Synthetic IRIS spectra of the solar transition region: Effect of high-energy tails

The solar transition region satisfies the conditions for presence of non-Maxwellian electron energy distributions with high-energy tails at energies corresponding to the ionization potentials of many ions emitting in the EUV and UV portions of the spectrum. We calculate the synthetic Si IV, O IV, and S IV spectra in the far ultra-violet (FUV) channel of the Interface Region Imaging Spectrograph (IRIS). Ionization, recombination, and excitation rates are obtained by integration of the cross-sections or their approximations over the model electron distributions considering particle propagation from the hotter corona. The ionization rates are significantly affected by the presence of high-energy tails. This leads to the peaks of the relative abundance of individual ions to be broadened with pronounced low-temperature shoulders. As a result, the contribution functions of individual lines observable by IRIS also exhibit low-temperature shoulders, or their peaks are shifted to temperatures an order of magnitude lower than for the Maxwellian distribution. The integrated emergent spectra can show enhancements of Si IV compared toO IV by more than a factor of two. The high-energy particles can have significant impact on the emergent spectra and their presence needs to be considered even in situations without strong local acceleration

Activated sampling in complex materials at finite temperature: the properly-obeying-probability activation-relaxation technique

While the dynamics of many complex systems is dominated by activated events, there are very few simulation methods that take advantage of this fact. Most of these procedures are restricted to relatively simple systems or, as with the activation-relaxation technique (ART), sample the conformation space efficiently at the cost of a correct thermodynamical description. We present here an extension of ART, the properly-obeying-probability ART (POP-ART), that obeys detailed balance and samples correctly the thermodynamic ensemble. Testing POP-ART on two model systems, a vacancy and an interstitial in crystalline silicon, we show that this method recovers the proper thermodynamical weights associated with the various accessible states and is significantly faster than MD in the diffusion of a vacancy below 700 K.Comment: 10 pages, 3 figure

Probabilistic Phase Space Trajectory Description for Anomalous Polymer Dynamics

It has been recently shown that the phase space trajectories for the anomalous dynamics of a tagged monomer of a polymer --- for single polymeric systems such as phantom Rouse, self-avoiding Rouse, Zimm, reptation, and translocation through a narrow pore in a membrane; as well as for many-polymeric system such as polymer melts in the entangled regime --- is robustly described by the Generalized Langevin Equation (GLE). Here I show that the probability distribution of phase space trajectories for all these classical anomalous dynamics for single polymers is that of a fractional Brownian motion (fBm), while the dynamics for polymer melts between the entangled regime and the eventual diffusive regime exhibits small, but systematic deviations from that of a fBm.Comment: 8 pages, two figures, 3 eps figure files, minor changes, supplementary material included moved to the appendix, references expanded, to appear in J. Phys.: Condens. Matte

Oxidative Activity of Human Polymorphonuclear Leukocytes Stimulated by the Long-Chain Phosphatidic Acids

Summary It has already been suggested that phosphatidic acids (PAs) play an important role in the regulation of signaling pathways involved in the production of reactive oxygen species (ROS) by human polymorphonuclear leukocytes (PMNs). The present study was performed to elucidate the effects of extracellularly added PAs -1,2-distearoyl-(DSPA) and 1-stearoyl-2-arachidonoyl-sn-glycero-phosphate (SAPA) -on the ROS production and on the elastase release by human PMNs. ROS production was monitored by luminol-amplified chemiluminescence and the elastase activity was measured in the supernatant of the PA-stimulated human PMNs by colorimetric assay. Obtained effects were compared with those of cells stimulated by either a chemotactic tripeptide, phorbol ester or calcium ionophore. Our results show that long-chain PAs at concentrations higher than 3 × 10 -5 mol/l stimulate the ROS production by human PMNs, whereas they were ineffective in promoting the elastase release. The chemiluminescence pattern of the SAPA-stimulated cells exhibited a biphasic curve, whereas cell stimulation with DSPA resulted in a monophasic chemiluminescence curve. Stimulation of the ROS production by PAs in dependence of the fatty acid composition required the activity of protein kinases

Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule

Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which the elements of the secondary structure can be determined is limited by thermal fluctuations. We present a detailed study of these thermal fluctuations, including the frequency spectrum, and show that these rule out single-nucleotide resolution under the experimental conditions which we simulated. Two possible ways to improve this resolution are strong stretching of the RNA with a back-pulling voltage across the membrane, and stiffening of the translocated part of the RNA by biochemical means.Comment: Significantly expanded compared to previous version, 13 pages, 4 figures, to appear in J. Phys.: Condens. Matte

