Related papers: Bubble propagation in a helicoidal molecular chain
We propose a model for DNA dynamics by introducing the helical structure through twist deformation in analogy with the structure of helimagnet and cholesteric liquid crystal system. The dynamics in this case is found to be governed by the…
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…
Measurements of electron transfer rates as well as of charge transport characteristics in DNA produced a number of seemingly contradictory results, ranging from insulating behaviour to the suggestion that DNA is an efficient medium for…
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…
We propose a model Hamiltonian for describing charge transport through short homogeneous double stranded DNA molecules. We show that the hybridization of the overlapping pi orbitals in the base-pair stack coupled to the backbone is…
We study the spreading of initially localized excitations in 1D disordered granular crystals. We thereby investigate localization phenomena in strongly nonlinear systems, which we demonstrate to be fundamentally different from localization…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…
Transcription factors are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional…
We demonstrate that period-doubled discrete breathers appear from the anti-continuum limit of the driven Peyrard-Bishop-Dauxois model of DNA. These novel breathers result from a stability overlap between sub-harmonic solutions of the driven…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
It has been suggested by several authors that nonlinear excitations, in particular solitary waves, could play a fundamental functional role in the process of DNA transcription, effecting the opening of the double chain needed for RNA…
We investigate the dynamics of entanglement in the excitation transfer through a chain of interacting molecules. In the case of two-molecule coupled to noisy environments we show that entanglement can be further enhanced if the distance…
We study the electrical conductance $G$ and the thermopower $S$ of single-molecule junctions, and reveal signatures of different transport mechanisms: off-resonant tunneling, on-resonant coherent (ballistic) motion, and multi-step hopping.…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…