Critical behavior of self-assembled rigid rods on triangular and honeycomb lattices

Using Monte Carlo simulations and finite-size scaling analysis, the critical behavior of self-assembled rigid rods on triangular and honeycomb lattices at intermediate density has been studied. The system is composed of monomers with two attractive (sticky) poles that, by decreasing temperature or increasing density, polymerize reversibly into chains with three allowed directions and, at the same time, undergo a continuous isotropic-nematic (IN) transition. The determination of the critical exponents, along with the behavior of Binder cumulants, indicate that the IN transition belongs to the q=1 Potts universality class.Comment: 6 pages, 5 figure

De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function.

The splicing regulator Polypyrimidine Tract Binding Protein (PTBP1) has four RNA binding domains that each binds a short pyrimidine element, allowing recognition of diverse pyrimidine-rich sequences. This variation makes it difficult to evaluate PTBP1 binding to particular sites based on sequence alone and thus to identify target RNAs. Conversely, transcriptome-wide binding assays such as CLIP identify many in vivo targets, but do not provide a quantitative assessment of binding and are informative only for the cells where the analysis is performed. A general method of predicting PTBP1 binding and possible targets in any cell type is needed. We developed computational models that predict the binding and splicing targets of PTBP1. A Hidden Markov Model (HMM), trained on CLIP-seq data, was used to score probable PTBP1 binding sites. Scores from this model are highly correlated (ρ = -0.9) with experimentally determined dissociation constants. Notably, we find that the protein is not strictly pyrimidine specific, as interspersed Guanosine residues are well tolerated within PTBP1 binding sites. This model identifies many previously unrecognized PTBP1 binding sites, and can score PTBP1 binding across the transcriptome in the absence of CLIP data. Using this model to examine the placement of PTBP1 binding sites in controlling splicing, we trained a multinomial logistic model on sets of PTBP1 regulated and unregulated exons. Applying this model to rank exons across the mouse transcriptome identifies known PTBP1 targets and many new exons that were confirmed as PTBP1-repressed by RT-PCR and RNA-seq after PTBP1 depletion. We find that PTBP1 dependent exons are diverse in structure and do not all fit previous descriptions of the placement of PTBP1 binding sites. Our study uncovers new features of RNA recognition and splicing regulation by PTBP1. This approach can be applied to other multi-RRM domain proteins to assess binding site degeneracy and multifactorial splicing regulation

Entropy-driven phase transition in a system of long rods on a square lattice

The isotropic-nematic (I-N) phase transition in a system of long straight rigid rods of length k on square lattices is studied by combining Monte Carlo simulations and theoretical analysis. The process is analyzed by comparing the configurational entropy of the system with the corresponding to a fully aligned system, whose calculation reduces to the 1D case. The results obtained (1) allow to estimate the minimum value of k which leads to the formation of a nematic phase and provide an interesting interpretation of this critical value; (2) provide numerical evidence on the existence of a second phase transition (from a nematic to a non-nematic state) occurring at density close to 1 and (3) allow to test the predictions of the main theoretical models developed to treat the polymers adsorption problem.Comment: 14 pages, 6 figures. Accepted for publication in JSTA

Coupling Between Thermal Oscillations in the Surface of a Micro-Cylinder and Vortex Shedding

his article studies the coupling between prescribed thermal oscillations in the surface of a micro-cylinder and vortex shedding. We deal with the unsteady, laminar, compressible flow regime where the aerodynamics forces have a periodic behavior. It is shown that appropriate spatial and time-dependent temperature oscillations on the surface of the micro-cylinder create a resonance that controls the amplitude and frequency of both lift and drag coefficients. In practice, what we study is a mechanism to modulate the amplitude and frequency of mechanical loads of aerodynamics origin in a micro-structure by using surface temperature fluctuations as the control parameter

Microscopic cluster model for the description of (18O,16O) two-neutron transfer reactions

Excitation energy spectra and absolute cross-section angular distributions were measured for the 13C(18O,16O)15C two-neutron transfer reaction at 84 MeV incident energy. Exact finite-range coupled reaction channel calculations are used to analyse the data considering both the direct two-neutron transfer and the two-step sequential mechanism. For the direct calculations, two approaches are discussed: The extreme cluster and the newly introduced microscopic cluster. The latter makes use of spectroscopic amplitudes in the centre-of-mass reference frame, derived from shell-model calculations. The results describe well the experimental cross sections

Microscopic cluster model for the description of new experimental results on the C 13 (O 18, O 16) C 15 two-neutron transfer at 84 MeV incident energy

The C13(O18,O16)C15 reaction is studied at 84 MeV incident energy. Excitation energy spectra and absolute cross-section angular distributions for the strongest transitions are measured with good energy and angular resolutions. Strong selectivity for two-neutron configurations in the states of the residual nucleus is found. The measured cross-section angular distributions are analyzed by exact finite-range coupled reaction channel calculations. The two-particle wave functions are extracted using the extreme cluster and the independent coordinate scheme with shell-model derived coupling strengths. A new approach also is introduced, the microscopic cluster, in which the spectroscopic amplitudes in the center-of-mass reference frame are derived from shell-model calculations using the Moshinsky transformation brackets. This new model is able to describe well the experimental cross section and to highlight cluster configurations in the involved wave functions

Water extract of Cryphaea heteromalla (Hedw.) D. Mohr bryophyte as a natural powerful source of biologically active compounds

Bryophytes comprise of the mosses, liverworts, and hornworts. Cryphaea heteromalla, (Hedw.) D. Mohr, is a non-vascular lower plant belonging to mosses group. To the date, the most chemically characterized species belong to the liverworts, while only 3.2% and 8.8% of the species belonging to the mosses and hornworts, respectively, have been investigated. In this work, we present Folin–Ciocalteu and oxygen radical absorbance capacity (ORAC) data related to crude extracts of C. heteromalla obtained by three different extraction solvents: pure water (WT), methanol:water (80:20 v/v) (MET), and ethanol:water (80:20 v/v) (ETH). The water extract proved to be the best solvent showing the highest content of biophenols and the highest ORAC value. The C. heteromalla-WT extract was investigated by HPLC-TOF/MS (High Performance Liquid Chromatography-Time of Flight/Mass Spectrometry) allowing for the detection of 14 compounds, five of which were phenolic compounds, derivatives of benzoic, caffeic, and coumaric acids. Moreover, the C. heteromalla WT extract showed a protective effect against reactive oxygen species (ROS) generation induced by tert-butyl hydroperoxide (TBH) on the murine NIH-3T3 fibroblast cell line