Dynamical Transition of Myoglobin and Cu／Zn Superoxide Dismutase Revealed by Molecular Dynamics Simulation

We have carried out parallel moecular dynamics simulations of solvated and non-solvated myoglobin and solvated Cu/Zn superoxide dismutase at different temperatures.By analysis of several methods,the simulati8ons reproduce the quasielastic neutron scattering experimental reults.Below 200K these two proteins behave as harmonic solids with essentially only vibrational motion,while above this temperature,there is a striking dynamic transition into anharmonic motion.Moreover,the simulations further show that water molecules play an important role for this dynamical transition.There is no such sharp dynamical transition in non-solvated proteins and the higher the solvate density is ,the steeper at transition point the curve of mean square displacement versus temperature will be.The simulations also display that the dynamical transition is a general propoerty for globular protein and this transition temperature is a demarcation of enzyme activity.     

Copper Nanobelt Reorientation by Molecular Dynamics Simulation

Atomic simulations using embedded atom method （EAM） are performed for Cu （100） nanobelts to study the structural and mechanical behaviour. Cu （100） nanobelts are along[001] taken as the z-axis and have a rectangular cross section in the x - y plane, with [100] and [010] taken as x and y axes. The periodic boundary is used along the z-axis to simulate an infinitely long nanobelt, and other surfaces are free. The simulations are carried out under the mechanical loading with an elongation strain rate of 8.0×10^8 s^-1 along the z-axis. The results show that the nanobelt undergoes a transition from the initial structure with a （100） axis and {100} lateral surfaces to a new structure with the （112） as the z-axis and the lateral surfaces are {111} and {110} respectively, instead of the original {100} surfaces. The mechanism of the structural transition is ascribed to the dislocation propagation through the nanobelt under the external stresses.     

Gold Nanobelt Reorientation by Molecular Dynamics Simulation

The embedded atom method is used to study the structure stability of gold nanobelt. The Au nanobelts have a rectangular cross-section with （100） orientation along the x^-,γ- and z-axes. Free surfaces are used along the x- and y-directions, and periodic boundary condition is used along z-direction. The simulation is performed at different temperatures and cross-section sizes. Our results show that the structure stability of the Au nanobelts depends on the nanobelt size, initial orientation, boundary conditions and temperature. A critical temperature exists for Au nanobelts to transform from initial （100） nanobelt to final （110） nanobelt. The mechanism of the reorientation is the slip and spread of dislocation through the nanobelt under compressive stress caused by tensile surface-stress components.     

Rarefied Gas Flow in Rough Microchannels by Molecular Dynamics Simulation

The molecular dynamics simulation method is applied to investigate the rarefied gas flow in a submicron channel with surface roughness which is modelled by an array of triangle modules. The boundary conditions are found to be determined not only by the Knudsen number but also the roughness, which implies that the breakdown of the Maxwell slip model under the conditions that the surface roughness is comparable to the molecular mean free path. The effects of the rarefaction and the surface roughness on the boundary conditions and the flow characteristics are strongly coupled. The flow friction increases with increasing roughness and with decreasing Knudsen number.     

Structural and Dynamic Properties of Amorphous Silicon： Tight-Binding Molecular Dynamics Simulation

The tight-binding molecular dynamics simulation has been performed to study structural and dynamical properties of amorphous silicon. It is found that the radial distribution function and static structure factor are in good agreement with the experimental measurements. The bond order parameters Q1 are sensitive to the structure change at different quenching rates. For the dynamical properties, we have calculated the vibration and electronic density of states. The simulation results show that the transverse acoustic is in good agreement with the experimental data, and the high frequency transverse optical (TO) peak shifts to the right of the experimental TO peak.     

Modeling the Stretch Behavior of the Single-Crystal Ni–Al Alloy and Its Molecular Dynamics Simulation

Physics of the Solid State - Molecular dynamics simulation was employed in this study to investigate the atomistic mechanisms involved in the Ni–Al alloy homogeneous deformation and the...     

Molecular Dynamics Simulation on Charge Transfer Relaxation between Myoglobin and Water

Dynamical processes of myoglobin after photon-excited charge transfer between Fe ion and surrounding water anion are simulated by a molecular dynamics model. The roles of Coulomb interaction effect and water effect in the relaxation process are discussed. It is found that the relaxations before and after charge transfer are similar. Strong Coulomb interactions and less water mobility decrease Coulomb energy fluctuations. An extra transferred charge of Fe ion has impact on water packing with a distance up to 0.86nm.     

