1,782 research outputs found
Ab initio molecular dynamics study of collective excitations in liquid HO and DO: 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 50C. 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 DO,
and in a long-wavelength LO-TO gap of 24 ps (127 cm).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 , for
various values of . Results for the Ising spins system are obtained in two
dimensions at vanishing bulk magnetic field 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 for the Ising film
is repulsive and decays for large wall separations in the same fashion as
the boundary field , whereas for temperatures larger than
the bulk critical temperature is attractive and the asymptotic decay
is . For the LJ fluid system is always
repulsive away from the critical region and decays for large 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 , 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 -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 % -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
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