611 research outputs found
Ab initio simulations of Cu binding sites in the N-terminal region of PrP
The prion protein (PrP) binds Cu2+ ions in the octarepeat domain of the
N-terminal tail up to full occupancy at pH=7.4. Recent experiments show that
the HGGG octarepeat subdomain is responsible for holding the metal bound in a
square planar coordination. By using first principle ab initio molecular
dynamics simulations of the Car-Parrinello type, the Cu coordination mode to
the binding sites of the PrP octarepeat region is investigated. Simulations are
carried out for a number of structured binding sites. Results for the complexes
Cu(HGGGW)+(wat), Cu(HGGG) and the 2[Cu(HGGG)] dimer are presented. While the
presence of a Trp residue and a H2O molecule does not seem to affect the nature
of the Cu coordination, high stability of the bond between Cu and the amide
Nitrogens of deprotonated Gly's is confirmed in the case of the Cu(HGGG)
system. For the more interesting 2[Cu(HGGG)] dimer a dynamically entangled
arrangement of the two monomers, with intertwined N-Cu bonds, emerges. This
observation is consistent with the highly packed structure seen in experiments
at full Cu occupancy.Comment: 4 pages, conference proceedin
Metals in Alzheimer's disease: A combined experimental and numerical approach
Alzheimer disease is a pathology causing severe problems with memory, thinking and behavior. It accounts for the majority of dementia cases and is the sixth leading cause of death in developed countries. Unfortunately a real cure is still missing and the drug treatments today available can only reduce symptoms. It belongs to a large class of diseases, called amyloidosis, in which endogenous proteins or peptides undergo a misfolding process switching from the physiological soluble configuration to a pathological fibrillar insoluble state. An important, but not yet fully elucidated, rôle appears to be played in these processes by transition metals (mainly copper and zinc) that have been observed to be present in fairly large amounts in patient's neurological plaques. In this review we will show that the challenging problem of understanding the physico-chemical basis of protein misfolding and aggregation can be successfully investigated with a combination of modern spectroscopic techniques and advanced first principle numerical simulations. In particular, it will be shown that different metals can rival in peptide binding thus adding support to the hypothesis that metal dyshomeostasis may be relevant in the Alzheimer disease development
A simple atomistic model for the simulation of the gel phase of lipid bilayers
In this paper we present the results of a large-scale numerical investigation
of structural properties of a model of cell membrane, simulated as a bilayer of
flexible molecules in vacuum. The study was performed by carrying out extensive
Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two
systems of different sizes (2x32 and 2x256 molecules), over a fairly large set
of temperatures and densities, using parallel platforms and more standard
serial computers. Depending on the dimension of the system, the dynamics was
followed for physical times that go from few hundred of picoseconds for the
largest system to 5--10 nanoseconds for the smallest one. We find that the
bilayer remains stable even in the absence of water and neglecting Coulomb
interactions in the whole range of temperatures and densities we have
investigated. The extension of the region of physical parameters that we have
explored has allowed us to study significant points in the phase diagram of the
bilayer and to expose marked structural changes as density and temperature are
varied, which are interpreted as the system passing from a crystal to a gel
phase.Comment: 41 pages, 13 figure
A photon transport problem with a time-dependent point source
We consider a time-dependent problem of photon transport in an interstellar cloud with a point photon source modeled by a Dirac δ functional. The existence of a unique distributional solution to this problem is established by using the theory of continuous semigroups of operators on locally convex spaces coupled with a constructive approach for producing spaces of generalized functions
Parallel computing and molecular dynamics of biological membranes
In this talk I discuss the general question of the portability of Molecular
Dynamics codes for diffusive systems on parallel computers of the APE family.
