Coarse graining of slow variables in dynamic simulations of soft matter

A new Brownian dynamics model is presented to describe the coarse grain dynamics of particles with long-lived memory. Instead of solving a set of generalized Langevin equations we introduce a set of variables describing the slowly fluctuating thermodynamic state of the ignored degrees of freedom. These variables give rise to additional transient forces on the simulated particles, whose interpretation provides a new way of thinking about memory effects in soft-matter physics. We illustrate the proposed method by simulating shear thinning of synthetic resins.\u

Measuring the Wilson depression of sunspots using the divergence-free condition of the magnetic field vector

Context: The Wilson depression is the difference in geometric height of unit continuum optical depth between the sunspot umbra and the quiet Sun. Measuring the Wilson depression is important for understanding the geometry of sunspots. Current methods suffer from systematic effects or need to make assumptions on the geometry of the magnetic field. This leads to large systematic uncertainties of the derived Wilson depressions. Aims: We aim at developing a robust method for deriving the Wilson depression that only requires the information about the magnetic field that is accessible from spectropolarimetry, and that does not rely on assumptions on the geometry of sunspots or on their magnetic field. Methods: Our method is based on minimizing the divergence of the magnetic field vector derived from spectropolarimetric observations. We focus on large spatial scales only in order to reduce the number of free parameters. Results: We test the performance of our method using synthetic Hinode data derived from two sunspot simulations. We find that the maximum and the umbral averaged Wilson depression for both spots determined with our method typically lies within 100 km of the true value obtained from the simulations. In addition, we apply the method to Hinode observations of a sunspot. The derived Wilson depression (about 600 km) is consistent with results typically obtained from the Wilson effect. We also find that the Wilson depression obtained from using horizontal force balance gives 110 - 180 km smaller Wilson depressions than both, what we find and what we deduce directly from the simulations. This suggests that the magnetic pressure and the magnetic curvature force contribute to the Wilson depression by a similar amount.Comment: 12 pages, 8 figures. Accepted for publication in Astronomy & Astrophysic

Effect of Pulp Protection Technique on the Clinical Performance of Amalgam Restorations: Three-Year Results

This study evaluated the influence of the pulp protection technique on clinical performance of amalgam restorations after three years, with particular reference to post-operative sensitivity and secondary caries. One hundred and twenty (120) Class II amalgam restorations (68 premolars, 52 molars; 78 MOD, 42 OD/MO) were placed in 30 participants (four restorations per participant).The restorations were divided into four groups according to the pulp protection technique used: copal varnish; 2% neutral sodium fluoride; adhesive resin and no pulp protection. The parameters evaluated were post-operative sensitivity, staining of the dental structure, tooth vitality, partial or total loss of the restoration and secondary caries. One hundred and eight (108)restorations were available for evaluation after three years. No partial or total loss of restorations had occurred; all teeth were vital, no tooth structure staining or secondary caries was detected in any of the restored teeth. Post-operative sensitivity was observed only in two restorations at baseline and at seven-days. The three year clinical performance of teeth restored with a high copper dispersed phase amalgam was not affected by the choice of pulp protection technique

Quasiperiodic Dynamics in Bose-Einstein Condensates in Periodic Lattices and Superlattices

We employ KAM theory to rigorously investigate quasiperiodic dynamics in cigar-shaped Bose-Einstein condensates (BEC) in periodic lattices and superlattices. Toward this end, we apply a coherent structure ansatz to the Gross-Pitaevskii equation to obtain a parametrically forced Duffing equation describing the spatial dynamics of the condensate. For shallow-well, intermediate-well, and deep-well potentials, we find KAM tori and Aubry-Mather sets to prove that one obtains mostly quasiperiodic dynamics for condensate wave functions of sufficiently large amplitude, where the minimal amplitude depends on the experimentally adjustable BEC parameters. We show that this threshold scales with the square root of the inverse of the two-body scattering length, whereas the rotation number of tori above this threshold is proportional to the amplitude. As a consequence, one obtains the same dynamical picture for lattices of all depths, as an increase in depth essentially only affects scaling in phase space. Our approach is applicable to periodic superlattices with an arbitrary number of rationally dependent wave numbers.Comment: 29 pages, 6 figures (several with multiple parts; higher-quality versions of some of them available at http://www.its.caltech.edu/~mason/papers), to appear very soon in Journal of Nonlinear Scienc

Inclinations of small quiet-Sun magnetic features based on a new geometric approach

