Related papers: Alternative Splicing and Genomic Stability
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Evolution occurs in populations of reproducing individuals. It is well known that population structure can affect evolutionary dynamics. Traditionally, natural selection is studied between mutants that differ in reproductive rate, but are…
Many life-history traits, like the age at maturity or adult longevity, are important determinants of the generation time. For instance, semelparous species whose adults reproduce once and die have shorter generation times than iteroparous…
We have analysed the possibility of scaling the sexual Penna ageing model. Assuming that the number of genes expressed before the reproduction age grows linearly with the genome size and that the mutation rate per genome and generation is…
Sensory mechanisms in biology, from cells to humans, have the property of adaptivity, whereby the response produced by the sensor is adapted to the overall amplitude of the signal; reducing the sensitivity in the presence of strong…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
The stability of model proteins with designed sequences is assessed in terms of the number of sequences (obtained from the designed sequence through mutations), which fold into 5the ``native'' conformation. By a complete enumeration of the…
As automatic optimization techniques find their way into industrial applications, the behavior of many complex systems is determined by some form of planner picking the right actions to optimize a given objective function. In many cases,…
Genomic expression depends critically both on the ability of regulatory proteins to locate specific target sites on a DNA within seconds and on the formation of long lived (many minutes) complexes between these proteins and the DNA.…
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…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
Darwin introduced the concept of the "living fossil" to describe species belonging to lineages that have experienced little evolutionary change, and suggested that species in more slowly evolving lineages are more prone to extinction (1).…
We analyze the advantage of cell size control strategies in growing populations under mortality constraints. We demonstrate a general advantage of the adder control strategy in the presence of growth-dependent mortality, and for different…
This paper summarizes previous work linking protein aggregation to the heterozygosity of organisms. It also cites the literature showing a correlation between species' morphological complexity and the lengths of their proteins. These two…
Metabolism of living organisms is a foundation of life. The metabolic rate (energy production per unit time) increases slower than organisms' mass. When this phenomenon is considered across different species, it is called interspecific…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Biological soft tissues exhibit elastic properties which can be dramatically different from rubber-type materials (elastomers). To gain a better understanding of the role of constitutive relationships in determining material responses under…