Ab initio molecular dynamics study of collective excitations in liquid H2_2O and D2_2O: Effect of dispersion corrections

The collective dynamics in liquid water is an active research topic experimentally, theoretically and via simulations. Here, ab initio molecular dynamics simulations are reported in heavy and ordinary water at temperature 323.15 K, or 50$^\circ$C. The simulations in heavy water were performed both with and without dispersion corrections. We found that the dispersion correction (DFT-D3) changes the relaxation of density-density time correlation functions from a slow, typical of a supercooled state, to exponential decay behaviour of regular liquids. This implies an essential reduction of the melting point of ice in simulations with DFT-D3. Analysis of longitudinal (L) and transverse (T) current spectral functions allowed us to estimate the dispersions of acoustic and optic collective excitations and to observe the L-T mixing effect. The dispersion correction shifts the L and T optic (O) modes to lower frequencies and provides by almost thirty per cent smaller gap between the longest-wavelength LO and TO excitations, which can be a consequence of a larger effective high-frequency dielectric permittivity in simulations with dispersion corrections. Simulation in ordinary water with the dispersion correction results in frequencies of optic excitations higher than in D$_2$O, and in a long-wavelength LO-TO gap of 24 ps$^{-1}$ (127 cm$^{-1}$).Comment: 14 pages, 9 figure

Pressure-driven flow of oligomeric fluid in nano-channel with complex structure. A dissipative particle dynamics study

We develop a simulational methodology allowing for simulation of the pressure-driven flow in the pore with flat and polymer-modified walls. Our approach is based on dissipative particle dynamics and we combine earlier ideas of fluid-like walls and reverse flow. As a test case we consider the oligomer flow through the pore with flat walls and demonstrate good thermostatting qualities of the proposed method. We found the inhomogeneities in both oligomer shape and alignment across the pore leading to a non-parabolic velocity profiles. The method is subsequently applied to a nano-channel decorated with a polymer brush stripes arranged perpendicularly to the flow direction. At certain threshold value of a flow force we find a pillar-to-lamellar morphological transition, which leads to the brush enveloping the pore wall by a relatively smooth layer. At higher flow rates, the flow of oligomer has similar properties as in the case of flat walls, but for the narrower effective pore size. We observe stretching and aligning of the polymer molecules along the flow near the pore walls.Comment: 14 pages, 12 figure

Solvation force for long ranged wall-fluid potentials

The solvation force of a simple fluid confined between identical planar walls is studied in two model systems with short ranged fluid-fluid interactions and long ranged wall-fluid potentials decaying as $-Az^{-p}, z\to \infty$, for various values of $p$. Results for the Ising spins system are obtained in two dimensions at vanishing bulk magnetic field $h=0$ by means of the density-matrix renormalization-group method; results for the truncated Lennard-Jones (LJ) fluid are obtained within the nonlocal density functional theory. At low temperatures the solvation force $f_{solv}$ for the Ising film is repulsive and decays for large wall separations $L$ in the same fashion as the boundary field $f_{solv}\sim L^{-p}$, whereas for temperatures larger than the bulk critical temperature $f_{solv}$ is attractive and the asymptotic decay is $f_{solv}\sim L^{-(p+1)}$. For the LJ fluid system $f_{solv}$ is always repulsive away from the critical region and decays for large $L$ with the the same power law as the wall-fluid potential. We discuss the influence of the critical Casimir effect and of capillary condensation on the behaviour of the solvation force.Comment: 48 pages, 12 figure

Density functional approach for inhomogeneous star polymers

We propose microscopic density functional theory for inhomogeneous star polymers. Our approach is based on fundamental measure theory for hard spheres, and on Wertheim's first- and second-order perturbation theory for the interparticle connectivity. For simplicity we consider a model in which all the arms are of the same length, but our approach can be easily extended to the case of stars with arms of arbitrary lengths.Comment: 4 pages, 3 figures, submitte

Density functional theory for colloidal mixtures of hard platelets, rods, and spheres