Pore-blockade Times for Field-Driven Polymer Translocation

We study pore blockade times for a translocating polymer of length $N$, driven by a field $E$ across the pore in three dimensions. The polymer performs Rouse dynamics, i.e., we consider polymer dynamics in the absence of hydrodynamical interactions. We find that the typical time the pore remains blocked during a translocation event scales as $\sim N^{(1+2\nu)/(1+\nu)}/E$, where $\nu\simeq0.588$ is the Flory exponent for the polymer. In line with our previous work, we show that this scaling behaviour stems from the polymer dynamics at the immediate vicinity of the pore -- in particular, the memory effects in the polymer chain tension imbalance across the pore. This result, along with the numerical results by several other groups, violates the lower bound $\sim N^{1+\nu}/E$ suggested earlier in the literature. We discuss why this lower bound is incorrect and show, based on conservation of energy, that the correct lower bound for the pore-blockade time for field-driven translocation is given by $\eta N^{2\nu}/E$, where $\eta$ is the viscosity of the medium surrounding the polymer.Comment: 14 pages, 6 figures, slightly shorter than the previous version; to appear in J. Phys.: Cond. Ma

Multifrequency behaviour of the anomalous events of PSR J0922+0638

PSR J0922+0638 (B0919+06) shows unexplained anomalous variations in the on-pulse phase, where the pulse appears to episodically move to an earlier longitude for a few tens of rotations before reverting to the usual phase for approximately several hundred to more than a thousand rotations. These events, where the pulse moves in phase by up to 5$^{\circ}$, have been previously detected in observations from $\sim$300 to 2000 MHz. We present simultaneous observations from the Effelsberg 100-m radio telescope at 1350 MHz and the Bornim (Potsdam) station of the LOw Frequency ARray at 150 MHz. Our observations present the first evidence for an absence of the anomalous phase-shifting behaviour at 150 MHz. Instead, the observed intensity at the usual pulse-phase typically decreases, often showing a pseudo-nulling feature corresponding to the times when phase shifts are observed at 1350 MHz. The presence of weak emission at the usual pulse-phase supports the theory that these shifts may result from processes similar to the 'profile-absorption' expected to operate for PSR J0814+7429 (B0809+74). A possible mechanism for this could be intrinsic variations of the emission within the pulsar's beam combined with absorption by expanding shells of electrons in the line of sight.Comment: 5 pages, 3 figures, accepted for publication in MNRAS Letter

Anomalous zipping dynamics and forced polymer translocation

We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high temperature equilibrium configuration to a low temperature state, so that the two strands zip up by closing up a "Y"-fork. In unzipping, the polymers are brought from a low temperature double stranded configuration to high temperatures, so that the two strands separate. Simulations show that the unzipping time, $\tau_u$, scales as a function of the polymer length as $\tau_u \sim L$, while the zipping is characterized by anomalous dynamics $\tau_z \sim L^\alpha$ with $\alpha = 1.37(2)$. This exponent is in good agreement with simulation results and theoretical predictions for the scaling of the translocation time of a forced polymer passing through a narrow pore. We find that the exponent $\alpha$ is robust against variations of parameters and temperature, whereas the scaling of $\tau_z$ as a function of the driving force shows the existence of two different regimes: the weak forcing ($\tau_z \sim 1/F$) and strong forcing ($\tau_z$ independent of $F$) regimes. The crossover region is possibly characterized by a non-trivial scaling in $F$, matching the prediction of recent theories of polymer translocation. Although the geometrical setup is different, zipping and translocation share thus the same type of anomalous dynamics. Systems where this dynamics could be experimentally investigated are DNA (or RNA) hairpins: our results imply an anomalous dynamics for the hairpins closing times, but not for the opening times.Comment: 15 pages, 9 figure

Solar off-limb line widths: Alfven waves, ion-cyclotron waves, and preferential heating

Alfven waves and ion-cyclotron absorption of high-frequency waves are frequently brought into models devoted to coronal heating and fast solar-wind acceleration. Signatures of ion-cyclotron resonance have already been observed in situ in the solar wind (HELIOS spacecrafts) and, recently, in the upper corona (UVCS/SOHO remote-sensing results). We propose a method to constrain both the Alfven wave amplitude and the preferential heating induced by ion-cyclotron resonance, above a partially developed polar coronal hole observed with the SUMER/SOHO spectrometer. The instrumental stray light contribution is first substracted from the spectra. By supposing that the non-thermal velocity is related to the Alfven wave amplitude, it is constrained through a density diagnostic and the gradient of the width of the Mg X 625 A line. The temperatures of several coronal ions, as functions of the distance above the limb, are then determined by substracting the non-thermal component to the observed line widths. The effect of stray light explains the apparent decrease with height in the width of several spectral lines, this decrease usually starting about 0.1-0.2 Rs above the limb. This result rules out any direct evidence of damping of the Alfven waves, often suggested by other authors. We also find that the ions with the smallest charge-to-mass ratios are the hottest ones at a fixed altitude and that they are subject to a stronger heating, as compared to the others, between 57" and 102" above the limb. This constitutes a serious clue to ion-cyclotron preferential heating.Comment: 15 pages, 12 figures, 3 table