Related papers: Nonlinear waves in double-stranded DNA
Hysteretic damping is often modeled by means of linear viscoelastic approaches such as "nearly constant Attenuation (NCQ)" models. These models do not take into account nonlinear effects either on the stiffness or on the damping, which are…
Biological and physical systems that can be classified as oscillatory media give rise to interesting phenomena like target patterns and spiral waves. The existence of these structures has been proven in the case of systems with local…
We study the evolution of fronts in a bistable reaction-diffusion system when the nonlinear reaction term is spatially non-homogeneous. This equation has been used to model wave propagation in various biological systems. Extending previous…
We present a mechanism to generate unidirectional pulse-shaped propagating waves, tamed to exponential growth and dispersion, in active systems with nonreciprocal and nonlinear couplings. In particular, when all bulk modes are exponentially…
The oscillatory response of nonlinear systems exhibits characteristic phenomena such as multistability, discontinuous jumps and hysteresis. These can be utilized in applications leading, e.g., to precise frequency measurement, mixing,…
Surface curvature of magnetic systems can lead to many static and dynamic effects which are not present in flat systems of the same material. These emergent magnetochiral effects can lead to frequency nonreciprocity of spin waves, which has…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
Cavity dressing of molecular vibrational dynamics expands the role of characteristic vibrations as spectroscopic markers of underlying ultrafast dynamics. Interacting vibrational modes exhibit a pronounced excited state delocalization due…
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.…
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…
A simple generalized model (GM) for coated bubbles accounting for the effect of compressibility of the liquid is presented. The GM was then coupled with nonlinear ODEs that account for the thermal effects. Starting with mass and momentum…
In a previous paper, we modeled the oscillations of a thermally-supported (Bonnor-Ebert) sphere as non-radial, linear perturbations following a standard analysis developed for stellar pulsations. The predicted column density variations and…
The duality between deformations of elastic bodies and non-inertial flows in viscous liquids has been a guiding principle in decades of research. However, this duality is broken when a spheroidal or other doubly-curved liquid film is…
To fully understand, analyze, and determine the behavior of dynamical systems, it is crucial to identify their intrinsic modal coordinates. In nonlinear dynamical systems, this task is challenging as the modal transformation based on the…
We propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We…
The status of the hydrodynamical modelling of nonlinear multi-mode stellar pulsations is discussed. The hydrodynamical modelling of steady double-mode (DM) pulsations has been a long-standing quest that is finally being concluded. Recent…