Related papers: Nonlinear Dynamics of DNA Chain
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
We explore a recently proposed locally resonant granular system bearing harmonic internal resonators in a chain of beads interacting via Hertzian elastic contacts. In this system, we propose the existence of two types of configurations: (a)…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
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…
Quasi-crystals formed by charged mesoscopic dust grains (dust lattices), observed since hardly a decade ago, are an exciting paradigm of a nonlinear chain. In laboratory discharge experiments, these quasi-lattices are formed spontaneously…
We study nonlinear wave phenomena in coupled ring resonator optical waveguides in the tight coupling regime. A discrete model for the system dynamics is put forward and its steady state nonlinear Bloch modes are derived. The switching…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
The question whether a nonlinear localized mode (discrete soliton/breather) can be mobile in a lattice has a standard interpretation in terms of the Peierls-Nabarro (PN) potential barrier. For the most commonly studied cases, the PN barrier…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
Step meandering due to a deterministic morphological instability on vicinal surfaces during growth is studied. We investigate nonlinear dynamics of a step model with asymmetric step kinetics, terrace and line diffusion, by means of a…
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 introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
In this work we report on unusual nonlinear dynamics measured in the resonance response of NbN superconducting microwave resonators. The nonlinear dynamics, occurring at relatively low input powers (2-4 orders of magnitude lower than Nb),…