Related papers: Molecular dynamics simulation of multivalent ion m…
An efficient approach for the simulation of ion scattering from solids is proposed. For every encountered atom, we take multiple samples of its thermal displacements among those which result in scattering with high probability to finally…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Understanding how the electronic excitation of DNA changes in response to different high-energy particles is central to advancing ion beam cancer therapy. While protons have been the predominant ion of choice in beam cancer therapy, heavier…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
The ion-electron coupling properties for a ion impurity in an electron gas and for a two component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely…
The interaction of mass-selected atomic clusters and nanoparticles with surfaces attracts strong interest in view of fundamental research and technological applications. Understanding dynamics of the deposition process is important for…
In plasma wakefield accelerators, the wave excited in the plasma eventually breaks and leaves behind slowly changing fields and currents that perturb the ion density background. We study this process numerically using the example of a FACET…
Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, we observed that the length of lambda-DNA molecules was extended to about 1.6 times…
The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is…
In this paper we propose an ab initio method to solve quantum many-body problems of molecular dynamics where both the electronic and the nuclear degrees are represented by ensembles of trajectories and guiding waves in physical space. Both…
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and…
The recently developed modified Donnan (mD) model provides a simple and useful description of the electrical double layer in microporous carbon electrodes, suitable for incorporation in porous electrode theory. By postulating an attractive…
The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
We present a 2D lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single Oxygen at the center of a site and two Hydrogen atoms on each…
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer…
To comprehend the complexities of the ice-water interface, we perform a study that attempts to correlate the altered dynamics of water to its perturbed structure at, and due to, the interface. The deviation from bulk values of structural…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
A recently proposed classical-trajectory dynamical screening model for the description of multiple ionization and capture during ion-water molecule collisions is extended to incorporate dynamical screening on both the multi-center target…