Matrix Domain Research Articles

Liquid crystalline collagen assemblies as substrates for directed alignment of human Schwann cells.

Collagen is a key component of the extracellular matrix (ECM) and well-oriented domains of collagen are important for mimicking the local cell environment in vitro. While there has been significant attention directed towards the alignment of collagen, formation of large-scale oriented domains remains a key challenge. Type I collagen self-assembles to form liquid crystalline (LC) mesophases in acidic conditions at concentrations above 100 mg mL-1. The LC mesophase provides an efficient platform for large-scale alignment and patterning of collagen coated substrates. However, there still exist challenges related to solubilizing and processing of collagen at such high concentrations in order to replicate the native ECM. In this contribution, we report on centimeter-scale alignment in collagen-coated glass substrates using solutions that are well below the LC-forming concentrations. Importantly, we are also able to extend this method to macroscopic 3-D LC-collagen hydrogels with programmed anisotropy within them to create a mimic of the native ECM. We show that the orientation and aspect ratio of human Schwann cells are strongly coupled with the alignment of the collagen substrate/hydrogel. We use a simple model to estimate the critical magnetic field strength needed for a given concentration of collagen to permit macroscopic alignment-enabling guidance for future studies on alignment of collagen at high concentrations.

Validation of an evaluation matrix for the nursing process in the hospital context.

To validate the content of an evaluation matrix for the nursing process in the hospital context. A methodological study conducted in four stages, carried out from March to December 2022. Including: bibliographic research and selection of structuring foundations; construction of the logical model and analysis and judgment matrix; content validation by a committee of judges (n=11) using the Delphi technique; analysis of content validation data by calculating the Concordance Rate and Content Validity Index. At the end of the two rounds, the matrix had a concordance rate of 90% regarding format and 100% regarding other structural aspects. It also had a 100% concordance rate regarding the scope and representativeness of the matrix domains. Regarding the average Content Validity Index, the values were 0.97 and 0.98, for clarity and representativeness, respectively. The evaluation matrix - consisting of four dimensions and fourteen evaluation items referring to the necessary stages for the implementation and operationalization of the nursing process - demonstrated excellent content validity, which can contribute to supporting institutional initiatives for its consolidation in hospital nursing services.

Mesoscale migration of oil in tight sandstone reservoirs by multi-field coupled two-phase flow

The oil migration process plays a pivotal role in determining the distribution and scale of oil reservoirs in tight sandstone formations, while also simultaneously influencing their development outcomes. However, the mechanisms governing oil migration in these tight formations remain poorly understood. This study conducted numerical simulations to investigate the oil migration characteristics in tight sandstone at the mesoscale. Multivariate regression analysis was used to characterize the micromechanical parameters of a 3D digital core. In addition, the main equations describing the two-phase flow that couples the stress and seepage fields were proposed, thereby elucidating the oil migration process. Finally, the effects of the reservoir space type, pressure gradient, and stress on the oil migration efficiency were assessed. The results showed that: (1) Compared with the porous-type model, the fractured-type model had a higher level and more concentrated distribution of damage, better connectivity, and higher oil migration efficiency due to the seepage-stress coupling effect; (2) High fluid pressure gradients improved the efficiency of oil migration and enhanced the control of the three-dimensional distribution of the pore domain over oil distribution in the matrix domain. (3) When σ1 >σ3, the oil phase migration efficiency improves with the increasing axial stress. When σ1 <σ3, the oil phase migration efficiency decreases with the increasing confining stress. When σ1 = σ3, high stress leads to low oil phase migration efficiency. This study reveals the mesoscopic-scale mechanism of oil migration in tight sandstone reservoirs and may prove useful in the exploration and development in such reservoirs.

