Related papers: Optimal Placement of Origins for DNA Replication
Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $\xi_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Biological information processing manifests a huge variety in its complexity and capability among different organisms, which presumably stems from the evolutionary optimization under limited computational resources. Starting from the…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
We examine fluctuation effects due to the low copy number of proteins involved in pattern-forming dynamics within a bacterium. We focus on a stochastic model of the oscillating MinCDE protein system regulating accurate cell division in E.…
Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…
Bacteria are able to maintain a narrow distribution of cell sizes by regulating the timing of cell divisions. In rich nutrient conditions, cells divide much faster than their chromosomes replicate. This implies that cells maintain multiple…
Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect…
The emergence of self-replication and information transmission in life's origin remains unexplained despite extensive research on the topic. A hypothesis explaining the transition from a simple organic world to a complex RNA world is…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
The Moran model with recombination is considered, which describes the evolution of the genetic composition of a population under recombination and resampling. There are $n$ sites (or loci), a finite number of letters (or alleles) at every…
DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its normal role as a {\it polymerase} catalyzing the elongation of a new DNA molecule by adding a…
Genetic stability is a key factor in maintaining, survival and reproduction of biological cells. It relies on many processes, but one of the most important is a {\it homologous recombination}, in which the repair of breaks in…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…