The viscoelastic properties of strongly coupled Yukawa liquids are characterized by computing the complex shear viscosity η(ω) . This is done using three methods of molecular-dynamics simulation: equilibrium, nonequilibrium, and Langevin dynamics, all with a mutually repulsive Yukawa interparticle potential. A change from viscous to elastic response is observed with increasing frequency, as wel...

When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms ar...

langevin equation for a nano-particle suspended in a laminar fluid flow was analytically studied. the brownian motion generated from molecular bombardment was taken as a wiener stochastic process and approximated by a gaussian white noise. euler-maruyama method was used to solve the langevin equation numerically. the accuracy of brownian simulation was checked by performing a series of simulati...

– Dissipative particle dynamics (DPD) and multi-particle collision (MPC) dynamics are powerful tools to study mesoscale hydrodynamic phenomena accompanied by thermal fluctuations. To understand the advantages of these types of mesoscale simulation techniques in more detail, we propose new two methods, which are intermediate between DPD and MPC — DPD with a multibody thermostat (DPD-MT), and MPC...

The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...

Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. The accumulated influence of these fluctuations is crucial ...

We study the influence of the bulk dynamics of a growing cluster of particles on the properties of its interface. First, we define a general bulk growth model by means of a continuum Master equation for the evolution of the bulk density field. This general model just considers an arbitrary addition of particles (though it can be easily generalized to consider subtraction) with no other physical...

This paper shows that in molecular dynamics (MD) when constant-energy (NVE) simulations of Newton’s equations of motion are attempted using the multiple time stepping (MTS) integrator Verlet-I/r-RESPA/Impulse, there are nonlinear instabilities when the longest step size is a third or possibly a fourth of the period(s) of the fastest motion(s) in the system. This is demonstrated both through a t...

This paper shows that in molecular dynamics (MD) when constantenergy (NVE) simulations of Newton’s equations of motion are attempted using the multiple time stepping (MTS) integrator Verlet-I/r-RESPA/Impulse, there are nonlinear instabilities when the longest step size is a third or possibly a fourth of the period(s) of the fastest motion(s) in the system. This is demonstrated both through a th...