Consistent treatment of shear failure in embedded discrete fracture models using XFVM

AbstractUnderstanding deformations and fluid flow in fractured rocks is of central importance for many subsurface flow applications. Thus, numerical frameworks are needed that capture the coupled mechanical and hydraulic behaviour, including scenarios with complex fracture networks. This paper employs the extended finite volume method to represent fracture manifolds in a poroelastic matrix domain and to compute shear and tensile displacements of fracture segments. However, using embedded fractures with non‐conforming grids can lead to severe convergence issues while computing shear slip and tensile opening of intersecting and parallel fractures, particularly if they have similar slopes. Our proposed solution of this problem is to slightly deform the fracture geometry by merging critical segments. We discuss and show examples of which attributes the merged segment has to adopt to ensure the correct slip behaviour at an intersection. Thereby it is crucial that the flow topology remains unaltered. Analysing failures of kinked fractures and fracture intersections show the flexibility of the devised algorithm. Moreover, it is demonstrated that deformation and opening patterns of a natural network with more than 200 fractures are qualitatively predicted very well. This method is a simple solution to treat multiple fracture segments in a grid cell, hence it can be used for any model embedding fractures in non‐conforming grids.

Integrated approach to improve numerical and geostatistical performance on a naturally fractured carbonate reservoir

The numerical simulation of carbonate reservoirs, while keeping the heterogeneous behavior in a reasonable development time, is a challenge. This study introduces a new method to improve simulation of complex carbonate reservoirs, balancing speed and accuracy by using multiple stochastic techniques and hierarchical upscaling. The methodology has five main steps: (1) develop the geological model, (2) hierarchical upscaling and numerical validation, (3) define the probabilistic workflow, (4) Discretized Latin Hypercube combined with geostatistical realizations, and (5) computational cost. The methodology is applied to a Brazilian pre-salt field. The time consumption for the numerical simulation and geomodelling of the proposed workflow was compared against conventional procedures. Notably, the hierarchical upscaling approach allowed the use of a reference model for the dynamic matching procedure. Innovative elements include implicit modeling of small-scale fractures within the matrix domain using analytical averaging techniques, the incorporation of pseudo-functions, and the direct integration of the discrete fracture network into the simulation grid. These advancements result in a remarkable reduction of 20% in simulation time and a 60% decrease in the time required to generate new geostatistical images. The innovative approach presented herein promises to address critical challenges in carbonate reservoir simulation, advancing the field’s understanding and practice.

Modeling density-driven flow and solute transport in heterogeneous reservoirs with micro/macro fractures

In this paper, a numerical model is presented to simulate the density-driven flow in heterogeneous porous media with micro- and macro-fractures. The micro-fractures (like fissures) with relatively small fracture lengths compared to the reservoir are modeled using an equivalent continuum model. The macro-fractures (like faults) with large fracture lengths are modeled using the extended finite element method (XFEM). Governing equations are based on the mass conservation equation for both the matrix and fracture domains together with the proper constitutive laws for the fluid velocity, dispersive velocity of solute, and equation of state for density of fluid phase. Several parameter studies are performed to investigate the effects of fracture characteristics on the solute spread in the medium. It is demonstrated that in the absence of macro-fractures, the influence of micro-fractures’ aperture on the solute spread is fully substantial and predictable. However, in the presence of macro-fractures, there is a region where the macro-fracture performs like a vacuum diminishing the influence of nearby micro-fractures. Finally, a real hydrological problem of the Gödöllő Hills reservoir located in Hungary with five different layers and eight faults, which is full of saline water is numerically modeled to investigate the effect of pressure gradient, anisotropy, and density difference on the solute transport. It is illustrated that in the top layers of the Gödöllő Hills reservoir, the gravitational force and vertical permeability are mostly accountable for the solute flow across the faults, whereas in the bottom layers, the horizontal pressure gradient is primarily responsible for the solute transport.

Preparation and Properties of Immiscible Poly(lactic acid)/Ethyl Cellulose Bioplastic Blends with Good Transparency and Optical Control by Drawing

In this study we prepared a poly(lactic acid)/ethyl cellulose (PLA/EC) bioplastic blend film by melt pressing after solvent casting and investigated the optical, thermal, and mechanical properties in relation to the structural changes revealed by various microscopies and scattering measurements. Despite the immiscibility of PLA and EC, the blend film exhibited good optical transparency due to the close match in their refractive indices. A second run of differential scanning calorimetry during heating revealed a decrease in the glass transition temperature () and melting point () of PLA with EC although EC had the higher values. Thermomechanical analysis suggested that these decreases were due to the negative pressure generated due to the suppression of PLA shrinkage below and above during cooling. Furthermore, ductile drawing of the blend film (70/30) at an optimal temperature of 70 °C above resulted in a uniform whitening near 100% strain. Delamination at the interface between the PLA matrix and EC domain led to the formation of micrometer-sized oriented voids, which enhanced the refractive index difference in the phase-separated structure, thereby scattering light and achieving the uniform and oriented white blend film.

