Related papers: Manipulating a single adsorbed DNA for a critical …
The interactions between Rydberg atoms and microwave fields provide a valuable framework for studying the complex dynamics out of equilibrium, exotic phases, and critical phenomena in many-body physics. This unique interplay allows us to…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We demonstrate that absorbing phase transitions in one dimension may be induced by the dynamics of a single site. As an example we consider a one-dimensional model of diffusing particles, where a single site at the boundary evolves…
We consider a model of a random copolymer at a selective interface which undergoes a localization/delocalization transition. In spite of the several rigorous results available for this model, the theoretical characterization of the phase…
A simple model of the driven motion of interacting particles in a two dimensional random medium is analyzed, focusing on the critical behavior near to the threshold that separates a static phase from a flowing phase with a steady-state…
Trapping, linearization, and imaging of single molecule DNA is of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analyzing methods such as optical mapping. In this study, single DNA…
A phase transition is an example of a ``topological defect'' in the space of parameters of a quantum or classical many-body systems. In this paper, we consider phase diagram topological defects of higher codimension. These have the property…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…
We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front…
We investigate the critical properties of the two-dimensional Z(5) vector model. For this purpose, we propose a new cluster algorithm, valid for Z(N) models with odd values of N. The two-dimensional Z(5) vector model is conjectured to…
DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…
Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…
We consider a self-avoiding walk on the $d$-dimensional hypercubic lattice, terminally attached to an impenetrable hyperplane at which it can adsorb. When a force is applied the walk can be pulled off the surface and we consider the…
We use a two-level simulation method to analyse the critical point associated with demixing of binary hard sphere mixtures. The method exploits an accurate coarse-grained model with two-body and three-body effective interactions. Using this…
Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…
Using exact enumeration methods and Monte Carlo simulations we study the phase diagram relative to the conformational transitions of a two dimensional diblock copolymer. The polymer is made of two homogeneous strands of monomers of…
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds…
Using theory and simulations, we carried out a first systematic characterization of DNA unzipping via nanopore translocation. Starting from partially unzipped states, we found three dynamical regimes depending on the applied force, f: (i)…