PyRETIS 2: An improbability drive for rare events

The algorithmic development in the field of path sampling has made tremendous progress in recent years. Although the original transition path sampling method was mostly used as a qualitative tool to sample reaction paths, the more recent family of interface-based path sampling methods has paved the way for more quantitative rate calculation studies. Of the exact methods, the replica exchange transition interface sampling (RETIS) method is the most efficient, but rather difficult to implement. This has been the main motivation to develop the open-source Python-based computer library PyRETIS that was released in 2017. PyRETIS is designed to be easily interfaced with any molecular dynamics (MD) package using either classical or ab initio MD. In this study, we report on the principles and the software enhancements that are now included in PyRETIS 2, as well as the recent developments on the user interface, improvements of the efficiency via the implementation of new shooting moves, easier initialization procedures, analysis methods, and supported interfaced software. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.     

Minimizing singularities of generic plane disks with immersed boundaries

A cooriented circle immersion into the plane can be extended to a stable map of the disk which is an immersion in a neighborhood of the boundary and with outward normal vector field along the boundary equal to the given coorienting normal vector field. We express the minimal number of fold components of such a stable map as a function of its number of cusps and of the normal degree of its boundary. We also show that this minimum is attained for any cooriented circle immersion of normal degree not equal to one. The first author is a research fellow of the Royal Swedish Academy of Sciences sponsored by the Knut and Alice Wallenberg foundation.     

Ferromagnetic erbium studied by μSR

The ferromagnetic cone phase of erbium has been studied with μSR. Two precessing muon signals were observed with nearly equal intensities at T\approx15\ K. At lower temperatures, one of the signals is gradually reduced and disappeared below 5 K. The two observed muon frequencies and their depolarisation behaviour show that the magnetic structure deduced from neutron and X‐ray scattering must be modified and that a “squaring up” of the structure is likely to occur as the temperature is lowered. This revised version was published online in July 2006 with corrections to the Cover Date.     

Optical analysis of dichroism measurements in polymer science

The polarization properties of an optical system, source–interferometer–polarizer–polymer film–detector, have been calculated. Using Mueller matrices, the intensity has been obtained as a function of polarizer angle. It is shown in some detail how polarization of the beam in both interferometer and detector optics distort the spectra. The contributions from the finite extinction ratio of the polarizer are also calculated and intensity variations caused by beam-wandering are discussed. It is shown that the commonly used procedure for correcting the spectra is wrong. Better methods for correcting the spectra are proposed. The influence of a uniaxial refractive index on the data is discussed, and experimental methods that can deal with refraction effects are presented. © 1993 John Wiley & Sons, Inc.     

Novel synthesis of hydrazide-hydrazone derivatives and their utilization in the synthesis of coumarin, pyridine, thiazole and thiophene derivatives with antitumor activity

The reaction of cyanoacetyl hydrazine (1) with 3-acetylpyridine (2) gave the hydrazide-hydrazone derivative 3. The latter compound undergoes a series of heterocyclization reactions to give new heterocyclic compounds. The antitumor evaluation of the newly synthesized products against three cancer cell lines, namely breast adenocarcinoma (MCF-7), non-small cell lung cancer (NCI-H460) and CNS cancer (SF-268) was performed. Most of the synthesized compounds showed high inhibitory effects.     

Atomic layer deposition of organic-inorganic hybrid materials based on saturated linear carboxylic acids

