Related papers: Optimal Placement of Origins for DNA Replication
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
Gene transcription is a stochastic process that involves thousands of reactions. The first set of these reactions, which happen near a gene promoter, are considered to be the most important in the context of stochastic noise. The most…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells, is, however, a wide open question. We present a…
We consider a problem of replication of random vectors by ordinary integrals in the setting when a underlying random variable is generated by a Wiener process. The goal is to find an optimal adapted process such that its cumulative integral…
Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA.…
Motivated by recent single molecule studies of proteins sliding on a DNA molecule, we explore the targeting dynamics of N particles ("proteins") sliding diffusively along a line ("DNA") in search of their target site (specific target…
How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that the individual repair enzymes do not work independently of each other, but rather interact with…
Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises…
In distributed computing systems with stragglers, various forms of redundancy can improve the average delay performance. We study the optimal replication of data in systems where the job execution time is a stochastically decreasing and…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential…
A central challenge in the study of protein evolution is the identification of historic amino acid sequence changes responsible for creating novel functions observed in present-day proteins. To address this problem, we developed a new…