Experimental data showing the effect of wetting on soil structure transformations: 3D images.

Structure of the pore network of the soil controls many processes in the soil. Soil moistening have a profound impact on soil structure, which may affect a soil functions. This dataset presents the non-destructive three-dimensional (3D) visualization of the same soil sample under two different saturation conditions: air-dried and saturated beyond the field capacity [1]. The data were obtained by X-ray computed tomography and stored as three-dimensional 8-bit grayscale arrays. Two reconstructed images of the same sample were produced for future research. This dataset provides a valuable and unique insight for the qualitative and quantitative analysis.

Calcium-dependent insulin resistance in hepatocytes: mathematical model.

Hepatocyte insulin resistance is one of the early factors of developing type II diabetes. If insulin resistance is treated early, type II diabetes could be prevented. In recent years, scientists have been conducting extensive research on the underlying issues on a cellular and molecular level. It was found that the modulation of IP3-receptors, the mitochondrial ability to form the mitochondria-associated membranes (MAMs) and the endoplasmic reticulum stress during Ca2+ signaling play a key role in hepatocyte being able to maintain euglycemia and provide metabolic flexibility. However, researchers cannot agree on what factor is the key one in resulting in insulin resistance. In this work, we propose a mathematical model of Ca2+ signaling. We included in the model all the major contributors of a proper Ca2+ signaling during both the fasting and the postprandial state. Our modeling results are in good agreement with available experimental data. The analysis of modeling results suggests that MAMs dysfunction alone cannot result in abnormal Ca2+ signaling and the wrong modulation of IP3-receptors is a more definite reason. However, both the MAMs dysfunction and the IP3 signaling dysregulation combined can lead to a robust Ca2+ signal and improper glucose release. In addition, our model results suggest a strong dependence of Ca2+ oscillations pattern on morphological characteristics of the ER and the mitochondria.

Effect of Cold-Sintering Parameters on Structure, Density, and Topology of Fe-Cu Nanocomposites.

The design of advanced nanostructured materials with predetermined physical properties requires knowledge of the relationship between these properties and the internal structure of the material at the nanoscale, as well as the dependence of the internal structure on the production (synthesis) parameters. This work is the first report of computer-aided analysis of high pressure consolidation (cold sintering) of bimetallic nanoparticles of two immiscible (Fe and Cu) metals using the embedded atom method (EAM). A detailed study of the effect of cold sintering parameters on the internal structure and properties of bulk Fe-Cu nanocomposites was conducted within the limitations of the numerical model. The variation of estimated density and bulk porosity as a function of Fe-to-Cu ratio and consolidation pressure was found in good agreement with the experimental data. For the first time, topological analysis using Minkowski functionals was applied to characterize the internal structure of a bimetallic nanocomposite. The dependence of topological invariants on input processing parameters was described for various components and structural phases. The model presented allows formalizing the relationship between the internal structure and properties of the studied nanocomposites. Based on the obtained topological invariants and Hadwiger's theorem we propose a new tool for computer-aided design of bimetallic Fe-Cu nanocomposites.

New direct dynamic models of protein interactions coupled to photosynthetic electron transport reactions.

This review covers the methods of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. A direct multiparticle simulation method that simulates reactions describing interactions of ensembles of molecules in the heterogeneous interior of a cell is developed. In the models, protein molecules move according to the laws of Brownian dynamics, mutually orient themselves in the electrical field, and form complexes in the 3D scene. The method allows us to visualize the processes of molecule interactions and to calculate the rate constants for protein complex formation reactions in the solution and in the photosynthetic membrane. Three-dimensional multiparticle computer models for simulating the complex formation kinetics for plastocyanin with photosystem I and cytochrome bf complex, and ferredoxin with photosystem I and ferredoxin:NADP+-reductase are considered. Effects of ionic strength are featured for wild type and mutant proteins. The computer multiparticle models describe nonmonotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions.