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 .     

Horizontal bridges in polar dielectric liquids

When a high-voltage direct-current is applied to two beakers filled with polar liquid dielectrica like water or methanol, a horizontal bridge forms between the two beakers. By repeating a version of Pellat’s experiment, it is shown that a horizontal bridge is stable by the action of electrohydrodynamic pressure. Thus, the static and dynamic properties of the phenomenon called a ‘floating water bridge’ can be explained by the gradient of Maxwell pressure, replenishing the liquid within the bridge against any drainage mechanism. It is also shown that a number of liquids can form stable and long horizontal bridges. The stability of such a connection, and the asymmetry in mass flow through such bridges caused by the formation of ion clouds in the vicinity of the electrodes, is also discussed by two further experiments.     

Size‐Dependence of the Melting Temperature of Individual Au Nanoparticles

Nanoparticles have an immense importance in various fields, such as medicine, catalysis, and various technological applications. Nanoparticles exhibit a significant depression in melting point as their size goes below ≈10 nm. However, nanoparticles are frequently used in high temperature applications such as catalysis where temperatures often exceed several 100 degrees which makes it interesting to study not only the melting temperature depression, but also how the melting progresses through the particle. Using high‐resolution transmission electron microscopy, the melting process of gold nanoparticles in the size range of 2–20 nm Au nanoparticles combined with molecular dynamics studies is investigated. A linear dependence of the melting temperature on the inverse particle size is confirmed; electron microscopy imaging reveals that the particles start melting at the surface and the liquid shell formed then rapidly expands to the particle core.     

Three Short Stories about Hexaarylbenzene–Porphyrin Scaffolds

A feasible two‐step synthesis and characterization of a full series of hexaarylbenzene (HAB) substituted porphyrins and tetrabenzoporphyrins is presented. Key steps represent the microwave‐assisted porphyrin condensation and the statistical Diels–Alder reaction to the desired HAB‐porphyrins. Regarding their applications, they proved to be easily accessible and effective high molecular mass calibrants for (MA)LDI mass spectrometry. The free‐base and zinc(II) porphyrin systems, as well as the respective tetrabenzoporphyrins, demonstrate in solid state experiments strong red‐ and near‐infrared‐light emission and are potentially interesting for the application in “truly organic” light‐emitting devices. Lastly, they represent facile precursors to large polycyclic aromatic hydrocarbon (PAH) substituted porphyrins. We prepared the first tetra‐hexa‐peri‐hexabenzocoronene substituted porphyrin, which represents the largest prepared PAH‐porphyrin conjugate to date.     

Diffusion effects on the CPMG relaxation rate in a dipolar field

The diffusion in the magnetic dipolar field around a sphere is considered. The diffusion is restricted to the space between two concentric spheres, where the inner sphere is the source of the magnetic dipolar field. Analytical expressions for the CPMG transverse relaxation rate as well as the free induction decay and the spin echo time evolution are given in the Gaussian approximation. The influence of the inter-echo time is analyzed. The limiting cases of small and large inter-echo times as well as the short and long time behavior are evaluated.     

Phenylene-Bridged Perylene Monoimides as Acceptors for Organic Solar Cells: A Study on the Structure–Property Relationship

A series of non-fullerene acceptors based on perylene monoimides coupled in the peri position through phenylene linkers were synthesized via Suzuki-coupling reactions. Various substitution patterns were investigated using density functional theory (DFT) calculations in combination with experimental data to elucidate the geometry and their optical and electrochemical properties. Further investigations of the bulk properties with grazing incidence wide angle X-ray scattering (GIWAXS) gave insight into the stacking behavior of the acceptor thin films. Electrochemical and morphological properties correlate with the photovoltaic performance of devices with the polymeric donor PBDB-T and a maximum efficiency of 3.17 % was reached. The study gives detailed information about structure–property relationships of perylene-linker-perylene compounds.     

Scaling laws for transverse relaxation times

Simple scaling laws are useful tools in understanding the effect of changing parameters in MRI experiments. In this paper the general scaling behavior of the transverse relaxation times is discussed. We consider the dephasing of spins diffusing around a field inhomogeneity inside a voxel. The strong collision approximation is used to describe the diffusion process. The obtained scaling laws are valid over the whole dynamic range from motional narrowing to static dephasing. The dependence of the relaxation times on the external magnetic field, diffusion coefficients of the surrounding medium, and the characteristic scale of the field inhomogeneity is analyzed. For illustration the generally valid scaling laws are applied to the special case of a capillary, usually used as a model of the myocardial BOLD effect.     

Sensory Perception of Non-Deuterated and Deuterated Organic Compounds

The chemical background of olfactory perception has been subject of intensive research, but no available model can fully explain the sense of smell. There are also inconsistent results on the role of the isotopology of molecules. In experiments with human subjects it was found that the isotope effect is weak with acetone and D₆-acetone. In contrast, clear differences were observed in the perception of octanoic acid and D₁₅-octanoic acid. Furthermore, a trained sniffer dog was initially able to distinguish between these isotopologues of octanoic acid. In chromatographic measurements, the respective deuterated molecule showed weaker interaction with a non-polar liquid phase. Quantum chemical calculations give evidence that deuterated octanoic acid binds more strongly to a model receptor than non-deuterated. In contrast, the binding of the non-deuterated molecule is stronger with acetone. The isotope effect is calculated in the framework of statistical mechanics. It results from a complicated interplay between various thermostatistical contributions to the non-covalent free binding energies and it turns out to be very molecule-specific. The vibrational terms including non-classical zero-point energies play about the same role as rotational/translational contributions and are larger than bond length effects for the differential isotope perception of odor for which general rules cannot be derived.     

Photochemical Hydrogen Evolution at Metal Centers Probed with Hydrated Aluminium Cations,Al+(H2O)n,n=1–10

Hydrated aluminium cations have been investigated as a photochemical model system with up to ten water molecules by UV action spectroscopy in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Intense photodissociation was observed starting at 4.5 eV for two to eight water molecules with loss of atomic hydrogen, molecular hydrogen and water molecules. Quantum chemical calculations for n=2 reveal that solvation shifts the intense 3s–3p excitations of Al⁺ into the investigated photon energy range below 5.5 eV. During the photochemical relaxation, internal conversion from S₁ to T₂ takes place, and photochemical hydrogen formation starts on the T₂ surface, which passes through a conical intersection, changing to T₁. On this triplet surface, the electron that was excited to the Al 3p orbital is transferred to a coordinated water molecule, which dissociates into a hydroxide ion and a hydrogen atom. If the system remains in the triplet state, this hydrogen radical is lost directly. If the system returns to singlet multiplicity, the reaction may be reversed, with recombination with the hydroxide moiety and electron transfer back to aluminium, resulting in water evaporation. Alternatively, the hydrogen radical can attack the intact water molecule, forming molecular hydrogen and aluminium dihydroxide. Photodissociation is observed for up to n=8. Clusters with n=9 or 10 occur exclusively as HAlOH⁺(H₂O)_n-1 and are transparent in the investigated energy range. For n=4–8, a mixture of Al⁺(H₂O)_n and HAlOH⁺(H₂O)_n-1 is present in the experiment.