Related papers: Molecular dynamics simulation of multivalent ion m…
The friction kernel (or memory function) $\gamma(t)$ characterizing single-molecule dynamics in strongly bound liquids exhibits two distinct relaxations with the longer time-scale relaxation associated with attractive intermolecular forces.…
Continuum simulation is employed to study ion transport and fluid flow through a nanopore in a solid-state membrane under an applied potential drop. Results show the existence of concentration polarization layers on the surfaces of the…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
Crystal nucleation is relevant across the domains of fundamental and applied sciences. However, in many cases its mechanism remains unclear due to a lack of temporal or spatial resolution. To gain insights to the molecular details of…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
A simple model is presented for the appearance of attraction between two like charged polyions inside a polyelectrolyte solution. The polyions are modeled as rigid cylinders in a continuum dielectric solvent. The strong electrostatic…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
We study the aging dynamics in a model for dense simple liquids, in which particles interact through a hard-core repulsion complemented by a short-ranged attractive potential, of the kind found in colloidal suspensions. In this system, at…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
The effects of monovalent (Na+, K+) and divalent (Mg2+, Ca2+, Mn2+) ions on the interaction between DNA and histone are studied using the molecular combing technique. Lamda-DNA molecules and DNA-histone complexes incubated with metal…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent…
The effective interaction between two probe particles in a one-dimensional driven system is studied. The analysis is carried out using an asymmetric simple exclusion process with nearest-neighbor interactions. It is found that the driven…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
Systems of dense spheres interacting through very short-ranged attraction are known from theory, simulations and colloidal experiments to exhibit dynamical reentrance. The liquid state can thus be fluidized to higher densities than…
In a recent letter [P.K. Shukla and B. Eliasson, Phys. Rev. Lett. 108, 165007 (2012)] the discovery of a new attractive force between protons in a hydrogen plasma was reported that would be responsible for the formation of molecules and of…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…