ATAD3 Proteins: Unique Mitochondrial Proteins Essential forLife inDiverse Eukaryotic Lineages.

ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.

Modeling two-phase flow behaviour in a shale gas reservoir with complex fracture networks and flow dynamics

In this work, a robust and pragmatic method has been developed, validated, and applied to describe two-phase flow behaviour of a multifractured horizontal well (MFHW) in a shale gas formation. As for a fracture subsystem, its permeability modulus, non-Darcy flow coefficient, and slippage factor have been defined and embedded into the governing equation, while an iterative method is applied to update the gas/water saturation in each fracture segment within discrete fracture networks. Different from the traditional treatment that a water-source/sink in the matrix is simplified by assuming it as a constant term, a skin factor on a fracture face is defined and introduced to represent the change in relative permeability in the matrix domain at each timestep, while the adsorption/desorption term is incorporated into the diffusivity equation to accurately calculate the shale gas production by taking the adsorbed gas in nanoscale porous media into account. Then, the theoretical model can be applied to accurately capture the two-phase flow behaviour in different subdomains. The accuracy of this newly developed model has been confirmed by the numerical simulation and then it is extended to field applications with excellent performance. The stress-sensitivity, non-Darcy flow, and slippage effect in a hydraulic fracture (HF) are found to be obvious during the production, while the initial gas saturation in a matrix and HFs imposes an evident influence on the production profile. As for an HF with a high gas saturation, the dewatering stage is missing and water from the matrix can be neglected during a short production time. For the matrix subsystem, a high-water saturation in the matrix near an HF can affect gas production during the entire stage since gas relative permeability in the HF remains low. In addition, the adsorption/desorption in the matrix subsystem can increase gas production but decrease water production. Compared to the observed gas/water production rates for field applications, the solutions obtained from the method in this work are found to be well matched, confirming its reliability and robustness.

Evolutionary conservation of an ancient retroviral gagpol gene in Artiodactyla.

The genomes of mammals contain fingerprints of past infections by ancient retroviruses that invaded the germline of their ancestors. Most of these endogenous retroviruses (ERVs) contain only remnants of the original retrovirus; however, on rare occasions, ERV genes can be co-opted for a beneficial host function. While most studies of co-opted ERVs have focused on envelope genes, including the syncytins that function in placentation, there are examples of co-opted gag genes including one we recently discovered in simian primates. Here, we searched for other intact gag genes in non-primate mammalian lineages. We began by examining the genomes of extant camel species, which represent a basal lineage in the order Artiodactyla. This identified a gagpol gene with a large open reading frame (ORF) (>3,500 bp) in the same orthologous location in Artiodactyla species but that is absent in other mammals. Thus, this ERV was fixed in the common ancestor of all Artiodactyla at least 64 million years ago. The amino acid sequence of this gene, termed ARTgagpol, contains recognizable matrix, capsid, nucleocapsid, and reverse transcriptase domains in ruminants, with an RNase H domain in camels and pigs. Phylogenetic analysis and structural prediction of its reverse transcriptase and RNase H domains groups ARTgagpol with gammaretroviruses. Transcriptomic analysis shows ARTgagpol expression in multiple tissues suggestive of a co-opted host function. These findings identify the oldest and largest ERV-derived gagpol gene with an intact ORF in mammals, an intriguing milestone in the co-evolution of mammals and retroviruses. IMPORTANCE Retroviruses are unique among viruses that infect animals as they integrate their reverse-transcribed double-stranded DNA into host chromosomes. When this happens in a germline cell, such as sperm, egg, or their precursors, the integrated retroviral copies can be passed on to the next generation as endogenous retroviruses (ERVs). On rare occasions, the genes of these ERVs can be domesticated by the host. In this study we used computational similarity searches to identify an ancient ERV with an intact viral gagpol gene in the genomes of camels that is also found in the same genomic location in other even-toed ungulates suggesting that it is at least 64 million years old. Broad tissue expression and predicted preservation of the reverse transcriptase fold of this protein suggest that it may be domesticated for a host function. This is the oldest known intact gagpol gene of an ancient retrovirus in mammals.

