Formalising the Pathways to Life Using Assembly Spaces

Assembly theory (referred to in prior works as pathway assembly) has been developed to explore the extrinsic information required to distinguish a given object from a random ensemble. In prior work, we explored the key concepts relating to deconstructing an object into its irreducible parts and then evaluating the minimum number of steps required to rebuild it, allowing for the reuse of constructed sub-objects. We have also explored the application of this approach to molecules, as molecular assembly, and how molecular assembly can be inferred experimentally and used for life detection. In this article, we formalise the core assembly concepts mathematically in terms of assembly spaces and related concepts and determine bounds on the assembly index. We explore examples of constructing assembly spaces for mathematical and physical objects and propose that objects with a high assembly index can be uniquely identified as those that must have been produced using directed biological or technological processes rather than purely random processes, thereby defining a new scale of aliveness. We think this approach is needed to help identify the new physical and chemical laws needed to understand what life is, by quantifying what life does.     

A structure determination protocol based on combined analysis of 3D-ED data,powder XRD data,solid-state NMR data and DFT-D calculations reveals the structure of a new polymorph of l-tyrosine

We report the crystal structure of a new polymorph of l-tyrosine (denoted the β polymorph), prepared by crystallization from the gas phase following vacuum sublimation. Structure determination was carried out by combined analysis of three-dimensional electron diffraction (3D-ED) data and powder X-ray diffraction (XRD) data. Specifically, 3D-ED data were required for reliable unit cell determination and space group assignment, with structure solution carried out independently from both 3D-ED data and powder XRD data, using the direct-space strategy for structure solution implemented using a genetic algorithm. Structure refinement was carried out both from powder XRD data, using the Rietveld profile refinement technique, and from 3D-ED data. The final refined structure was validated both by periodic DFT-D calculations, which confirm that the structure corresponds to an energy minimum on the energy landscape, and by the fact that the values of isotropic ¹³C NMR chemical shifts calculated for the crystal structure using DFT-D methodology are in good agreement with the experimental high-resolution solid-state ¹³C NMR spectrum. Based on DFT-D calculations using the PBE0-MBD method, the β polymorph is meta-stable with respect to the previously reported crystal structure of l-tyrosine (now denoted the α polymorph). Crystal structure prediction calculations using the AIRSS approach suggest that there are three other plausible crystalline polymorphs of l-tyrosine, with higher energy than the α and β polymorphs.

A new polymorph of l-tyrosine is reported, with the crystal structure determined by combined analysis of 3D-ED data and powder XRD data, augmented by information from periodic DFT-D calculations and solid-state ¹³C NMR data.     

Modelling of a novel high-impedance matching layer for high frequency (>30 MHz) ultrasonic transducers

This work describes a new approach to impedance matching for ultrasonic transducers. A single matching layer with high acoustic impedance of 16 MRayls is demonstrated to show a bandwidth of around 70%, compared with conventional single matching layer designs of around 50%. Although as a consequence of this improvement in bandwidth, there is a loss in sensitivity, this is found to be similar to an equivalent double matching layer design. Designs are calculated by using the KLM model and are then verified by FEA simulation, with very good agreement Considering the fabrication difficulties encountered in creating a high-frequency double matched design due to the requirement for materials with specific acoustic impedances, the need to accurately control the thickness of layers, and the relatively narrow bandwidths available for conventional single matched designs, the new approach shows advantages in that alternative (and perhaps more practical) materials become available, and offers a bandwidth close to that of a double layer design with the simplicity of a single layer design. The disadvantage is a trade-off in sensitivity. A typical example of a piezoceramic transducer matched to water can give a 70% fractional bandwidth (comparable to an ideal double matched design of 72%) with a 3 dB penalty in insertion loss.     

