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

On Carbuncles and Other Excrescences

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/77358/1/AIAA-2005-4872-769.pd

Re-entrant ferroelectricity in liquid crystals

The ferroelectric (Sm C$^*$) -- antiferroelectric (Sm C$^*_A$) -- reentrant ferroelectric (re Sm C$^*$) phase temperature sequence was observed for system with competing synclinic - anticlinic interactions. The basic properties of this system are as follows (1) the Sm C$^*$ phase is metastable in temperature range of the Sm C$^*_A$ stability (2) the double inversions of the helix handedness at Sm C$^*$ -- Sm C$^*_A$ and Sm C$^*_A$% -- re-Sm C$^*$ phase transitions were found (3) the threshold electric field that is necessary to induce synclinic ordering in the Sm C$^*_A$ phase decreases near both Sm C$^*_A$ -- Sm C$^*$ and Sm C$^*_A$ -- re-Sm C$^*$ phase boundaries, and it has maximum in the middle of the Sm C$^*_A$ stability region. All these properties are properly described by simple Landau model that accounts for nearest neighboring layer steric interactions and quadrupolar ordering only.Comment: 10 pages, 5 figures, submitted to PR

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

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

The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome

Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome

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