A quasi-conforming embedded reproducing kernel particle method for heterogeneous materials

We present a quasi-conforming embedded reproducing kernel particle method (QCE-RKPM) for modeling heterogeneous materials that makes use of techniques not available to mesh-based methods such as the finite element method (FEM) and avoids many of the drawbacks in current embedded and immersed formulations which are based on meshed methods. The different material domains are discretized independently thus avoiding time-consuming, conformal meshing. In this approach, the superposition of foreground (inclusion) and background (matrix) domain integration smoothing cells are corrected by a quasi-conforming quadtree subdivision on the background integration smoothing cells. Due to the non-conforming nature of the background integration smoothing cells near the material interfaces, a variationally consistent (VC) correction for domain integration is introduced to restore integration constraints and thus optimal convergence rates at a minor computational cost. Additional interface integration smoothing cells with area (volume) correction, while non-conforming, can be easily introduced to further enhance the accuracy and stability of the Galerkin solution using VC integration on non-conforming cells. To properly approximate the weak discontinuity across the material interface by a penalty-free Nitsche’s method with enhanced coercivity, the interface nodes on the surface of the foreground discretization are also shared with the background discretization. As such, there are no tunable parameters, such as those involved in the penalty type method, to enforce interface compatibility in this approach. The advantage of this meshfree formulation is that it avoids many of the instabilities in mesh-based immersed and embedded methods. The effectiveness of QCE-RKPM is illustrated with several examples.

Effect of fracture geometry, topology and connectivity on energy recovery from enhanced geothermal systems

A combination of hydraulic fracturing and horizontal wells is now being used to tap geothermal energy from naturally fractured reservoirs. Fully grid-based numerical models are currently used to simulate heat recovery from enhanced geothermal systems (EGS). Such models require a fine unstructured mesh and are computationally expensive. In this paper we present a computationally efficient model that allows us to accurately simulate fracture propagation, fluid flow, and heat transfer in networks of natural fractures that may be created in naturally fractured geothermal reservoirs.The integrated simulator is developed by combining the displacement discontinuity method (DDM) for fracture propagation in naturally fractured reservoirs with a general Green's function solution for fluid and heat flow from the matrix to the fracture. This eliminates the need to discretize the matrix domain resulting in a very computationally efficient solution. A discrete fracture network (DFN) approach is used to represent the pre-existing natural fractures.The model is first validated against an analytical solution for fluid flow and heat transfer in a rock matrix with a single fracture. The computation time with and without discretizing the rock matrix shows a 100-fold reduction in computation cost with very little loss in accuracy. Parametric studies are conducted to investigate the effect of the distribution of natural fracture density, length, and orientation. The results show that the efficiency of tapping geothermal energy is impacted by geometrical and topological complexities of the fracture network and in particular the connectivity of backbone fractures. It is, therefore, important to optimize (not maximize) the connectivity and complexity of the backbone fracture network. The computationally efficient model presented here provides a practical tool for optimizing operational parameters for efficient geothermal production.

Water distribution in human hair microstructure elucidated by spin contrast variation small-angle neutron scattering

