2,168 research outputs found
Escaping free-energy minima
We introduce a novel and powerful method for exploring the properties of the
multidimensional free energy surfaces of complex many-body systems by means of
a coarse-grained non-Markovian dynamics in the space defined by a few
collective coordinates.A characteristic feature of this dynamics is the
presence of a history-dependent potential term that, in time, fills the minima
in the free energy surface, allowing the efficient exploration and accurate
determination of the free energy surface as a function of the collective
coordinates. We demonstrate the usefulness of this approach in the case of the
dissociation of a NaCl molecule in water and in the study of the conformational
changes of a dialanine in solution.Comment: 3 figure
Ciona intestinalis galectin (CiLgals-a and CiLgals-b) genes are differentially expressed in endostyle zones and challenged by LPS
Immunohistochemical and in situ hybridization assays were performed to answer the question whether
the endostyle, that is the initial gastro-intestinal trait of Ciona intestinalis pharynx, is involved in galectin
(CiLgals-a and CiLgals-b) production during the pharynx inflammatory response to LPS inoculation.
Specific anti-CiLgal-a and anti-CiLgals-b antibodies, and oligonucleotide probes, that mark inflammatory
hemocytes inside the pharynx vessels and vessel epithelium as shown by a previous paper, were assayed
on endostyle histological sections. For the first time, we show that galectins are produced by endostyle
zones, and both CiLgals-a and eb genes are upregulated by LPS. CiLgals-a and CiLgals-b are constitutively
expressed in the endostyle zone 2 and 3, respectively, both genes are upregulated by LPS in the zone 2,
and CiLgals-b in the zone 3 and 4. The antibody-reacting material contained in intracellular and extracellular
large vesicles suggest an unexpected vesicle-dependent transporting mechanism of galectins not
provided with signal peptide. Differential expression and gene upregulation in not-treated and LPStreated
specimens, support the role of endostyle galectins both in filter feeding and defense responses
Momentum distribution, vibrational dynamics and the potential of mean force in ice
By analyzing the momentum distribution obtained from path integral and phonon
calculations we find that the protons in hexagonal ice experience an
anisotropic quasi-harmonic effective potential with three distinct principal
frequencies that reflect molecular orientation. Due to the importance of
anisotropy, anharmonic features of the environment cannot be extracted from
existing experimental distributions that involve the spherical average. The
full directional distribution is required, and we give a theoretical prediction
for this quantity that could be verified in future experiments. Within the
quasi-harmonic context, anharmonicity in the ground state dynamics of the
proton is substantial and has quantal origin, a finding that impacts the
interpretation of several spectroscopies
Displaced path integral formulation for the momentum distribution of quantum particles
The proton momentum distribution, accessible by deep inelastic neutron
scattering, is a very sensitive probe of the potential of mean force
experienced by the protons in hydrogen-bonded systems. In this work we
introduce a novel estimator for the end to end distribution of the Feynman
paths, i.e. the Fourier transform of the momentum distribution. In this
formulation, free particle and environmental contributions factorize. Moreover,
the environmental contribution has a natural analogy to a free energy surface
in statistical mechanics, facilitating the interpretation of experiments. The
new formulation is not only conceptually but also computationally advantageous.
We illustrate the method with applications to an empirical water model,
ab-initio ice, and one dimensional model systems
A self-learning algorithm for biased molecular dynamics
A new self-learning algorithm for accelerated dynamics, reconnaissance
metadynamics, is proposed that is able to work with a very large number of
collective coordinates. Acceleration of the dynamics is achieved by
constructing a bias potential in terms of a patchwork of one-dimensional,
locally valid collective coordinates. These collective coordinates are obtained
from trajectory analyses so that they adapt to any new features encountered
during the simulation. We show how this methodology can be used to enhance
sampling in real chemical systems citing examples both from the physics of
clusters and from the biological sciences.Comment: 6 pages, 5 figures + 9 pages of supplementary informatio
Predicting crystal structures: the Parrinello-Rahman method revisited
By suitably adapting a recent approach [A. Laio and M. Parrinello, PNAS, 99,
12562 (2002)] we develop a powerful molecular dynamics method for the study of
pressure-induced structural transformations. We use the edges of the simulation
cell as collective variables. In the space of these variables we define a
metadynamics that drives the system away from the local minimum towards a new
crystal structure. In contrast to the Parrinello-Rahman method our approach
shows no hysteresis and crystal structure transformations can occur at the
equilibrium pressure. We illustrate the power of the method by studying the
pressure-induced diamond to simple hexagonal phase transition in a model of
silicon.Comment: 5 pages, 2 Postscript figures, submitte
The Ciona intestinalis immune-related galectin genes (CiLgals-a and CiLgals-b) are expressed by the gastric epithelium
The transcription of two Ciona intestinalis galectin genes (CiLgals-a and CiLgalseb) is uparegulated by LPS
in the pharynxis (hemocytes, vessel epithelium, endostilar zones) which is retained the main organ of
the immunity. In this ascidian, for the first time we show, by immunohistochemistry and in situ hybridization
methods, that these two immune-related genes are expressed in the gastric epithelium of
na\uefve ascidians, whereas the galectins appear to be only contained in the intestine columnar epithelium.
In addition, according to previous results on the pharynx, the genes are also expressed and galectins
produced by hemocytes scattered in the connective tissue surrounding the gut. The genes expression and
galectin localization in several tissues, including the previous findings on the transcription upregulation,
the constitutive expression of these genes by endostylar zones and by the gastric epithelium suggest a
potential multifunctional role of these galectins. In this respect, it is of interest to define where the
CiLgals are normally found as related to the tissue functions. Such an approach should be a starting point
for further investigations
Upregulated transcription of phenoloxidase genes in the pharynx and endostyle of Ciona intestinalis in response to LPS
We investigated the role of phenoloxidases (POs) in ascidians inflammatory reaction, a components of a
copper-containing protein family involved in invertebrate immune system. In Ciona intestinalis two phenoloxidases
(CinPO-1, CinPO-2) have been sequenced. In the present study, real time PCR analysis showed
that both CinPO-1 and CinPO-2 genes were modulated by LPS inoculation suggesting that they are inducible
and highly expressed in the inflamed pharynx. In situ hybridization disclosed CinPO-1 and CinPO-2
transcripts in pharynx hemocytes (granulocytes) and, mainly, in unilocular refractile granulocytes (URG)
which mainly populated the inflamed tunic matrix. Interestingly, the genes are also upregulated by LPS in
the endostyle (zones 7, 8 and 9) that is considered homolog to the vertebrate thyroid
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