A Holistic and Probabilistic Approach to the Ground-based and Spaceborne Data of HAT-P-19 System

We update the main physical and orbital properties of the transiting hot Saturn planet HAT-P-19 b, based on a global modelling of high-precision transit and occultation light curves, taken with ground-based and space telescopes, archive spectra and radial velocity measurements, brightness values from broadband photometry, and Gaia parallax. We collected 65 light curves by amateur and professional observers, measured mid-transit times, analyzed their differences from calculated transit timings based on reference ephemeris information, which we update as a result. We haven’t found any periodicity in the residuals of a linear trend, which we attribute to the accumulation of uncertainties in the reference mid-transit time and the orbital period. We comment on the scenarios describing the formation and migration of this hot-Saturn type exoplanet with a bloated atmosphere yet a small core, although it is orbiting a metal-rich ([Fe/H] = 0.24 dex) host star. Finally, we review the planetary mass-radius, the orbital period-radius and density, and the stellar metallicity-core mass diagrams, based on the parameters we derive for HAT-P-19 b and those of the other seventy transiting Saturn-mass planets from the NASA Exoplanet Archive

Reoccurring patterns in hierarchical protein materials and music: The power of analogies

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.Comment: 13 pages, 3 figure

Rough Fibrils Provide a Toughening Mechanism in Biological Fibers

Spider silk is a fascinating natural composite material. Its combination of strength and toughness is unrivalled in nature, and as a result, it has gained considerable interest from the medical, physics, and materials communities. Most of this attention has focused on the one to tens of nanometer scale: predominantly the primary (peptide sequences) and secondary (β sheets, helices, and amorphous domains) structure, with some insights into tertiary structure (the arrangement of these secondary structures) to describe the origins of the mechanical and biological performance. Starting with spider silk, and relating our findings to collagen fibrils, we describe toughening mechanisms at the hundreds of nanometer scale, namely, the fibril morphology and its consequences for mechanical behavior and the dissipation of energy. Under normal conditions, this morphology creates a nonslip fibril kinematics, restricting shearing between fibrils, yet allowing controlled local slipping under high shear stress, dissipating energy without bulk fracturing. This mechanism provides a relatively simple target for biomimicry and, thus, can potentially be used to increase fracture resistance in synthetic materials

Sacrificial Ionic Bonds Need To Be Randomly Distributed To Provide Shear Deformability

Multivalent ions are known to allow for reversible cross-linking in soft biological materials, providing stiffness and extensibility via sacrificial bonds. We present a simple model where stiff nanoscale elements carrying negative charges are coupled in shear by divalent mobile cations in aqueous media. Such a shear coupling through a soft glue has, indeed, been proposed to operate in biological nanocomposites. While the coupling is elastic and brittle when the negative charges are periodically arranged, sufficient randomness in their distribution allows for large irreversible deformation. Dependent on their function, biological as well as technical materials have to possess different, often contradictory, properties. In load-bearing materials, such as bone, a high stiffness has to be reconciled with an elevated toughness. A high stiffness, defined as the initial slope of the stress-strain curve, means that the material deforms only little with applied load. On the other hand, toughness is a measure of how much energy has to be put into the material to break it. In one-component materials, stiffness and toughness are typically contradictory properties. A strategy often followed by natur

Strength of Hydrogen Bond Network Takes Crucial Roles in the Dissociation Process of Inhibitors from the HIV-1 Protease Binding Pocket

To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions

Category Theoretic Analysis of Hierarchical Protein Materials and Social Networks

Materials in biology span all the scales from Angstroms to meters and typically consist of complex hierarchical assemblies of simple building blocks. Here we describe an application of category theory to describe structural and resulting functional properties of biological protein materials by developing so-called ologs. An olog is like a “concept web” or “semantic network” except that it follows a rigorous mathematical formulation based on category theory. This key difference ensures that an olog is unambiguous, highly adaptable to evolution and change, and suitable for sharing concepts with other olog. We consider simple cases of beta-helical and amyloid-like protein filaments subjected to axial extension and develop an olog representation of their structural and resulting mechanical properties. We also construct a representation of a social network in which people send text-messages to their nearest neighbors and act as a team to perform a task. We show that the olog for the protein and the olog for the social network feature identical category-theoretic representations, and we proceed to precisely explicate the analogy or isomorphism between them. The examples presented here demonstrate that the intrinsic nature of a complex system, which in particular includes a precise relationship between structure and function at different hierarchical levels, can be effectively represented by an olog. This, in turn, allows for comparative studies between disparate materials or fields of application, and results in novel approaches to derive functionality in the design of de novo hierarchical systems. We discuss opportunities and challenges associated with the description of complex biological materials by using ologs as a powerful tool for analysis and design in the context of materiomics, and we present the potential impact of this approach for engineering, life sciences, and medicine.Presidential Early Career Award for Scientists and Engineers (N000141010562)United States. Army Research Office. Multidisciplinary University Research Initiative (W911NF0910541)United States. Office of Naval Research (grant N000141010841)Massachusetts Institute of Technology. Dept. of MathematicsStudienstiftung des deutschen VolkesClark BarwickJacob Luri

Hierarchical, multilayered cell walls reinforced by recycled silk cocoons enhance the structural integrity of honeybee combs

We reveal the sophisticated and hierarchical structure of honeybee combs and measure the elastic properties of fresh and old natural honeycombs at different scales by optical microscope, environmental scanning electron microscope, nano/microindentation, and by tension and shear tests. We demonstrate that the comb walls are continuously strengthened and stiffened without becoming fragile by the addition of thin wax layers reinforced by recycled silk cocoons reminiscent of modern fiber-reinforced composite laminates. This is done to increase its margin of safety against collapse due to a temperature increase. Artificial engineering honeycombs mimic only the macroscopic geometry of natural honeycombs, but have yet to achieve the microstructural sophistication of their natural counterparts. The natural honeycombs serve as a prototype of truly biomimetic cellular materials with hitherto unattainable improvement in stiffness, strength, toughness, and thermal stability

Demonstration of ethyl glucuronide in dental tissue samples by liquid chromatography/electro-spray tandem mass spectrometry

PubMedID: 23910866Introduction: Ethyl glucuronide (EtG) has been studied in various tissues and body fluid for determination of alcohol intake. However, no study, dealing with EtG analysis in dental tissue, was performed so far. In this study, we aimed to demonstrate EtG levels in dental tissue. Materials and methods: Michigan Alcohol Screening Test (MAST) was performed to 29 participants. Following the test, cases were divided into three groups as non-hazardous alcohol users, alcohol abusers and 6 controls who verbally declared that they were abstainers. A total of 29 tooth specimens, obtained from participants, was included in the study. These specimens were analyzed using LC/MS/MS. Results: All of the participants included in the study were male. According to the MAST outcomes 14 of the participants were non-hazardous alcohol users, and 9 were alcohol abusers, while 6 patients verbally declared that they were abstainers. Dental tissue analyses revealed EtG levels ranging between EtG < LOD and 23.39 pg/mg. EtG levels were observed to be <LOD in dental specimens of 6 abstainer cases. A significant correlation was found between EtG levels measured in the dental tissues and MAST outcomes on the statistical analyses (r = 0.914). Conclusion: The findings of the present study demonstrated that dental tissue can be used for detection of alcohol intake, using LC/MS/MS. © 2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved