319 research outputs found
Towards a mesoscopic model of water-like fluids with hydrodynamic interactions
We present a mesoscopic lattice model for non-ideal fluid flows with
directional interactions, mimicking the effects of hydrogen-bonds in water. The
model supports a rich and complex structural dynamics of the orientational
order parameter, and exhibits the formation of disordered domains whose size
and shape depend on the relative strength of directional order and thermal
diffusivity. By letting the directional forces carry an inverse density
dependence, the model is able to display a correlation between ordered domains
and low density regions, reflecting the idea of water as a denser liquid in the
disordered state than in the ordered one
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
Electro-osmotic flows under nanoconfinement: a self-consistent approach
We introduce a theoretical and numerical method to investigate the properties
of electro-osmotic flows under conditions of extreme confinement. The present
approach, aiming to provide a simple modeling of electrolyte solutions
described as ternary mixtures, which comprises two ionic species and a third
uncharged component, is an extension of our recent work on binary neutral
mixtures. The approach, which combines elements of kinetic theory, density
functional theory with Lattice-Boltzmann algorithms, is microscopic and
self-consistent and does not require the us e of constitutive equations to
determine the fluxes. Numerical solutions are obtained by solving the resulting
coupled equations for the one-particle phase-space distributions of the species
by means of a Lattice Boltzmann discretization procedure. Results are given for
the microscopic density and velocity profiles and for the volumetric and charge
flow.Comment: 5 pages and 3 figures; Europhysics Letters 201
Lattice Boltzmann Method for mixtures at variable Schmidt number
When simulating multicomponent mixtures via the Lattice Boltzmann Method, it
is desirable to control the mutual diffusivity between species while
maintaining the viscosity of the solution fixed. This goal is herein achieved
by a modification of the multicomponent Bhatnagar-Gross-Krook (BGK) evolution
equations by introducing two different timescales for mass and momentum
diffusion. Diffusivity is thus controlled by an effective drag force acting
between species. Numerical simulations confirm the accuracy of the method for
neutral binary and charged ternary mixtures in bulk conditions. The simulation
of a charged mixture in a charged slit channel show that the conductivity and
electro-osmotic mobility exhibit a departure from the Helmholtz-Smoluchowski
prediction at high diffusivity.Comment: 18 pages, 6 figure
Carbon nanotubes and catalysis: the many facets of a successful marriage
Carbon nanotubes have emerged as unique carbon allotropes that bear very interesting prospects in catalysis. Their use is mostly related to that of supports for inorganic metal catalysts, including molecular catalysts, metal nanoparticles, metal oxides or even more complex hierarchical hybrids. However, several reports have shown that they can intriguingly act as metal-free catalysts, with performance often superior to that of other carbon materials, in particular when ad hoc organic functional groups are attached prior to catalytic screening. The range of catalytic reactions is quite wide, and it includes standard organic synthesis, electrocatalysis, photocatalysis as well as other important industrial processes. In the last few years, the energy sector has acquired a dominant role as one of the most sought-after fields of application, given its ever-increasing importance in society
Stabilized Lattice Boltzmann-Enskog method for compressible flows and its application to one and two-component fluids in nanochannels
A numerically stable method to solve the discretized Boltzmann-Enskog
equation describing the behavior of non ideal fluids under inhomogeneous
conditions is presented. The algorithm employed uses a Lagrangian
finite-difference scheme for the treatment of the convective term and a forcing
term to account for the molecular repulsion together with a
Bhatnagar-Gross-Krook relaxation term. In order to eliminate the spurious
currents induced by the numerical discretization procedure, we use a
trapezoidal rule for the time integration together with a version of the
two-distribution method of He et al. (J. Comp. Phys 152, 642 (1999)). Numerical
tests show that, in the case of one component fluid in the presence of a
spherical potential well, the proposed method reduces the numerical error by
several orders of magnitude. We conduct another test by considering the flow of
a two component fluid in a channel with a bottleneck and provide information
about the density and velocity field in this structured geometry.Comment: to appear in Physical Review
hMENA11a contributes to HER3-mediated resistance to PI3K inhibitors in HER2-overexpressing breast cancer cells.
