A simple model for DNA denaturation

Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases, are reduced to a single short range binding term. Furthermore, base-pair misalignments are forbidden, implying that this binding term exists only for corresponding (same curvilinear abscissae) monomers of the two chains. We take into account the excluded volume repulsion between monomers of the two chains, but neglect intra-chain repulsion. We find that the excluded volume term generates an effective repulsive interaction between the chains, which decays as $1/r^{d-2}$. Due to this long-range repulsion between the chains, the denaturation transition is first order in any dimension, in agreement with previous studies.Comment: 10 page

Ground State Energy of the One-Component Charged Bose Gas

The model considered here is the `jellium' model in which there is a uniform, fixed background with charge density $-e\rho$ in a large volume $V$ and in which $N=\rho V$ particles of electric charge $+e$ and mass $m$ move --- the whole system being neutral. In 1961 Foldy used Bogolubov's 1947 method to investigate the ground state energy of this system for bosonic particles in the large $\rho$ limit. He found that the energy per particle is $-0.402 r_s^{-3/4} {me^4}/{\hbar^2}$ in this limit, where $r_s=(3/4\pi \rho)^{1/3}e^2m/\hbar^2$. Here we prove that this formula is correct, thereby validating, for the first time, at least one aspect of Bogolubov's pairing theory of the Bose gasComment: 38 pages latex. Typos corrected.Lemma 6.2 change

Aplicação de parser baseado na compreensão e execução de diálogos entre usuários e computadores: sistema compor

O presente artigo visa apresentar o sistema Compor; um sistema que viabiliza a execução de um diálogo entre usuários e computadores através da compreensão da linguagem natural. Voltado ao idioma português, este sistema recebe as sentenças de entrada do usuário, efetua o processo de compreensão e na seqüência emite respostas coerentes com esta entrada. Utilizando uma abordagem diferenciada – a de Parser Baseado em Casos – o sistema Compor efetua a compreensão a partir de uma memória pré-modelada que representa os conceitos sobre o domínio do conhecimento, as informações sobre o tratamento da linguagem natural e ainda os procedimentos que conduzem o diálogo de forma inteligente. Como um todo, a intenção é aproximar-se dos processos cognitivos humanos e construir um sistema artificial controlado que reproduza a compreensão de linguagem natural.Eje: Teoría (TEOR)Red de Universidades con Carreras en Informática (RedUNCI

Mesenchymal stem cell-derived extracellular vesicles protect human corneal endothelial cells from endoplasmic reticulum stress-mediated apoptosis

Corneal endothelial dystrophy is a relevant cause of vision loss and corneal transplantation worldwide. In the present study, we analyzed the effect of mesenchymal stem cell (MSC)-derived extracellular vesicles (MSC-EVs) in an in vitro model of corneal dystrophy, characterized by endoplasmic reticulum stress. The effects of MSC-EVs were compared with those of serum-derived EVs, reported to display a pro-angiogenic activity. MSC-EVs were able to induce a significant down-regulation of the large majority of endoplasmic reticulum stress-related genes in human corneal endothelial cells after exposure to serum deprivation and tunicamycin. In parallel, they upregulated the Akt pathway and limited caspase-3 activation and apoptosis. At variance, the effect of the serum EVs was mainly limited to Akt phosphorylation, with minimal or absent effects on endoplasmic reticulum stress modulation and apoptosis prevention. The effects of MSC-EVs were correlated to the transfer of numerous endoplasmic reticulum (ER)-stress targeting miRNAs to corneal endothelial cells. These data suggest a potential therapeutic effect of MSC-EVs for corneal endothelial endoplasmic reticulum stress, a major player in corneal endothelial dystrophy

