Related papers: Quantitative approach to facilitated diffusion wit…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
We study how Cas9, a central component of the CRISPR/Cas9 system, searches for a target sequence on the DNA. We propose a model that includes as key ingredients 3D diffusion, 1D sliding along the DNA, and the effect of short binding…
Recent experiments indicated that disorder effect in DNA may lead to a transition of the charge transport mechanism from band resonant tunnelling to thermal activated hopping. In this letter, based on Mott's variable-range hopping theory we…
In gene expression, various kinds of proteins need to bind to specific locus of DNA. It is still not clear how these proteins find their target locus. In this study, the mean first-passage time (FPT) of protein binding to its target locus…
Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to non-specific adsorption of proteins to DNA and subsequent one-dimensional…
We study the search process of a target on a rapidly folding polymer (`DNA') by an ensemble of particles (`proteins'), whose search combines 1D diffusion along the chain, Levy type diffusion mediated by chain looping, and volume exchange. A…
Transcription factors perform facilitated diffusion (3D diffusion in the cytosol and 1D diffusion on the DNA) when binding to their target sites to regulate gene expression. Here, we investigated the influence of this binding mechanism on…
The insertion of HIV and other DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of these insertions are not random and occupy specific positions within the genome but the physical mechanisms…
Membrane targeting domains play crucial roles in the association of signalling molecules to the plasma membrane. For most peripheral proteins, the protein-to-membrane interaction is transient. After proteins dissociate from the membrane…
To ensure fast gene activation, Transcription Factors (TF) use a mechanism known as facilitated diffusion to find their DNA promoter site. Here we analyze such a process where a TF alternates between 3D and 1D diffusion. In the latter (TF…
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation…
Modeling of DNA-protein interactions is a complex process involving many important time and length scales. This can be facilitated through the use of coarse-grained models which reduce the number of degrees of freedom and allow efficient…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
We study the target searching on the DNA for proteins in the presence of non-constant drift and non-Gaussian $\alpha$-stable L\'evy fluctuations. The target searching is realized by the facilitated diffusion process. The existing works are…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We use a large single particle tracking data set to analyze the short time and small spatial scale motion of quantum dots labeling proteins in cell membranes. Our analysis focuses on the jumps which are the changes in the position of the…