Human Mena (hMENA), an actin regulatory protein of the ENA/VASP family, cooperates with ErbB receptor family signaling in breast cancer. It is overexpressed in high-risk preneoplastic lesions and in primary breast tumors where it correlates with HER2 overexpression and an activated status of AKT and MAPK. The concomitant overexpression of hMENA and HER2 in breast cancer patients is indicative of a worse prognosis. hMENA is expressed along with alternatively expressed isoforms, hMENA11a and hMENAΔv6 with opposite functions. A novel role for the epithelial-associated hMENA11a isoform in sustaining HER3 activation and pro-survival pathways in HER2-overexpressing breast cancer cells has been identified by reverse phase protein array and validated in vivo in a series of breast cancer tissues. As HER3 activation is crucial in mechanisms of cell resistance to PI3K inhibitors, we explored whether hMENA11a is involved in these resistance mechanisms. The specific hMENA11a depletion switched off the HER3-related pathway activated by PI3K inhibitors and impaired the nuclear accumulation of HER3 transcription factor FOXO3a induced by PI3K inhibitors, whereas PI3K inhibitors activated hMENA11a phosphorylation and affected its localization. At the functional level, we found that hMENA11a sustains cell proliferation and survival in response to PI3K inhibitor treatment, whereas hMENA11a silencing increases molecules involved in cancer cell apoptosis. As shown in three-dimensional cultures, hMENA11a contributes to resistance to PI3K inhibition because its depletion drastically reduced cell viability upon treatment with PI3K inhibitor BEZ235. Altogether, these results indicate that hMENA11a in HER2-overexpressing breast cancer cells sustains HER3/AKT axis activation and contributes to HER3-mediated resistance mechanisms to PI3K inhibitors. Thus, hMENA11a expression can be proposed as a marker of HER3 activation and resistance to PI3K inhibition therapies, to select patients who may benefit from these combined targeted treatments. hMENA11a activity could represent a new target for antiproliferative therapies in breast cancer
IMAGE: A New Tool for the Prediction of Transcription Factor Binding Sites
IMAGE is an application tool, based on the vector quantization method, aiding the discovery of nucleotidic sequences corresponding to Transcription Factor binding sites. Starting from the knowledge of regulation regions of a number of co-expressed genes, the software is able to predict the occurrence of specific motifs of different lengths (starting from 6 base pairs) with a defined number of punctual mutations
Eco-Physiological Screening of Different Tomato Genotypes in Response to High Temperatures: A Combined Field-to-Laboratory Approach
High temperatures represent a limitation for growth and development of many crop species. Several studies have demonstrated that the yield reduction of tomato under high temperatures and drought is mainly due to a photosynthetic decline. In this paper, a set of 15 tomato genotypes were screened for tolerance to elevated temperatures by cultivating plants under plastic walk-in tunnels. To assess the potential tolerance of tomato genotypes to high temperatures, measurements of chlorophyll fluorescence, pigments content and leaf functional traits have been carried out together with the evaluation of the final yields. Based on the greenhouse trials, a group of eight putative heat-sensitive and heat-tolerant tomato genotypes was selected for laboratory experiments aimed at investigating the effects of short-term high temperatures treatments in controlled conditions. The chlorophyll fluorescence induction kinetics were recorded on detached leaves treated for 60 min at 35 °C or at 45 °C. The last treatment significantly affected the photosystem II (PSII) photochemical efficiency (namely maximum PSII quantum efficiency, Fv/Fm, and quantum yield of PSII electron transport, ΦPSII) and the non-photochemical quenching (NPQ) in the majority of genotypes. The short-term heat shock treatments also led to significant differences in the shape of the slow Kautsky kinetics and its significant time points (chlorophyll fluorescence levels minimum O, peak P, semi-steady state S, maximum M, terminal steady state T) compared to the control, demonstrating heat shock-induced changes in PSII functionality. Genotypes potentially tolerant to high temperatures have been identified. Our findings support the idea that chlorophyll fluorescence parameters (i.e., ΦPSII or NPQ) and some leaf functional traits may be used as a tool to detect high temperatures-tolerant tomato cultivars
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