Related papers: Localization of Denaturation Bubbles in Random DNA…
We study a partially disordered one-dimensional system with interacting particles. Concretely, we impose a disorder potential to only every other site, followed by a clean site. Our numerical analysis of eigenstate properties is based on…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
With the aim to understand the role of the constraints in the thermalisation of quantum systems, we study the dynamics of a family of kinetically constrained models arising through duality from the XXZ spin chain. We find that integrable…
The horizontal dynamics of a bouncing ball interacting with an irregular surface is investigated and is found to demonstrate behavior analogous to a random walk. Its stochastic character is substantiated by the calculation of a permutation…
We investigate the dynamics of a single tracer particle performing Brownian motion in a two-dimensional course of randomly distributed hard obstacles. At a certain critical obstacle density, the motion of the tracer becomes anomalous over…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Cyclization of DNA with sticky ends is commonly used to construct DNA minicircles and to measure DNA bendability. The cyclization probability of short DNA (< 150 bp) has a strong length dependence, but how it depends on the rotational…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…
Anderson localization1 in a random system is sensitive to a distance dependence of the excitation transfer amplitude V(r). If V(r) decreases with the distance r slower than 1/r^d in a d-dimensional system then all excitations are…
Topological defects in low-dimensional non-linear systems feature a sliding-to-pinning transition of relevance for a variety of research fields, ranging from biophysics to nano- and solid-state physics. We find that the dynamics after a…
Metastability is a quintessential feature of first order quantum phase transitions, which is lost either by dynamical instability or by nucleating bubbles of a true vacuum through quantum tunneling. By considering a drive across the first…
The dynamics of supercooled liquids slow down and become increasingly heterogeneous as they are cooled. Recently, local structural variables identified using machine learning, such as "softness", have emerged as predictors of local…
We investigate real-space localization in the few-particle regime of the XXZ spin-$1/2$ chain with a random magnetic field. Our investigation focuses on the time evolution of the spatial variance of non-equilibrium densities, as resulting…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
We present detailed molecular dynamics results for the displacement autocorrelation spectra of the Peyrard-Bishop model of thermal DNA denaturation. As the phase transition is approached, the spectra depend on whether the wavelength is…
The deformation of finite-sized bubbles in intense turbulence exhibits complex geometries beyond simple spheroids as the bubbles exchange energy with the surrounding eddies across a wide range of scales. This study investigates deformation…
The inertia of particles driven by the turbulent flow of the surrounding fluid makes them prefer certain regions of the flow. The heavy particles lag behind the flow and tend to accumulate in the regions with less vorticity, while the light…