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Search results for: HETEROGENEOUS LIPID BILAYER
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Localization and Orientation of Xanthophylls in a Lipid Bilayer
PublicationXanthophylls (polar carotenoids) play diverse biological roles, among which are modulation of the physical properties of lipid membranes and protection of biomembranes against oxidative damage. Molecular mechanisms underlying these functions are intimately related to the localization and orientation of xanthophyll molecules in lipid membranes. In the present work, we address the problem of localization and orientation of two xanthophylls...
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Water Behavior Near the Lipid Bilayer
PublicationIn this chapter, we focus on the dynamics of water molecules situated in the vicinity of a phospholipid bilayer. Using a molecular dynamics simulation method, we studied interactions between water and the bilayer and tracked trajectories of the water molecules. Based on the hypothesis that molecules trapped inside the bilayer make different motions than the ones which are either attached to the surface or move freely in the water...
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublicationAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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A review on homogeneous and heterogeneous catalytic microalgal lipid extraction and transesterification for biofuel production
PublicationExtracting lipids from microalgal biomass presents significant potential as a cost-effective approach for clean energy generation. This can be achieved through the chemical conversion of lipids to produce fatty acid methyl esters via transesterification. The extraction mainly involves free fatty acids, phospholipids, and triglycerides, and requires less energy, making it an attractive option for satisfying the growing demand for...
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublicationMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
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Direct injection liquid chromatography-mass spectrometry (DI-LC-MS) analysis for rapid lipidomic profiling of extracellular vesicles
PublicationExtracellular vesicles (EVs) are small, spherical particles produced by eukaryotic and prokaryotic cells, surrounded by a bilayer membrane and carrying various bioactive molecules, such as proteins, surface receptors, membrane and soluble proteins, lipids, and nucleic acids. EVs are of substantial interest because of their important roles in cell communication, epigenetic regulation and possible application in disease diagnosis...
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Sodium alginate decreases the permeability of intestinal mucus
PublicationIn the small intestine the nature of the environment leads to a highly heterogeneous mucus layer primarily composed of the MUC2 mucin. We set out to investigate whether the soluble dietary fibre sodium alginate could alter the permeability of the mucus layer. The alginate was shown to freely diffuse into the mucus and to have minimal effect on the bulk rheology when added at concentrations below 0.1%. Despite this lack of interaction...
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Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
PublicationC99 is the C-terminal membrane-bound fragment of the amyloid precursor protein that is cleaved by γ-secretase to release Aβ peptides, the hallmark of Alzheimer’s disease (AD). Specific interactions of C99 with cholesterol have been proposed to underlie the recognized role of cholesterol in promoting amyloidogenesis. By using molecular dynamics simulations, we studied cholesterol binding to C99 in a lipid bilayer. We determined...
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Regulated Control of the Assembly and Diversity of LPS by Noncoding sRNAs
PublicationThe outer membrane (OM) of Gram-negative bacteria is asymmetric due to the presence of lipopolysaccharide (LPS) facing the outer leaflet of the OM and phospholipids facing the periplasmic side. LPS is essential for bacterial viability, since it provides a permeability barrier and is a major virulence determinant in pathogenic bacteria. In Escherichia coli, several steps of LPS biosynthesis and assembly are regulated by the RpoE...
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How do sterols determine the antufungal activitiy of amphotericin B? Free energy of binding between the drug and its membrane targets.
PublicationAmphotericin B (AmB) is a well-known polyene antibiotic used to treat systemic fungal infections. It is commonly accepted that the presence of sterols in the membrane is essential for the AmB biological activity, that is, for the formation of transmembrane ion channels. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against...
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A BODIPY‐Based Molecular Rotor in Giant Unilamellar Vesicles: A Case Study by Polarization‐Resolved Time‐Resolved Emission and Transient Absorption Spectroscopy
PublicationBODIPY and BODIPY-derived systems are widely applied as fluorophores and as probes for viscosity detection in solvents and biological media. Their orientational and rotational dynamics in biological media are thus of vital mechanistic importance and extensively investigated. In this contribution, polarization-resolved confocal microscopy is used to determine the orientation of an amphiphilic BODIPY-cholesterol derivative in homogeneous...
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Gender-Related Differences in Trimethylamine and Oxidative Blood Biomarkers in Cardiovascular Disease Patients
PublicationGender differences in the burden of cardiovascular disease (CVD) have been observed worldwide. In this study, plasmatic levels of trimethylamine (TMA) and blood oxidative biomarkers have been evaluated in 358 men (89 controls and 269 CVD patients) and 189 women (64 control and 125 CVD patients). The fluorescence technique was applied to determine erythrocyte membrane fluidity using 1,6-diphenyl-1,3,5-hexatriene (DPH) and Laurdan,...
