Related papers: Dynamics of a bubble formed in double stranded DNA
Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of…
We study the statistics, in stationary conditions, of the work $W_\tau$ done by the active force in different systems of self-propelled particles in a time $\tau$. We show the existence of a critical value $W_\tau ^\dag$ such that…
We use the bond fluctuation model to study the contraction process of two polymer loops with $N$ segments that are connected each to the bottom and top part of a Feringa engine. The change in the size of the molecules as well as the folding…
Starting from a spectral expansion of the Fokker-Plank equation for the membrane potential density in a network of spiking neurons, a low-dimensional dynamics of the collective firing rate is derived. As a result a $n$-order ordinary…
We explore the dynamics of active elements performing persistent random motion with fluctuating active speed and in the presence of translational noise in a $d$-dimensional harmonic trap, modeling active speed generation through an…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
We describe the dynamics of a bound state of an attractive $\delta$-well under displacement of the potential. Exact analytical results are presented for the suddenly moved potential. Since this is a quantum system, only a fraction of the…
Fokker-Planck equation with the velocity-dependent coefficients is considered for various isotropic systems on the basis of probability transition (PT) approach. This method provides the self-consistent and universal description of friction…
Examples of self propulsion in strongly fluctuating environment is abound in nature, e.g., molecular motors and pumps operating in living cells. Starting from Langevin equation of motion, we develop a fluctuating thermodynamic description…
We provide an analytical solution for the time-dependent Fokker-Planck equation for a two-dimensional active Brownian particle trapped in an isotropic harmonic potential. Using the passive Brownian particle as basis states we show that the…
The strong well-posedness of the Vlasov-Fokker-Planck-Dean-Kawasaki (VFPDK) equation with correlated noise is established. This equation can be interpreted as the fluctuating mean-field limit of second-order Newtonian particle systems,…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
We investigate the tagged-particle motion in a strongly interacting quasi-confined liquid using periodic boundary conditions along the confining direction. Within a mode-coupling theory of the glass transition (MCT) we calculate the…
Solid state nanopores have emerged as powerful tools for single-molecule sensing, yet the rapid uncontrolled translocation of the molecule through the pore remains a key limitation. We have previously demonstrated that an active…
Using the three-site Hubbard model and Floquet theorem, we investigate the dynamical behaviors of two electrons which are confined in a line-shape three quantum dot molecule driven by an AC electric field. Because the Hamiltonian contains…
We consider self-propelled particles undergoing run-and-tumble dynamics (as exhibited by E. coli) in one dimension. Building on previous analyses at drift-diffusion level for the one-particle density, we add both interactions and noise,…
We study the dynamics of a kink in a one-lane asymmetric simple exclusion process with detachment and attachment of the particle at arbitrary sites. For a system with one site of detachment and attachment we find that the kink is trapped by…
We predict that two correlated particles hopping on a one-dimensional Hubbard lattice can show transient self-acceleration and self-induced Bloch oscillations as a result of anti-Newtonian dynamics. Self-propulsion occurs for two particles…
We consider a two-dimensional disordered conductor in the regime when the superconducting phase is destroyed by the magnetic field. We analyze a combination of fluctuations of different origin which results in an effective interaction…