The ionic atmosphere around nucleic acids remains only partially understood at atomic-level detail. Ion counting (IC) experiments provide a quantitative measure of the ionic atmosphere around nucleic acids and, as such, are a natural route for testing quantitative theoretical approaches. In this article, we replicate IC experiments involving duplex DNA in NaCl(aq) using molecular dynamics (MD) ...

Molecular dynamics (MD) is a computer simulation technique where the time evolution of a set of interacting atoms is approximated by integrating their equations of motion. Our goal is to explain the mathematical background of MD for practitioners and researchers in numerical analysis and computational mechanics. The vast majority of these practitioners and researchers work with continuum mechan...

In most of the cases, the experimental study of Nanotechnology involves high cost for Laboratory set-up and the experimentation processes were also slow. So, one cannot rely on experimental nanotechnology alone. As such, the Computer-Based molecular simulations and modeling are one of the foundations of computational nanotechnology. The computer based modeling and simulations were also referred...

We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of tw...

Electron paramagnetic resonance (EPR) spectroscopy using site-directed spin-labeling is an appropriate technique to analyze the structure and dynamics of flexible protein regions as well as protein-protein interactions under native conditions. The analysis of a set of protein mutants with consecutive spin-label positions leads to the identification of secondary and tertiary structure elements. ...

In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD) simulation and binding free energy (ΔGbind) calculation were performed in this work. Molecular docking was carr...

We report results from molecular dynamics (MD) simulations and quasielastic neutron-scattering (QENS) measurements on the rotational dynamics of propane in Na-Y zeolite at room temperature with a loading of four molecules per alpha cage. Rotational part of the intermediate scattering function F(Q,t) obtained from the MD simulation suggests that rotational motion is faster relative to the transl...

In this study, a multi-grid sampling multi-scale (MGSMS) method is proposed by coupling with finite element (FEM), extended (XFEM) and molecular dynamics (MD) methods. Crack studied comprehensively from microscopic initiations to macroscopic propagation MGSMS method. order establish the relationship between model, FEM used transmit displacement boundary conditions atomic model XFEM feedback cra...

We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport informat...

Solution state x-ray diffraction fingerprinting is demonstrated as a method for experimentally assessing the accuracy of molecular dynamics (MD) simulations. Fourier transforms of coordinate data from MD simulations are used to produce reciprocal space "fingerprints" of atomic pair distance correlations that are characteristic of the ensemble and are the direct numerical analogues of experiment...