This tutorial paper provides a step-by-step guide to developing a comprehensive understanding of the different forms of the deformation gradient used in Abaqus, and outlines a number of key issues that must be considered when developing an Abaqus user defined material subroutine (UMAT) in which the Cauchy stress is computed from the deformation gradient. Firstly, we examine the \"classical\" forms of global and local deformation gradients. We then show that Abaqus/Standard does not use the classical form of the local deformation gradient when continuum elements are used, and we highlight the important implications for UMAT development. We outline the key steps that must be implemented in developing an anisotropic fibre-reinforced hyperelastic UMAT for use with continuum elements and local orientation systems. We also demonstrate that a classical local deformation gradient is provided by Abaqus/Standard if structural (shell and membrane) elements are used, and by Abaqus/Explicit for all element types. We emphasise, however, that the majority of biomechanical simulations rely on the use of continuum elements with a local coordinate system in Abaqus/Standard, and therefore the development of a hyperelastic UMAT requires an in-depth and precise understanding of the form of the non-classical deformation gradient provided as input by Abaqus. Several worked examples and case studies are provided for each section, so that the details and implications of the form of the deformation gradient can be fully understood. For each worked example in this tutorial paper the source files and code (Abaqus input files, UMATs, and Matlab script files) are provided, allowing the reader to efficiently explore the implications of the form of the deformation gradient in the development of a UMAT.

In the last decade, technological advances in chemistry and photonics have enabled real-time measurement of temperature at the nanoscale. Nanothermometers, probes specifically designed to relay these nanoscale temperature changes, provide a high degree of temperature, temporal, and spatial resolution and precision. Several different approaches have been proposed, including microthermocouples, luminescence and fluorescence polarization anisotropy-based nanothermometers. Anisotropy-based nanothermometers excel in terms of biocompatibility because they can be built from endogenous proteins conjugated to dyes, minimizing any system perturbation. Moreover, the resulting fluorescent proteins can retain their native structure and activity while performing the temperature measurement, allowing precise temperature recordings from the native environment or during an enzymatic reaction in any given experimental system. To facilitate the future use of these nanothermometers in research, here we present a theoretical model that predicts the optimal sensitivity for anisotropy-based thermometers starting with any protein or dye, based on protein size and dye fluorescence lifetime. Using this model, most proteins and dyes can be converted to nanothermometers. The utilization of these nanothermometers by a broad spectrum of disciplines within the scientific community will bring new knowledge and understanding that today remains unavailable with current techniques.

A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal-organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.

Magnetic nanoparticles are of immense current interest because of their possible use in biomedical and technological applications. Here we demonstrate that the large magnetic anisotropy of FePt nanoparticles can be significantly modified by surface design. We employ X-ray absorption spectroscopy offering an element-specific approach to magnetocrystalline anisotropy and the orbital magnetism. Experimental results on oxide-free FePt nanoparticles embedded in Al are compared with large-scale density functional theory calculations of the geometric- and spin-resolved electronic structure, which only recently have become possible on world-leading supercomputer architectures. The combination of both approaches yields a more detailed understanding that may open new ways for a microscopic design of magnetic nanoparticles and allows us to present three rules to achieve desired magnetic properties. In addition, concrete suggestions of capping materials for FePt nanoparticles are given for tailoring both magnetocrystalline anisotropy and magnetic moments.

Since the publication of AAPM Task Group 60 report in 1999, a considerable amount of dosimetry data for the three coronary brachytherapy systems in use in the United States has been reported. A subgroup, Task Group 149, of the AAPM working group on Special Brachytherapy Modalities (Bruce Thomadsen, Chair) was charged to develop recommendations for dose calculation formalisms and the related consensus dosimetry parameters. The recommendations of this group are presented here. For the Cordis 192Ir and Novoste 90Sr/90Y systems, the original TG-43 formalism in spherical coordinates should be used along with the consensus values of the dose rate constant, geometry function, radial dose function, and anisotropy function for the single seeds. Contributions from the single seeds should be added linearly for the calculation of dose distributions from a source train. For the Guidant 32P wire system, the modified TG-43 formalism in cylindrical coordinates along with the recommended data for the 20 and 27 mm wires should be used. Data tables for the 6, 10, 14, 18, and 22 seed trains of the Cordis system, 30, 40, and 60 mm seed trains of the Novoste system, and the 20 and 27 mm wires of the Guidant system are presented along with our rationale and methodology for selecting the consensus data. Briefly, all available datasets were compared with each other and the consensus dataset was either an average of available data or the one obtained from the most densely populated study; in most cases this was a Monte Carlo calculation.