track on which it moves as a motor utilizing chemical energy input. The time it spends at each…
It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and…
The problem of RNA genomes packaged inside spherical viruses is studied. The viral capsid is modeled as a hollowed sphere. The attraction between RNA molecules and the inner viral capsid is assumed to be non-specific and occurs at the inner…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
We study the population dynamics of lytic viruses which replicate slowly in dividing host cells within an organism or cell culture, and find a range of viral replication rates that allows viruses to persist, avoiding extinction of host…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
The cowpea chlorotic mottle virus (CCMV) has emerged as an exemplary model system to assess the balance between electrostatic and topological features of ssRNA viruses, specifically in the context of the viral self-assembly process. Yet, in…
The steady state properties of the mean density population of infected cells in a viral spread is simulated by a general forest fire like cellular automaton model with two distinct populations of cells ( permissive and resistant ones) and…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how…
Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…
Antimicrobial resistance (AMR) poses a significant threat to public health by increasing mortality, extending hospital stays, and increasing healthcare costs. It affects people of all ages and affects health services, veterinary medicine,…
We study two simple mathematical models of the epidemic. At first, we study the repetitive infection spreading in a simplified SIRS model including the effect of the decay of the acquired immune. The model is an intermediate model of the…
Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which…
In this work, we aim to study that the dynamics behavior for cumulative number of SARS-CoV-2 pandemic can provide information on the overall behavior of the spread over daily time.The cumulative data can be synthesized in an empirical form…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
The rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much…
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-protein interactions. However, many commonly used methods to predict these effects perform poorly in important…
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…