Related papers: Nonlinear molecular excitations in a completely in…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
We study the dynamics of soliton solutions to the perturbed mKdV equation $\partial_t u = \partial_x(-\partial_x^2 u -2u^3) + \epsilon V u$, where $V\in \mathcal{C}^1_b(\mathbb{R})$, $0<\epsilon\ll 1$. This type of perturbation is…
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a…
A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially…
Charge transport through a short DNA oligomer (Dickerson dodecamer) in presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure…
We investigate dynamically and statistically diffusive motion in a Klein-Gordon particle chain in the presence of disorder. In particular, we examine a low energy (subdiffusive) and a higher energy (self-trapping) case and verify that…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
Instabilities driven by strong gradients appear in a wide variety of physical systems, including plasmas, neutral fluids, and self-gravitating systems. This work develops an analytic formulation to describe the transport structure and…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
We consider the reflectionless transport of sine-Gordon solitons on a line. Transparent boundary conditions for the sine-Gordon equation on a line are derived using the so-called potential approach. Our numerical implementation of these…
We present a very simple model for the study of charge transport in a molecule patterned on B-DNA. In this model we use a discrete non-linear Schr\"{o}dinger equation to describe electrons propagating along the sugar-phosphate backbone of…
We study properties of the localized solitons to the sine-Gordon equation excited on the attractive impurity by a moving kink. The cases of one- and two-dimensional spatially extended impurities are considered. For the case of…
We consider the two-dimensional quantum field theory of a scalar field self-interacting via two periodic terms of frequencies $\alpha$ and $\beta$. Looking at the theory as a perturbed Sine-Gordon model, we use Form Factor Perturbation…
We consider KdV-type equations with $C^1$ nonhomogeneous nonlinearities and small dispersion $\varepsilon$. The first result consists in the conclusion that, in the leading term with respect to $\varepsilon$, the solitary waves in this…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
The conditions under which stable evolution of two nonlinear interacting waves are derived within the context of nematic crystals. Two cases are considered: plane waves and solitons. In the first case, the modulation instability analysis…
The concept of soliton complex in a nonlinear dispersive medium is proposed. It is shown that strongly interacting identical topological solitons in the medium can form bound soliton complexes which move without radiation. This phenomenon…
We unravel stationary states in the form of dark soliton stripes, bubbles, and kinks embedded in a two-dimensional droplet-bearing setting emulated by an extended Gross-Pitaevskii approach. The existence of these configurations is…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
We consider a quasi-one-dimensional two-component Bose-Einstein condensate subject to a coherent coupling between its components, such as realized in spin-orbit coupled condensates. We study how nonlinearity modifies the dynamics of the…