Calcium magneto-optical trap loaded from a decelerated atomic beam

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOWe describe a new system for laser cooling and trapping of neutral Calcium atoms employing the ¹S0 -¹ P1 resonant transition at 423 nm. An on-axis magneto-optical trap (MOT) is loaded from a Zeeman decelerated atomic beam. When a single laser is used, in order to avoid perturbation of the trap by the deceleration laser beam, this one has been tightly focused near the MOT center, with a waist size much smaller than the atomic cloud. In order to test the efficiency of this novel technique, we have then employed a second, independent decelerating laser, with a profile mode matched to the atomic beam. For an oven temperature of 580±C this system can load 1.2 (2) x 10(7) atoms in 16 (1) ms. By the spatial extension of the atomic cloud the one dimension rms velocity was estimated to be 136 (12) cm/s, corresponding to a temperature of 9 (2) mK. The variation of the number of trapped atoms as a function of laser detuning and intensity, trap magnetic field gradient and oven temperature is analyzed. Spatial structures of the trapped atoms, like stable rings created by vortex forces, have been observed. This is the first time that these structures, already observed in alkali-metal elements, are reported in MOTs of alkaline-earth elements.We describe a new system for laser cooling and trapping of neutral Calcium atoms employing the ¹S0 -¹ P1 resonant transition at 423 nm. An on-axis magneto-optical trap (MOT) is loaded from a Zeeman decelerated atomic beam. When a single laser is used, in order to avoid perturbation of the trap by the deceleration laser beam, this one has been tightly focused near the MOT center, with a waist size much smaller than the atomic cloud. In order to test the efficiency of this novel technique, we have then employed a second, independent decelerating laser, with a profile mode matched to the atomic beam. For an oven temperature of 580±C this system can load 1.2 (2) x 10(7) atoms in 16 (1) ms. By the spatial extension of the atomic cloud the one dimension rms velocity was estimated to be 136 (12) cm/s, corresponding to a temperature of 9 (2) mK. The variation of the number of trapped atoms as a function of laser detuning and intensity, trap magnetic field gradient and oven temperature is analyzed. Spatial structures of the trapped atoms, like stable rings created by vortex forces, have been observed. This is the first time that these structures, already observed in alkali-metal elements, are reported in MOTs of alkaline-earth elements.We describe a new system for laser cooling and trapping of neutral Calcium atoms employing the ¹S0 -¹ P1 resonant transition at 423 nm. An on-axis magneto-optical trap (MOT) is loaded from a Zeeman decelerated atomic beam. When a single laser is used, in order to avoid perturbation of the trap by the deceleration laser beam, this one has been tightly focused near the MOT center, with a waist size much smaller than the atomic cloud. In order to test the efficiency of this novel technique, we have then employed a second, independent decelerating laser, with a profile mode matched to the atomic beam. For an oven temperature of 580±C this system can load 1.2 (2) x 10(7) atoms in 16 (1) ms. By the spatial extension of the atomic cloud the one dimension rms velocity was estimated to be 136 (12) cm/s, corresponding to a temperature of 9 (2) mK. The variation of the number of trapped atoms as a function of laser detuning and intensity, trap magnetic field gradient and oven temperature is analyzed. Spatial structures of the trapped atoms, like stable rings created by vortex forces, have been observed. This is the first time that these structures, already observed in alkali-metal elements, are reported in MOTs of alkaline-earth elements.332355362FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOSem informaçãoSem informaçãoSem informaçãoWe would like to acknowledge the glass shop of the UNICAMP Physics Institute for the very well done work in the construction of the atomic beam and MOT glass chamber. We also would like to thank the machine shop and J.B.Rodrigues for the mechanical parts. This work was supported by FAPESP, CAPES and CNPq and FAEPUNICAMP, Brazilian government agencies. Support for RLCF was through CAPES graduate research scholarship and for DAM and DRO through FAPESP graduate and undergraduate scholarships respectively

Hybrid Particle-Continuum Simulations of Nonequilibrium Hypersonic Blunt-Body Flowfields

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77319/1/AIAA-30216-565.pd

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

The genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors