Linearized model Fokker-Planck collision operators for gyrokinetic simulations. II. Numerical implementation and tests

A set of key properties for an ideal dissipation scheme in gyrokinetic simulations is proposed, and implementation of a model collision operator satisfying these properties is described. This operator is based on the exact linearized test-particle collision operator, with approximations to the field-particle terms that preserve conservation laws and an H-Theorem. It includes energy diffusion, pitch-angle scattering, and finite Larmor radius effects corresponding to classical (real-space) diffusion. The numerical implementation in the continuum gyrokinetic code GS2 is fully implicit and guarantees exact satisfaction of conservation properties. Numerical results are presented showing that the correct physics is captured over the entire range of collisionalities, from the collisionless to the strongly collisional regimes, without recourse to artificial dissipation.Comment: 13 pages, 8 figures, submitted to Physics of Plasmas; typos fixe

‘The Invisible Chain by Which All Are Bound to Each Other’: Civil Defence Magazines and the Development of Community During the Second World War

This article uses local collaboratively produced civil defence magazines to examine how community spirit was developed and represented within the civil defence services during the Second World War. It highlights the range of functions which the magazines performed, as well as the strategies employed by civil defence communities to manage their emotions in order to keep morale high and distract personnel from the fear and boredom experienced while on duty. The article also discusses silences in the magazines — especially around the experience of air raids — and argues that this too reflects group emotional management strategies. The significance of local social groups in developing narratives about civil defence and their workplace communities is demonstrated, and the article shows how personnel were able to engage with and refashion dominant cultural narratives of the ‘people’s war’ in order to assert their own status within the war effort

A blind detection of a large, complex, Sunyaev--Zel'dovich structure

We present an interesting Sunyaev-Zel'dovich (SZ) detection in the first of the Arcminute Microkelvin Imager (AMI) 'blind', degree-square fields to have been observed down to our target sensitivity of 100{\mu}Jy/beam. In follow-up deep pointed observations the SZ effect is detected with a maximum peak decrement greater than 8 \times the thermal noise. No corresponding emission is visible in the ROSAT all-sky X-ray survey and no cluster is evident in the Palomar all-sky optical survey. Compared with existing SZ images of distant clusters, the extent is large (\approx 10') and complex; our analysis favours a model containing two clusters rather than a single cluster. Our Bayesian analysis is currently limited to modelling each cluster with an ellipsoidal or spherical beta-model, which do not do justice to this decrement. Fitting an ellipsoid to the deeper candidate we find the following. (a) Assuming that the Evrard et al. (2002) approximation to Press & Schechter (1974) correctly gives the number density of clusters as a function of mass and redshift, then, in the search area, the formal Bayesian probability ratio of the AMI detection of this cluster is 7.9 \times 10^4:1; alternatively assuming Jenkins et al. (2001) as the true prior, the formal Bayesian probability ratio of detection is 2.1 \times 10^5:1. (b) The cluster mass is MT,200 = 5.5+1.2\times 10^14h-1M\odot. (c) Abandoning a physical model with num- -1.3 70 ber density prior and instead simply modelling the SZ decrement using a phenomenological {\beta}-model of temperature decrement as a function of angular distance, we find a central SZ temperature decrement of -295+36 {\mu}K - this allows for CMB primary anisotropies, receiver -15 noise and radio sources. We are unsure if the cluster system we observe is a merging system or two separate clusters.Comment: accepted MNRAS. 12 pages, 9 figure

The Impact of Antiretroviral Therapy in a Cohort of HIV Infected Patients Going in and out of the San Francisco County Jail

BackgroundJails are an important venue of HIV care and a place for identification, treatment and referral for care. HIV infected inmates in the San Francisco County jail are offered antiretroviral treatment (ART), which many take only while in jail. We evaluated the effect of ART administration in a cohort of jail inmates going in and out of jail over a nine year period.Methodology/Principal FindingsIn this retrospective study, we examined inmates with HIV going in and out of jail. Inmates were categorized by patterns of ART use: continuous ART - ART both in and out of jail, [...] more likely to have higher VL than inmates on continuous ART. Furthermore, Inmates on intermittent ART and never-on ART lost 1.60; 95%CI (1.06, 2.13) and 1.97; 95%CI (0.96, 3.00) more CD4 cells per month, respectively, compared to continuously treated inmates. The continuous ART inmates gained 0.67CD4 cells/month.Conclusions/SignificanceContinuous ART therapy in jail inmate's benefits CD4 cell counts and control of VL especially compared to those who never took ART. Although jail inmates on intermittent ART were more likely to lose CD4 cells and experience higher VL over time than those on continuous ART, CD4 cell loss was slower in these inmates as compared to inmates never on ART. Further studies are needed to evaluate whether or not intermittent ART provides some benefit in outcome if continuous ART is not possible or likely

Moment Closure - A Brief Review

Moment closure methods appear in myriad scientific disciplines in the modelling of complex systems. The goal is to achieve a closed form of a large, usually even infinite, set of coupled differential (or difference) equations. Each equation describes the evolution of one "moment", a suitable coarse-grained quantity computable from the full state space. If the system is too large for analytical and/or numerical methods, then one aims to reduce it by finding a moment closure relation expressing "higher-order moments" in terms of "lower-order moments". In this brief review, we focus on highlighting how moment closure methods occur in different contexts. We also conjecture via a geometric explanation why it has been difficult to rigorously justify many moment closure approximations although they work very well in practice.Comment: short survey paper (max 20 pages) for a broad audience in mathematics, physics, chemistry and quantitative biolog

