Related papers: Comparative classical and ab initio Molecular Dyna…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…
The "melting" of self-formed rigid structures made of a small number of interacting classical particles confined in an irregular two-dimensional space is investigated using Monte Carlo simulations. It is shown that the interplay of…
The structural evolution of laser-excited systems of gold has previously been measured through ultrafast MeV electron diffraction. However, there has been a long-standing inability of atomistic simulations to provide a consistent picture of…
Molecular dynamics (MD) simulations are performed to investigate the thermal and mass accommodation coefficients (TAC and MAC, respectively) for the combination of iron(-oxide) and air. The obtained values of TAC and MAC are then used in a…
We consider the Langevin dynamics of a many-body system of interacting particles in $d$ dimensions, in a very general setting suitable to model several out-of-equilibrium situations, such as liquid and glass rheology, active self-propelled…
Thermal and mechanical properties of two-dimensional nanomaterials are commonly studied by calculating force constants using the density functional theory (DFT) and classical molecular dynamics (MD) simulations. Although DFT simulations…
We consider the modified Emden equation (MEE) and introduce its most general solution, using the most general solution for the simple harmonic oscillator's linear dynamical equation (i.e., the initial conditions shall be identified by the…
The study of optomechanical systems has attracted much attention, most of which are concentrated in the physics in the small-amplitude regime. While in this article, we focus on optomechanics in the extremely-large-amplitude regime and…
The structural and dynamic properties of silica melts under high pressure are studied using molecular dynamics (MD) computer simulation. The interactions between the ions are modeled by a pairwise-additive potential, the so-called CHIK…
Quantum Molecular Dynamics models (QMD) are Monte Carlo approaches targeted at the description of nucleon-ion and ion-ion collisions. We have developed a QMD code, which has been used for the simulation of the fast stage of ion-ion…
We have carried out molecular dynamics simulations to understand the dynamics of a tagged pair of atoms in a strongly non-ideal glass-forming binary Lennard-Jones mixture (commonly known as Kob-Andersen model). The generalized…
The dynamics of stability and collapse of a trapped atomic Bose-Einstein condensate (BEC) coupled to a molecular one is studied using the time-dependent Gross-Pitaevskii (GP) equation including a nonlinear interaction term which can…
In this study some properties of the methanol-water mixture such as diffusivity, density, viscosity, and hydrogen bonding were calculated at different temperatures and atmospheric pressure using molecular dynamics simulations (MDS). The…
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…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
Generalizing the mode-coupling theory for ideal liquid-glass transitions, equations of motion are derived for the correlation functions describing the glassy dynamics of a diatomic probe molecule immersed in a simple glass-forming system.…
In Born-Oppenheimer molecular dynamics (BOMD) simulations based on density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…