We provide an overview of ongoing work using large scale Molecular Dynamics (MD) simulations to study systems comprising macromolecules and explicit fluid in various contexts relevant to emerging bioanalytical microdevices and single molecule manipulation techniques. In particular, we discuss the application of MD simulations to polymer translocation through a nanopore, electroosmotic flow cont...

In this paper, a multiscale method is developed to predict Young's modulus of fullerene-reinforced polymer nanocomposites (FRPNs). Polymethyl methacrylate chosen as the matrix, while C60 fullerene considered reinforcement. First, molecular dynamics (MD) simulations are conducted calculate Young nanocomposite unit cell with different weight fractions fullerene. Then, micromechanics model for com...

Properties of biomolecules are often investigated using Molecular Dynamics (MD) simulations whereby atoms and molecules interact for a period of time, thus revealing the time dependent behavior of the system. Whereas the atom positions of the starting structures for such MD runs are usually derived from X-ray crystallography or NMR experiments, properties such as charges or bonds are specified ...

Molecular dynamics (MD) simulations at 37 degrees C have been performed on three phospholipid bilayer systems composed of the lipids DLPE, DOPE, and DOPC. The model used included 24 explicit lipid molecules and explicit waters of solvation in the polar head group regions, together with constant-pressure periodic boundary conditions in three dimensions. Using this model, a MD simulation samples ...

The compatibilities of polymer blends, Polypropylene(PP) and Polyamide12(PA12), was simulated by molecular dynamics(MD) simulations. Density, cohesive energy density (CED) ,and solubility parameters(δ) of pure substances and PP/PA12 blends were calculated by MD simulations with the COMPASS force field for the prediction of polymer blends compatibility . Results showed that PP/PA12 is not miscri...

Large-scale molecular dynamics (MD) simulations on two-phase immiscible flows show that, associated with the moving contact line, there is a very large 1/x partial-slip region where x denotes the distance from the contact line. This power-law partial-slip region is verified in large-scale adaptive continuum calculations based on a local, continuum hydrodynamic formulation, which has proved succ...

MOTIVATION Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields. Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always con...

The interaction of ions with interfaces and, in particular, the high specificity of these interactions to the particular ions considered, are central questions in the field of surface forces. Here we study the effect of different salts (NaI, NaCl, CaCl₂ and MgCl₂) on monolayers made of cholesterol molecules, both experimentally (surface area vs. lateral pressure isotherms measured by a Langmuir...

The photoisomerization reaction dynamics of a retinal chromophore in the visual receptor rhodopsin was investigated by means of hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations. The photoisomerization reaction of retinal constitutes the primary step of vision and is known as one of the fastest reactions in nature. To elucidate the molecular mechanism of...

in this work, the thermal reaction of aluminum (al) and nickel oxide (nio) was investigated by molecular dynamics simulations. some effective features of reaction such as reaction temperature, the reaction mechanism, and diffusion rate of oxygen into aluminum structure were studied. reaxff force field was performed to study the al/nio thermite reaction behavior at five different temperatures (5...