A geometry-based density functional theory is presented for mixtures of hard spheres, hard needles and hard platelets; both the needles and the platelets are taken to be of vanishing thickness. Geometrical weight functions that are characteristic for each species are given and it is shown how convolutions of pairs of weight functions recover each Mayer bond of the ternary mixture and hence ensure the correct second virial expansion of the excess free energy functional. The case of sphere-platelet overlap relies on the same approximation as does Rosenfeld's functional for strictly two-dimensional hard disks. We explicitly control contributions to the excess free energy that are of third order in density. Analytic expressions relevant for the application of the theory to states with planar translational and cylindrical rotational symmetry, e.g. to describe behavior at planar smooth walls, are given. For binary sphere-platelet mixtures, in the appropriate limit of small platelet densities, the theory differs from that used in a recent treatment [L. Harnau and S. Dietrich, Phys. Rev. E 71, 011504 (2004)]. As a test case of our approach we consider the isotropic-nematic bulk transition of pure hard platelets, which we find to be weakly first order, with values for the coexistence densities and the nematic order parameter that compare well with simulation results.Comment: 39 pages, 8 figure

Depletion potentials near geometrically structured substrates

Using the recently developed so-called White Bear version of Rosenfeld's Fundamental Measure Theory we calculate the depletion potentials between a hard-sphere colloidal particle in a solvent of small hard spheres and simple models of geometrically structured substrates: a right-angled wedge or edge. In the wedge geometry, there is a strong attraction beyond the corresponding one near a planar wall that significantly influences the structure of colloidal suspensions in wedges. In accordance with an experimental study, for the edge geometry we find a free energy barrier of the order of several $k_B T$ which repels a big colloidal particle from the edge.Comment: 7 pages, 7 figure

Velocity autocorrelations across the molecular-atomic fluid transformation in hydrogen under pressure

Non-monotonous changes in velocity autocorrelations across the transformation from molecular to atomic fluid in hydrogen under pressure are studied by ab initio molecular dynamics simulations at the temperature 2500 K. We report diffusion coefficients in a wide range of densities from purely molecular fluid up to metallic atomic fluid phase. An analysis of contributions to the velocity autocorrelation functions from the motion of molecular centers-of-mass, rotational and intramolecular vibrational modes is performed, and a crossover in the vibrational density of intramolecular modes across the transition is discussed.Comment: 7 pages, 5 figure

A new procedure for microarray experiments to account for experimental noise and the uncertainty of probe response

Although microarrays are routine analysis tools in biomedical research, theystill yield noisy output that often requires experimental confirmation. Manystudies have aimed at optimizing probe design and statistical analysis totackle this problem. However, less emphasis has been placed on controlling thenoise inherent to the experimental approach. To address this problem, weinvestigate here a procedure that controls for such experimental variance andcombine it with an assessment of probe performance. Two custom arrays were usedto evaluate the procedure: one based on 25mer probes from an Affymetrix designand the other based on 60mer probes from an Agilent design. To assessexperimental variance, all probes were replicated ten times. To assess probeperformance, the probes were calibrated using a dilution series of targetmolecules and the signal response was fitted to an absorption model. We foundthat significant variance of the signal could be controlled by averaging acrossprobes and removing probes that are nonresponsive. Thus, a more reliable signalcould be obtained using our procedure than conventional approaches. We suggestthat once an array is properly calibrated, absolute quantification of signalsbecomes straight forward, alleviating the need for normalization and referencehybridizations.<br

What is the value of water contact angle on silicon?

Silicon is a widely applied material and the wetting of silicon surface is an important phenomenon. However, contradictions in the literature appear considering the value of the water contact angle (WCA). The purpose of this study is to present a holistic experimental and theoretical approach to the WCA determination. To do this, we checked the chemical composition of the silicon (1,0,0) surface by using the X-ray photoelectron spectroscopy (XPS) method, and next this surface was purified using different cleaning methods. As it was proved that airborne hydrocarbons change a solid wetting properties the WCA values were measured in hydrocarbons atmosphere. Next, molecular dynamics (MD) simulations were performed to determine the mechanism of wetting in this atmosphere and to propose the force field parameters for silica wetting simulation. It is concluded that the best method of surface cleaning is the solvent-reinforced de Gennes method, and the WCA value of silicon covered by SiO2 layer is equal to 20.7° (at room temperature). MD simulation results show that the mechanism of pure silicon wetting is similar to that reported for graphene, and the mechanism of silicon covered by SiO2 layer wetting is similar to this observed recently for a MOF