Related papers: DNA confined in a two-dimensional strip geometry
In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand,…
We study a class of Landau-de Gennes energy functionals with a sextic bulk energy density in a three-dimensional domain. We examine the asymptotic behavior of uniformly bounded minimizers in two distinct scenarios: one where their energy…
We present dynamic light scattering (DLS) measurements of soft polymethyl-methacrylate (PMMA) and polyacrylamide(PA) polymer gels prepared with trapped bodies (latex spheres or maghemite nanoparticles). We show that the anomalous…
We study a modified Landau-de Gennes model for nematic liquid crystals, where the elastic term is assumed to be of subquadratic growth in the gradient. We analyze the behaviour of global minimizers in two- and three-dimensional domains,…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
In these proceedings, we first summarize some general properties of phase transitions in the presence of quenched disorder, with emphasis on the following points: the need to distinguish typical and averaged correlations, the possible…
We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC)…
The properties of semiflexible polymers tethered by one end to an impenetrable wall and exposed to oscillatory shear flow are investigated by mesoscale simulations. A polymer, confined in two dimensions, is described by a linear bead-spring…
We investigate the properties of natural two-dimensional (2D) magnetoplasma modes in laterally confined electron systems, such as 2D materials, quantum wells, or inversion layers in semiconductors, with an elliptic Fermi surface. The…
The dynamics of a single chain tethered to an interface and in contact with a cross-linked network is examined numerically. When the network is put in contact with the tethered chain, the chain moves with dynamics that are highly…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
Filamentary structures are ubiquitous in molecular clouds, and have been recently argued to play an important role in regulating the size and mass of embedded clumps through fragmentation and mass accretion. Here, we reveal the dynamical…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
We analyse how simple local constraints in two dimensions lead a defect to exhibit robust, non-transient, and tunable, subdiffusion. We uncover a rich dynamical phenomenology realised in ice- and dimer-type models. On the microscopic scale…
In a recent work on fluid infiltration in a Hele-Shaw cell with the pore-block geometry of Sierpinski carpets (SCs), the area filled by the invading fluid was shown to scale as F~t^n, with n<1/2, thus providing a macroscopic realization of…
Two-dimensional (2D) nanomaterials exhibit unique properties that are promising for diverse applications, including those relevant to concentration-gradient-driven transport of electrolyte solutions through porous membranes made from these…
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
The nanoscale fluctuation dynamics of semi dilute high molecular weight polymer solutions of Polyethylenoxide (PEO) in D2O under non-equilibrium flow conditions were studied by the neutron spin-echo technique. The sample cell was in…