NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

2,3,7,8,12,13-Hexakis[2-(2-methoxyethoxy)ethoxy]tricycloquinazoline: a discogen which allows enhanced levels of n-doping

A synthesis has been developed for 2,3,7,8,12,13-hexakis[2-(2-methoxyethoxy)ethoxy]-tricycloquinazoline (TCQ6EO2M) in which the ethylenoxy side chains are introduced before elaboration of the heterocylic core. This discogen gives a hexagonal columnar phase (Col_h) between 77 and 233°C. n-Doping using potassium metal is facilitated firstly by the electron poor/π-deficient nature of the core and secondly by the polyethylenoxy side chains which complex the potassium K⁺ counter-ions. The conductivity of the Col_h phase of TCQ6EO2M doped with 10 mol % potassium (σ _∥ = 1.1 x 10^-3 S m^-1) is substantially higher than that previously reported for 2,3,7,8,12,13-hexa(hexylthio)tricycloquinazoline doped with 6 mol % potassium (σ _∥ = 2.9 x 10^-5 S m^-1). Photoconductivity studies of TCQ6EO2M using a time of flight sample configuration show transient photocurrents for both holes and electrons. From these an upper limit on the mobility for the electrons is estimated as ~10^-4 cm² V^-1 s^-1 at 150°C which is of the same magnitude as that for hole mobilities in other columnar discotic liquid crystals.     

X-ray photoelectron spectroscopy and Raman microscopy of a ferroan platinum crystal from the Kondyor Massif,Russian Far East

X-ray Photoelectron Spectroscopy was used to study a ferroan platinum crystal from the Kondyor Massif, Russian Far East. Prior to the X-ray Photoelectron Spectroscopic analyses, the nature of the crystal was confirmed by X-ray diffraction. The survey scan showed mainly the presence of Pt and Fe, with smaller amounts of O and Si. The high resolutions spectra of the Pt 4f and Fe 2p showed 18.3 atom% Fe in the crystal, which puts the composition on the lower boundary for ferroan platinum and confirms earlier analyses using other methods such as Scanning Electron Microscopy-Energy Dispersive X-ray analysis/microprobe. The binding energy of the Pt 4f5/2 was 74.0?eV and Pt 4f7/2 70.5?eV, while the Fe 2p3/2 for metallic Fe was observed at 707.2?eV. The Fe 2p3/2 for metallic Fe was significantly sharper than that of Fe 2p3/2 at 710.7?eV associated with surface material. The Raman spectrum was dominated by the Pt–Pt stretching mode at 253?cm^?1. Changed orientation resulted in the observation of two bands at 127 and 139?cm^?1, interpreted as being due to stretching modes of two Pt–Pt bonds with the third bond to Fe and Pt fixed. The presence of Ca-Fe-Al-Mg-Si-O on the surface was probably associated with the presence of a clinopyroxene. These minerals can be expected since the crystal came originally from a clinopyroxenite-dunite matrix. The spectra showed a variety of interferences, e.g. Al 2p with Pt 4f, Mg 2p with Fe 3p, and Ca 2p1/2 with Mg Auger, making exact determinations of the ratios of these elements difficult.     

Physical Properties and Erosion Behavior of Poly(trimethylene carbonate‐co‐ε‐caprolactone) Networks

Form‐stable resorbable networks are prepared by gamma irradiating trimethylene carbonate (TMC)‐ and ε‐caprolactone (CL)‐based (co)polymer films. To evaluate their suitability for biomedical applications, their physical properties and erosion behavior are investigated. Homopolymer and copolymer networks that are amorphous at room temperature are flexible and rubbery with elastic moduli ranging from 1.8 ± 0.3 to 5.2 ± 0.4 MPa and permanent set values as low as 0.9% strain. The elastic moduli of the semicrystalline networks are higher and range from 61 ± 3 to 484 ± 34 MPa. The erosion behavior of (co)polymer networks is investigated in vitro using macrophage cultures, and in vivo by subcutaneous implantation in rats. In macrophage cultures, as well as upon implantation, a surface erosion process is observed for the amorphous (co)polymer networks, while an abrupt decrease in the rate and a change in the nature of the erosion process are observed with increasing crystallinity. These resorbable and form‐stable networks with tuneable properties may find application in a broad range of biomedical applications.