The intrinsic single precision arithmetics of the today available APE platforms
does not seem to affect the numerical accuracy of the simulations, while the
absence of integer addressing from CPU to individual nodes puts strong
constraints on the possible programming strategies. Liquids can be very
satisfactorily simulated using the "systolic" method. For more complex systems,
like the biological ones at which we are ultimately interested in, the "domain
decomposition" approach is best suited to beat the quadratic growth of the
inter-molecular computational time with the number of elementary components of
the system. The promising perspectives of using this strategy for extensive
simulations of lipid bilayers are briefly reviewed.Comment: 4 pages LaTeX, 2 figures included, espcrc2.sty require
Constraints of T conformation of carp azide hemoglobin on Fe site structure
AbstractThe iron site structure modifications induced by the transition from the quaternary R to T structure in ferric carp azide hemoglobin have been detected from analysis of multiple scattering resonances in the XANES (X-ray absorption near edge structure) spectra. High signal-to-noise XANES spectra measured at the Frascati ‘wiggler’ synchrotron radiation facility reveal that the forces on the Fe active site, due to the transition from the R to T quaternary conformation, only induce the tilting of the porphyrin plane and probably also of the proximal histidine. The variation of the Fe-N mean distance is not detected by XANES spectroscopy and therefore it is less than 0.01 Å
Electrical properties of individual tin oxide nanowires contacted to platinum electrodes
A simple and useful experimental alternative to field-effect transistors for measuring electrical properties
free electron concentration nd, electrical mobility , and conductivity in individual nanowires has been
developed. A combined model involving thermionic emission and tunneling through interface states is proposed
to describe the electrical conduction through the platinum-nanowire contacts, fabricated by focused ion
beam techniques. Current-voltage I-V plots of single nanowires measured in both two- and four-probe
configurations revealed high contact resistances and rectifying characteristics. The observed electrical behavior
was modeled using an equivalent circuit constituted by a resistance placed between two back-to-back Schottky
barriers, arising from the metal-semiconductor-metal M-S-M junctions. Temperature-dependent I-V measurements
revealed effective Schottky barrier heights up to BE= 0.4 eV
Efeitos de doses e formas de aplicação de reguladores de crescimento em uvas sem sementes, cv. BRS Clara, em região tropical.
O objetivo deste trabalho foi avaliar o efeito do uso dos reguladores vegetais, ácido giberélico e tidiazuron, no tamanho de bagas da cultivar BRS Clara em Região Tropical. Os experimentos foram conduzidos em 2006 e 2007, na Estação Experimental de Viticultura Tropical, em Jales-SP, região noroeste do Estado de São Paulo, em plantas da cv. BRS Clara. Foram testadas diferentes concentrações de GA3 aplicadas isoladamente, combinadas com Crop Set ou tidiazuron, em aplicações únicas ou sequênciais (2 e 4 vezes). As avaliações foram feitas por ocasião da maturação das uvas, considerando-se a massa fresca dos cachos, dos engaços e das bagas, determinadas por meio de balança analítica; o comprimento e o diâmetro médio das bagas, utilizando-se de paquímetro; e o teor de sólidos solúveis (SS), por meio de refratômetro manual. Os experimentos foram conduzidos em delineamento experimental de blocos casualizados, representados por uma planta, com 15 repetições, no ano de 2006, e 10 repetições, no ano de 2007. Os dados foram submetidos à análise de variância e, para a comparação das médias dos tratamentos, foi utilizado o teste Skott Nott, ao nível de 5% de probabilidade. Observou-se que o uso dos reguladores promoveu o crescimento das bagas na cultivar BRS Clara em todos os tratamentos, diferindo da testemunh
Ultimate response dynamics achieved with gas sensors based on self-heated nanowires
Bias current applied to conductometric gas sensors consisting of individual metal oxide nanowires can be used to heat them up to the temperature necessary for sensing. This approach in combination with the good sensitivity and stability of metal-oxide nanowires, can be used to develop prototypes with low power requirements (few tens of microwatts). Here, we present new sensors devices based on this approach that display fast dynamic performance only limited by the gas-solid interaction kinetics,. © 2009
Direct correlation of crystal structure and optical properties in wurtzite/zinc-blende GaAs nanowire heterostructures
A novel method for the direct correlation at the nanoscale of structural and
optical properties of single GaAs nanowires is reported. Nanowires consisting
of 100% wurtzite and nanowires presenting zinc-blende/wurtzite polytypism are
investigated by photoluminescence spectroscopy and transmission electron
microscopy. The photoluminescence of wurtzite GaAs is consistent with a band
gap of 1.5 eV. In the polytypic nanowires, it is shown that the regions that
are predominantly composed of either zinc-blende or wurtzite phase show
photoluminescence emission close to the bulk GaAs band gap, while regions
composed of a nonperiodic superlattice of wurtzite and zinc-blende phases
exhibit a redshift of the photoluminescence spectra as low as 1.455 eV. The
dimensions of the quantum heterostructures are correlated with the light
emission, allowing us to determine the band alignment between these two
crystalline phases. Our first-principles electronic structure calculations
within density functional theory, employing a hybrid-exchange functional,
predict band offsets and effective masses in good agreement with experimental
results
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