Molecular Dynamical Simulation of Ice Phase Transition： Ice Ih to High-Density Amorphous

We put 5kbar and 12kbar on perfect ice Ih lattice at 77K and 180K. After 30000 simulation steps （in units of 10^-15 s）, high-density amorphous ice is formed. Four-site simple-pair potential TIP4P is used for molecular interactions and the rigid molecular model is employed. Phase transition processes are fitted by an exponential function, and different phase transition times τ are obtained from O-O radial distribution functions （366 and 359fs for 77K and 180K） and O-O-O angle distribution functions （126 and 116fs for 77K and 180K）.     

The Interaction of Polyphenol Flavonoids with β-lactoglobulin: Molecular Docking and Molecular Dynamics Simulation Studies

The interaction of quercetin, quercitrin, and rutin, as natural polyphenolic compounds, with β-lactoglobulin (BLG) using molecular docking and molecular dynamics simulation methods was examined. Molecular docking studies showed that quercetin and quercitrin were bounded to the internal cavity of protein, while rutin was bounded to the entrance of the cavity because of its large structural volume. It was found that there were one-, three-, and four-hydrogen bond interactions between BLG and quercetin, quercitrin, and rutin respectively. This showed that with an increase in the number of OH groups in the flavonoid structure, there was an increase in the number of hydrogen bond interactions. The binding constants for the binding of quercetin, quercitrin, and rutin to BLG were 1.2 × 10⁶, 1.9 × 10⁶, and 7.4 × 10⁴ M^?1 respectively. The results of molecular dynamics simulation showed that the root mean square deviation (RMSD) of non-liganded BLG and BLG–ligand complexes reached equilibration after 3500 ps. The study of the radius of gyration revealed that BLG and BLG–ligand complexes were stabilized around 2500 ps, and unlike the two other complexes, there was no conformational change for BLG–quercetin. Finally, analyzing the RMS fluctuations suggested that the structure of the ligand binding site remained approximately rigid during simulation.     

Molecular Dynamics Simulation of the Structure I Empty Gas Hydrate

The 368 water molecule structure I empty gas hydrates with three possible hydrogen orientations are calculated using TIP4P potential molecular dynamical simulations.The thermodynamic properties and hydrogen bonding are compared with ice Ih.The density of states is analysed based on experimental measurements.The empty gas hydrate at low temperature is stable without gas molecules encaged.     

Molecular Dynamics Simulation of Myoglobin Collision with Low Energy Ions

Collisions of a low energy heavy ion with a myoglobin in water are simulated by molecular dynamics model. The increase of total energy is very small. The mean squared fluctuation decreases at 300 K and increases at 250K. This is an important novel cooling effect that protects the protein from ion damage. The possible collision side effect is the change of tertiary structure that blocks the normal functions of the myoglobin.     

Molecular Dynamics Simulation of Elongation of Copper–Platinum Nanocontacts

Journal of Experimental and Theoretical Physics - The formation of nanocontacts consisting of copper (Cu) and platinum (Pt) atoms at various temperatures (0–300 K), relative concentrations of...     

Fokker–Planck Equation,Molecular Friction,and Molecular Dynamics for Brownian Particle Transport near External Solid Surfaces

The Fokker–Planck (FP) equation describing the dynamics of a single Brownian particle near a fixed external surface is derived using the multiple-time-scales perturbation method, previously used by Cukier and Deutch and Nienhuis in the absence of any external surfaces, and Piasecki et al. for two Brownian spheres in a hard fluid. The FP equation includes an explicit expression for the (time-independent) particle friction tensor in terms of the force autocorrelation function and equilibrium average force on the particle by the surrounding fluid and in the presence of a fixed external surface, such as an adsorbate. The scaling and perturbation analysis given here also shows that the force autocorrelation function must decay rapidly on the zeroth-order time scale ₀, which physically requires N _Kn1, where N _Kn is the Knudsen number (ratio of the length scale for fluid intermolecular interactions to the Brownian particle length scale). This restricts the theory given here to liquid systems where N _Kn1. For a specified particle configuration with respect to the external surface, equilibrium canonical molecular dynamics (MD) calculations are conducted, as shown here, in order to obtain numerical values of the friction tensor from the force autocorrelation expression. Molecular dynamics computations of the friction tensor for a single spherical particle in the absence of a fixed external surface are shown to recover Stokes' law for various types of fluid molecule–particle interaction potentials. Analytical studies of the static force correlation function also demonstrate the remarkable principle of force-time parity whereby the particle friction coefficient is nearly independent of the fluid molecule–particle interaction potential. Molecular dynamics computations of the friction tensor for a single spherical particle near a fixed external spherical surface (adsorbate) demonstrate a breakdown in continuum hydrodynamic results at close particle–surface separation distances on the order of several molecular diameters.     

