Related papers: Molecular dynamics simulation of multivalent ion m…
Ion-mediated interaction is important for the properties of polyelectrolytes such as colloids and nucleic acids. The effective pair interactions between two polyelectrolytes have been investigated extensively, but the many-body effect for…
New interlayer intermolecular potential model was proposed and it represented ``ABAB'' staking of graphite. Hydrogen atom sputtering on graphite surface was investigated using molecular dynamics simulation. In the initial short time period,…
Iron, cobalt and nickel nanoparticles, grown in the gas phase, are known to arrange in chains and bracelet-like rings due to the long-range dipolar interaction between the ferromagnetic (or super-paramagnetic) particles. We investigate the…
The heavy-ion fusion reactions induced by neutron-rich nuclei are investigated with the improved quantum molecular dynamics (ImQMD) model. With a subtle consideration of the neutron skin thickness of nuclei and the symmetry potential, the…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
DNA is the most important biological molecule, and its hydration contributes essentially to the structure and functions of the double helix. We analyze the microhydration of the individual bases of nucleic acids and their methyl derivatives…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Ionic transport in nanopores or nanochannels is key to many cellular processes and is now being explored as a method for DNA/polymer sequencing and detection. Although apparently simple in its scope, the study of ionic dynamics in confined…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
Molecular dynamics simulations of ultrathin water film confined between atomically flat rigid diamond plates are described. Films with thickness of one and two molecular diameters are concerned and TIP4P model is used for water molecules.…
The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs)…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
In the present work an attempt has been made to study the dynamics of a diatomic molecule N2 in water. The proposed model consists of Langevin stochastic differential equation whose solution is obtained through Euler's method. The proposed…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Acid ionization in aprotic media is studied using Molecular Dynamics techniques. In particular, models for HCl ionization in acetonitrile and dimethylsulfoxide are investigated. The proton is treated quantum mechanically using Feynman path…
We present an extension of the multiparticle collision dynamics method for flows with complex interfaces, including supramolecular near-contact interactions mimicking the effect of surfactants. The new method is demonstrated for the case of…
Molecular dynamics simulations have been used extensively to determine equilibrium properties of the electrode-electrolyte interface in supercapacitors held at various potentials. While such studies are essential to understand and optimize…
We have studied by Molecular Dynamics computer simulations the dynamics of water confined in ionic surfactants phases, ranging from well ordered lamellar structures to micelles at low and high water loading, respectively. We have analysed…
Molecular dynamics simulations have been used to study the driving force of ion irradiation induced interfacial mixing in metal bilayers in which the relative mass of the constituents is considerable. We find no apparent effect of chemical…