Observational data needs for plasma phenomena

Bright comets display a rich variety of interesting plasma phenomena which occur over an enormous range of spatial scales, and which require different observational techniques to be studied effectively. Wide-angle photography of high time resolution is probably the best method of studying the phenomenon of largest known scale: the plasma tail disconnection event (DE), which has been attributed to magnetic reconnection at interplanetary sector boundary crossings. These structures usually accelerate as they recede from the head region and observed velocities are typically in the range 50 V km/s. They are often visible for several days following the time of disconnection, and are sometimes seen out past 0.2 AU from the cometary head. The following areas pertaining to plasma phenomena in the ionoshere are addressed: the existence, size, and heliocentric distance variations of the contact surface, and the observational signatures of magnetic reconnection at sector boundary crossings

Interaction of the plasma tail of comet Bradfield 1979L on 1980 February 6 with a possibly flare-generated solar-wind disturbance

Solar wind plasma data from the ISEE-3 and Helios 2 spacecraft were examined to explain a uniquely rapid 10 deg turning of the plasma tail of comet Bradfield 1979L on 1980 February 6. It was suggested that the tail position angle change occurred in response to a solar wind velocity shear across which the polar component changed by approx. 50 km s-1. The present activity was caused by noncorotating, disturbed plasma flows probably associated with an Importance 1B solar flare

Mn12_{12}-Acetate Complexes Studied as Single Molecules

The phenomenon of single molecule magnet (SMM) behavior of mixed valent Mn12 coordination clusters of general formula [Mn$^{III}$$_{8}$Mn$^{IV}$$_{4}$O$_{12}$(RCOO)$_{16}$(H$_{2}$O)$_{4}$] had been exemplified by bulk samples of the archetypal [Mn$^{III}$$_{8}$Mn$^{IV}$$_{4}$O$_{12}$(CH$_{3}$COO)$_{16}$(H$_{2}$O)$_{4}$] (4) molecule, and the molecular origin of the observed magnetic behavior has found support from extensive studies on the Mn12 system within crystalline material or on molecules attached to a variety of surfaces. Here we report the magnetic signature of the isolated cationic species [Mn$_{12}$O$_{12}$(CH$_{3}$COO)$_{15}$(CH$_{3}$CN)]$^{+}$ (1) by gas phase X-ray Magnetic Circular Dichroism (XMCD) spectroscopy, and we find it closely resembling that of the corresponding bulk samples. Furthermore, we report broken symmetry DFT calculations of spin densities and single ion tensors of the isolated, optimized complexes [Mn$_{12}$O$_{12}$(CH$_{3}$COO)$_{15}$(CH$_{3}$CN)]$^{+}$ (1), [[Mn$_{12}$O$_{12}$(CH$_{3}$COO)$_{16}$] (2), [Mn$_{12}$O$_{12}$(CH$_{3}$COO)$_{16}$(H$_{2}$O)$_{4}$] (3), and the complex in bulk geometry [Mn$^{III}$$_{8}$Mn$^{IV}$$_{4}$O$_{12}$(CH$_{3}$COO)$_{16}$(H$_{2}$O)$_{4}$] (5). The found magnetic fingerprints – experiment and theory alike – are of a remarkable robustness: The Mn$^{IV}$$_{4}$ core bears almost no magnetic anisotropy while the surrounding MnIII8 ring is highly anisotropic. These signatures are truly intrinsic properties of the Mn$_{12}$ core scaffold within all of these complexes and largely void of the environment. This likely holds irrespective of bulk packing effects

The Science of Sungrazers, Sunskirters, and Other Near-Sun Comets

This review addresses our current understanding of comets that venture close to the Sun, and are hence exposed to much more extreme conditions than comets that are typically studied from Earth. The extreme solar heating and plasma environments that these objects encounter change many aspects of their behaviour, thus yielding valuable information on both the comets themselves that complements other data we have on primitive solar system bodies, as well as on the near-solar environment which they traverse. We propose clear definitions for these comets: We use the term near-Sun comets to encompass all objects that pass sunward of the perihelion distance of planet Mercury (0.307 AU). Sunskirters are defined as objects that pass within 33 solar radii of the Sun’s centre, equal to half of Mercury’s perihelion distance, and the commonly-used phrase sungrazers to be objects that reach perihelion within 3.45 solar radii, i.e. the fluid Roche limit. Finally, comets with orbits that intersect the solar photosphere are termed sundivers. We summarize past studies of these objects, as well as the instruments and facilities used to study them, including space-based platforms that have led to a recent revolution in the quantity and quality of relevant observations. Relevant comet populations are described, including the Kreutz, Marsden, Kracht, and Meyer groups, near-Sun asteroids, and a brief discussion of their origins. The importance of light curves and the clues they provide on cometary composition are emphasized, together with what information has been gleaned about nucleus parameters, including the sizes and masses of objects and their families, and their tensile strengths. The physical processes occurring at these objects are considered in some detail, including the disruption of nuclei, sublimation, and ionisation, and we consider the mass, momentum, and energy loss of comets in the corona and those that venture to lower altitudes. The different components of comae and tails are described, including dust, neutral and ionised gases, their chemical reactions, and their contributions to the near-Sun environment. Comet-solar wind interactions are discussed, including the use of comets as probes of solar wind and coronal conditions in their vicinities. We address the relevance of work on comets near the Sun to similar objects orbiting other stars, and conclude with a discussion of future directions for the field and the planned ground- and space-based facilities that will allow us to address those science topics

ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer

Protein kinases are a large and diverse family of enzymes that are genomically altered in many human cancers. Targeted cancer genome sequencing efforts have unveiled the mutational profiles of protein kinase genes from many different cancer types. While mutational data on protein kinases is currently catalogued in various databases, integration of mutation data with other forms of data on protein kinases such as sequence, structure, function and pathway is necessary to identify and characterize key cancer causing mutations. Integrative analysis of protein kinase data, however, is a challenge because of the disparate nature of protein kinase data sources and data formats., where the mutations are spread over 82 distinct kinases. We also provide examples of how ontology-based data analysis can be used to generate testable hypotheses regarding cancer mutations.

The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems