Helical ensembles outperform ideal helices in molecular replacement

The conventional approach in molecular replacement is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterized families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high, albeit local, structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolutions. Here, the performance of libraries of helical ensembles created by clustering helical segments is explored. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. A 30% increase in the number of solutions obtained by AMPLE was observed when using this new set of ensembles compared with the performance with ideal helices. The boost in performance was notable across three different fold classes: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction in the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the `helical ensembles' mode.

Helical ensembles out-perform ideal helices in Molecular Replacement

The conventional approach in molecular replacement (MR) is the use of a related structure as a search model. However, this is not always possible as the availability of such structures can be scarce for poorly characterised families of proteins. In these cases, alternative approaches can be explored, such as the use of small ideal fragments that share high albeit local structural similarity with the unknown protein. Earlier versions of AMPLE enabled the trialling of a library of ideal helices, which worked well for largely helical proteins at suitable resolution. Here we explore the performance of libraries of helical ensembles created by clustering helical segments. The impacts of different B-factor treatments and different degrees of structural heterogeneity are explored. We observed a 30% increase in the number of solutions obtained by AMPLE when using this new set of ensembles compared to performance with ideal helices. The boost of performance was notable across three different folds: transmembrane, globular and coiled-coil structures. Furthermore, the increased effectiveness of these ensembles was coupled to a reduction of the time required by AMPLE to reach a solution. AMPLE users can now take full advantage of this new library of search models by activating the “helical ensembles” mode.

The role of subjective age in sustaining wellbeing and health in the second half of life

Subjective age (SA) is a core indicator of the individual ageing experience, with important consequences for successful ageing. The aim of the current study was to investigate the directions of the longitudinal associations between domains of SA and subjective wellbeing and physical functioning in the second half of life. We used three-wave survey data (2002, 2007 and 2017) spanning 15 years from the Norwegian Lifecourse, Ageing and Generation Study, including 6,292 persons born between 1922 and 1961. SA was measured with felt-age and ideal-age discrepancies, wellbeing with the Satisfaction of Life Scale and physical functioning with the Short-Form 12. Three-wave cross-lagged panel models were applied to assess the temporal relationships between the different domains of SA, life satisfaction and physical functioning, adjusted for age, gender and education. Findings indicated that wanting to be younger was negatively associated with life satisfaction and physical functioning over time. Felt-age discrepancies did not predict subsequent wellbeing or physical functioning. The results did not reveal any evidence for reversed effects, i.e. from functioning or life satisfaction to SA. Our findings support the psychological pathway from satisfaction with age(ing) to subjective wellbeing and physical functioning over time. Small ideal-age discrepancies reflect positive self-perceptions of ageing, which may help to accumulate psychological resources, guide behavioural regulation and support health.

Crystal Structure and Mechanical Properties of ThBC2

Thorium borocarbide compounds have fascinating physical properties and diverse structures, and hence have stimulated great interest. In this work, we determine the ground state structure of ThBC2 by the unbiased structure prediction method based on first-principles calculations. The dynamical and elastic stabilities of our proposed ThBC2 are verified by the calculations of phonon spectrum and elastic constants. To study the mechanical properties fundamentally, we estimated the elastic anisotropy of ThBC2. The results show that the Young’s and shear moduli possess high degree of anisotropy. The ideal strength calculations reveal that ThBC2 readily collapses upon applied stress due to small ideal strengths. The cleavage fracture probably occurs along the [111] direction while slip may easily appear along the [ 1 ¯ 10 ] direction on the (111) plane for ThBC2. In addition, we provide an atomic explanation for the different characteristics of the strain–stress curves under different strains.

THREE-DIMENSIONAL BILLIARDS WITH TIME MACHINE

Self-collision of a nonrelativistic classical point-like body, or particle, in the spacetime containing closed time-like curves (time-machine spacetime) is considered. A point-like body (particle) is an idealization of a small ideal elastic billiard ball. The known model of a time machine is used containing a wormhole leading to the past. If the body enters one of the mouths of the wormhole, it emerges from another mouth in an earlier time so that both the particle and its “incarnation” coexist during some time and may collide. Such self-collisions are considered in the case when the size of the body is much less than the radius of the mouth, and the latter is much less than the distance between the mouths. Three-dimensional configurations of trajectories with a self-collision are presented. Their dynamics is investigated in detail. Configurations corresponding to multiple wormhole traversals are discussed. It is shown that, for each world line describing self-collision of a particle, dynamically equivalent configurations exist in which the particle collides not with itself but with an identical particle having a closed trajectory (Jinnee of Time Machine).

On the small and essential ideals in certain classes of rings

It is well known that for a ring with identity the Brown-McCoy radical is the maximal small ideal. However, in certain subrings of complete matrix rings, which we call structural matrix rings, the maximal small and minimal essential ideals coincide.In this paper we characterize a class of commutative and a class of non-commutative rings for which this coincidence occurs, namely quotients of Prüfer domains and structural matrix rings over Brown-McCoy semisimple rings. A similarity between these two classes is obtained.

XII.—Magnetisation and Temperature in Crystals

In previous papers (Proc. R. S. Edin., 1905, 1907, 1912) on the subject of crystalline magnetic quality, all questions of temperature were left aside. Molecular heat motions were regarded as non-existent, and the magnetic atoms or molecules were considered as representable by small ideal magnets centred upon a geometrical space lattice. No other mode of representation is possible until explicit notions regarding the origin and seat of molecular magnetic quality become definitely possible; and the general nature of magnetic actions and properties indicate that the general nature of the conclusions thus arrived at will not be fundamentally altered by particular assumptions regarding the nature of the magnetic molecules themselves. The crystalline quality of the magnetisation is due to the geometrical spacing of the atoms or molecules, and is manifested under the control afforded by the magnetic fields originating in surrounding molecules. This is essentially, when freed from the restriction to crystals, the statement of the modern Theory of Molecular Magnetism, which was definitely put forward by Weber in 1852, in all its features, and was recognised by Maxwell, who, in the state of experimental knowledge at the time, contented himself with an addition to Weber's representation of the law of force by postulation instead of by direct deduction. The first explicit applications to crystalline, or randomly crystalline, solid materials were made by Ewing, who obtained approximate quantitative results, relatively to ordinary magnetic materials such as iron, by neglecting the effect of all but closely neighbouring molecules, a condition which, though only strictly justifiable under the postulate of small pole clearance, is sufficient to give a good-elucidation of the effects. The action of his models was not so narrowly restricted.