Related papers: DNA toroid condensation as analytic solutions
As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
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…
We use quantum sine-Gordon model to describe the low energy dynamics of a pair of coupled one-dimensional condensates of interacting atoms. We show that the nontrivial excitation spectrum of the quantum sine-Gordon model, which includes…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
An effective approach for solving the three-dimensional Dirac equation for spherically symmetric local interactions, which we have introduced recently, is reviewed and consolidated. The merit of the approach is in producing Schrodinger-like…
DNA-coated colloids are a popular model system for self-assembly through tunable interactions. The DNA-encoded linkages between particles theoretically allow for very high specificity, but generally no directionality or long-range…
In this paper, we consider a damped Navier-Stokes-Bardina model posed on the whole three-dimensional. These equations have an important physical motivation and they arise from some oceanic model. From the mathematical point of view, they…
In this note we analyze the large time behavior of solutions to an initial/boundary problem involving a damped nonlinear beam equation. We show that under physically realistic conditions on the nonlinear terms in the equation of motion the…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We explicitly give all stationary solutions to the focusing cubic NLS on the line, in the presence of a defect of the type Dirac's delta or delta prime. The models proves interesting for two features: first, they are exactly solvable and…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
A theory of condensation and resolubilization of a dilute DNA solution with growing concentration of multivalent cations, N is suggested. It is based on a new theory of screening of a macroion by multivalent cations, which shows that due to…
Attraction between two indentical objects uniformly charged in solution seems intuitively surprising on the one hand because we know that such objects do repel in vacuum and on another hand because this simple mental picture is still…
We study theoretically a binary system in which an attraction of unlike particles is combined with a type-independent soft core repulsion. The possible experimental implementation of the system is a mixture of DNA-covered colloids, in which…
We present an exact expression for the evolution of the wavefunction of $N$ interacting atoms in an arbitrarily time-dependent, $d$-dimensional parabolic trap potential $\omega(t)$. The interaction potential between atoms is taken to be of…