Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl-) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration....

Besides experimental methods, numerical simulations bring benefits and great opportunities to characterize and predict mechanical behaviors of materials especially at nanoscale. In this study, a nano-single crystal aluminum (Al) as a typical face centered cubic (FCC) metal was modeled based on molecular dynamics (MD) method and by applying tensile and compressive strain loadings its mechanical ...

We have performed NMR spin-lattice relaxation experiments and molecular dynamics (MD) computer simulations on atactic polystyrene (a-PS). The segmental correlation times of three different molecular weight a-PS (Mn ) 1600, 2100, 10 900 g/mol) were extracted from NMR by measuring the 2H spin-lattice relaxation times (T1) over a broad temperature range (390-510 K). MD simulations of an a-PS melt ...

Molecular dynamics (MD) simulation, in which the classical equations of motion for all particles of a system are integrated over finite period of time, is one of the theoretical methods to investigate dynamical properties of molecular systems [1]. The problem which arises in performing MD simulations of such systems is that only short simulations can be performed due to the high-frequency motio...

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...

We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, approximately 250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and...

The inhibition performances of nafcillin (III), methicillin (II) and penicillin G (I) on the corrosion of copper in HCl was studied and tested by weight loss, Tafel polarization, SEM, UV-vis spectrophotometry, molecular dynamics method and quantum chemical calculations. Polarization curves indicated that the studied inhibitors act as mixed-type inhibitors. The values of inhibition efficiency an...

Pyrabactin receptors (PYR) play a central role in abscisic acid (ABA) signal transduction; they are ABA receptors that inhibit type 2C protein phosphatases (PP2C). Molecular aspects contributing to increased basal activity of PYR against PP2C are studied by molecular dynamics (MD) simulations. An extensive series of MD simulations of the apo-form of mutagenized PYR1 as a homodimer and in comple...