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

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

Density functional theory and demixing of binary hard rod-polymer mixtures

A density functional theory for a mixture of hard rods and polymers modeled as chains built of hard tangent spheres is proposed by combining the functional due to Yu and Wu for the polymer mixtures [J. Chem. Phys. {\bf 117}, 2368 (2002)] with the Schmidt's functional [Phys. Rev. E {\bf 63}, 50201 (2001)] for rod-sphere mixtures. As a simple application of the functional, the demixing transition into polymer-rich and rod-rich phases is examined. When the chain length increases, the phase boundary broadens and the critical packing fraction decreases. The shift of the critical point of a demixing transition is most noticeable for short chains.Comment: 4 pages,2 figures, in press, PR

School violence, school differences and school discourses

This article highlights one strand of a study which investigated the concept of the violenceresilient school. In six inner-city secondary schools, data on violent incidents in school and violent crime in the neighbourhood were gathered, and compared with school practices to minimise violence, accessed through interviews. Some degree of association between the patterns of behaviour and school practices was found: schools with a wider range of wellconnected practices seemed to have less difficult behaviour. Interviews also showed that the different schools had different organisational discourses for construing school violence, its possible causes and the possible solutions. Differences in practices are best understood in connection with differences in these discourses. Some of the features of school discourses are outlined, including their range, their core metaphor and their silences. We suggest that organisational discourse is an important concept in explaining school effects and school differences, and that improvement attempts could have clearer regard to this concept

Density functional formalism in the canonical ensemble

Density functional theory, when applied to systems with $T\neq 0$, is based on the grand canonical extension of the Hohenberg-Kohn-Sham theorem due to Mermin (HKSM theorem). While a straightforward canonical ensemble generalization fails, work in nanopore systems could certainly benefit from such extension. We show that, if the asymptotic behaviour of the canonical distribution functions is taken into account, the HKSM theorem can be extended to the canonical ensemble. We generate $N$-modified correlation and distribution functions hierarchies and prove that, if they are employed, either a modified external field or the density profiles can be indistinctly used as independent variables. We also write down the $N$% -modified free energy functional and prove that its minimum is reached when the equilibrium values of the new hierarchy are used. This completes the extension of the HKSM theorem.Comment: revtex, to be submitted to Phys. Rev. Let