Radiation-enhanced diffusion and fission gas release from recrystallised grains in high burn-up hbox{UO}_{2} nuclear fuel

The effective diffusion coefficient that gives a steady-state xenon concentration of 0.2-0.3wt% in the recrystallised grains of high burn-up UO 2 fuel is calculated to lie in the range 10 m 24 to 10 m 22 m 2 s m 1 . These values are one to three orders of magnitude lower than the value currently accepted for the radiation-enhanced diffusion coefficient. The time required to reach the steady-state concentration depends on the local fission rate, the grain size distribution and the precise magnitude of the radiation-enhanced diffusion coefficient, and can take from 2 to 10 years. Additional calculations reveal that substantially less than 10% of the fission gas inventory is released from the original UO 2 grains in the outer region of the fuel prior to recrystallisation. In contrast, with a diffusion coefficient of 10 m 22 m 2 s m 1 more than 80% of the fission gas is released from the recrystallised grains of the high burn-up structure in one year.     

Spectroscopic fingerprints of valence and spin states in manganese oxides and fluorides

We performed a systematic study of soft X-ray absorption spectroscopy in various manganese oxides and fluorides. Both Mn L-edges and ligand (O and F) K-edges are presented and compared with each other. Despite the distinct crystal structure and covalent/ionic nature in different systems, the Mn-L spectra fingerprint the Mn valence and spin states through spectral lineshape and energy position consistently and evidently. The clear O- and F-K pre-edge features in our high resolution spectra enable a quantitative definition of the molecular orbital diagram with different Mn valence. In addition, while the binding energy difference of the O-1s core electrons leads to a small shift of the O-K leading edges between trivalent and quadrivalent manganese oxides, a significant edge shift, with an order of magnitude larger in energy, was found between divalent and trivalent compounds, which is attributed to the spin exchange stabilization of half-filled 3d system. This shift is much enhanced in the ionic fluoride system. This work provides the spectroscopic foundation for further studies of complicated Mn compounds.     

Free (open) boundary condition: some experiences with viscous flow simulations

The free (or open) boundary condition (FBC, OBC) was proposed by Papanastasiou et al. (A new outflow boundary condition, International Journal for Numerical Methods in Fluids, 1992; 14:587–608) to handle truncated domains with synthetic boundaries where the outflow conditions are unknown. In the present work, implementation of the FBC has been tested in several benchmark problems of viscous flow in fluid mechanics. The FEM is used to provide numerical results for both cases of planar and axisymmetric domains under laminar, isothermal or non‐isothermal, steady‐state conditions, for Newtonian fluids. The effects of inertia, gravity, compressibility, pressure dependence of the viscosity, slip at the wall, and surface tension are all considered individually in the extrudate‐swell benchmark problem for a wide range of the relevant parameters. The present results extend previous ones regarding the applicability of the FBC and show cases where the FBC is inappropriate, namely in the extrudate‐swell problem with gravity or surface‐tension effects. Particular emphasis has been given to the pressure at the outflow, which is the most sensitive quantity of the computations. In all cases where FBC is appropriate, excellent agreement has been found in comparisons with results from very long domains. The formulation for Picard‐type iterations is given in some detail, and the differences with the Newton–Raphson formulation are highlighted regarding some computational aspects. Copyright © 2011 John Wiley & Sons, Ltd.     

Recycling of Informational Units Leads to Selection of Replicators in a Prebiotic Soup

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Highlights? Recycling of genetic material is important for the origins of life ? Simulation studies show recycling leads to the selection of genotypes from a pool ? Recycling can lead to the sudden emergence of a high-fitness RNA genotype ? Experimental studies with the Azoarcus ribozyme show fragment recycling     

The Acetoxyfulvene Synthesis of Prostaglandins: A New,Versatile Synthesis of dl-PGF1δ, dl-PGF2α, dl-PGE1 and dl-PGE2 from a Common Intermediate

Abstract

In the Corey¹ synthesis of prostaglandins and in our recently published modifications^2,3 a synthon containing carbon atoms 14 to 20^θ is first added to a bicyclic intermediate (C-6 to C-13) and completion of the prostaglandin skeleton by addition of a second synthon containing carbon atoms 1 to 5 forms a subsequent step. In a modification^4,5 of the Corey synthesis¹ PGF_1α and PGE₁ were made by reversing the order in which these two synthons were added to the cyclopentane ring (C-6 to C-13). The major limitation of this modified route^4,5 is that it is restricted to the preparation of prostaglandins of the 1-series,^? because hydrogenolysis of the benzyl group of the intermediate ester (1) reduces the C-5, C-6 double bond to form the saturated alcohol (2), which cannot be converted into prostaglandins of the 2-series^?.