Intermolecular correlations are necessary to explain diffuse scattering from protein crystals

Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to advance our understanding of biological dynamics. However, recent work challenged this prevailing view, suggesting instead that diffuse scattering primarily originates from rigid body motions and could therefore be applied to improve structure determination. To investigate the nature of the disorder giving rise to diffuse scattering, and thus the potential applications of this signal, a diverse repertoire of disorder models was assessed for its ability to reproduce the diffuse signal reconstructed from three protein crystals. This comparison revealed that multiple models of intramolecular conformational dynamics, including ensemble models inferred from the Bragg data, could not explain the signal. Models of rigid body or short-range liquid-like motions, in which dynamics are confined to the biological unit, showed modest agreement with the diffuse maps, but were unable to reproduce experimental features indicative of long-range correlations. Extending a model of liquid-like motions to include disorder across neighboring proteins in the crystal significantly improved agreement with all three systems and highlighted the contribution of intermolecular correlations to the observed signal. These findings anticipate a need to account for intermolecular disorder in order to advance the interpretation of diffuse scattering to either extract biological motions or aid structural inference.Comment: 12 pages, 5 figures (not including Supplementary Information

Accelerated X-ray Structure Elucidation of a 36 kDa Muramidase/Transglycosylase Using wARP

The X-ray structure of the 36kDa soluble lytic transglycosylase from Escherichia coli has been determined starting with the multiple isomorphous replacement method with inclusion of anomalous scattering at 2.7 Å resolution. Subsequently, before any model building was carried out, phases were extended to 1.7 Å, resolution with the weighted automated refinement procedure wARP, which gave a dramatic improvement in the phases. The electron-density maps from wARP were of outstanding quality for both the main chain and the side chains of the protein, which allowed the time spent on the tracing, interpretation and building of the X-ray structure to be substantially shortened. The structure of the soluble lyric transglycosylase was refined at 1.7 Å, resolution with X-PLOR to a final crystallographic R factor of 18.9%. Analysis of the wARP procedure revealed that the use of the maximum-likelihood refinement in wARP gave much better phases than least-squares refinement, provided that the ratio of reflections to protein atom parameters was approximately 1.8 or higher. Furthermore, setting aside 5% of the data for an Rfree test set had a negative effect on the phase improvement. The mean WwARP, a weight determined at the end of the wARP procedure and based on the variance of structure factors from six individually refined wARP models, proved to be a better indicator than the Rfree factor to judge different phase improvement protocols. The elongated Slt35 structure has three domains named the alpha, beta and core domains. The alpha domain contains mainly α-helices, while the beta domain consists of a five-stranded antiparallel β-sheet flanked by a short α-helix. Sandwiched between the alpha and beta domains is the core domain, which bears some resemblance to the fold of the catalytic domain of the previously elucidated 70 kDa soluble lytic transglycosylase from E. coli. The putative active site is at the bottom of a large deep groove in the core domain.

Model-free reconstruction of magnetic correlations in frustrated magnets

Frustrated magnetic systems exhibit extraordinary physical properties but quantification of their magnetic correlations poses a serious challenge to experiment and theory. Current insight into frustrated magnetic correlations relies on modelling techniques such as reverse Monte Carlo methods, which require knowledge about the exact ordered atomic structure. Here we present a method for direct reconstruction of magnetic correlations in frustrated magnets by three-dimensional difference pair distribution function analysis of neutron total scattering data. The methodology is applied to the disordered frustrated magnet bixbyite, (Mn1-xFex)2O3, which reveals nearest-neighbor antiferromagnetic correlations for the metal sites up to a range of approximately 15 {\AA}. Importantly, this technique allows for magnetic correlations to be determined directly from the experimental data without any assumption about the atomic structure

Patching task-level robot controllers based on a local µ-calculus formula

We present a method for mending strategies for GR(1) specifications. Given the addition or removal of edges from the game graph describing a problem (essentially transition rules in a GR(1) specification), we apply a µ-calculus formula to a neighborhood of states to obtain a “local strategy” that navigates around the invalidated parts of an original synthesized strategy. Our method may thus avoid global resynthesis while recovering correctness with respect to the new specification. We illustrate the results both in simulation and on physical hardware for a planar robot surveillance task

Signatures of Spin and Charge Energy Scales in the Local Moment and Specific Heat of the Two-Dimensional Hubbard Model

Local moment formation driven by the on--site repulsion $U$ is one of the most fundamental features in the Hubbard model. At the simplest level, the temperature dependence of the local moment is expected to have a single structure at $T \sim U$, reflecting the suppression of the double occupancy. In this paper we show new low temperature Quantum Monte Carlo data which emphasize that the local moment also has a signature at a lower energy scale which previously had been thought to characterize only the temperatures below which moments on {\it different} sites begin to correlate locally. We discuss implications of these results for the structure of the specific heat, and connections to quasiparticle resonance and pseudogap formation in the density of states.Comment: 13 pages, 19 figure

Thermally activated magnetization reversal in bulk BiFe0.5Mn0.5O3

We report on the synthesis and characterization of BiFe0.5Mn0.5O3, a potential type-I multiferroic compound displaying temperature induced magnetization reversal. Bulk samples were obtained by means of solid state reaction carried out under the application of hydrostatic pressure at 6 GPa and 1100{\deg}C. The crystal structure is an highly distorted perovskite with no cation order on the B site, where, besides a complex scheme of tilt and rotations of the TM-O6 octahedra, large off-centering of the bismuth ions is detected. Below T1 = 420 K the compound undergoes a first weak ferromagnetic transition related to the ordering of iron rich clusters. At lower temperatures (just below RT) two distinct thermally activated mechanisms are superimposed, inducing at first an enhancement of the magnetization at T2 = 288 K, then a spontaneous reversal process centered at T3 = 250 K, finally giving rise to a negative response. The application of fields higher than 1500 Oe suppresses the process, yielding a ferromagnetic like behaviour. The complementary use of SQuID magnetometry and M\"ossbauer spectroscopy allowed the interpretation of the overall magnetic behaviour in terms of an uncompensated weak competitive coupling between non-equivalent clusters of interactions characterized by different critical temperatures and resultant magnetizations. PACS numbers: 75.85.+t, 75.60.Jk, 76.80.+y, 75.30.Et, 75.30.KzComment: 30 pages, 13 figure

Eksperimentalna usporedba metoda izgradnje mrežastih karata prostora korištenjem ultrazvučnih senzora

For successful usage of mobile robots in human working areas several navigation problems have to be solved. One of the navigational problems is the creation and update of the model or map of a mobile robot working environment. This article describes most used types of the occupancy grid maps based sonar range readings. These maps are: (i) Bayesian map, (ii) Dempster-Shafer map, (iii) Fuzzy map, (iv) Borenstein map, (v) MURIEL map, and (vi) TBF map. Besides the maps description, a memory consumption and computation time comparison is done. Simulation validation is done using the AMORsim mobile robot simulator for Matlab and experimental validation is done using a Pioneer 3DX mobile robot. Obtained results are presented and compared regarding resulting map quality.Za uspješnu primjenu mobilnih robota u radnim prostorima s ljudima potrebno je riješiti različite probleme navigacije. Jedan od problema navigacije jest kreiranje modela i uključivanje novih informacija o radnoj okolini mobilnog robota u model radne okoline ili kartu. Članak opisuje često korištene tipove mrežastih karata prostora zasnovanih na očitanjima ultrazvučnih osjetila udaljenosti. Obrađeni modeli prostora su: (i) Bayesova karta, (ii) Dempster-Shaferova karta, (iii) neizrazita karta, (iv) Borensteinova karta, (v) MURIEL karta i (vi) TBF karta. Osim opisa, u članku je dana i usporedba implementiranih algoritama prema memorijskim i računskim zahtjevima. Simulacijska provjera napravljena je korištenjem AMORsim simulatora mobilnog robota za programski paket Matlab, a eksperimentalna provjera napravljena je korištenjem Pioneer 3DX mobilnog robota. Također su prikazani dobiveni rezultati uz usporedbu njihove kakvoće