2,909 research outputs found
Evolution of structure of SiO2 nanoparticles upon cooling from the melt
Evolution of structure of spherical SiO2 nanoparticles upon cooling from the
melt has been investigated via molecular-dynamics (MD) simulations under
non-periodic boundary conditions (NPBC). We use the pair interatomic potentials
which have weak Coulomb interaction and Morse type short-range interaction. The
change in structure of SiO2 nanoparticles upon cooling process has been studied
through the partial radial distribution functions (PRDFs), coordination number
and bond-angle distributions at different temperatures. The core and surface
structures of nanoparticles have been studied in details. Our results show
significant temperature dependence of structure of nanoparticles. Moreover,
temperature dependence of concentration of structural defects in nanoparticles
upon cooling from the melt toward glassy state has been found and discussed.Comment: 12 pages, 6 figure
On the form of growing strings
Patterns and forms adopted by Nature, such as the shape of living cells, the
geometry of shells and the branched structure of plants, are often the result
of simple dynamical paradigms. Here we show that a growing self-interacting
string attached to a tracking origin, modeled to resemble nascent polypeptides
in vivo, develops helical structures which are more pronounced at the growing
end. We also show that the dynamic growth ensemble shares several features of
an equilibrium ensemble in which the growing end of the polymer is under an
effective stretching force. A statistical analysis of native states of proteins
shows that the signature of this non-equilibrium phenomenon has been fixed by
evolution at the C-terminus, the growing end of a nascent protein. These
findings suggest that a generic non-equilibrium growth process might have
provided an additional evolutionary advantage for nascent proteins by favoring
the preferential selection of helical structures.Comment: 4 pages, 3 figures. Accepted for publication in Phys. Rev. Let
Pathways to folding, nucleation events and native geometry
We perform extensive Monte Carlo simulations of a lattice model and the Go
potential to investigate the existence of folding pathways at the level of
contact cluster formation for two native structures with markedly different
geometries. Our analysis of folding pathways revealed a common underlying
folding mechanism, based on nucleation phenomena, for both protein models.
However, folding to the more complex geometry (i.e. that with more non-local
contacts) is driven by a folding nucleus whose geometric traits more closely
resemble those of the native fold. For this geometry folding is clearly a more
cooperative process.Comment: Accepted in J. Chem. Phy
Structural motifs of biomolecules
Biomolecular structures are assemblies of emergent anisotropic building
modules such as uniaxial helices or biaxial strands. We provide an approach to
understanding a marginally compact phase of matter that is occupied by proteins
and DNA. This phase, which is in some respects analogous to the liquid crystal
phase for chain molecules, stabilizes a range of shapes that can be obtained by
sequence-independent interactions occurring intra- and intermolecularly between
polymeric molecules. We present a singularityfree self-interaction for a tube
in the continuum limit and show that this results in the tube being positioned
in the marginally compact phase. Our work provides a unified framework for
understanding the building blocks of biomolecules.Comment: 13 pages, 5 figure
The Vietnamese Version of the Brief Illness Perception Questionnaire and the Beliefs about Medicines Questionnaire:Translation and Cross-cultural Adaptation
OBJECTIVE: To translate and cross-culturally adapt the Brief Illness Perception Questionnaire (BIPQ) and the Beliefs about Medicines Questionnaire (BMQ) into Vietnamese. METHODS: We followed the guideline by Beaton et al. (2000 & 2007). Stage I: two translators (informed and uninformed) translated the questionnaires. Stage II: the translations were synthesized. Stage III: back translation was performed by two translators fluent in both Vietnamese and English but naïve to the outcome measurement. Stage IV: seven experts reached consensus on the pre-final Vietnamese version (BIPQ-V and BMQ-V). Stage V: field test of the questionnaires on 16 twelve-year-old students and 31 Vietnamese patients. In addition, we determined the internal consistency and test-retest reliability of the questionnaires in 34 Vietnamese patients with acute coronary syndrome. RESULTS: All experts agreed that there was semantic, idiomatic, experiential, and conceptual equivalence between the original and pre-final Vietnamese versions of the BIPQ and BMQ. Cronbach's alpha coefficients of the internal consistency were acceptable for the BMQ-V Specific-Necessity (0.64), BMQ-V Specific-Concerns (0.62), and BMQ-V General-Harm (0.60), with the exception of BMQ-V General-Overuse (0.27). Intra-class correlation coefficients of the test-retest reliability was acceptable for the subscales of BMQ-V (range: 0.77-0.86), and BIPQ-V items (range: 0.62-0.85) with the exception of BIPQ-V 1 (0.44, 95% CI -014-0.72) and BIPQ-V 4 (0.57, 95% CI 0.22-0.81). CONCLUSIONS: The Vietnamese version of BIPQ and BMQ are reliable tools to assess illness perceptions and beliefs about medicines of patients with acute coronary syndrome. Psychometric properties of these questionnaires should be tested in different patient populations
Geometry and symmetry presculpt the free-energy landscape of proteins
We present a simple physical model which demonstrates that the native state
folds of proteins can emerge on the basis of considerations of geometry and
symmetry. We show that the inherent anisotropy of a chain molecule, the
geometrical and energetic constraints placed by the hydrogen bonds and sterics,
and hydrophobicity are sufficient to yield a free energy landscape with broad
minima even for a homopolymer. These minima correspond to marginally compact
structures comprising the menu of folds that proteins choose from to house
their native-states in. Our results provide a general framework for
understanding the common characteristics of globular proteins.Comment: 23 pages, 5 figure
Status of water use and potential of rainwater harvesting for replacing centralized supply system in remote mountainous areas: a case study.
The failure of the centralized water supply system forced XY community to become more dependent on uncertain and unstable water sources. The results of surveying 50 households showed that 89.18% of total households depended on water collected from rivers, which contributed 58.3% of the total water volume used for the domestic demands. The average water volume consumed was 19.5 liters/person/day (l/p/d), and 86.5% of households used more than one source; 13.5% of households collected water only from rivers, and 45.94% of families had rainwater harvesting (RWH) for their activities (domestic water demand); however, RWH only provided 9.9% of total water consumption. In this study, basic methods were applied to calculate the storage tanks necessary to balance the water deficit created by drought months. Three levels of water demand (14, 20, and 30 l/p/d) can be the best choices for RWH; for a higher demand (40 and 60 l/p/d), small roof area (30-40 m2), and many people (six to seven) per family, RWH might be impractical because of unsuitable rainfall or excessively large storage tanks
Dynamical chaos and power spectra in toy models of heteropolymers and proteins
The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied
by molecular dynamics simulations. It is shown that two nearby trajectories
quickly diverge from each other if the heteropolymer corresponds to a random
sequence. For good folders, on the other hand, two nearby trajectories may
initially move apart but eventually they come together. Thus good folders are
intrinsically non-chaotic. A choice of a distance of the initial conformation
from the native state affects the way in which a separation between the twin
trajectories behaves in time. This observation allows one to determine the size
of a folding funnel in good folders. We study the energy landscapes of the toy
models by determining the power spectra and fractal characteristics of the
dependence of the potential energy on time. For good folders, folding and
unfolding trajectories have distinctly different correlated behaviors at low
frequencies.Comment: 8 pages, 9 EPS figures, Phys. Rev. E (in press
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