     

A new approach to untargeted integration of high resolution liquid chromatography–mass spectrometry data

Because of its high sensitivity and specificity, hyphenated mass spectrometry has become the predominant method to detect and quantify metabolites present in bio-samples relevant for all sorts of life science studies being executed. In contrast to targeted methods that are dedicated to specific features, global profiling acquisition methods allow new unspecific metabolites to be analyzed. The challenge with these so-called untargeted methods is the proper and automated extraction and integration of features that could be of relevance. We propose a new algorithm that enables untargeted integration of samples that are measured with high resolution liquid chromatography–mass spectrometry (LC–MS). In contrast to other approaches limited user interaction is needed allowing also less experienced users to integrate their data. The large amount of single features that are found within a sample is combined to a smaller list of, compound-related, grouped feature-sets representative for that sample. These feature-sets allow for easier interpretation and identification and as important, easier matching over samples. We show that the automatic obtained integration results for a set of known target metabolites match those generated with vendor software but that at least 10 times more feature-sets are extracted as well. We demonstrate our approach using high resolution LC–MS data acquired for 128 samples on a lipidomics platform. The data was also processed in a targeted manner (with a combination of automatic and manual integration) using vendor software for a set of 174 targets. As our untargeted extraction procedure is run per sample and per mass trace the implementation of it is scalable. Because of the generic approach, we envision that this data extraction lipids method will be used in a targeted as well as untargeted analysis of many different kinds of TOF-MS data, even CE- and GC–MS data or MRM. The Matlab package is available for download on request and efforts are directed toward a user-friendly Windows executable.     

On the “Tertiary Structure” of Poly‐Carbenes; Self‐Assembly of sp3‐Carbon‐Based Polymers into Liquid‐Crystalline Aggregates

The self‐assembly of poly(ethylidene acetate) (st‐PEA) into van der Waals‐stabilized liquid‐crystalline (LC) aggregates is reported. The LC behavior of these materials is unexpected, and unusual for flexible sp³‐carbon backbone polymers. Although the dense packing of polar ester functionalities along the carbon backbone of st‐PEA could perhaps be expected to lead directly to rigid‐rod behavior, molecular modeling reveals that individual st‐PEA chains are actually highly flexible and should not reveal rigid‐rod induced LC behavior. Nonetheless, st‐PEA clearly reveals LC behavior, both in solution and in the melt over a broad elevated temperature range. A combined set of experimental measurements, supported by MM/MD studies, suggests that the observed LC behavior is due to self‐aggregation of st‐PEA into higher‐order aggregates. According to MM/MD modeling st‐PEA single helices adopt a flexible helical structure with a preferred trans‐gauche syn‐syn‐anti‐anti orientation. Unexpectedly, similar modeling experiments suggest that three of these helices can self‐assemble into triple‐helical aggregates. Higher‐order assemblies were not observed in the MM/MD simulations, suggesting that the triple helix is the most stable aggregate configuration. DLS data confirmed the aggregation of st‐PEA into higher‐order structures, and suggest the formation of rod‐like particles. The dimensions derived from these light‐scattering experiments correspond with st‐PEA triple‐helix formation. Langmuir–Blodgett surface pressure–area isotherms also point to the formation of rod‐like st‐PEA aggregates with similar dimensions as st‐PEA triple helixes. Upon increasing the st‐PEA concentration, the viscosity of the polymer solution increases strongly, and at concentrations above 20 wt % st‐PEA forms an organogel. STM on this gel reveals the formation of helical aggregates on the graphite surface–solution interface with shapes and dimensions matching st‐PEA triple helices, in good agreement with the structures proposed by molecular modeling. X‐ray diffraction, WAXS, SAXS and solid state NMR spectroscopy studies suggest that st‐PEA triple helices are also present in the solid state, up to temperatures well above the melting point of st‐PEA. Formation of higher‐order aggregates explains the observed LC behavior of st‐PEA, emphasizing the importance of the “tertiary structure” of synthetic polymers on their material properties.     

Formation of cellulose microspheres and nanocrystals from mildly carboxylated fibers

Cellulose - The ultrastructure of mildly carboxylated swollen tracheids from which cellulose microspheres and cellulose nanocrystals (CNC) were formed was investigated. A mild etherification of...     

Production of textile filaments from carboxymethylated cellulosic pulps

Cellulose - Textile filaments were fabricated from a solution obtained from carboxymethylated cellulose dissolved in aqueous NaOH solution, by wet spinning in an acid coagulation bath. Spinning is...     

Solvent induced enhancement of nonlinear optical response of graphdiyne

Flat and crystalline materials with exceptional nonlinear optical(NLO) properties are highly desirable for their potential applications in integrated NLO photonic devices.Graphdiyne(GD),a new twodimensional(2 D) carbon allotrope,has recently evoked burgeoning research attention by virtue of its tunable bandgap along with a high carrier mobility and extended π-conjugation compared with most conventional optical materials.Here,we experimentally probe the third-order nonlinear optical response of GD dispersed in several common solvents(alcohols) using a femtosecond Z-scan technique.The measured nonlinear optical refractive index is in the order of ~10^-8 cm²/W,which is approximately one order of magnitude higher than that of most 2 D materials.In particular,we find that different NLO responses can be observed from GD when dispersed in different solvents,with the strongest NLO response when dispersed in 1-propanol.It is proposed that some intrinsic properties of the solvents,such as the polarity and viscosity,could influence the NLO response of GD materials.Our experimental results confirm the assumptions on the NLO behavior in GD and demonstrate its great potential for future generations of Kerr-effect-based NLO materials and devices.