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

Coherent phenomena in semiconductors

A review of coherent phenomena in photoexcited semiconductors is presented. In particular, two classes of phenomena are considered: On the one hand the role played by optically-induced phase coherence in the ultrafast spectroscopy of semiconductors; On the other hand the Coulomb-induced effects on the coherent optical response of low-dimensional structures. All the phenomena discussed in the paper are analyzed in terms of a theoretical framework based on the density-matrix formalism. Due to its generality, this quantum-kinetic approach allows a realistic description of coherent as well as incoherent, i.e. phase-breaking, processes, thus providing quantitative information on the coupled ---coherent vs. incoherent--- carrier dynamics in photoexcited semiconductors. The primary goal of the paper is to discuss the concept of quantum-mechanical phase coherence as well as its relevance and implications on semiconductor physics and technology. In particular, we will discuss the dominant role played by optically induced phase coherence on the process of carrier photogeneration and relaxation in bulk systems. We will then review typical field-induced coherent phenomena in semiconductor superlattices such as Bloch oscillations and Wannier-Stark localization. Finally, we will discuss the dominant role played by Coulomb correlation on the linear and non-linear optical spectra of realistic quantum-wire structures.Comment: Topical review in Semiconductor Science and Technology (in press) (Some of the figures are not available in electronic form

Dust from AGBs: relevant factors and modelling uncertainties

The dust formation process in the winds of Asymptotic Giant Branch stars is discussed, based on full evolutionary models of stars with mass in the range $1$M$_{\odot} \leq$M$\leq 8$M$_{\odot}$, and metallicities $0.001 < Z <0.008$. Dust grains are assumed to form in an isotropically expanding wind, by growth of pre--existing seed nuclei. Convection, for what concerns the treatment of convective borders and the efficiency of the schematization adopted, turns out to be the physical ingredient used to calculate the evolutionary sequences with the highest impact on the results obtained. Low--mass stars with M$\leq 3$M$_{\odot}$ produce carbon type dust with also traces of silicon carbide. The mass of solid carbon formed, fairly independently of metallicity, ranges from a few $10^{-4}$M$_{\odot}$, for stars of initial mass $1-1.5$M$_{\odot}$, to $\sim 10^{-2}$M$_{\odot}$ for M$\sim 2-2.5$M$_{\odot}$; the size of dust particles is in the range $0.1 \mu$m$\leq a_C \leq 0.2\mu$m. On the contrary, the production of silicon carbide (SiC) depends on metallicity. For $10^{-3} \leq Z \leq 8\times 10^{-3}$ the size of SiC grains varies in the range $0.05 \mu {\rm m} < {\rm a_{SiC}} < 0.1 \mu$m, while the mass of SiC formed is $10^{-5}{\rm M}_{\odot} < {\rm M_{SiC}} < 10^{-3}{\rm M}_{\odot}$. Models of higher mass experience Hot Bottom Burning, which prevents the formation of carbon stars, and favours the formation of silicates and corundum. In this case the results scale with metallicity, owing to the larger silicon and aluminium contained in higher--Z models. At Z=$8\times 10^{-3}$ we find that the most massive stars produce dust masses $m_d \sim 0.01$M$_{\odot}$, whereas models of smaller mass produce a dust mass ten times smaller. The main component of dust are silicates, although corundum is also formed, in not negligible quantities ($\sim 10-20\%$).Comment: Paper accepted for publication in Monthly Notices of the Royal Astronomical Society Main Journal (2014 January 4

Methylglyoxal-dependent glycative stress and deregulation of SIRT1 functional network in the ovary of PCOS mice

Advanced glycation end-products (AGEs) are involved in the pathogenesis and consequences of polycystic ovary syndrome (PCOS), a complex metabolic disorder associated with female infertility. The most powerful AGE precursor is methylglyoxal (MG), a byproduct of glycolysis, that is detoxified by the glyoxalase system. By using a PCOS mouse model induced by administration of dehydroepiandrosterone (DHEA), we investigated whether MG-dependent glycative stress contributes to ovarian PCOS phenotype and explored changes in the Sirtuin 1 (SIRT1) functional network regulating mitochondrial functions and cell survival. In addition to anovulation and reduced oocyte quality, DHEA ovaries revealed altered collagen deposition, increased vascularization, lipid droplets accumulation and altered steroidogenesis. Here we observed increased intraovarian MG-AGE levels in association with enhanced expression of receptor for AGEs (RAGEs) and deregulation of the glyoxalase system, hallmarks of glycative stress. Moreover, DHEA mice exhibited enhanced ovarian expression of SIRT1 along with increased protein levels of SIRT3 and superoxide dismutase 2 (SOD2), and decreased peroxisome proliferator-activated receptor gamma co-activator 1 alpha (PGC1 alpha), mitochondrial transcriptional factor A (mtTFA) and translocase of outer mitochondrial membrane 20 (TOMM20). Finally, the presence of autophagy protein markers and increased AMP-activated protein kinase (AMPK) suggested the involvement of SIRT1/AMPK axis in autophagy activation. Overall, present findings demonstrate that MG-dependent glycative stress is involved in ovarian dysfunctions associated to PCOS and support the hypothesis of a SIRT1-dependent adaptive response

Quark masses with Nf=2 twisted mass lattice QCD

We present the results of the recent high precision lattice calculation of the average up/down, strange and charm quark masses performed by ETMC with Nf=2 twisted mass Wilson fermions. The analysis includes data at four values of the lattice spacing and pion masses as low as ~270 MeV, allowing for accurate continuum limit and chiral extrapolation. The strange and charm masses are extracted by using several methods, based on different observables: the kaon and the eta_s meson for the strange quark and the D, D_s and eta_c mesons for the charm. The quark mass renormalization is carried out non-perturbatively using the RI-MOM method. The results for the quark masses in the MSbar scheme read: m_ud(2 GeV)= 3.6(2) MeV, m_s(2 GeV)=95(6) MeV and m_c(m_c)=1.28(4) GeV. We have also obtained the ratios m_s/m_ud=27.3(9) and m_c/m_s=12.0(3). Moreover, we provide the updated result for the bottom quark mass, m_b(m_b)=4.3(2) GeV, obtained using the method presented in 0909.3187 [hep-lat].Comment: 7 pages, 7 figures, talk given at the XXVIII International Symposium on Lattice Field Theory (Lattice 2010), June 14-19 2010, Villasimius, Ital

Dissipation and Decoherence in Nanodevices: a Generalized Fermi's Golden Rule

We shall revisit the conventional adiabatic or Markov approximation, which --contrary to the semiclassical case-- does not preserve the positive-definite character of the corresponding density matrix, thus leading to highly non-physical results. To overcome this serious limitation, originally pointed out and partially solved by Davies and co-workers almost three decades ago, we shall propose an alternative more general adiabatic procedure, which (i) is physically justified under the same validity restrictions of the conventional Markov approach, (ii) in the semiclassical limit reduces to the standard Fermi's golden rule, and (iii) describes a genuine Lindblad evolution, thus providing a reliable/robust treatment of energy-dissipation and dephasing processes in electronic quantum devices. Unlike standard master-equation formulations, the dependence of our approximation on the specific choice of the subsystem (that include the common partial trace reduction) does not threaten positivity, and quantum scattering rates are well defined even in case the subsystem is infinitely extended/has continuous spectrum.Comment: 6 pages, 0 figure

Dissipation and Decoherence in Nanodevices: a Generalized Fermi's Golden Rule

We shall revisit the conventional adiabatic or Markov approximation, which --contrary to the semiclassical case-- does not preserve the positive-definite character of the corresponding density matrix, thus leading to highly non-physical results. To overcome this serious limitation, originally pointed out and partially solved by Davies and co-workers almost three decades ago, we shall propose an alternative more general adiabatic procedure, which (i) is physically justified under the same validity restrictions of the conventional Markov approach, (ii) in the semiclassical limit reduces to the standard Fermi's golden rule, and (iii) describes a genuine Lindblad evolution, thus providing a reliable/robust treatment of energy-dissipation and dephasing processes in electronic quantum devices. Unlike standard master-equation formulations, the dependence of our approximation on the specific choice of the subsystem (that include the common partial trace reduction) does not threaten positivity, and quantum scattering rates are well defined even in case the subsystem is infinitely extended/has continuous spectrum.Comment: 6 pages, 0 figure

Dissipation and Decoherence in Nanodevices: a Generalized Fermi's Golden Rule

We shall revisit the conventional adiabatic or Markov approximation, which --contrary to the semiclassical case-- does not preserve the positive-definite character of the corresponding density matrix, thus leading to highly non-physical results. To overcome this serious limitation, originally pointed out and partially solved by Davies and co-workers almost three decades ago, we shall propose an alternative more general adiabatic procedure, which (i) is physically justified under the same validity restrictions of the conventional Markov approach, (ii) in the semiclassical limit reduces to the standard Fermi's golden rule, and (iii) describes a genuine Lindblad evolution, thus providing a reliable/robust treatment of energy-dissipation and dephasing processes in electronic quantum devices. Unlike standard master-equation formulations, the dependence of our approximation on the specific choice of the subsystem (that include the common partial trace reduction) does not threaten positivity, and quantum scattering rates are well defined even in case the subsystem is infinitely extended/has continuous spectrum.Comment: 6 pages, 0 figure