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...

Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based acc...

In this paper, an SIR epidemic model with an infectious period and a non-linear Beddington-DeAngelis type incidence rate function is considered. The dynamics of this model depend on the reproduction number R0. Accurately, if R0 < 1, we show the global asymptotic stability of the disease-free equilibrium by analyzing the corresponding characteristic equation and using compa...

In the current research, thermal conductivity of magnetite (Fe3O4) has been calculated using molecular dynamic simulation. The rNEMD Molecular Dynamics Method provided in the LMMPS package is used for the simulation of the thermal conductivity. The effects of magnetite layer size and temperature on the thermal conductivity have been investigated. The numerical results have...

This paper investigates the mechanism of water transportation through aquaporin-4(AQP4) of ratbrain cells by means of molecular dynamics simulation with CHARMM software. The AQP4 wasembedded into a bilayer made of Dimystroilphosphatylcholine (DMPC). The results illustrate thatwater molecules move through AQP4's channel with change of orientation of oxygen of eachwater molecule.

We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the cis side subchain. We present theoretical and numerical evidence that the non-universal behavior observed in experiments and simulations are due to finite chain length effects that persist well beyond the relevant ex...

Despite providing robustness, high-gain observers impose a peaking phenomenon, which may cause instability, on the system states. In this paper, an adaptive saturation is proposed to attenuate the undesirable mentioned phenomenon in high-gain observers. A real-valued and differentiable sigmoid function is considered as the saturating element whose parameters (height and slope) are adaptively tu...