Automated Analysis of MUTEX Algorithms with FASE

In this paper we study the liveness of several MUTEX solutions by representing them as processes in PAFAS s, a CCS-like process algebra with a specific operator for modelling non-blocking reading behaviours. Verification is carried out using the tool FASE, exploiting a correspondence between violations of the liveness property and a special kind of cycles (called catastrophic cycles) in some transition system. We also compare our approach with others in the literature. The aim of this paper is twofold: on the one hand, we want to demonstrate the applicability of FASE to some concrete, meaningful examples; on the other hand, we want to study the impact of introducing non-blocking behaviours in modelling concurrent systems.Comment: In Proceedings GandALF 2011, arXiv:1106.081

Neutral and Charged Polymers at Interfaces

Chain-like macromolecules (polymers) show characteristic adsorption properties due to their flexibility and internal degrees of freedom, when attracted to surfaces and interfaces. In this review we discuss concepts and features that are relevant to the adsorption of neutral and charged polymers at equilibrium, including the type of polymer/surface interaction, the solvent quality, the characteristics of the surface, and the polymer structure. We pay special attention to the case of charged polymers (polyelectrolytes) that have a special importance due to their water solubility. We present a summary of recent progress in this rapidly evolving field. Because many experimental studies are performed with rather stiff biopolymers, we discuss in detail the case of semi-flexible polymers in addition to flexible ones. We first review the behavior of neutral and charged chains in solution. Then, the adsorption of a single polymer chain is considered. Next, the adsorption and depletion processes in the many-chain case are reviewed. Profiles, changes in the surface tension and polymer surface excess are presented. Mean-field and corrections due to fluctuations and lateral correlations are discussed. The force of interaction between two adsorbed layers, which is important in understanding colloidal stability, is characterized. The behavior of grafted polymers is also reviewed, both for neutral and charged polymer brushes.Comment: a review: 130 pages, 30 ps figures; final form, added reference

Evaluating the successful implementation of evidence into practice using the PARiHS framework : theoretical and practical challenges

Background The PARiHS framework (Promoting Action on Research Implementation in Health Services) has proved to be a useful practical and conceptual heuristic for many researchers and practitioners in framing their research or knowledge translation endeavours. However, as a conceptual framework it still remains untested and therefore its contribution to the overall development and testing of theory in the field of implementation science is largely unquantified. Discussion This being the case, the paper provides an integrated summary of our conceptual and theoretical thinking so far and introduces a typology (derived from social policy analysis) used to distinguish between the terms conceptual framework, theory and model – important definitional and conceptual issues in trying to refine theoretical and methodological approaches to knowledge translation. Secondly, the paper describes the next phase of our work, in particular concentrating on the conceptual thinking and mapping that has led to the generation of the hypothesis that the PARiHS framework is best utilised as a two-stage process: as a preliminary (diagnostic and evaluative) measure of the elements and sub-elements of evidence (E) and context (C), and then using the aggregated data from these measures to determine the most appropriate facilitation method. The exact nature of the intervention is thus determined by the specific actors in the specific context at a specific time and place. In the process of refining this next phase of our work, we have had to consider the wider issues around the use of theories to inform and shape our research activity; the ongoing challenges of developing robust and sensitive measures; facilitation as an intervention for getting research into practice; and finally to note how the current debates around evidence into practice are adopting wider notions that fit innovations more generally. Summary The paper concludes by suggesting that the future direction of the work on the PARiHS framework is to develop a two-stage diagnostic and evaluative approach, where the intervention is shaped and moulded by the information gathered about the specific situation and from participating stakeholders. In order to expedite the generation of new evidence and testing of emerging theories, we suggest the formation of an international research implementation science collaborative that can systematically collect and analyse experiences of using and testing the PARiHS framework and similar conceptual and theoretical approaches. We also recommend further refinement of the definitions around conceptual framework, theory, and model, suggesting a wider discussion that embraces multiple epistemological and ontological perspectives

Magnetism, FeS colloids, and Origins of Life

A number of features of living systems: reversible interactions and weak bonds underlying motor-dynamics; gel-sol transitions; cellular connected fractal organization; asymmetry in interactions and organization; quantum coherent phenomena; to name some, can have a natural accounting via $physical$ interactions, which we therefore seek to incorporate by expanding the horizons of `chemistry-only' approaches to the origins of life. It is suggested that the magnetic 'face' of the minerals from the inorganic world, recognized to have played a pivotal role in initiating Life, may throw light on some of these issues. A magnetic environment in the form of rocks in the Hadean Ocean could have enabled the accretion and therefore an ordered confinement of super-paramagnetic colloids within a structured phase. A moderate H-field can help magnetic nano-particles to not only overcome thermal fluctuations but also harness them. Such controlled dynamics brings in the possibility of accessing quantum effects, which together with frustrations in magnetic ordering and hysteresis (a natural mechanism for a primitive memory) could throw light on the birth of biological information which, as Abel argues, requires a combination of order and complexity. This scenario gains strength from observations of scale-free framboidal forms of the greigite mineral, with a magnetic basis of assembly. And greigite's metabolic potential plays a key role in the mound scenario of Russell and coworkers-an expansion of which is suggested for including magnetism.Comment: 42 pages, 5 figures, to be published in A.R. Memorial volume, Ed Krishnaswami Alladi, Springer 201

Genome‐Wide DNA Methylation Study Identifies Significant Epigenomic Changes in Osteoarthritic Cartilage

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/108665/1/art38762.pd

Observation of charge-dependent azimuthal correlations and possible local strong parity violation in heavy ion collisions

