<i>N</i>-body simulations of planet formation via pebble accretion:II. How various giant planets form

Aims. The connection between initial disc conditions and final orbital and physical properties of planets is not well-understood. In this paper, we numerically study the formation of planetary systems via pebble accretion and investigate the effects of disc properties such as masses, dissipation timescales, and metallicities on planet formation outcomes. Methods. We improved the N-body code SyMBA that was modified for our Paper I by taking account of new planet–disc interaction models and type II migration. We adopted the ‘two-α’ disc model to mimic the effects of both the standard disc turbulence and the mass accretion driven by the magnetic disc wind. Results. We successfully reproduced the overall distribution trends of semi-major axes, eccentricities, and planetary masses of extrasolar giant planets. There are two types of giant planet formation trends, depending on whether or not the disc’s dissipation timescales are comparable to the planet formation timescales. When planet formation happens fast enough, giant planets are fully grown (Jupiter mass or higher) and are distributed widely across the disc. On the other hand, when planet formation is limited by the disc’s dissipation, discs generally form low-mass cold Jupiters. Our simulations also naturally explain why hot Jupiters (HJs) tend to be alone and how the observed eccentricity-metallicity trends arise. The low-metallicity discs tend to form nearly circular and coplanar HJs in situ, because planet formation is slower than high-metallicity discs, and thus protoplanetary cores migrate significantly before gas accretion. The high-metallicity discs, on the other hand, generate HJs in situ or via tidal circularisation of eccentric orbits. Both pathways usually involve dynamical instabilities, and thus HJs tend to have broader eccentricity and inclination distributions. When giant planets with very wide orbits (“super-cold Jupiters”) are formed via pebble accretion followed by scattering, we predict that they belong to metal-rich stars, have eccentric orbits, and tend to have (~80%) companions interior to their orbits

A new and simple prescription for planet orbital migration and eccentricity damping by planet-disc interactions based on dynamical friction

During planet formation gravitational interaction between a planetary embryo and the protoplanetary gas disc causes orbital migration of the planetary embryo, which plays an important role in shaping the final planetary system. While migration sometimes occurs in the supersonic regime, wherein the relative velocity between the planetary embryo and the gas is higher than the sound speed, migration prescriptions proposed thus far describing the planet-disc interaction force and the timescales of orbital change in the supersonic regime are inconsistent with one another. Here we discuss the details of existing prescriptions in the literature and derive a new simple and intuitive formulation for planet-disc interactions based on dynamical friction that can be applied in both supersonic and subsonic cases. While the existing prescriptions assume particular disc models, ours include the explicit dependence on the disc parameters; hence it can be applied to discs with any radial surface density and temperature dependence (except for the local variations with radial scales less than the disc scale height). Our prescription will reduce the uncertainty originating from different literature formulations of planet migration and will be an important tool to study planet accretion processes, especially when studying the formation of close-in low-mass planets that are commonly found in exoplanetary systems.Comment: 10 pages, 1 figure, accepted for publication in MNRAS; typos corrected, the reference list was complete

Effects of Dynamical Evolution of Giant Planets on Survival of Terrestrial Planets

The orbital distributions of currently observed extrasolar giant planets allow marginally stable orbits for hypothetical, terrestrial planets. In this paper, we propose that many of these systems may not have additional planets on these "stable" orbits, since past dynamical instability among giant planets could have removed them. We numerically investigate the effects of early evolution of multiple giant planets on the orbital stability of the inner, sub-Neptune-like planets which are modeled as test particles, and determine their dynamically unstable region. Previous studies have shown that the majority of such test particles are ejected out of the system as a result of close encounters with giant planets. Here, we show that secular perturbations from giant planets can remove test particles at least down to 10 times smaller than their minimum pericenter distance. Our results indicate that, unless the dynamical instability among giant planets is either absent or quiet like planet-planet collisions, most test particles down to ~0.1 AU within the orbits of giant planets at a few AU may be gone. In fact, out of ~30 % of survived test particles, about three quarters belong to the planet-planet collision cases. We find a good agreement between our numerical results and the secular theory, and present a semi-analytical formula which estimates the dynamically unstable region of the test particles just from the evolution of giant planets. Finally, our numerical results agree well with the observations, and also predict the existence of hot rocky planets in eccentric giant planet systems.Comment: 12 pages, 12 figures, published in Ap

