Related papers: DNA Transcription Mechanism with a Moving Enzyme
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
Recent papers have considered moving breathers (MBs) in DNA models including long range interaction due to the dipole moments of the hydrogen bonds. We have recalculated the value of the charge transfer when hydrogen bonds stretch using…
Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We…
We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
Charge migration along DNA molecules has attracted scientific interest for over half a century. Reports on possible high rates of charge transfer between donor and acceptor through the DNA, obtained in the last decade from solution…
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
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…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…