Simulation of Ab Initio Molecular Dynamics of Shock Wave on Copper

The relation between particle velocity Up, up to 4 km/s, and shock wave velocity Us in copper has been simulated with ab initio molecular dynamics. The simulated relationship without considering the correction of zero-point and finite temperature effects is Us = 4.23 1.53Up. After considering the correction the relation becomes Us = 4.08 1.53Up, which is consistent with the experimental result.     

Molecular Dynamics Simulation of Ion Implantation into HfO2 and HfO2／Si Multi-Layer Structure

We simulate the B, As and P implantations into HfO2 from 3keY to 40keY by a simulator LEACS developed based on molecular dynamics method and by the traditional Monte Carlo simulator TSUPREM4 respectively. The LEACS results accurately fit with the SIMS (secondary ion mass spectroscopy) data, while the TSUPREM4 results deviate from the SIMS data obviously except B implantation. Based on the verification of the simulator, influence of the oxide thickness on the retained range profiles in the Si layer has been quantitatively investigated in the case of HfO2/Si and SiO2/Si structures. The range profiles in the Si layer through HfO2 shift to the surface obviously for about 0.68 times of the oxide layer thickness on the average in comparison to those through SiO2. It can be predicted that this effect will have a significant impact on MOSFET (metallic oxide semiconductor field effect transistor) device performance in the integrated circuit process of the next decade if HfO2 is used to replace SiO2 as the gate dielectric.     

Molecular Dynamics Simulation of Cage Effect in the Glass Transition of Argon

The glass transition process of argon is studied by molecular dynamics simulations with Lennard-Jones potential. The cage effect appears at about 24K. The Lindemann length of argon is found to be 0.55A. Two relaxation processes are clearly observed near the glass transition temperature, which is in agreement with the mode-coupling theory.     

Dynamics of α-Tocopherol Acetate: Proton Relaxation Studies Supported by Molecular Dynamics Simulations

Dynamical properties of α-tocopherol acetate (commonly known as vitamin E) have been investigated in a broad temperature range (below and above the glass transition) by means of proton spin–lattice relaxation. Two distinct relaxation processes have been detected in the studied temperature range. One of them, present in the solid phase, has been attributed to reorientation of methyl groups. In order to identify the motional process leading to the proton relaxation above the glass transition temperature (T _g), molecular dynamics (MD) simulations have been performed, which provided time correlation functions for several internuclear vectors in the molecule. The high-temperature relaxation process is primarily due to dynamics of the aromatic rings of the tocopherol molecule; however, a considerable contribution of diffusion of the aliphatic chain cannot be excluded. Comparing the nuclear magnetic resonance (NMR) results with MD and relaxation data of dielectric spectroscopy (DS) available in the literature (K. Kamiński, S. Maślanka, J. Zioło, M. Paluch, K.J. McGrath, C.M. Roland, Phys Rev E 75:011903-7, 2007; E. Szwajczak, J. Świergiel, R. Stagraczyński, J. Jadżyn, Phys Chem Liq 47:460–466, 2009), the motional process observed in NMR relaxation studies above T _g has been identified with the δ process observed in DS.     

In Silico Study on the Interaction of Thiazolidinediones and β-Lactoglobulin by Molecular Dynamics and Docking Approach

Thiazolidinediones are widely used in the treatment of diabetes mellitus type 2. An investigation of their interaction with a transport protein, such as β-lactoglobulin (BLG), at the atomic level could be a valuable factor in controlling their transport to biological sites. The interaction of troglitazone, pioglitazone, and rosiglitazone, as representative thiazolidinediones, and BLG, as a transport protein, was investigated using molecular docking and molecular dynamics (MD) simulation methods. The molecular docking results showed that these thiazolidinediones bind to the internal cavity of BLG and the BLG affinity for binding the thiazolidinediones decreases in the following order: troglitazone > pioglitazone > rosiglitazone. The analysis of MD simulation trajectories showed that the BLG and BLG-thiazolidinedione complexes became stable at approximately 2500 ps and that there was little conformational change in the BLG-thiazolidinedione complexes over a 10 ns timescale. In addition, the profiles of atomic fluctuations showed the rigidity of the ligand-binding site during the simulation time.     

Formation of NiZr2 Binary Metallic Glass： Experimental and Molecular Dynamics Analyses

The local atomic structure of an amorphous NiZr2 alloy is identified by using x-ray diffraction, transmission electron microscopy, and differential scanning calorimeter. Based on the experimental results, molecular dynamics simulation is performed to investigate the glass formation of liquid NiZr2 alloy. Some relevant features of the pair correlation functions are in good agreement with those obtained by experiment. The pair analysis parameters are calculated, suggesting that there exist icosahedral ordering, four-fold symmetrical bipyramid and triangular- faced polyhedral units in the amorphous NiZr2 structure. The result is beneficial to open avenues toward the understanding of fundamental theoretical problems of glass formation of simple binary alloys.