Structure and magnetic properties of mono- and bi-dispersed ferrofluids as revealed by simulations

Using a Langevin molecular dynamics simulation, we show that the magnetic properties of a mono- and bi-dispersed ferrofluid system depend on the volume fraction and the dipolar coupling parameter. For the bi-dispersed system, most of the chains are formed by the large particles, but the aggregation behavior of the large particles is hindered by the presence of the small particles, which are predominantly attached to the end of the particle chain. To further elucidate the microscopic fluid structure, anisotropic structure factors are calculated.

Structure and viscoelasticity of an electrorheological fluid in oscillatory shear: computer simulation investigation

The three-dimensional molecular dynamics simulation method has been used to study the dynamic responses of an electrorheological (ER) fluid in oscillatory shear. The structure and related viscoelastic behaviour of the fluid are found to be sensitive to the amplitude of the strain. With the increase of the strain amplitude, the structure formed by the particles changes from isolated columns to sheet-like structures which may be perpendicular or parallel to the oscillating direction. Along with the structure evolution, the field-induced moduli decrease significantly with an increase in strain amplitude. The viscoelastic behaviour of the structures obtained in the cases of different strain amplitudes was examined in the linear response regime and an evident structure dependence of the moduli was found. The reason for this lies in the anisotropy of the arrangement of the particles in these structures. Short-range interactions between the particles cannot be neglected in determining the viscoelastic behaviour of ER fluids at small strain amplitude, especially for parallel sheets. The simulation results were compared with available experimental data and good agreement was reached for most of them.

Mode-specificity and transition state-specific energy redistribution in the chemisorption of CH4 on Ni{100}

We have investigated methane (CH4) dissociative chemisorption on the Ni{100} surface by first-principles molecular dynamics (MD) simulations. Our results show that this reaction is mode-specific, with the n1 state being the most strongly coupled to efficient energy flow into the reaction coordinate when the molecule reaches the transition state. By performing MD simulations for two different transition state (TS) structures we provide evidence of TS structure-specific energy redistribution in methane chemisorption. Our results are compared with recently reported state-resolved measurement of methane adsorption probability on nickel surfaces, and we find that a strong correlation exists between the highest vibrational efficacy measured on Ni{100} for the n1 state and the calculated highest fractional vibrational energy content in this mode.

Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design

Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids.

Simulating startup shear of entangled polymer melts

Start-up shear rheology is a standard experiment used for characterizing polymer flow, and to test various models of polymer dynamics. A rich phenomenology is developed for behavior of entangled monodisperse linear polymers in such tests, documenting shear stress overshoots as a function of shear rates and molecular weights. A tube theory does a reasonable qualitative job at describing these phenomena, although it involves several drastic approximations and the agreement can be fortuitous. Recently, Lu and coworkers published several papers [e.g. Lu {\it et al.} {\it ACS Macro Lett}. 2014, 3, 569-573] reporting results from molecular dynamics simulations of linear entangled polymers, which contradict both theory and experiment. Based on these observations, they made very serious conclusions about the tube theory, which seem to be premature. In this letter, we repeat simulations of Lu {\it et al.} and systematically show that neither their simulation results, nor their comparison with theory are confirmed.