Stuttering Min oscillations within E. coli bacteria: A stochastic polymerization model

We have developed a 3D off-lattice stochastic polymerization model to study subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding, and fragmentation of MinD filaments due to MinE. Each of processivity, protection, and fragmentation reduces stuttering, speeds oscillations, and reduces MinD filament lengths. Neither processivity or tip-protection were, on their own, sufficient to produce fast stutter-free oscillations. While filament fragmentation could, on its own, lead to fast oscillations with infrequent stuttering; high levels of fragmentation degraded oscillations. The infrequent stuttering observed in standard Min oscillations are consistent with short filaments of MinD, while we expect that mutants that exhibit higher stuttering frequencies will exhibit longer MinD filaments. Increased stuttering rate may be a useful diagnostic to find observable MinD polymerization in experimental conditions.Comment: 21 pages, 7 figures, missing unit for k_f inserte

Coulomb and nuclear breakup effects in the single neutron removal reaction 197Au(17C,16C gamma)X

We analyze the recently obtained new data on the partial cross sections and parallel momentum distributions for transitions to ground as well as excited states of the 16C core, in the one-neutron removal reaction 197Au(17C,16C gamma)X at the beam energy of 61 MeV/nucleon. The Coulomb and nuclear breakup components of the one-neutron removal cross sections have been calculated within a finite range distorted wave Born approximation theory and an eikonal model, respectively. The nuclear contributions dominate the partial cross sections for the core excited states. By adding the nuclear and Coulomb cross sections together, a reasonable agreement is obtained with the data for these states. The shapes of the experimental parallel momentum distributions of the core states are described well by the theory.Comment: Revtex format, two figures included, to appear in Phys. Rev. C. (Rapid communications

Three-body continuum discretization in a basis of transformed harmonic oscillator states

The inclusion of the continuum in the study of weakly-bound three-body systems is discussed. A transformed harmonic oscillator basis is introduced to provide an appropriate discrete and finite basis for treating the continuum part of the spectrum. As examples of the application of the method the strength functions corresponding to several operators that couple the ground state to the continuum are investigated, for 6He, and compared with previous calculations. It is found that the energy moments of these distributions are accurately reproduced with a small basis set.Comment: 12 figures, submitted to PR

Four-body continuum-discretized coupled-channels calculations using a transformed harmonic oscillator basis

The scattering of a weakly bound three-body system by a target is discussed. A transformed harmonic oscillator basis is used to provide an appropriate discrete and finite basis for treating the continuum part of the spectrum of the projectile. The continuum-discretized coupled channels framework is used for the scattering calculations. The formalism is applied to different reactions, 6He+12C at 229.8 MeV, 6He+64Zn at 10 and 13.6 MeV, and 6He+208Pb at 22 MeV, induced by the Borromean nucleus 6He. Both the Coulomb and nuclear interactions with a target are taken into account.Comment: Published in Phys. Rev.

Diagnosis delays in the UK according to pre- or post-migration acquisition of HIV

Objectives: To evaluate whether infection occurred pre- or post-migration and the associated diagnosis delay in migrants diagnosed with HIV in the UK. Design: We analysed a cohort of individuals diagnosed with HIV in the UK in 2014–2016 born in Africa or elsewhere in Europe. Inclusion criteria were arrival within 15 years before diagnosis, availability of HIV pol sequence and viral subtype shared by at least 10 individuals. Methods: We examined phylogenies for evidence of infection after entry into the UK and incorporated this information into a Bayesian analysis of timing of infection using biomarkers of CD4+ cell count, avidity assays, proportion of ambiguous nucleotides in viral sequences and last negative test dates where available. Results: 1256 individuals were included. The final model indicated that HIV was acquired post-migration for most men who have sex with men (MSM) born in Europe (posterior expectation 65%, 95% credibility interval 64%-67%) or Africa (65%, 62%-69%), whereas a minority (20%-30%) of men and women with heterosexual transmission acquired HIV post-migration. Estimated diagnosis delays were lower for MSM than for those with heterosexual transmission, and were lower for those with post-migration infection across all subgroups. For MSM acquiring HIV post-migration the estimated mean time to diagnosis was 5 years for all subgroups. Conclusions: Acquisition of HIV post-migration is common, particularly among MSM calling for prevention efforts aimed at migrant communities. Delays in diagnosis reinforce the need for targeted testing initiatives

Probing halo nucleus structure through intermediate energy elastic scattering

This work addresses the question of precisely what features of few body models of halo nuclei are probed by elastic scattering on protons at high centre-of-mass energies. Our treatment is based on a multiple scattering expansion of the proton-projectile transition amplitude in a form which is well adapted to the weakly bound cluster picture of halo nuclei. In the specific case of $^{11}$Li scattering from protons at 800 MeV/u we show that because core recoil effects are significant, scattering crosssections can not, in general, be deduced from knowledge of the total matter density alone. We advocate that the optical potential concept for the scattering of halo nuclei on protons should be avoided and that the multiple scattering series for the full transition amplitude should be used instead.Comment: 8 pages REVTeX, 1 eps figure, accepted for publication in Phys. Rev.