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Regulated Assembly of LPS, Its Structural Alterations and Cellular Response to LPS Defects
PublicationDistinguishing feature of the outer membrane (OM) of Gram-negative bacteria is its asymmetry due to the presence of lipopolysaccharide (LPS) in the outer leaflet of the OM and phospholipids in the inner leaflet. Recent studies have revealed the existence of regulatory controls that ensure a balanced biosynthesis of LPS and phospholipids, both of which are essential for bacterial viability. LPS provides the essential permeability...
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Searching by heterogeneous agents
PublicationIn this work we introduce and study a pursuit-evasion game in which the search is performed by heterogeneous entities. We incorporate heterogeneity into the classical edge search problem by considering edge-labeled graphs: once a search strategy initially assigns labels to the searchers, each searcher can be only present on an edge of its own label. We prove that this problem is not monotone even for trees and we give instances...
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Searching by Heterogeneous Agents
PublicationIn this work we introduce and study a pursuit-evasion game in which the search is performed by heterogeneous entities. We incorporate heterogeneity into the classical edge search problem by considering edge-labeled graphs. In such setting a searcher, once a search strategy initially decides on the label of the searcher, can be present on an edge only if the label of the searcher and the label of the edge are the same. We prove...
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Regulation of LPS assembly via controlled proteolysis and sensing of LPS stress in Escherichia coli
PublicationLipopolysaccharide (LPS) is a complex glycolipid, essential for the bacterial viability and along with phospholipids, it constitutes the major amphiphilic component of outer membrane (OM) in most of the Gram-negative bacteria, including Escherichia coli. LPS molecules confer an effective permeability barrier to the OM and play a crucial role in bacteria-environment and -host interactions. The synthesis and accumulation of this...
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Comparison of Properties of the Hybrid and Bilayer MWCNTs—Hydroxyapatite Coatings on Ti Alloy
PublicationCarbon nanotubes are proposed for reinforcement of the hydroxyapatite coatings to improve their adhesion, resistance to mechanical loads, biocompatibility, bioactivity, corrosion resistance, and antibacterial protection. So far, research has shown that all these properties are highly susceptible to the composition and microstructure of coatings. The present research is aimed at studies of multi-wall carbon nanotubes in three different...
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Characterization of various drinking waters by new potentiometric taste sensor with lipid, lipid-like polymer membranes
PublicationA new sensing system comprising five all-solid-state electrodes with lipid, lipid like-polymer membranes was applied for rapid qualitative and quantitative analysis of various drinking waters. The results elaborated by chemometric methods revealed sensitivity to CO2 content in drinking water, suggesting that this sensing system could be used as a taste sensor. The ability of taste sensor to perform quantitative analysis of minerals...
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Statistical significance of displacements in heterogeneous control networks
PublicationThis paper proposes a modification of the classical process for evaluating the statistical significance of displacements in the case of heterogeneous (e.g. linear-angular) control networks established to deformation measurements and analysis. The basis for the proposed solution is the idea of local variance factors. The theoretical discussion was complemented with an example of its application on a simulated horizontal control...
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Integration of heterogeneous web services in exceptional situations
PublicationWeb services are intended to enable interoperability between heterogeneous distributed systems. Although the technology has been widely adopted and accepted, there are still differences between runtime platforms in exception structure and handling. This results in difficulties in effective handling of exceptions during Web services invocation. The paper presents a solution that enables coordinated exception handling between different...
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Ranking of Heterogeneous Catalysts Metals by Their Greenness
PublicationCatalysis is very important process in industry and laboratory practice, especially from the point of green chemistry principles. However, eco-friendly character of heterogeneous catalysts, containing transition metal components has not been evaluated, yet. Therefore, we perform a comprehensive assessment of 18 heterogeneous metal catalysts (Pd, Pt, V, Co, Ni, Mo, Ru, Mn, Au, Cu, Cd, Zr, Fe, Rh, Ir, Sn, Zn, Ag) using multicriteria...
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Application of Spinel and Hexagonal Ferrites in Heterogeneous Photocatalysis
PublicationSemiconducting materials display unique features that enable their use in a variety of applications, including self-cleaning surfaces, water purification systems, hydrogen generation, solar energy conversion, etc. However, one of the major issues is separation of the used materials from the process suspension. Therefore, chemical compounds with magnetic properties have been proposed as crucial components of photocatalytic composites,...
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ELECTRON ATTACHMENT TO HETEROGENEOUS MOLECULAR CLUSTERS
PublicationHeterogeneous clusters are unique model species enabling studies of bulk and surface processes by vacuum restricted methods. This is of particular importance for the reactions of low-energy electrons which have extremely short penetration depth in bulk environments. This contribution overviews our recent experiments with low-energy electrons and clusters prepared by different techniques. First, the deposition of molecules on argon...
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A concept of heterogeneous numerical model of concrete for GPR simulations
PublicationThe Ground Penetrating Radar (GPR) method, which is increasingly being used in the non-destructive diagnostics of reinforced concrete structures, often needs more accurate interpretation tools for analysis of experimental data. Recently, there has been growing interest in developing of various numerical models for exhaustive understanding of GPR data. This paper presents the concept of a heterogeneous numerical model of concrete,...
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Thermal Buckling Analysis of Circular Bilayer Graphene sheets Resting on an Elastic Matrix Based on Nonlocal Continuum Mechanics
PublicationIn this article, the thermal buckling behavior of orthotropic circular bilayer graphene sheets embedded in the Winkler–Pasternak elastic medium is scrutinized. Using the nonlocal elasticity theory, the bilayer graphene sheets are modeled as a nonlocal double–layered plate that contains small scale effects and van der Waals (vdW) interaction forces. The vdW interaction forces between the layers are simulated as a set of linear springs...
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Integrating heterogeneous systems with high-dependability requirements by means of web services
PublicationWeb services are commonly used on boundaries of heterogeneous components in Service Oriented Architecture (SOA) as they provide a universal communication channel not bound to any particular programming language or run-time platform. This paper describes how web services can be used to integrate heterogeneous systems which serve purposes requiring high dependability, reliability and availability. Examples of such systems include...
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Ubiquity of client access in heterogeneous access environment
PublicationWith popularization of mobile computing and diverse offer of mobile devices providing functionality comparable to stationary computers, the necessity of providing network access for such users cannot be disputed. The requirement is further reinforced by emergence of general purpose mobile operating systems which provide their full functionality only with network connectivity available and popular XaaS (Anything as a Service) approach....
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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublicationIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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Rendezvous of heterogeneous mobile agents in edge-weighted networks
PublicationWe introduce a variant of the deterministic rendezvous problem for a pair of heterogeneous agents operating in an undirected graph, which differ in the time they require to traverse particular edges of the graph. Each agent knows the complete topology of the graph and the initial positions of both agents. The agent also knows its own traversal times for all of the edges of the graph, but is unaware of the corresponding traversal...
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Rendezvous of Heterogeneous Mobile Agents in Edge-Weighted Networks
PublicationWe introduce a variant of the deterministic rendezvous problem for a pair of heterogeneous agents operating in an undirected graph, which differ in the time they require to traverse particular edges of the graph. Each agent knows the complete topology of the graph and the initial positions of both agents. The agent also knows its own traversal times for all of the edges of the graph, but is unaware of the corresponding traversal...
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A Novel Bitrate Adaptation Method for Heterogeneous Wireless Body Area Networks
PublicationIn the article, a novel bitrate adaptation method for data streams allocation in heterogeneous Wireless Body Area Networks (WBANs) is presented. The efficiency of the proposed algorithm was compared with other known algorithms of data stream allocation using computer simulation. A dedicated simulator has been developed using results of measurements in the real environment. The usage of the proposed adaptive data streams allocation...
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A Novel Bitrate Adaptation Method for Heterogeneous Wireless Body Area Networks
PublicationIn the article, a novel bitrate adaptation method for data streams allocation in heterogeneous Wireless Body Area Networks (WBANs) is presented. The efficiency of the proposed algorithm was compared with other known algorithms of data stream allocation using computer simulation. A dedicated simulator has been developed using results of measurements in the real environment. The usage of the proposed adaptive data streams allocation...
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Modeling of photovoltaic properties of bilayer organic systems
PublicationPraca prezentuje teoretyczny opis charakterystyki prądowo-napięciowej i efektu fotowoltaicznego układu zbudowanego z dwóch warstw organicznych i elektrod. Rozpatrywane jest przybliżenie stałego pola elektrycznego oraz wpływ pułąpkowania nośników ładunku.
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Category-Based Workload Modeling for Hardware Load Prediction in Heterogeneous IaaS Cloud
PublicationThe paper presents a method of hardware load prediction using workload models based on application categories and high-level characteristics. Application of the method to the problem of optimization of virtual machine scheduling in a heterogeneous Infrastructure as a Service (IaaS) computing cloud is described.
