Related papers: Bubble relaxation dynamics in homopolymer DNA sequ…
A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence…
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice Boltzmann (LB) method for the solvent…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
When illuminated by a laser, nano particles immersed in water can very quickly and strongly heat up, leading to the nucleation of so called vapor bubbles, which have huge application potential in e.g. solar light-harvesting, catalysis, and…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
We conducted molecular dynamics simulations to investigate chain conformations in adsorbed layers during polymer capillary imbibition. While the imbibition length adheres to the classical Lucas-Washburn equation, a notable deviation in…
Antibubbles, which consist of a shell of a low-density fluid inside a high-density fluid, have several promising applications. We show, via extensive direct numerical simulations (DNSs), in both two and three dimensions (2D and 3D), that…
Molecular dynamics simulations are performed to investigate heterogeneous dynamics in amorphous glassy materials under oscillatory shear strain. We consider three-dimensional binary Lennard-Jones mixture well below the glass transition…
We present the results of molecular dynamics computer simulations of a binary Lennard-Jones liquid confined between two parallel rough walls. These walls are realized by frozen amorphous configurations of the same liquid and therefore the…
The interaction lifetimes between condensate-forming biomolecules can dictate both the specificity of the condensate-forming species as well as the fluidity and exchange dynamics of these condensates. Using a heuristic modeling approach, we…
[abridged] Energy relaxation around a massive black hole (MBH) is key to establishing the dynamical state of galactic nuclei, and the nature of close stellar interactions with the MBH. The standard description of relaxation as diffusion…
The non-linear dynamics of driven oscillations in the size of a spherical bubble are mapped to the dynamics of a Newtonian particle in a potential within the incompressible liquid regime. The compressible liquid regime, which is important…
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…
Diffusion on a diluted hypercube has been proposed as a model for glassy relaxation and is an example of the more general class of stochastic processes on graphs. In this article we determine numerically through large scale simulations the…
The connection between domain relaxations at individual scales and the collective heterogeneous response in non-equilibrium systems is a topic of profound interest in recent times. In a model sys- tem of constantly driven oppositely charged…
The disorder function formalism [Gunaratne et.al., Phys. Rev. E, {\bf 57}, 5146 (1998)]^M is used to show that pattern relaxation in an experiment on a vibrated layer of brass beads^M occurs in three distinct stages. During stage I, all…
Locally (re)structuring colloidal gels $\unicode{x2013}$ micron-sized particles forming a connected network with arrested dynamics $\unicode{x2013}$ enables precise tuning of the micromechanical and -rheological properties of the system. A…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…