Related papers: Tautomeric Transitions in DNA
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…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
We study the transition from laminar to chaotic behavior in deterministic chaotic coupled map lattices and in an extension of the stochastic Domany--Kinzel cellular automaton [DK]. For the deterministic coupled map lattices we find evidence…
Ionic currents accompanying DNA translocation strongly depend on molarity of the electrolyte solution and the shape and surface charge of the nanopore. By means of the Poisson-Nernst-Planck equations it is shown how conductance is modulated…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
When double stranded DNA is turned in experiments it undergoes a transition. We use an interacting self-avoiding walk on a three-dimensional fcc lattice weighted by writhe to relate to these experiments and treat this problem via…
Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules e.g.…
The potential energy surface of the H13 proton in base cytosine of the DNA molecules is calculated {\it ab initio} at the Gaussian98 MP2/6-311G(d,p) level. Two potential wells are found. One corresponds to the normal cytosine, while the…
Dynamics of solitons of the Ablowitz-Ladik model in the presence of a random potential is studied. In absence of the random potential it is an integrable model and the solitons are stable. As a result of the random potential this stability…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
The Yakushevich model of DNA torsion dynamics supports soliton solutions, which are supposed to be of special interest for DNA transcription. In the discussion of the model, one usually adopts the approximation $\ell_0 \to 0$, where…
It is well known that transcription can induce torsional stress in DNA, affecting the activity of nearby genes or even inducing structural transitions in the DNA duplex. It has long been assumed that the generation of significant torsional…
In columnar assemblies of helical bio-molecules the azimuthal degrees of freedom, i.e. rotations about the long axes of molecules, may be important in determining the structure of the assemblies especially when the interaction energy…
Crystals form regular and robust structures that under extreme conditions can melt and recrystallize into different arrangements in a process that is called crystal metamorphism. While crystals exist due to the breaking of a continuous…
Photo-ionization induced ultrafast electron dynamics is considered as a precursor to the slower nuclear dynamics associated with molecular dissociation. Here, using ab initio multielectron wave-packet propagation method, we study the…
DNA in sperm cells must undergo an extreme compaction to almost crystalline packing levels. To produce this dense packing, DNA is condensed by protamine, a positively charged protein that loops the DNA into a toroid. Our goal is to…
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…