Dynamic nuclear polarization (DNP) is effective for controlling the neutron scattering length of protons and can be utilized for contrast variation in small-angle neutron scattering (SANS). Using the TEMPOL solution soaking method as electron spin doping, the DNP–SANS technique was applied to human hair fiber for the first time. For dry and D2O-swollen hair samples, a drastic change in the SANS profile was observed at high polarization conditions (|P H P N| ∼ 60%, where P H and P N are the proton and neutron spin polarization, respectively). The SANS profile as a function of the magnitude of the scattering vector, q, was composed of a low-q upturn, a middle-q oscillation and a high-q flat region. The low-q upturn was assumed to be a combination of two power-law functions, q −4 due to a large structure interface (Porod's law) and q −2 due to random coil. The middle-q oscillation was well reproduced by numerical calculation based on the structure model of intermediate filaments (IFs) as proposed by Er Rafik et al. [Biophys. J. (2004), 86, 3893–3904]: one pair of keratin coiled-coils is located at the center and surrounded by seven pairs of keratin coiled-coils located in a circle (called the `7 + 1' model), and a collection of IFs is arranged in a quasi-hexagonal manner. For the observed SANS profiles for different P H P N, the IF term contribution maintained a constant q-dependent profile, despite significant changes in intensity. This indicates that the macrofibril is composed of two domains (keratin coiled-coils and matrix). In addition, D2O swelling enhanced the IF term intensity and shifted the polarization-dependent local minimum to higher P H P N. This behavior was reproduced by contrast factor calculation based on the two-domain model. Scattering length densities of keratin coiled-coil and surrounding matrix domains were calculated by use of the known amino acid composition, considering the hydrogen–deuterium exchange reaction during soaking with D2O solution of TEMPOL. As a result, it was found that for keratin coiled-coil domains, about 40% of the peptide backbone amide NH protons were replaced with deuterons. This means that 68% of the α-helix domain is rigid, but the rest is flexible to allow dynamic dissociation of the hydrogen bond. Furthermore, the local mass density of each domain was precisely evaluated. The obtained data are expected to be a guide for further detailed investigation of keratin and keratin-associated protein distribution. This approach is expected to be applied to a wide variety of bio-derived materials, which are water absorbing in general.

Influence of HIV-1 Genomic RNA on the Formation of Gag Biomolecular Condensates

Biomolecular condensates (BMCs) play an important role in the replication of a growing number of viruses, but many important mechanistic details remain to be elucidated. Previously, we demonstrated that the pan-retroviral nucleocapsid (NC) and HIV-1 pr55Gag (Gag) proteins phase separate into condensates, and that HIV-1 protease (PR)-mediated maturation of Gag and Gag-Pol precursor proteins yields self-assembling BMCs that have HIV-1 core architecture. Using biochemical and imaging techniques, we aimed to further characterize the phase separation of HIV-1 Gag by determining which of its intrinsically disordered regions (IDRs) influence the formation of BMCs, and how the HIV-1 viral genomic RNA (gRNA) could influence BMC abundance and size. We found that mutations in the Gag matrix (MA) domain or the NC zinc finger motifs altered condensate number and size in a salt-dependent manner. Gag BMCs were also bimodally influenced by the gRNA, with a condensate-promoting regime at lower protein concentrations and a gel dissolution at higher protein concentrations. Interestingly, incubation of Gag with CD4+ T cell nuclear lysates led to the formation of larger BMCs compared to much smaller ones observed in the presence of cytoplasmic lysates. These findings suggest that the composition and properties of Gag-containing BMCs may be altered by differential association of host factors in nuclear and cytosolic compartments during virus assembly. This study significantly advances our understanding of HIV-1 Gag BMC formation and provides a foundation for future therapeutic targeting of virion assembly.

Application of Leak 2D to Describe Preferential Water Flow in a Soil Containing Artificial Macropores

Leak 2D is a new two-dimensional dual permeability mathematical model for the simulation of the preferential flow in the vadose zone. In this model, water flow in the soil matrix domain is described by the two-dimensional h-based Richards’ equation. Water flow in the fracture domain is estimated using the kinematic wave approach. Richards’ equation is solved by a combination of the alternating direction implicit (A.D.I.) method and the Douglas and Jones predictor−corrector method. The kinematic wave equation is solved explicitly. In the present paper, Leak 2D is calibrated and validated with data obtained in a Hele–Shaw apparatus filled with sand. Preferential flow is achieved by inserting four artificial macropores of various sizes into the soil. Six irrigations of various intensities and durations were used for the calibration and validation process. The water content at various depths was recorded by five sensors that were inserted into the soil. A comparison of the simulated water content with the measured profiles shows that Leak 2D can sufficiently describe preferential flow into the unsaturated zone of the soil, even under extreme irrigation conditions.

