Related papers: Anomalous dynamics of DNA hairpin folding
We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase…
We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice represents a DNA strand while each of the particles that hop on…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
We use nonequilibrium molecular dynamics simulations to verify recent tube-model predictions that associative polymer networks exhibit broad stretch fluctuations during elongational flow. Simulations further show that these fluctuating…
DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two…
Using a simple model, we study the fluctuating dynamics of inextensible, semiflexible polar filaments interacting with active and directed force generating centres such as molecular motors. Taking into account the fact that the activity…
A generalization of the Drude model is studied. On the one hand, the free motion of the particles is allowed to be sub- or superdiffusive; on the other hand, the distribution of the time delay between collisions is allowed to have a long…
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation…
We study a discrete model of an heterogeneous elastic line with internal disorder, submitted to thermal fluctuations. The monomers are connected through random springs with independent and identically distributed elastic constants drawn…
We show through intensive simulations that the paradigmatic features of anomalous diffusion are indeed the features of a (continuous-time) random walk driven by two different Markovian hopping-trap mechanisms. If $p \in (0,1/2)$ and $1-p$…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
Probing the anomalous nanoscale intermixing using molecular dynamics (MD) simulations in Pt/Ti bilayer we characterize the superdiffusive nature of interfacial atomic transport. In particular, the low-energy ($0.5$ keV) ion-sputtering…
Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA…
Sub-diffusion in biological systems is conventionally treated as anomalous, requiring fractional derivatives, heavy-tailed waiting times, or fitted memory kernels. We argue that this anomaly is an artifact of an incomplete phase space.…
Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction…
We investigate a generic non-phase invariant Hamiltonian model that governs the dynamics of nonlinear dispersive waves. We give evidence that initial data characterized by random phases naturally evolve into phase correlations between…
In this paper, we mathematically describe the time evolution of protein folding features via Iori et al.'s heteropolymer model. More specifically, we identify that the folding amino acid chain evolve according to a power law $D \sim…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…
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…