Spectroscopy of 35^{35}P using the one-proton knockout reaction

The structure of $^{35}$P was studied with a one-proton knockout reaction at88~MeV/u from a $^{36}$S projectile beam at NSCL. The $\gamma$ rays from thedepopulation of excited states in $^{35}$P were detected with GRETINA, whilethe $^{35}$P nuclei were identified event-by-event in the focal plane of theS800 spectrograph. The level scheme of $^{35}$P was deduced up to 7.5 MeV using$\gamma-\gamma$ coincidences. The observed levels were attributed to protonremovals from the $sd$-shell and also from the deeply-bound $p\_{1/2}$ orbital.The orbital angular momentum of each state was derived from the comparisonbetween experimental and calculated shapes of individual ($\gamma$-gated)parallel momentum distributions. Despite the use of different reactions andtheir associate models, spectroscopic factors, $C^2S$, derived from the$^{36}$S $(-1p)$ knockout reaction agree with those obtained earlier from$^{36}$S($d$,\nuc{3}{He}) transfer, if a reduction factor $R\_s$, as deducedfrom inclusive one-nucleon removal cross sections, is applied to the knockout transitions.In addition to the expected proton-hole configurations, other states were observedwith individual cross sections of the order of 0.5~mb. Based on their shiftedparallel momentum distributions, their decay modes to negative parity states,their high excitation energy (around 4.7~MeV) and the fact that they were notobserved in the ($d$,\nuc{3}{He}) reaction, we propose that they may resultfrom a two-step mechanism or a nucleon-exchange reaction with subsequent neutronevaporation. Regardless of the mechanism, that could not yet be clarified, thesestates likely correspond to neutron core excitations in \nuc{35}{P}. Thisnewly-identified pathway, although weak, offers the possibility to selectivelypopulate certain intruder configurations that are otherwise hard to produceand identify.Comment: 5 figures, 1 table, accepted for publication in Physical Review

Neutron knockout of 12Be populating neutron-unbound states in 11Be

Neutron-unbound resonant states of 11Be were populated in neutron knock-out reactions from 12Be and identified by 10Be-n coincidence measurements. A resonance in the decay-energy spectrum at 80(2) keV was attributed to a highly excited unbound state in 11Be at 3.949(2) MeV decaying to the 2+ excited state in 10Be. A knockout cross section of 15(3) mb was inferred for this 3.949(2) MeV state suggesting a spectroscopic factor near unity for this 0p3/2- level, consistent with the detailed shell model calculations.Comment: 5 pages, 2 figures \pacs{29.38.Db, 29.30.Hs, 24.50.+g, 21.10.Pc, 21.10.Hw, 27.20.+n} \keywords{neutron decay spectroscopy, neutron-unbound states in 11Be

The fidelity of dynamic signaling by noisy biomolecular networks

This is the final version of the article. Available from Public Library of Science via the DOI in this record.Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error) can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments.We acknowledge support from a Medical Research Council and Engineering and Physical Sciences Council funded Fellowship in Biomedical Informatics (CGB) and a Scottish Universities Life Sciences Alliance chair in Systems Biology (PSS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Inverse-kinematics one-neutron pickup with fast rare-isotope beams

New measurements and reaction model calculations are reported for single neutron pickup reactions onto a fast \nuc{22}{Mg} secondary beam at 84 MeV per nucleon. Measurements were made on both carbon and beryllium targets, having very different structures, allowing a first investigation of the likely nature of the pickup reaction mechanism. The measurements involve thick reaction targets and $\gamma$-ray spectroscopy of the projectile-like reaction residue for final-state resolution, that permit experiments with low incident beam rates compared to traditional low-energy transfer reactions. From measured longitudinal momentum distributions we show that the \nuc{12}{C} (\nuc{22}{Mg},\nuc{23}{Mg}+\gamma)X reaction largely proceeds as a direct two-body reaction, the neutron transfer producing bound \nuc{11}{C} target residues. The corresponding reaction on the \nuc{9}{Be} target seems to largely leave the \nuc{8}{Be} residual nucleus unbound at excitation energies high in the continuum. We discuss the possible use of such fast-beam one-neutron pickup reactions to track single-particle strength in exotic nuclei, and also their expected sensitivity to neutron high-$\ell$ (intruder) states which are often direct indicators of shell evolution and the disappearance of magic numbers in the exotic regime.Comment: 8 pages, 5 figure