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The advent of advanced crystallographic techniques has shifted structural biology from static, single-conformer models toward probing protein dynamics. Extracting cooperative motions from temporally and spatially averaged electron density…

Quantitative Methods · Quantitative Biology 2025-09-08 Avinash Mandaiya , Veit Elser

A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…

Tissues and Organs · Quantitative Biology 2018-05-01 Andrew L. Krause , Dmitry Beliaev , Robert A. Van Gorder , Sarah L. Waters

Predicting the geometrical evolution of the pore space in geological formations due to fluid-solid interactions has applications in reservoir engineering, oil recovery, and geological storage of carbon dioxide. However, modeling frameworks…

Multilayer networks provide a powerful framework for modeling complex systems that capture different types of interactions between the same set of entities across multiple layers. Core-periphery detection involves partitioning the nodes of…

Physics and Society · Physics 2025-05-08 Kai Bergermann , Francesco Tudisco

Film flow through networks of corners and capillary bridges can establish connections between seemingly isolated clusters during drainage in porous media. Coupled with drainage through the bulk of pores and throats, the flow through these…

In this paper, we present a new multiscale model reduction technique for the Stokes flows in heterogeneous perforated domains. The challenge in the numerical simulations of this problem lies in the fact that the solution contains many…

Numerical Analysis · Mathematics 2016-08-26 Eric T. Chung , Maria Vasilyeva , Yating Wang

The numerical simulation of large-scale multiphase flow in porous media is of considerable importance across various application fields, particularly in the petroleum industry. The fully implicit method is preferred in reservoir simulations…

Numerical Analysis · Mathematics 2026-04-13 Shizhe Li , Li Zhao , Chen-Song Zhang

Heterogeneous networks provide a universal framework for extracting subsystem-level features of a complex system, which are critical in graph colouring, pattern classification, and motif identification. When abstracting physical systems…

Optics · Physics 2025-07-31 Seungmok Youn , Kunwoo Park , Ikbeom Lee , Gitae Lee , Namkyoo Park , Sunkyu Yu

Fast prediction of permeability directly from images enabled by image recognition neural networks is a novel pore-scale modeling method that has a great potential. This article presents a framework that includes (1) generation of porous…

Computational Physics · Physics 2018-09-11 Jin-Long Wu , Xiao-Long Yin , Heng Xiao

Core-periphery detection aims to separate the nodes of a complex network into two subsets: a core that is densely connected to the entire network and a periphery that is densely connected to the core but sparsely connected internally. The…

Numerical Analysis · Mathematics 2024-05-29 Kai Bergermann , Martin Stoll , Francesco Tudisco

The convergence between effective medium theory and pore-network modelling is examined. Electrical conductance on two and three-dimensional cubic resistor networks is used as an example of transport through composite materials or porous…

Materials Science · Physics 2021-09-17 Jack Edwards , Peter Berg

Coarse-scale surrogate models in the context of numerical homogenization of linear elliptic problems with arbitrary rough diffusion coefficients rely on the efficient solution of fine-scale sub-problems on local subdomains whose solutions…

Numerical Analysis · Mathematics 2022-09-07 Fabian Kröpfl , Roland Maier , Daniel Peterseim

We investigate the chemical dissolution of porous media using a network model in which the system is represented as a series of interconnected pipes with the diameter of each segment increasing in proportion to the local reactant…

Fluid Dynamics · Physics 2015-06-12 Agnieszka Budek , Piotr Szymczak

Profiling core-periphery structures in networks has attracted significant attention, leading to the development of various methods. Among these, the rich-core method is distinguished for being entirely parameter-free and scalable to large…

Physics and Society · Physics 2025-04-17 Jiaqi Nie , Qi Xuan , Dehong Gao , Zhongyuan Ruan

The study of multiphase flows in porous media is fundamental to various fields, including oil recovery, CO2 sequestration, hydrogeology, and others. Accurate predictions of fluid behavior in these systems can enhance process efficiency…

Fluid Dynamics · Physics 2025-09-17 Roberto Lange , Gabriel M. Magalhães , Franciane F. Rocha , Hélio R. Neto

The paper is devoted to the homogenization of porous piezoelectric materials saturated by electrically inert fluid. The solid part of a representative volume element consists of the piezoelectric skeleton with embedded conductors. The pore…

Computational Physics · Physics 2018-08-01 Eduard Rohan , Vladimír Lukeš

Recent advances in 3D X-ray Computed Tomographic (CT) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. Voxel-based description (up to hundreds…

Computer Vision and Pattern Recognition · Computer Science 2023-09-06 Olivier Monga , Zakaria Belghali , Mouad Klai , Lucie Druoton , Dominique Michelucci , Valerie Pot

The growing use of composite materials in engineering applications has accelerated the demand for computational methods to accurately predict their complex behavior. Multiscale modeling based on computational homogenization is a potentially…

Numerical Analysis · Mathematics 2024-10-18 N. Kovács , M. A. Maia , I. B. C. M. Rocha , C. Furtado , P. P. Camanho , F. P. van der Meer

We use the periodic unfolding technique to derive corrector estimates for a reaction-diffusion system describing concrete corrosion penetration in the sewer pipes. The system, defined in a periodically-perforated domain, is semi-linear,…

Analysis of PDEs · Mathematics 2012-01-30 Tasnim Fatima , adrian Muntean , Mariya Ptashnyk

We present multiscale graph-based reduction algorithms for upscaling heterogeneous and anisotropic diffusion problems. The proposed coarsening approaches begin by constructing a partitioning of the computational domain into a set of…

Numerical Analysis · Mathematics 2025-10-14 Maria Vasilyeva , James Brannick , Ben S. Southworth