The curious case of Mars' formation

Dynamical models of planet formation coupled with cosmochemical data from martian meteorites show that Mars' isotopic composition is distinct from that of Earth. Reconciliation of formation models with meteorite data require that Mars grew further from the Sun than its present position. Here, we evaluate this compositional difference in more detail by comparing output from two $N$-body planet formation models. The first of these planet formation models simulates what is termed the "Classical" case wherein Jupiter and Saturn are kept in their current orbits. We compare these results with another model based on the "Grand Tack", in which Jupiter and Saturn migrate through the primordial asteroid belt. Our estimate of the average fraction of chondrite assembled into Earth and Mars assumes that the initial solid disk consists of only sources of enstatite chondrite composition in the inner region, and ordinary chondrite in the outer region. Results of these analyses show that both models tend to yield Earth and Mars analogues whose accretion zones overlap. The Classical case fares better in forming Mars with its documented composition (29% to 68% enstatite chondrite plus 32% to 67% ordinary chondrite) though the Mars analogues are generally too massive. However, if we include the restriction of mass on the Mars analogues, the Classical model does not work better. We also further calculate the isotopic composition of $^{17} \rm O$, $^{50} \rm Ti$, $^{54} \rm Cr$, $^{142} \rm Nd$, $^{64} \rm Ni$, and $^{92} \rm Mo$ in the martian mantle from the Grand Tack simulations. We find that it is possible to match the calculated isotopic composition of all the above elements in Mars' mantle with their measured values, but the resulting uncertainties are too large to place good restriction on the early dynamical evolution and birth place of Mars.Comment: 14 pages, 8 figures, presented in the 2017 DPS meeting, 2018 Solar system symposium in Sapporo and 2018 AOGS annual meeting, Accepted for publishing in A&

Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus

Detailed investigation of extremely severe pathological conditions in ancient human skeletons is important as it could shed light on the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate an ancient human skeletal individual with severe oral pathology, focusing our research on bacterial pathogenic factors and host defense response. This female skeleton, from the Okhotsk period (i.e., fifth to thirteenth century) of Northern Japan, poses relevant amounts of abnormal dental calculus deposition and exhibits oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from the calculus of the subject. We identified two pathogenic or bioinvasive proteins originating from two of the three "red complex" bacteria, the core species associated with severe periodontal disease in modern humans, as well as two additional bioinvasive proteins of periodontal-associated bacteria. Moreover, we discovered defense response system-associated human proteins, although their proportion was mostly similar to those reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily more intense in ancient individuals with significant amounts of abnormal dental calculus deposition

Structure of the inhibitor complex of old yellow enzyme from Trypanosoma cruzi

The structures of old yellow enzyme from Trypanosoma cruzi which produces prostaglandin F2α from PGH2 have been determined in the presence or absence of menadione

Frequent Transmission of Streptococcus pneumoniae Serotype 35B and 35D, Clonal Complex 558 Lineage, across Continents and the Formation of Multiple Clades in Japan

Streptococcus pneumoniae is a common bacterial pathogen that causes infections in children worldwide, even after administration of the pneumococcal conjugate vaccine. S. pneumoniae serotype 35B, especially the clonal complex 558 (CC558) lineage, has emerged globally following implementation of the 13-valent pneumococcal conjugate vaccine. Serotype 35B strains are also associated with multidrug resistance to both β-lactams and non-β-lactam drugs. In addition, a novel serotype, 35D, which is closely related to 35B and differs in polysaccharide structure, was recently reported. However, the genetic relationship among globally disseminating serotype 35B and D (35B/D) strains remains unknown. To investigate the molecular epidemiology of global serotype 35B/D strains, we conducted a genomic analysis of serotype 35B/D strains from various continents, including those from the Japanese national surveillance collection. A total of 87 isolates were identified as serotype 35B/D in the Japanese surveillance collection (n = 1, 358). All the isolates were assigned to either CC558 or CC2755. Serotype 35D isolates were interspersed with serotype 35B isolates. Phylogenetic analysis revealed the formation of multiple clusters by the Japanese serotype 35B/D-CC558 isolates among the foreign isolates, which suggested multiple events of introduction of the clone into Japan. The global 35B/D-CC558 strains were found to share specific penicillin-binding protein profiles, pbp1a-4, pbp2b-7, and pbp2x-7, associated with penicillin, cephalosporin, and carbapenem nonsusceptibility. Moreover, 88.5% of the Japanese 35B/D-CC558 and 35B/D-CC2755 isolates were found to harbor the Tn916-like integrative and conjugative elements Tn2009, Tn2010, and Tn6002, associated with multidrug resistance to macrolides and tetracyclines. The results of this study imply that serotype 35B/D-CC558 strains could be frequently transmitted intercontinentally

Approach for growth of high-quality and large protein crystals

Three crystallization methods, including crystallization in the presence of a semi-solid agarose gel, top-seeded solution growth (TSSG) and a large-scale hanging-drop method, have previously been presented. In this study, crystallization has been further evaluated in the presence of a semi-solid agarose gel by crystallizing additional proteins. A novel crystallization method combining TSSG and the large-scale hanging-drop method has also been developed