Related papers: Bubble relaxation dynamics in homopolymer DNA sequ…
We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the…
We present a computational investigation on the slow dynamics of a mixture of large and small soft spheres. By varying the size disparity at a moderate fixed composition different relaxation scenarios are observed for the small particles.…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
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…
Motivated by the desire to understand complex transient behaviour in fluid flows, we study the dynamics of an air bubble driven by the steady motion of a suspending viscous fluid within a Hele-Shaw channel with a centred depth perturbation.…
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
We analyze the properties of naturally formed nano-bubbles in Lennard-Jones molecular dynamics simulations of liquid-to-vapor nucleation in the boiling and the cavitation regimes. The large computational volumes provide a realistic…
When two bubbles submerged in a liquid are brought closely together, the intermediate liquid film separating the bubbles begins to drain. Once the film ruptures, the bubbles coalesce and form a neck that expands with time. The dynamics of…
Supercooled liquids display dynamics that are inherently heterogeneous in space. This essentially means that at temperatures below the melting point, particle dynamics in certain regions of the liquid can be orders of magnitude faster than…
Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
We study the relaxation of a Brownian particle with long range memory under confinement in one dimension. The particle diffuses in an arbitrary confining potential and resets at random times to previously visited positions, chosen with a…
Stress relaxation following deformation of an entangled polymeric liquid is thought to be affected by transient reforming of chain entanglements. In this work, we use single molecule techniques to study the relaxation of individual polymers…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
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…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…