Parity-odd domains, corresponding to non-trivial topological solutions of the QCD vacuum, might be created during relativistic heavy-ion collisions. These domains are predicted to lead to charge separation of quarks along the orbital momentum of the system created in non-central collisions. To study this effect, we investigate a three particle mixed harmonics azimuthal correlator which is a \P-even observable, but directly sensitive to the charge separation effect. We report measurements of this observable using the STAR detector in Au+Au and Cu+Cu collisions at $\sqrt{s_{NN}}$=200 and 62~GeV. The results are presented as a function of collision centrality, particle separation in rapidity, and particle transverse momentum. A signal consistent with several of the theoretical expectations is detected in all four data sets. We compare our results to the predictions of existing event generators, and discuss in detail possible contributions from other effects that are not related to parity violation.Comment: 17 pages, 14 figures, as accepted for publication in Physical Review C

Identified high-pTp_{T} spectra in Cu+Cu collisions at sNN\sqrt{s_{NN}}=200 GeV

We report new results on identified (anti)proton and charged pion spectra at large transverse momenta (3<$p_{T}$<10 GeV/c) from Cu+Cu collisions at $\sqrt{s_{NN}}$=200 GeV using the STAR detector at the Relativistic Heavy Ion Collider (RHIC). This study explores the system size dependence of two novel features observed at RHIC with heavy ions: the hadron suppression at high-$p_{T}$ and the anomalous baryon to meson enhancement at intermediate transverse momenta. Both phenomena could be attributed to the creation of a new form of QCD matter. The results presented here bridge the system size gap between the available pp and Au+Au data, and allow the detailed exploration for the on-set of the novel features. Comparative analysis of all available 200 GeV data indicates that the system size is a major factor determining both the magnitude of the hadron spectra suppression at large transverse momenta and the relative baryon to meson enhancement.Comment: Submitted to Phys. Rev. C, 9 pages, 5 figure

Strangeness Enhancement in Cu+Cu and Au+Au Collisions at \sqrt{s_{NN}} = 200 GeV

We report new STAR measurements of mid-rapidity yields for the $\Lambda$, $\bar{\Lambda}$, $K^{0}_{S}$, $\Xi^{-}$, $\bar{\Xi}^{+}$, $\Omega^{-}$, $\bar{\Omega}^{+}$ particles in Cu+Cu collisions at \sNN{200}, and mid-rapidity yields for the $\Lambda$, $\bar{\Lambda}$, $K^{0}_{S}$ particles in Au+Au at \sNN{200}. We show that at a given number of participating nucleons, the production of strange hadrons is higher in Cu+Cu collisions than in Au+Au collisions at the same center-of-mass energy. We find that aspects of the enhancement factors for all particles can be described by a parameterization based on the fraction of participants that undergo multiple collisions

Inclusive pi^0, eta, and direct photon production at high transverse momentum in p+p and d+Au collisions at sqrt(s_NN) = 200 GeV

We report a measurement of high-p_T inclusive pi^0, eta, and direct photon production in p+p and d+Au collisions at sqrt(s_NN) = 200 GeV at midrapidity (0 gamma gamma were detected in the Barrel Electromagnetic Calorimeter of the STAR experiment at the Relativistic Heavy Ion Collider. The eta -> gamma gamma decay was also observed and constituted the first eta measurement by STAR. The first direct photon cross section measurement by STAR is also presented, the signal was extracted statistically by subtracting the pi^0, eta, and omega(782) decay background from the inclusive photon distribution observed in the calorimeter. The analysis is described in detail, and the results are found to be in good agreement with earlier measurements and with next-to-leading order perturbative QCD calculations.Comment: 28 pages, 30 figures, 6 tables, the updated version that was accepted by Phys. Rev.

Charged and strange hadron elliptic flow in Cu+Cu collisions at sNN\sqrt{s_{NN}} = 62.4 and 200 GeV

We present the results of an elliptic flow analysis of Cu+Cu collisions recorded with the STAR detector at 62.4 and 200GeV. Elliptic flow as a function of transverse momentum is reported for different collision centralities for charged hadrons and strangeness containing hadrons $K_{S}^{0}$, $\Lambda$, $\Xi$, $\phi$ in the midrapidity region $|eta|<1.0$. Significant reduction in systematic uncertainty of the measurement due to non-flow effects has been achieved by correlating particles at midrapidity, $|\eta|<1.0$, with those at forward rapidity, $2.5<|\eta|<4.0$. We also present azimuthal correlations in p+p collisions at 200 GeV to help estimating non-flow effects. To study the system-size dependence of elliptic flow, we present a detailed comparison with previously published results from Au+Au collisions at 200 GeV. We observe that $v_{2}$($p_{T}$) of strange hadrons has similar scaling properties as were first observed in Au+Au collisions, i.e.: (i) at low transverse momenta, $p_T<2GeV/c$, $v_{2}$ scales with transverse kinetic energy, $m_{T}-m$, and (ii) at intermediate $p_T$, $2<p_T<4GeV/c$, it scales with the number of constituent quarks, $n_q$. We have found that ideal hydrodynamic calculations fail to reproduce the centrality dependence of $v_{2}$($p_{T}$) for $K_{S}^{0}$ and $\Lambda$. Eccentricity scaled $v_2$ values, $v_{2}/\epsilon$, are larger in more central collisions, suggesting stronger collective flow develops in more central collisions. The comparison with Au+Au collisions which go further in density shows $v_{2}/\epsilon$ depend on the system size, number of participants $N_{part}$. This indicates that the ideal hydrodynamic limit is not reached in Cu+Cu collisions, presumably because the assumption of thermalization is not attained.Comment: 18 pages, 14 figure