High levels of horizontal magnetic flux have been reported in the quiet-Sun internetwork, often based on Stokes profile inversions. Here we introduce a new method for deducing the inclination of magnetic elements and use it to test magnetic field inclinations from inversions. We determine accurate positions of a set of small, bright magnetic elements in high spatial resolution images sampling different photospheric heights obtained by the Sunrise balloon-borne solar observatory. Together with estimates of the formation heights of the employed spectral bands, these provide us with the inclinations of the magnetic features. We also compute the magnetic inclination angle of the same magnetic features from the inversion of simultaneously recorded Stokes parameters. Our new, geometric method returns nearly vertical fields (average inclination of around 14 deg with a relatively narrow distribution having a standard deviation of 6 deg). In strong contrast to this, the traditionally used inversions give almost horizontal fields (average inclination of 75+-8 deg) for the same small magnetic features, whose linearly polarised Stokes profiles are adversely affected by noise. The almost vertical field of bright magnetic features from our geometric method is clearly incompatible with the nearly horizontal magnetic fields obtained from the inversions. This indicates that the amount of magnetic flux in horizontal fields deduced from inversions is overestimated in the presence of weak Stokes signals, in particular if Stokes Q and U are close to or under the noise level. By combining the proposed method with inversions we are not just improving the inclination, but also the field strength. This technique allows us to analyse features that are not reliably treated by inversions, thus greatly extending our capability to study the complete magnetic field of the quiet Sun.Comment: 12 pages, 9 figures, 1 table; Accepted for publication in Astronomy & Astrophysic

No universal connection between the vertical magnetic field and the umbra-penumbra boundary in sunspots

Context. It has been reported that the boundary between the umbra and the penumbra of sunspots occurs at a canonical value of the strength of the vertical magnetic field, independently of the size of the spot. This critical field strength is interpreted as to be the threshold for the onset of magnetoconvection. Aims. Here we investigate the reasons why this criterion, also called the Jur\v{c}\'ak criterion in the literature, does not always identify the boundary between umbra and penumbra. Methods. We perform a statistical analysis of 23 sunspots observed with Hinode/SOT. We compare the properties of the continuum intensity and the vertical magnetic field between filaments and spines and how they vary between spots of different sizes. Results. We find that the inner boundary of the penumbra is not related to a universal value of the vertical magnetic field. The properties of spines and filaments vary between spots of different sizes. Both components are darker in larger spots and the spines exhibit stronger vertical magnetic field. These variations of the properties of filaments and spines with spot size are also the reason for the reported invariance of the averaged vertical magnetic field at 50% of the mean continuum intensity. Conclusions. The formation of filaments and the onset of magnetoconvection are not related to a canonical value of the strength of the vertical magnetic field. Such a seemingly unique magnetic field strength is rather an effect of the filling factor of spines and penumbral filaments.Comment: 15 pages, 11 figures. Accepted for publication in Astronomy and Astrophysic

Orchestration versus bookkeeping:How stakeholder pressures drive a healthcare purchaser’s institutional logics

BACKGROUND: Healthcare purchasers such as health insurers and governmental bodies are expected to strategically manage chronic care chains. In doing so, purchasers can contribute to the goal of improving task division and collaboration between chronic care providers as has been recommended by numerous studies. However, healthcare purchasing research indicates that, in most countries, purchasers still struggle to fulfil a proactive, strategic approach. Consequently, a typical pattern occurs in which care improvement initiatives are instigated, but not transformed into regular care. By acknowledging that healthcare purchasers are embedded in a care chain of stakeholders who have different, sometimes conflicting, interests and, by taking an institutional logics lens, we seek to explain why achieving strategic purchasing and sustainable improvement is so elusive. METHOD AND FINDINGS: We present a longitudinal case study in which we follow a health insurer and care providers aiming to improve the care of patients with Chronic Obstructive Pulmonary Disease (COPD) in a region of the Netherlands. Taking a theoretical lens of institutional logics, our aim was to answer ‘how stakeholder pressures influence a purchaser’s use of institutional logics when pursuing the right care at the right place’. The insurer by default predominantly expressed a bookkeeper’s logic, reflecting a focus on controlling short-term care costs by managing individual providers. Over time, a contrasting orchestrator’s logic emerged in an attempt to achieve chain-wide improvement, striving for better health outcomes and lower long-term costs. We established five types of stakeholder pressure to explain the shift in logic adoption: relationship pressures, cost pressures, medical demands, public health demands and uncertainty. Linking the changes in logic over time with stakeholder pressures showed that, firstly, the different pressures interact in influencing the purchaser. Secondly, we saw that the lack of intra-organisational alignment affects how the purchaser deals with the different stakeholder pressures. CONCLUSIONS: By highlighting the purchaser’s difficult position in the care chain and the consequences of their own internal responses, we now better understand why the intended orchestrator’s logic and thereby a strategic approach to purchasing chronic care proves unsustainable within the Dutch healthcare system of managed competition

Orthology prediction at scalable resolution by phylogenetic tree analysis

BACKGROUND: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. RESULTS: We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable. CONCLUSION: The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website