Dataset Information

Multiscale and multiresolution modeling of shales and their flow and morphological properties.

ABSTRACT: The need for more accessible energy resources makes shale formations increasingly important. Characterization of such low-permeability formations is complicated, due to the presence of multiscale features, and defies conventional methods. High-quality 3D imaging may be an ultimate solution for revealing the complexities of such porous media, but acquiring them is costly and time consuming. High-quality 2D images, on the other hand, are widely available. A novel three-step, multiscale, multiresolution reconstruction method is presented that directly uses 2D images in order to develop 3D models of shales. It uses a high-resolution 2D image representing the small-scale features to reproduce the nanopores and their network, a large scale, low-resolution 2D image to create the larger-scale characteristics, and generates stochastic realizations of the porous formation. The method is used to develop a model for a shale system for which the full 3D image is available and its properties can be computed. The predictions of the reconstructed models are in excellent agreement with the data. The method is, however, quite general and can be used for reconstructing models of other important heterogeneous materials and media. Two biological examples and from materials science are also reconstructed to demonstrate the generality of the method.

SUBMITTER: Tahmasebi P

PROVIDER: S-EPMC4642334 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Multiscale and multiresolution modeling of shales and their flow and morphological properties.

Tahmasebi Pejman P Javadpour Farzam F Sahimi Muhammad M

Scientific reports 20151112

The need for more accessible energy resources makes shale formations increasingly important. Characterization of such low-permeability formations is complicated, due to the presence of multiscale features, and defies conventional methods. High-quality 3D imaging may be an ultimate solution for revealing the complexities of such porous media, but acquiring them is costly and time consuming. High-quality 2D images, on the other hand, are widely available. A novel three-step, multiscale, multiresol ...[more]

PMID: 26560178

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Project description:Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid discrete molecular dynamics simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperatures, suggesting a mechanism of chromatin structural organization whereby histone tails regulate inter- and intranucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed "cold sites", which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A interhistone interfaces, indicating the necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows that bending across the H3-H3 is a prominent mode of intranucleosomal dynamics. We postulate that effects of salts on mononucleosomes can be modeled in discrete molecular dynamics by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mononucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin structure, mediated by salt-bridge interactions with adjacent DNA.

Dataset Information

Multiscale and multiresolution modeling of shales and their flow and morphological properties.

Publications

Multiscale and multiresolution modeling of shales and their flow and morphological properties.

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