Excluded volume effects in on‐ and off‐lattice reaction–diffusion models

Mathematical models are important tools to study the excluded volume effects on reaction–diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off‐lattice Brownian dynamics become computationally expensive in crowded environments. In this study, the authors therefore investigate to which extent on‐lattice approximations, the so‐called cellular automata models, can be used to simulate reactions and diffusion in the presence of crowding molecules. They show that the diffusion is most severely slowed down in the off‐lattice model, since randomly distributed obstacles effectively exclude more volume than those ordered on an artificial grid. Crowded reaction rates can be both increased and decreased by the grid structure and it proves important to model the molecules with realistic sizes when excluded volume is taken into account. The grid artefacts increase with increasing crowder density and they conclude that the computationally more efficient on‐lattice simulations are accurate approximations only for low crowder densities.Inspec keywords: reaction‐diffusion systems, cellular biophysics, biodiffusion, Brownian motion, cellular automata, molecular biophysics, molecular configurationsOther keywords: crowder density, grid artefacts, grid structure, crowded reaction rates, artificial grid, randomly distributed obstacles, crowding molecules, cellular automata models, on‐lattice approximations, crowded environments, off‐lattice Brownian dynamics, detailed microscopic simulations, living cells, mathematical models, off‐lattice reaction‐diffusion models, on‐lattice reaction‐diffusion models, excluded volume effects     

A computational framework for scale‐bridging in multi‐scale simulations

A computational framework for scale‐bridging in multi‐scale simulations is presented. The framework enables seamless combination of at‐scale models into highly dynamic hierarchies to build a multi‐scale model. Its centerpiece is formulated as a standalone module capable of fully asynchronous operation. We assess its feasibility and performance for a two‐scale model applied to two challenging test problems from impact physics. We find that the computational cost associated with using the framework may, as expected, become substantial. However, the framework has the ability of effortlessly combining at‐scale models to render complex multi‐scale models. The main source of the computational inefficiency of the framework is related to poor load balancing of the lower‐scale model evaluation We demonstrate that the load balancing can be efficiently addressed by recourse to conventional load‐balancing strategies. Copyright © 2016 John Wiley & Sons, Ltd.     

Noncontact Sonic NDE and Defect Imaging Via Local Defect Resonance

A selective acoustic activation of defects based on the concept of local defect resonance enables to enhance considerably the intensity of defect vibrations and makes it possible to reduce the input acoustic powers to the levels permissible for noncontact nondestructive inspection. Since for cm-size defects in composite materials, the LDR frequencies lie in the low kHz-range, the resonant noncontact activation shifts to an audible frequency range and can be provided by conventional sonic equipment. In this paper, the feasibility of the resonant noncontact inspection is validated for the most “problematic” methodologies of nonlinear, thermosonic and shearosonic NDE that usually require an elevated acoustic power and, therefore, a reliable contact between the specimen and the transducer. In contrast, the noncontact versions developed employ commercial loudspeakers which can simultaneously insonify large areas and be applied for a contactless sonic inspection of different materials and various scale components.     

Bootstrap- and permutation-based inference for the Mann–Whitney effect for right-censored and tied data

The Mann–Whitney effect is an intuitive measure for discriminating two survival distributions. Here we analyse various inference techniques for this parameter in a two-sample survival setting with independent right-censoring, where the survival times are even allowed to be discretely distributed. This allows for ties in the data and requires the introduction of normalized versions of Kaplan–Meier estimators from which adequate point estimates are deduced. Asymptotically exact inference procedures based on standard normal, bootstrap, and permutation quantiles are developed and compared in simulations. Here, the asymptotically robust and—under exchangeable data—even finitely exact permutation procedure turned out to be the best. Finally, all procedures are illustrated using a real data set.     

Single point incremental forming: state-of-the-art and prospects

Incremental sheet metal forming in general and Single Point Incremental Forming (SPIF) specifically have gone through a period of intensive development with growing attention from research institutes worldwide. The result of these efforts is significant progress in the understanding of the underlying forming mechanisms and opportunities as well as limitations associated with this category of flexible forming processes. Furthermore, creative process design efforts have enhanced the process capabilities and process planning methods. Also, simulation capabilities have evolved substantially. This review paper aims to provide an overview of the body of knowledge with respect to Single Point Incremental Forming. Without claiming to be exhaustive, each section aims for an up-to-date state-of-the-art review with corresponding conclusions on scientific progress and outlook on expected further developments.     

Ultraschallbasierte in situ Vorspannkraftermittlung an Schrauben ohne Referenzmessung im nicht verspannten Zustand durch Kombination von Longitudinal- und Transversalwellen

Ultrasonic based bolt preload evaluation is commonly performed using the mono-wave method. This method works by measuring the time of flight of longitudinal waves. Here, a reference measurement in the unloaded condition is necessary for each bolt. In this publication the longitudinal wave is complemented by another type of ultrasonic wave - the transverse wave. This method does not require a reference measurement in the unloaded condition for each bolt. Moreover, an analytic method for determining the bolt-specific K-value is introduced, which is needed for the ultrasonic bolt preload determination. The analytically calculated K-values are compared with experimental K-values from tensile tests. The influence of material, bolt property class and surface protection system were determined with cylindrical specimens. In component tests, the bolt preload was evaluated using the bi-wave method, a possible influence of the bolt assembly method was investigated and the results were interpreted regarding their accuracy.     

Co-capping studies reveal CD8/TCR interactions after capping CD8 beta polypeptides and intracellular associations of CD8 with p56(lck)

A reaction-diffusion model was developed to predict the fate of nitric oxide (NO) released by cells of the immune system. The model was used to analyze data obtained previously using macrophages attached to microcarrier beads suspended in a stirred vessel. Activated macrophages synthesize NO, which is oxidized in the culture medium by molecular oxygen and superoxide (O2-, also released by the cells), yielding mainly nitrite (NO2-) and nitrate (NO3-) as the respective end products. In the analysis the reactor was divided into a "stagnant film" with position-dependent concentrations adjacent to a representative carrier bead and a well-mixed bulk solution. It was found that the concentration of NO was relatively uniform in the film. In contrast, essentially all of the O2- was calculated to be consumed within approximately 2 microm of the cell surfaces, due to its reaction with NO to yield peroxynitrite. The decomposition of peroxynitrite caused its concentration to fall to nearly zero over a distance of approximately 30 microm from the cells. Although the film regions (which had an effective thickness of 63 microm) comprised just 2% of the reactor volume and were predicted to account for only 6% of the NO2- formation under control conditions, they were calculated to be responsible for 99% of the NO3- formation. Superoxide dismutase in the medium (at 3.2 microM) was predicted to lower the ratio of NO3- to NO2- formation rates from near unity to <0.5, in reasonable agreement with the data. The NO3-/NO2- ratio was predicted to vary exponentially with the ratio of O2- to NO release rates from the cells. Recently reported reactions involving CO2 and bicarbonate were found to have important effects on the concentrations of peroxynitrite and nitrous anhydride, two of the compounds that have been implicated in NO cytotoxicity and mutagenesis.     

A temperature-dependent Mössbauer study of mechanically activated and non-activated zinc ferrite

The changes of ZnFe₂O₄ caused by mechanical activation as well as the structural evolution of nonactivated and mechanically activated zinc ferrite occurring during heating, have been investigated by in situ Mössbauer spectroscopy. Attention is directed to mechanically induced changes in magnetic properties of zinc ferrite, the variation of nuclear quadrupolar interactions, the thermally induced changes of the Mössbauer shift, and also to the structural response of mechanically activated zinc ferrite to changes in temperature.     

GOST 34.10—A brief overview of Russia's DSA

GOST 34.10 is Russia's DSA. Like its US counterpart, GOST is an ElGamal-like signature scheme used in Schnorr mode. It is similar to NIST DSA in many aspects. In this paper we will overview GOST 34.10 and discuss the three main differences between the two algorithms, (i) GOST's principal design criterion does not seem to be computational efficiency: the algorithm is 1.6 times slower than the DSA and produces 512-bit signatures. This is mainly due to the usage of the modulus q which is at least 254 bits long. During verification, modular inverses are computed by exponentiation (while the Extended Euclidian algorithm is roughly 100 times faster for this parameter size) and the generation of the public parameters is much more complicated than in the DSA. This choice of the parameters makes GOST 34.10 very secure. (ii) GOST signers do not have to generate modular inverses as the basic signature equation is s = xr + mk (mod q) instead of (mod q). (iii) GOST's hash function (the Russian equivalent of the SHA) is the standard GOST 34.11 which uses the block cipher GOST 28147 (partially classified) as a building block. The hash function will be briefly described. Copyright