Interference of H-bonding and substituent effects in nitro- and hydroxy-substituted salicylaldehydes

Two intramolecular interactions, i.e., (1) hydrogen bond and (2) substituent effect, were analyzed and compared. For this purpose, the geometry of 4- and 5-X-substituted salicylaldehyde derivatives (X = NO2, H or OH) was optimized by means of B3LYP/6-311 + G(d,p) and MP2/aug-cc-pVDZ methods. The results obtained allowed us to show that substituents (NO2 or OH) in the para or meta position with respect to either OH or CHO in H-bonded systems interact more strongly than in the case of di-substituted species: 4- and 3-nitrophenol or 4- and 3-hydroxybenzaldehyde by ∼31%. The substituent effect due to the intramolecular charge transfer from the para-counter substituent (NO2) to the proton-donating group (OH) is ∼35% greater than for the interaction of para-OH with the proton-accepting group (CHO). The total energy of H-bonding for salicylaldehyde, and its derivatives, is composed of two contributions: ∼80% from the energy of H-bond formation and ∼20% from the energy associated with reorganization of the electron structure of the systems in question

Socio-demographic determinants of coinfections by HIV, hepatitis B and hepatitis C viruses in central Italian prisoners

BACKGROUND: The coinfections HIV/HCV/HBV are an important health issue in penitentiary communities. The aim of the study was to examine HIV, HBV and HCV coinfections determinants amongst prisoners in the jails of Southern Lazio (Central Italy), in the period 1995-2000. METHODS: Diagnosis of seropositivities for HIV, HBV and HCV was made using ELISA method. A multiple logistic regression analysis was conducted to verify the influence of socio-demographic factors on the HIV/HBV/HCV coinfections. RESULTS: HIV/HCV, HBV/HCV and HIV/HBV coinfections were detected in 42 (4%), 203 (17.9%) and 31 (2.9%) inmates, respectively. These coinfections are significantly associated with the status of drug addiction (OR = 16.02; p = 0.012; OR = 4.15; p < 0.001; OR = 23.57; p = 0.002), smoking habits (OR = 3.73; p = 0.033; OR = 1.42; p = 0.088; OR = 4.25; p = 0.053) and Italian nationality (OR = 7.05; p = 0.009; OR = 2.31; p < 0.001; OR = 4.61; p = 0.04). CONCLUSION: The prevalence of HIV, HBV and HCV seropositivity in jails suggests that information and education programs for inmates could be useful to reduce the spread of such infections

Insights into the Complex Formed by Matrix Metalloproteinase-2 and Alloxan Inhibitors: Molecular Dynamics Simulations and Free Energy Calculations

Matrix metalloproteinases (MMP) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. Hence, the development of potent and selective inhibitors targeting these enzymes continues to be eagerly sought. In this paper, a number of alloxan-based compounds, initially conceived to bias other therapeutically relevant enzymes, were rationally modified and successfully repurposed to inhibit MMP-2 (also named gelatinase A) in the nanomolar range. Importantly, the alloxan core makes its debut as zinc binding group since it ensures a stable tetrahedral coordination of the catalytic zinc ion in concert with the three histidines of the HExxHxxGxxH metzincin signature motif, further stabilized by a hydrogen bond with the glutamate residue belonging to the same motif. The molecular decoration of the alloxan core with a biphenyl privileged structure allowed to sample the deep S1′ specificity pocket of MMP-2 and to relate the high affinity towards this enzyme with the chance of forming a hydrogen bond network with the backbone of Leu116 and Asn147 and the side chains of Tyr144, Thr145 and Arg149 at the bottom of the pocket. The effect of even slight structural changes in determining the interaction at the S1′ subsite of MMP-2 as well as the nature and strength of the binding is elucidated via molecular dynamics simulations and free energy calculations. Among the herein presented compounds, the highest affinity (pIC50 = 7.06) is found for BAM, a compound exhibiting also selectivity (>20) towards MMP-2, as compared to MMP-9, the other member of the gelatinases

Electronic Properties of Vinylene-Linked Heterocyclic Conducting Polymers: Predictive Design and Rational Guidance from DFT Calculations

The band structure and electronic properties in a series of vinylene-linked heterocyclic conducting polymers are investigated using density functional theory (DFT). In order to accurately calculate electronic band gaps, we utilize hybrid functionals with fully periodic boundary conditions to understand the effect of chemical functionalization on the electronic structure of these materials. The use of predictive first-principles calculations coupled with simple chemical arguments highlights the critical role that aromaticity plays in obtaining a low band gap polymer. Contrary to some approaches which erroneously attempt to lower the band gap by increasing the aromaticity of the polymer backbone, we show that being aromatic (or quinoidal) in itself does not insure a low band gap. Rather, an iterative approach which destabilizes the ground state of the parent polymer towards the aromatic \leftrightarrow quinoidal level-crossing on the potential energy surface is a more effective way of lowering the band gap in these conjugated systems. Our results highlight the use of predictive calculations guided by rational chemical intuition for designing low band gap polymers in photovoltaic materials.Comment: Accepted by the Journal of Physical Chemistry