How to do an evaluation: pitfalls and traps

The recent literature is replete with papers evaluating computational tools (often those operating on 3D structures) for their performance in a certain set of tasks. Most commonly these papers compare a number of docking tools for their performance in cognate re-docking (pose prediction) and/or virtual screening. Related papers have been published on ligand-based tools: pose prediction by conformer generators and virtual screening using a variety of ligand-based approaches. The reliability of these comparisons is critically affected by a number of factors usually ignored by the authors, including bias in the datasets used in virtual screening, the metrics used to assess performance in virtual screening and pose prediction and errors in crystal structures used.     

A mild and general method for the synthesis of 5-substituted and 5,5-disubstituted fulleroprolines

The reductive ring-opening of fullerenyldihydropyrrole yields ethyl N-benzhydryl fullerenyl[60]glycinate, which is deprotected to give ethyl fullerenylglycinate. The free amine is able to react with a variety of aldehydes and ketones in a Mannich-type process to produce 5-substituted and 5,5-disubstituted fulleroprolines and represents a versatile and general strategy to this class of compounds.     

Duality properties of indicatrices of knots

The bridge index and superbridge index of a knot are important invariants in knot theory. We define the bridge map of a knot conformation, which is closely related to these two invariants, and interpret it in terms of the tangent indicatrix of the knot conformation. Using the concepts of dual and derivative curves of spherical curves as introduced by Arnold, we show that the graph of the bridge map is the union of the binormal indicatrix, its antipodal curve, and some number of great circles. Similarly, we define the inflection map of a knot conformation, interpret it in terms of the binormal indicatrix, and express its graph in terms of the tangent indicatrix. This duality relationship is also studied for another dual pair of curves, the normal and Darboux indicatrices of a knot conformation. The analogous concepts are defined and results are derived for stick knots.     

Fractal discrimination of random fractal aggregates and its application in biomarker analysis for blood coagulation

A recent rheological study has established that the fractal dimension, d_f, of an incipient clot, formed at the Gel Point (sol–gel transition) of coagulating blood is a significant new biomarker of haemostasis. In whole healthy blood, incipient clots show a clearly defined value of d_f = 1.7 within a narrow range, which represents a new ‘healthy index’ for normal clotting. The addition of unfractionated heparin significantly prolongs the onset of clot formation with a corresponding reduction of d_f as a function of heparin dose. However, as clots mature they exhibit (i) an expected increase in d_f and (ii) a significant increase to spread of these values, i.e. d_f’s in the range 2.0–2.5, limiting the use of d_f as a discriminant of clot microstructure.The present study, details how and why the spectral dimension, d_s, can be used to accommodate this shortcoming and allow discrimination of mature forms of clot microstructure in indistinguishable in terms of their fractal dimension. To elucidate why d_s permits discrimination a numerical experiment was conducted on computationally generated random fractal aggregates (RFAs) with a priori set value of d_f. Starting from RFAs with a d_f of 1.7, mature RFAs are evolved from these incipient templates by two differing growth processes achieving a final d_f of 2.1. Fractal and statistical analysis of the mature RFAs reveals, for the first time, that their differing internal structure is manifest in the magnitude of d_s. The potential clinical significance of these findings is discussed in terms of the possibility of exploiting the incipient clot’s ability to template the internal arrangement of the mature clot to better predict long term clot susceptibility to lysis.     

Germanium microsphere high-Q resonator

In this Letter, the fabrication and characterization of a microsphere resonator from the semiconductor germanium is demonstrated. Whispering gallery modes are excited in a 46 μm diameter germanium microsphere resonator using evanescent coupling from a tapered silica optical fiber with a waist diameter of 2 μm. Resonances with Q factors as high as 3.8×10(4) at wavelengths near 2 μm are observed. Because of their ultrahigh optical nonlinearities and extremely broad transparency window, germanium microsphere resonators offer the potential for optical processing devices, in particular at long wavelengths, such as around 2 μm.