516 research outputs found
Liquid state properties from first principles DFT calculations: Static properties
In order to test the Vibration-Transit (V-T) theory of liquid dynamics, ab
initio density functional theory (DFT) calculations of thermodynamic properties
of Na and Cu are performed and compared with experimental data. The
calculations are done for the crystal at T = 0 and T_m, and for the liquid at
T_m. The key theoretical quantities for crystal and liquid are the structural
potential and the dynamical matrix, both as function of volume. The theoretical
equations are presented, as well as details of the DFT computations. The
properties compared with experiment are the equilibrium volume, the isothermal
bulk modulus, the internal energy and the entropy. The agreement of theory with
experiment is uniformly good. Our primary conclusion is that the application of
DFT to V-T theory is feasible, and the resulting liquid calculations achieve
the same level of accuracy as does ab initio lattice dynamics for crystals.
Moreover, given the well established reliability of DFT, the present results
provide a significant confirmation of V-T theory itself.Comment: 9 pages, 3 figures, 5 tables, edited to more closely match published
versio
Peculiarities of anharmonic lattice dynamics and thermodynamics of alkaline-earth metals
The calculations are performed for a broad range of the properties of Ca and
Sr in the fcc and bcc phases. A detailed information on the magnitude and
character of temperature dependence of anharmonic effects in the lattice
dynamics over the entire Brillouin zone (frequency shifts and phonon damping,
Gruneisen parameters) is given. A detailed comparison of the computational
results for the heat capacity and thermal expansion with the experimental data
is carried out; the theoretical results are in good agreement with the
experiment.Comment: 16 pages, 19 Postscript figures, Revte
Thermodynamic properties of binary HCP solution phases from special quasirandom structures
Three different special quasirandom structures (SQS) of the substitutional
hcp binary random solutions (, 0.5, and 0.75) are
presented. These structures are able to mimic the most important pair and
multi-site correlation functions corresponding to perfectly random hcp
solutions at those compositions. Due to the relatively small size of the
generated structures, they can be used to calculate the properties of random
hcp alloys via first-principles methods. The structures are relaxed in order to
find their lowest energy configurations at each composition. In some cases, it
was found that full relaxation resulted in complete loss of their parental
symmetry as hcp so geometry optimizations in which no local relaxations are
allowed were also performed. In general, the first-principles results for the
seven binary systems (Cd-Mg, Mg-Zr, Al-Mg, Mo-Ru, Hf-Ti, Hf-Zr, and Ti-Zr) show
good agreement with both formation enthalpy and lattice parameters measurements
from experiments. It is concluded that the SQS's presented in this work can be
widely used to study the behavior of random hcp solutions.Comment: 15 pages, 8 figure
Efficient Isoparametric Integration over Arbitrary, Space-Filling Voronoi Polyhedra for Electronic-Structure Calculations
A numerically efficient, accurate, and easily implemented integration scheme
over convex Voronoi polyhedra (VP) is presented for use in {\it ab-initio}
electronic-structure calculations. We combine a weighted Voronoi tessellation
with isoparametric integration via Gauss-Legendre quadratures to provide
rapidly convergent VP integrals for a variety of integrands, including those
with a Coulomb singularity. We showcase the capability of our approach by first
applying to an analytic charge-density model achieving machine-precision
accuracy with expected convergence properties in milliseconds. For contrast, we
compare our results to those using shape-functions and show our approach is
greater than faster and more accurate. A weighted Voronoi
tessellation also allows for a physics-based partitioning of space that
guarantees convex, space-filling VP while reflecting accurate atomic size and
site charges, as we show within KKR methods applied to Fe-Pd alloys.Comment: 12 Pages, 9 Figures, 4 Tabl
First-principles equation of state and phase stability for the Ni-Al system under high pressures
The equation of state (EOS) of alloys at high pressures is generalized with
the cluster expansion method. It is shown that this provides a more accurate
description. The low temperature EOSs of Ni-Al alloys on FCC and BCC lattices
are obtained with density functional calculations, and the results are in good
agreement with experiments. The merits of the generalized EOS model are
confirmed by comparison with the mixing model. In addition, the FCC phase
diagram of the Ni-Al system is calculated by cluster variation method (CVM)
with both spin-polarized and non-spin-polarized effective cluster interactions
(ECI). The influence of magnetic energy on the phase stability is analyzed. A
long-standing discrepancy between ab initio formation enthalpies and
experimental data is addressed by defining a better reference state. This aids
both evaluation of an ab initio phase diagram and understanding the
thermodynamic behaviors of alloys and compounds. For the first time the
high-pressure behavior of order-disorder transition is investigated by ab
initio calculations. It is found that order-disorder temperatures follow the
Simon melting equation. This may be instructive for experimental and
theoretical research on the effect of an order-disorder transition on shock
Hugoniots.Comment: 27 pages, 12 figure
Interactions between Magnetic Nanowires and Living Cells : Uptake, Toxicity and Degradation
We report on the uptake, toxicity and degradation of magnetic nanowires by
NIH/3T3 mouse fibroblasts. Magnetic nanowires of diameters 200 nm and lengths
comprised between 1 {\mu}m and 40 {\mu}m are fabricated by controlled assembly
of iron oxide ({\gamma}-Fe2O3) nanoparticles. Using optical and electron
microscopy, we show that after 24 h incubation the wires are internalized by
the cells and located either in membrane-bound compartments or dispersed in the
cytosol. Using fluorescence microscopy, the membrane-bound compartments were
identified as late endosomal/lysosomal endosomes labeled with lysosomal
associated membrane protein (Lamp1). Toxicity assays evaluating the
mitochondrial activity, cell proliferation and production of reactive oxygen
species show that the wires do not display acute short-term (< 100 h) toxicity
towards the cells. Interestingly, the cells are able to degrade the wires and
to transform them into smaller aggregates, even in short time periods (days).
This degradation is likely to occur as a consequence of the internal structure
of the wires, which is that of a non-covalently bound aggregate. We anticipate
that this degradation should prevent long-term asbestos-like toxicity effects
related to high aspect ratio morphologies and that these wires represent a
promising class of nanomaterials for cell manipulation and microrheology.Comment: 21 pages 12 figure
Patient perspectives of managing fatigue in ankylosing spondylitis, and views on potential interventions: a qualitative study
<p>Background: Fatigue is a major component of living with ankylosing spondylitis (AS), though it has been largely over-looked, and currently there are no specific agreed management strategies.</p>
<p>Methods: This qualitative exploratory study involved participants who are members of an existing population-based ankylosing spondylitis (PAS) cohort. Participants residing in South West Wales were invited to participate in a focus group to discuss; (1) effects of fatigue, (2) self-management strategies and (3) potential future interventions. The focus groups were audio-recorded and the transcripts were analysed using thematic analysis.</p>
<p>Results: Participants consisted of 3 males/4 females (group 1) and 4 males/3 females (group 2), aged between 35 and 73 years (mean age 53 years). Three main themes were identified: (1) The effects of fatigue were multi-dimensional with participants expressing feelings of being ‘drained’ (physical), ‘upset’ (emotional) and experiencing ‘low-mood’ (psychological); (2) The most commonly reported self-management strategy for fatigue was a balanced combination of activity (exercise) and rest. Medication was reluctantly taken due to side-effects and worries over dependency; (3) Participants expressed a preference for psychological therapies rather than pharmacological for managing fatigue. Information on Mindfulness-Based Stress Reduction (MBSR) was received with interest, with recommendations for delivery in a group format with the option of distance-based delivery for people who were not able to attend a group course.</p>
<p>Conclusions: Patients frequently try and manage their fatigue without any formal guidance or support. Our research indicates there is a need for future research to focus on psychological interventions to address the multi-faceted aspects of fatigue in AS.</p>
Microscopic dynamics in liquid metals: the experimental point of view
The experimental results relevant for the understanding of the microscopic
dynamics in liquid metals are reviewed, with special regards to the ones
achieved in the last two decades. Inelastic Neutron Scattering played a major
role since the development of neutron facilities in the sixties. The last ten
years, however, saw the development of third generation radiation sources,
which opened the possibility of performing Inelastic Scattering with X rays,
thus disclosing previously unaccessible energy-momentum regions. The purely
coherent response of X rays, moreover, combined with the mixed
coherent/incoherent response typical of neutron scattering, provides enormous
potentialities to disentangle aspects related to the collectivity of motion
from the single particle dynamics.
If the last twenty years saw major experimental developments, on the
theoretical side fresh ideas came up to the side of the most traditional and
established theories. Beside the raw experimental results, therefore, we review
models and theoretical approaches for the description of microscopic dynamics
over different length-scales, from the hydrodynamic region down to the single
particle regime, walking the perilous and sometimes uncharted path of the
generalized hydrodynamics extension. Approaches peculiar of conductive systems,
based on the ionic plasma theory, are also considered, as well as kinetic and
mode coupling theory applied to hard sphere systems, which turn out to mimic
with remarkable detail the atomic dynamics of liquid metals. Finally, cutting
edges issues and open problems, such as the ultimate origin of the anomalous
acoustic dispersion or the relevance of transport properties of a conductive
systems in ruling the ionic dynamic structure factor are discussed.Comment: 53 pages, 41 figures, to appear in "The Review of Modern Physics".
Tentatively scheduled for July issu
The structure of the PapD-PapGII pilin complex reveals an open and flexible P5 pocket
P pili are hairlike polymeric structures that mediate binding of uropathogenic Escherichia coli to the surface of the kidney via the PapG adhesin at their tips. PapG is composed of two domains: a lectin domain at the tip of the pilus followed by a pilin domain that comprises the initial polymerizing subunit of the 1,000-plus-subunit heteropolymeric pilus fiber. Prior to assembly, periplasmic pilin domains bind to a chaperone, PapD. PapD mediates donor strand complementation, in which a beta strand of PapD temporarily completes the pilin domain's fold, preventing premature, nonproductive interactions with other pilin subunits and facilitating subunit folding. Chaperone-subunit complexes are delivered to the outer membrane usher where donor strand exchange (DSE) replaces PapD's donated beta strand with an amino-terminal extension on the next incoming pilin subunit. This occurs via a zip-in-zip-out mechanism that initiates at a relatively accessible hydrophobic space termed the P5 pocket on the terminally incorporated pilus subunit. Here, we solve the structure of PapD in complex with the pilin domain of isoform II of PapG (PapGIIp). Our data revealed that PapGIIp adopts an immunoglobulin fold with a missing seventh strand, complemented in parallel by the G1 PapD strand, typical of pilin subunits. Comparisons with other chaperone-pilin complexes indicated that the interactive surfaces are highly conserved. Interestingly, the PapGIIp P5 pocket was in an open conformation, which, as molecular dynamics simulations revealed, switches between an open and a closed conformation due to the flexibility of the surrounding loops. Our study reveals the structural details of the DSE mechanism
Kochen-Specker Vectors
We give a constructive and exhaustive definition of Kochen-Specker (KS)
vectors in a Hilbert space of any dimension as well as of all the remaining
vectors of the space. KS vectors are elements of any set of orthonormal states,
i.e., vectors in n-dim Hilbert space, H^n, n>3 to which it is impossible to
assign 1s and 0s in such a way that no two mutually orthogonal vectors from the
set are both assigned 1 and that not all mutually orthogonal vectors are
assigned 0. Our constructive definition of such KS vectors is based on
algorithms that generate MMP diagrams corresponding to blocks of orthogonal
vectors in R^n, on algorithms that single out those diagrams on which algebraic
0-1 states cannot be defined, and on algorithms that solve nonlinear equations
describing the orthogonalities of the vectors by means of statistically
polynomially complex interval analysis and self-teaching programs. The
algorithms are limited neither by the number of dimensions nor by the number of
vectors. To demonstrate the power of the algorithms, all 4-dim KS vector
systems containing up to 24 vectors were generated and described, all 3-dim
vector systems containing up to 30 vectors were scanned, and several general
properties of KS vectors were found.Comment: 19 pages, 6 figures, title changed, introduction thoroughly
rewritten, n-dim rotation of KS vectors defined, original Kochen-Specker 192
(117) vector system translated into MMP diagram notation with a new graphical
representation, results on Tkadlec's dual diagrams added, several other new
results added, journal version: to be published in J. Phys. A, 38 (2005). Web
page: http://m3k.grad.hr/pavici
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