Complexation of DNA with positive spheres: phase diagram of charge inversion and reentrant condensation

The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres these "artificial chromatin" complexes are negative, while at large enough concentrations of spheres the charge of DNA is inverted by the adsorbed spheres. Charges of complexes stabilize their solutions. In the plane of concentrations of DNA and spheres the phases with positive and negative complexes are separated by another phase, which contains the condensate of neutral DNA-spheres complexes. Thus when the concentration of spheres grows, DNA-spheres complexes experience condensation and resolubilization (or reentrant condensation). Phenomenological theory of the phase diagram of reentrant condensation and charge inversion is suggested. Parameters of this theory are calculated by microscopic theory. It is shown that an important part of the effect of a monovalent salt on the phase diagram can be described by the nontrivial renormalization of the effective linear charge density of DNA wound around a sphere, due to the Onsager-Manning condensation. We argue that our phenomenological phase diagram or reentrant condensation is generic to a large class of strongly asymmetric electrolytes. Possible implication of these results for the natural chromatin are discussed.Comment: Many corrections to text. SUbmitted to J. Chem. Phy

Modelling Citation Networks

The distribution of the number of academic publications as a function of citation count for a given year is remarkably similar from year to year. We measure this similarity as a width of the distribution and find it to be approximately constant from year to year. We show that simple citation models fail to capture this behaviour. We then provide a simple three parameter citation network model using a mixture of local and global search processes which can reproduce the correct distribution over time. We use the citation network of papers from the hep-th section of arXiv to test our model. For this data, around 20% of citations use global information to reference recently published papers, while the remaining 80% are found using local searches. We note that this is consistent with other studies though our motivation is very different from previous work. Finally, we also find that the fluctuations in the size of an academic publication's bibliography is important for the model. This is not addressed in most models and needs further work.Comment: 29 pages, 22 figure

Problems in rain making

CER47-52THE27.From Public Works, July 1951

HLA-B27 Positivity: associated health implications

HLA-B27 positivity makes the onset of autoimmune diseases such as uveitis, ankylosing spondylitis and Crohn's disease more likely to occur. Ankylosing spondylitis and Crohn's disease are two types of HLA-B27 positive diseases that demonstrate a direct association with uveitis. Although the possession of HLA-B27 positivity is not mandatory for autoimmune diseases such as uveitis to occur, HLA-B27 positivity not only makes it more likely but may modify the clinical picture in which a patient presents. In relation to assessment and diagnosis it is imperative that the medical history of patients is thoroughly examined to ensure pathological sequelae are appropriately treated. Nurses play an important role in assessing patients that have uveitis and should suspect ankylosing spondylitis or Crohn's disease may be present

Keplerian discs around post-AGB stars: a common phenomenon?

Aims: We aim at showing that the broad-band SED characteristics of our sample of post-AGB stars are best interpreted, assuming the circumstellar dust is stored in Keplerian rotating passive discs. Methods: We present a homogeneous and systematic study of the Spectral Energy Distributions (SEDs) of a sample of 51 post-AGB objects. The selection criteria to define the whole sample were tuned to cover the broad-band characteristics of known binary post-AGB stars. The whole sample includes 20 dusty RV Tauri stars from the General Catalogue of Variable Stars (GCVS). We supplemented our own Geneva optical photometry with literature data to cover a broad range of fluxes from the UV to the far-IR. Results: All the SEDs display very similar characteristics: a large IR excess with a dust excess starting near the sublimation temperature, irrespective of the effective temperature of the central star. Moreover, when available, the long wavelength fluxes show a black-body slope indicative of the presence of a component of large mm sized grains. Conclusions: We argue that in all systems, gravitationally bound dusty discs are present. The discs must be puffed-up to cover a large opening angle for the central star and we argue that the discs have some similarity with the passive discs detected around young stellar objects. We interpret the presence of a disc to be a signature for binarity of the central object, but this will need confirmation by long-term monitoring of the radial velocities. We argue that dusty RV Tauri stars are those binaries which happen to be in the Population II instability strip.Comment: 29 pages, 5 figures, accepted for publication in A&

Marginalising instrument systematics in HST WFC3 transit lightcurves

Hubble Space Telescope (HST) Wide Field Camera 3 (WFC3) infrared observations at 1.1-1.7$\mu$m probe primarily the H$_2$O absorption band at 1.4$\mu$m, and has provided low resolution transmission spectra for a wide range of exoplanets. We present the application of marginalisation based on Gibson (2014) to analyse exoplanet transit lightcurves obtained from HST WFC3, to better determine important transit parameters such as R$_p$/R$_*$, important for accurate detections of H$_2$O. We approximate the evidence, often referred to as the marginal likelihood, for a grid of systematic models using the Akaike Information Criterion (AIC). We then calculate the evidence-based weight assigned to each systematic model and use the information from all tested models to calculate the final marginalised transit parameters for both the band-integrated, and spectroscopic lightcurves to construct the transmission spectrum. We find that a majority of the highest weight models contain a correction for a linear trend in time, as well as corrections related to HST orbital phase. We additionally test the dependence on the shift in spectral wavelength position over the course of the observations and find that spectroscopic wavelength shifts $\delta_\lambda(\lambda)$, best describe the associated systematic in the spectroscopic lightcurves for most targets, while fast scan rate observations of bright targets require an additional level of processing to produce a robust transmission spectrum. The use of marginalisation allows for transparent interpretation and understanding of the instrument and the impact of each systematic evaluated statistically for each dataset, expanding the ability to make true and comprehensive comparisons between exoplanet atmospheres.Comment: 19 pages, 13 figures, 8 tables, Accepted to Ap

An Ising-Like model for protein mechanical unfolding

The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a model is generalized by including the effect of an external force, and its thermodynamics turns out to be exactly solvable. We consider two molecules, the 27th immunoglobulin domain of titin and protein PIN1. In the case of titin we determine equilibrium force-extension curves and study nonequilibrium phenomena in the frameworks of dynamic loading and force clamp protocols, verifying theoretical laws and finding the position of the kinetic barrier which hinders the unfolding of the molecule. The PIN1 molecule is used to check the possibility of computing the free energy landscape as a function of the molecule length by means of an extended form of the Jarzynski equality.Comment: 4 pages + appendi

Hard rod gas with long-range interactions: Exact predictions for hydrodynamic properties of continuum systems from discrete models

One-dimensional hard rod gases are explicitly constructed as the limits of discrete systems: exclusion processes involving particles of arbitrary length. Those continuum many-body systems in general do not exhibit the same hydrodynamic properties as the underlying discrete models. Considering as examples a hard rod gas with additional long-range interaction and the generalized asymmetric exclusion process for extended particles ($\ell$-ASEP), it is shown how a correspondence between continuous and discrete systems must be established instead. This opens up a new possibility to exactly predict the hydrodynamic behaviour of this continuum system under Eulerian scaling by solving its discrete counterpart with analytical or numerical tools. As an illustration, simulations of the totally asymmetric exclusion process ($\ell$-TASEP) are compared to analytical solutions of the model and applied to the corresponding hard rod gas. The case of short-range interaction is treated separately.Comment: 19 pages, 8 figure