Atomic layer deposition (ALD) has successfully provided thin films of organic-inorganic hybrid materials based on saturated linear carboxylic acids and trimethylaluminium (TMA). Films were grown for seven carboxylic acids: oxalic, malonic, succinic, glutaric, pimelic, suberic and sebacic acid, i.e. ranging from 2 to 10 carbon atoms in the molecular structure. These processes show exceptionally high growth rates; up to 4.3 nm/cycle for the pimelic acid-TMA system. Quartz crystal microbalance measurements of the growth dynamics indicate that all systems are of a self limiting ALD-type. Nevertheless, temperature dependent growth was observed in several systems. The width of the ALD windows shows correlations with the length of the carbon chains. Fourier transform infrared spectroscopy clearly proved that the deposited films are of a hybrid character, where the carboxylic acids primarily form bidentate complexes, though bridging complexes may also form. All films are X-ray amorphous as deposited. The films were further analyzed by atomic force microscopy for surface roughness and topography, UV-Vis spectroscopy and ellipsometry for optical properties, and the goniometer method for measuring sessile drops for surface wetting properties. Apart from the oxalic and malonic acid-TMA systems, the films are stable in contact with water. The films are generally smooth, transparent and have a refractive index close to 1.5. The complete coverage and accurate growth control offered by the ALD technique is here proven to provide surface-functionalized hybrid materials resembling metal-organic frameworks (MOF), probably as rather dense structures, yet with substantial potential for applications.     

Management of the risk of wind damage in forestry: a graph-based Markov decision process approach

This study deals with the problem of including the risk of wind damage in long-term forestry management. A model based on Graph-Based Markov Decision Processes (GMDP) is suggested for development of silvicultural management policies. The model can both take stochastic wind events into account and be applied to forest estates containing a large number of stands. The model is demonstrated for a forest estate in southern Sweden. Treatment of the stands according to the management policy specified by the GMDP model increased the expected net present value (NPV) of the whole forest only slightly, less than 2%, under different wind-risk assumptions. Most of the stands were managed in the same manner as when the risk of wind damage was not considered. For the stands that were treated differently, however, the expected NPV increased by 3% to 8%.     

On the development of a new pre-weld thermal treatment procedure for preventing heat-affected zone (HAZ) liquation cracking in nickel-base IN 738 superalloy

Hot cracking in the heat-affected zone (HAZ) of precipitation strengthened nickel-base superalloys, such as IN 738, during fusion welding remains a major factor limiting reparability of nickel-base gas turbine components. The problem of HAZ intergranular cracking can be addressed by modifying the microstructure of the pre-weld material through thermal treatment, which requires significant understanding of the critical factors controlling cracking behaviour. The decomposition of Mo-Cr-W-and Cr-rich borides in the alloy, among other factors, has been observed to contribute significantly to non-equilibrium intergranular liquation and, hence, intergranular liquation cracking during welding. Gleeble physical simulation of HAZ microstructure has also shown that non-equilibrium liquation is more severe in the vicinity of decomposed borides in the alloy and can occur at temperatures as low as 1,150 °C. Although currently existing pre-weld heat treatments for IN 738 superalloy minimize the contributions of dissolution of second phases, including borides, to HAZ intergranular liquation, these heat treatments are not industrially feasible due to process-related difficulties. Therefore, a new industrially feasible and effective pre-weld thermal treatment process, designated as FUMT, was developed during the present research by controlling both the formation of borides and the segregation of boron at the grain boundaries in the pre-weld heat-treated material. This thermal treatment was observed to very significantly reduce intergranular HAZ cracking in welded IN 738 superalloy. The details of the development process and developed procedure are presented in this paper.     

Density-functional calculations of the nuclear magnetic shielding and indirect nuclear spin–spin coupling constants of three isomers of C20

The parameters of the nuclear magnetic resonance (NMR) spectrum – shielding constants and indirect spin–spin coupling constants – of three isomers of C₂₀ are studied using density-functional theory. The performance of different exchange–correlation functionals is analysed by optimising the geometry for the ring, bowl and cage isomers, followed by a computation of the NMR constants at the optimised structure. The results are analysed and rationalised by performing comparisons of the three isomers with one another and with related systems such as polyynes (for the ring), o-benzyne (for the bowl) and C₆₀ (for the cage). The shielding and spin–spin parameters calculated using the Perdew–Burke–Ernzerhof (PBE) exchange–correlation functional are sufficiently reliable to assist in future experimental NMR studies of C₂₀ and, in particular, the identification of its isomers.