Relaxation of surface tension in the free-surface boundary layers of simple Lennard-Jones liquids

In this paper we use molecular dynamics to answer a classical question: how does the surface tension on a liquid/gas interface appear? After defining surface tension from the first principles and performing several consistency checks, we perform a dynamic experiment with a single simple liquid nanodroplet. At time zero, we remove all molecules of the interfacial layer of molecules, creating a fresh bare interface with the bulk arrangement of molecules. After that the system evolves towards equilibrium, and the expected surface tension is re-established. We found that the system relaxation consists of three distinct stages. First, the mechanical balance is quickly re-established. During this process the notion of surface tension is meaningless. In the second stage, the surface tension equilibrates, and the density profile broadens to a value which we call “intrinsic” interfacial width. During the third stage, the density profile continues to broaden due to capillary wave excitations, which does not however affect the surface tension.We have observed this scenario for monatomic Lennard-Jones (LJ) liquid as well as for binary LJ mixtures at different temperatures, monitoring a wide range of physical observables.

Relaxation of surface tension in the liquid-solid interfaces of Lennard-Jones liquids

We have established the surface tension relaxation time in the liquid-solid interfaces of Lennard-Jones (LJ) liquids by means of direct measurements in molecular dynamics (MD) simulations. The main result is that the relaxation time is found to be almost independent of the molecular structures and viscosity of the liquids (at seventy-fold change) used in our study and lies in such a range that in slow hydrodynamic motion the interfaces are expected to be at equilibrium. The implications of our results for the modelling of dynamic wetting processes and interpretation of dynamic contact angle data are discussed.

Reversible state transition in nanoconfined aqueous solutions

Using molecular dynamics simulations, we find a reversible transition between the dispersion and aggregation states of solute molecules in aqueous solutions confined in nanoscale geometry, which is not observed in macroscopic systems. The nanoscale confinement also leads to a significant increase of the critical aggregation concentration (CAC). A theoretical model based on Gibbs free energy calculation is developed to describe the simulation results. It indicates that the reversible state transition is attributed to the low free energy barrier (of order kBT) in between two energy minima corresponding to the dispersion and aggregation states, and the enhancement of the CAC results from the fact that at lower concentrations the number of solute molecules is not large enough to allow the formation of a stable cluster in the confined systems.

Regimes of conformational transitions of a diblock polyampholyte

The conformational properties of symmetric flexible diblock polyampholytes are investigated by scaling theory and molecular dynamics simulations. The electrostatically driven coil-globule transition of a symmetric diblock polyampholyte is found to consist of three regimes identified with increasing electrostatic interaction strength. In the first (folding) regime the electrostatic attraction causes the chain to fold through the overlap of the two blocks, while each block is slightly stretched by self-repulsion. The second (weak association or scrambled egg) regime is the classical collapse of the chain into a globule dominated by the fluctuation-induced attractions between oppositely charged sections of the chain. The structure of the formed globule can be represented as a dense packing of the charged chain sections (electrostatic attraction blobs). The third (strong association or ion binding) regime starts with direct binding of oppositely charged monomers (dipole formation), followed by a cascade of multipole formation (quadrupole, hexapole, octupole, etc.), leading to multiplets analogous to those found in ionomers. The existence of the multiplet cascade has also been confirmed in the simulations of solutions of short polymers with only one single charge (either positive or negative) in the middle of each chain. We use scaling theory to estimate the average chain size and the electrostatic correlation length as functions of the chain length, strength of electrostatic interactions, charge fraction, and solvent quality. The theoretically predicted scaling laws of these conformational properties are in very good agreement with our simulation results.

Computer simulations of the structure of colloidal ferrofluids

The structure of a ferrofluid under the influence of an external magnetic field is expected to become anisotropic due to the alignment of the dipoles into the direction of the external field, and subsequently to the formation of particle chains due to the attractive head to tail orientations of the ferrofluid particles. Knowledge about the structure of a colloidal ferrofluid can be inferred from scattering data via the measurement of structure factors. We have used molecular-dynamics simulations to investigate the structure of both monodispersed and polydispersed ferrofluids. The results for the isotropic structure factor for monodispersed samples are similar to previous data by Camp and Patey that were obtained using an alternative Monte Carlo simulation technique, but in a different parameter region. Here we look in addition at bidispersed samples and compute the anisotropic structure factor by projecting the q vector onto the XY and XZ planes separately, when the magnetic field was applied along the z axis. We observe that the XY- plane structure factor as well as the pair distribution functions are quite different from those obtained for the XZ plane. Further, the two- dimensional structure factor patterns are investigated for both monodispersed and bidispersed samples under different conditions. In addition, we look at the scaling exponents of structure factors. Our results should be of value to interpret scattering data on ferrofluids obtained under the influence of an external field.

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.

Applying the chain formation model to magnetic properties of aggregated ferrofluids

The magnetization properties of aggregated ferrofluids are calculated by combining the chain formation model developed by Zubarev with the modified mean-field theory. Using moderate assumptions for the inter- and intrachain interactions we obtain expressions for the magnetization and initial susceptibility. When comparing the results of our theory to molecular dynamics simulations of the same model we find that at large dipolar couplings (lambda>3) the chain formation model appears to give better predictions than other analytical approaches. This supports the idea that chain formation is an important structural ingredient of strongly interacting dipolar particles.

