Related papers: Molecular dynamics simulation of multivalent ion m…
A simple model of the molecular crystal of $N$ atoms as a statistical mixture in real space of $NX$ atoms in excited and $N(1-X)$ atoms in well localized ground state is considered. The phase coherence of the atomic wave functions is…
Experiments on attractive Bose-Einstein condensates (BECs) have unlocked many intriguing out-of-equilibrium dynamics through the interplay between matter-wave dispersion and nonlinear attractive interaction. Competition between these…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
The properties of a strongly interacting quark plasma are investigated by molecular dynamics method including non-abelian quark-quark potential. Our main goal is to study the thermalization process in this system. We find an interesting…
From cement cohesion to DNA condensation, a proper statistical physics treatment of systems with long range forces is important for a number of applications in physics, chemistry, and biology. We compute here the effective force between…
Ion beam therapy is one of the most progressive methods in cancer treatment. Studies of the water radiolysis process show that the most long-living species that occur in the medium of a biological cell under the action of ionizing…
Belite -- dicalcium silicate Ca$_2$SiO$_4$ -- is a main constituent of low-carbon cement. In this work, we study several terminations of the (010) surface of $\gamma$-belite, its most stable polymorph, by molecular dynamics simulations. The…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…
Most organic and inorganic surfaces (e.g., glass, nucleic acids or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces. Stacks of like-charged…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous…
Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. Here we employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…
We introduce an efficient scheme for the molecular dynamics of electronic systems by means of quantum Monte Carlo. The evaluation of the (Born-Oppenheimer) forces acting on the ionic positions is achieved by two main ingredients: i) the…
Two different preparation methods (liquid-quenching and evaporation) of chalcogenide glasses have been investigated by molecular dynamics simulations. Our particular aim was to determine how the structural changes occur due to the different…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological…
We present a semi-quantitative model of condensation of short nucleic acid (NA) duplexes induced by tri-valent cobalt(III) hexammine (CoHex) ions. The model is based on partitioning of bound counterion distribution around singleNA duplex…
The forces between charged macromolecules, usually given in terms of osmotic pressure, are highly affected by the intervening ionic solution. While in most theoretical studies the solution is treated as a homogeneous structureless…