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Lipophagy and Lipolysis Status in Lipid Storage and Lipid Metabolism Diseases
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Multichannel taste sensors with lipid, lipid like – polymer membranes
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Untargeted Lipidomics Reveals Differences in the Lipid Pattern among Clinical Isolates of Staphylococcus aureus Resistant and Sensitive to Antibiotics
PublicationStaphylococcus aureus resistance to antibiotics is a significant clinical problem worldwide. In this study, an untargeted lipidomics approach was used to compare the lipid fingerprints of S. aureus clinical isolates that are resistant and sensitive to antibiotics. High-performance liquid chromatography coupled with time-of-flight mass spectrometry was employed to rapidly and comprehensively analyze bacterial lipids. Chemometric...
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Characterization of Mesorhizobium huakuii lipid A containing bothD-galacturonic acid and phosphate residues.
PublicationLipid A jest mieszaniną co najmniej 6 związków, różniących się stopniem fosforylacji i strukturą kwasów tłuszczowych przyłączonych do szkieletu polisacharydowego. Szkielet cukrowy zawiera beta(1'->6)połączone dwie cząsteczki 2,3-diamino-2,3-dideoksyglucosy (DAG)oraz aglikon kwas alfa-D-galaktouronowy.
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A novel heterogeneous model of concrete for numerical modelling of ground penetrating radar
PublicationThe ground penetrating radar (GPR) method has increasingly been applied in the non-destructive testing of reinforced concrete structures. The most common approach to the modelling of radar waves is to consider concrete as a homogeneous material. This paper proposes a novel, heterogeneous, numerical model of concrete for exhaustive interpretation of GPR data. An algorithm for determining the substitute values of the material constants...
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Implementation of FDTD-compatible Green's function on heterogeneous CPU-GPU parallel processing system
PublicationThis paper presents an implementation of the FDTD-compatible Green's function on a heterogeneous parallel processing system. The developed implementation simultaneously utilizes computational power of the central processing unit (CPU) and the graphics processing unit (GPU) to the computational tasks best suited to each architecture. Recently, closed-form expression for this discrete Green's function (DGF) was derived, which facilitates...
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Nonlinear material identification of heterogeneous isogeometric Kirchhoff–Love shells
PublicationThis work presents a Finite Element Model Updating inverse methodology for reconstructing heterogeneous materialdistributions based on an efficient isogeometric shell formulation. It uses nonlinear hyperelastic material models suitable fordescribing incompressible material behavior as well as initially curved shells. The material distribution is discretized by bilinearelements such that the nodal values...
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Two-phase flow in heterogeneous porous media with non-wetting phase trapping
PublicationThis article presents amathematical model describing flowof two fluid phases in a heterogeneous porous medium. Zaproponowano model matematyczny przepływu dwufazowego w drobnoziarnistym ośrodku porowatym zawierającym inkluzje gruboziarniste. Inkluzje charakteryzują się niższą wartością ciśnienia wejścia dla płynu niezwilżającego (np. powietrze, ropa naftowa) niż materiał podstawowy. Podczas nawadniania takiego ośrodka dochodzi do...
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Voltammetric and biological studies of folate-targeted non-lamellar lipid mesophases
PublicationFolate-targeted lipid nanostructures are promising strategies for the development of biocompatible drug delivery systems. The objective of this study was to evaluate the efficacy of drug delivery to cancer cells by folate-targeted lipid mesophases, cubosomes (CUB) and hexosomes (HEX), loaded with doxorubicin (DOX). Three cancer-derived cell lines (KB, HeLa, T98G) exhibiting different expressional levels of folate receptor protein...
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Molecular Dynamics of a Vasopressin V2 Receptor in a Phospholipid Bilayer Membrane
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Defining the thermal conductivity of thermally heterogeneous hollow wall bricks used as elements for increasing the comfort of buildings
PublicationThe article presents numerical calculation analysis in the scope of determining thermal conductivity coefficientλeq[W/(m·K)] of thermally heterogeneous hollow bricks of thermally heterogeneous structure (a combinationof structural material with thermal insulation material). Numerical calculations were conducted by means ofprofessional software TRISCO-KOBRU 86, serving thermal circulation analysis in a 2D field in stationary approach.The...
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Network-aware Data Prefetching Optimization of Computations in a Heterogeneous HPC Framework
PublicationRapid development of diverse computer architectures and hardware accelerators caused that designing parallel systems faces new problems resulting from their heterogeneity. Our implementation of a parallel system called KernelHive allows to efficiently run applications in a heterogeneous environment consisting of multiple collections of nodes with different types of computing devices. The execution engine of the system is open for...
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Influence of heterogeneous air entry pressure on large scale unsaturated flow in porous media
PublicationThe paper presents numerical simulations of water infiltration in unsaturated porous media containing coarse-textured inclusions embed- ded in fine-textured background material. The calculations are performed using the two-phase model for water and air flow and a simplified model known as the Richards equation. It is shown that the Richards equation cannot correctly describe flow in the presence of heterogeneities. How- ever, its...