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.

The effect of electric field direction on the-shear stress of ER fluids

The effect of the direction of external electric field on the shear stress of an ER fluid has been studied by molecular-dynamics simulation. Due to the formation of inclined chains, the shear stress strongly depends on the direction of the field, and it may be very large under some special field direction. And theoretical model of ideal microstructure of ER fluids has proved this result. Thus the ER effect may be greatly enhanced just by choosing an optimum direction for the field without any additional requirement, suggesting a promising way to the practical application of ER fluids.

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.

Selectivity in the mechanism of action of antimicrobial mastoparan peptide Polybia-MP1

Many potent antimicrobial peptides also present hemolytic activity, an undesired collateral effect for the therapeutic application. Unlike other mastoparan peptides, Polybia-MP1 (IDWKKLLDAAKQIL), obtained from the venom of the social wasp Polybia paulista, is highly selective of bacterial cells. The study of its mechanism of action demonstrated that it permeates vesicles at a greater rate of leakage on the anionic over the zwitterionic, impaired by the presence of cholesterol or cardiolipin; its lytic activity is characterized by a threshold peptide to lipid molar ratio that depends on the phospholipid composition of the vesicles. At these particular threshold concentrations, the apparent average pore number is distinctive between anionic and zwitterionic vesicles, suggesting that pores are similarly formed depending on the ionic character of the bilayer. To prospect the molecular reasons for the strengthened selectivity in Polybia-MP1 and its absence in Mastoparan-X, MD simulations were carried out. Both peptides presented amphipathic alpha-helical structures, as previously observed in Circular Dichroism spectra, with important differences in the extension and stability of the helix; their backbone solvation analysis also indicate a different profile, suggesting that the selectivity of Polybia-MP1 is a consequence of the distribution of the charged and polar residues along the peptide helix, and on how the solvent molecules orient themselves according to these electrostatic interactions. We suggest that the lack of hemolytic activity of Polybia-MP1 is due to the presence and position of Asp residues that enable the equilibrium of electrostatic interactions and favor the preference for the more hydrophilic environment.

Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel-like activity, and the role of the amidated C-terminus

Anoplin, an antimicrobial, helical decapeptide from wasp venom, looses its biological activities by mere deamidation of its C-terminus. Secondary structure determination, by circular dichroism spectroscopy in amphipathic environments, and lytic activity in zwitterionic and anionic vesicles showed quite similar results for the amidated and the carboxylated forms of the peptide. The deamidation of the C-terminus introduced a negative charge at an all-positive charged peptide, causing a loss of amphipathicity, as indicated by molecular dynamics simulations in TFE/water mixtures and this subtle modification in a peptide`s primary structure disturbed the interaction with bilayers and biological membranes. Although being poorly lytic, the amidated form, but not the carboxylated, presented ion channel-like activity on anionic bilayers with a well-defined conductance step; at approximately the same concentration it showed antimicrobial activity. The pores remain open at trans-negative potentials, preferentially conducting cations, and this situation is equivalent to the interaction of the peptide with bacterial membranes that also maintain a high negative potential inside. Copyright (C) 2007 European Peptide Society and John Wiley & Sons, Ltd.

Polarization and Spectral Shift of Benzophenone in Supercritical Water

Monte Carlo simulation and quantum mechanics calculations based on the INDO/CIS and TD-DFT methods were utilized to study the solvatochromic shift of benzophenone when changing the environment from normal water to supercritical (P = 340.2 atm and T = 673 K) condition. Solute polarization increases the dipole moment of benzophenone, compared to gas phase, by 88 and 35% in normal and supercritical conditions, giving the in-solvent dipole value of 5.8 and 4.2 D, respectively. The average number of solute-solvent hydrogen bonds was analyzed, and a large decrease of 2.3 in normal water to only 0.8 in the supercritical environment was found. By using these polarized models of benzophenone in the two different conditions of water, we performed MC simulations to generate statistically uncorrelated configurations of the solute surrounded by the solvent molecules and subsequent quantum mechanics calculations on these configurations. When changing from normal to supercritical water environment, INDO/CIS calculations explicitly considering all valence electrons of the 235 solvent water molecules resulted in a solvatochromic shift of 1425 cm(-1) for the most intense transition of benzophenone, that is, slightly underestimated in comparison with the experimentally inferred result of 1700 cm(-1). TD-B3LYP/6-311+G(2d,p) calculations on the same configurations but with benzophenone electrostatically embedded in the 320 water molecules resulted in a solvatochromic shift of 1715 cm(-1) for this transition, in very good agreement with the experimental result. When using the unpolarized model of the benzophenone, this calculated solvatochromic shift was only 640 cm(-1). Additional calculations were also made by using BHandHLYP/6-311+G(2d,p) to analyze the effect of the asymptotic decay of the exchange functional. This study indicates that, contrary to the general expectation, there is a sizable solute polarization even in the low-density regime of supercritical condition and that the inclusion of this polarization is important for a reliable description of the spectral shifts considered here.