Nafion Matrix and Ionic Domain Tuning for High‐Performance Composite Proton Exchange Membranes

AbstractAlthough proton exchange membranes (PEMs) are widely deployed in an array of commercial applications, limitations linked to their proton conductivity, water retention, and gas permeability still limit ultimate device performance. While ex situ studies have shown additives can enhance membrane stability and mass transport, to date few have demonstrated that these performance enhancements are maintained when tested in commercially relevant electrochemical technologies, such as fuel cells or electrolyzers. Herein, a new multifunctional additive, 2D poly(triazine imide) (PTI), is demonstrated for composite PEMs, which is shown to boost proton conductivity by 37% under optimal high relative humidity (RH) conditions and 67% at low RHs. PTI also enables major improvements (over 55%) in both current and power densities in industrially relevant PEM fuel cells (PEMFCs). Most importantly, in situ and ex situ characterization suggests that the enhanced performance is due to polymer aggregate‐PTI clusters that form with increasing 2D character and improved long‐range connectivity, while acid‐base interactions with pyridinic nitrogen facilitate the critical proton hopping mechanism at all RHs. Hence, this work offers both a new membrane concept with proven benefits for important electrochemical technologies, as well as design principles for future optimization of proton transport and water management within PEMs.

A numerical approach for modeling crack closure and infiltrated flow in cracked soils

Soil cracks generated in natural fields will change soil structure and provide pathways for preferential flow. Although most simulations have focused on the influences of surface cracks or subsurface cracks in the fields, few studies are conducted on the deformable cracks extending from soil surface to deep soil layer. The present study addresses a fundamental issue and investigates the differences in water flow during infiltration processes of deformable and non-deformable cracked soils. Based on the discrete crack network model, a two-dimensional numerical approach is proposed to investigate the preferential flow in deformable cracked soil. Numerical simulations on water flow are implemented for matrix domain and cracks with the finite element method, which are discretized into solid elements and zero thickness elements, respectively. The proposed model is validated through explicit modeling and experimental observation and then compared with deformable crack approach. It is further employed to simulate the infiltration process of deformable cracked soil revealing significant differences in infiltration characteristics between deformable and non-deformable cracked soils, even if the cracks all act as preferential flow pathways. Although the saturation in crack closure of numerical model is variable during infiltration process, the effect of saturation is still affected by the number of cracks. Furthermore, cracks do not entirely close over a long period of infiltration, and thus they can become preferential flow pathways in subsequent infiltration events. These findings highlight the gap in simulations of water infiltration in cracked soil and the potential for erroneous simulations of water condition when cracks cannot be deformable during infiltration process.

Continuum and discrete element modelling for describing coupled hydro-mechanical effects of earthworm burrow coatings on soil shrinkage

Structured soils with earthworm burrows are locally heterogeneous due to coatings along these biopore walls that are superimposed on the inter- and intra-aggregate pore network of the soil matrix. The partially compacted finer-textured and organic matter-rich coatings can limit the flow exchange between the macropores and the soil matrix during preferential flow. Still unknown are dynamic hydro-mechanical interrelations in coating and matrix domains that affect stress–strain behaviour at the macroscopic scale. Such hydro-mechanic interactions may be described with the discrete element method (DEM) coupled with a two-phase pore finite volume (2PFV) approach if relevant pore structures are represented in the model. The objective was to develop a coupled DEM-2PFV model together with a parameterization procedure. Major task was to create a parameterization procedure to calibrate micro parameters of the model by macro properties quantified from drainage experiments of soil samples with earthworm burrow wall coatings.The solid phase was modelled by particle aggregation creating inter and intra-aggregate pore network for the soil matrix in a cube of about 5 cm edge length and one side with the coating structure. This DEM model was coupled with a 2PFV model to simulate hydro-mechanic effects during drainage. Sand box drainage experiments were carried out on soil matrix and biopore samples with laser surface elevation measurements to obtain the mechanical stress–strain macro parameters necessary for model calibration. The poly-dispersed DEM-2PFV model was able to describe effects of two-phase air–water flow on stress–strain macro parameters. The micro parameters (i.e., particle stiffness and bond strength) of the pore scale model were obtained from macro parameters of the primary and secondary stress–strain stages by training a random forest meta-estimator. The model was able to reproduce the pore network of coating material and the inter- and intra-aggregate pore network of the matrix that are dynamically changing with the effective stress. The machine learning model revealed that the bond strength among particles within aggregates governed the shrinkage of soil matrix, while the particle stiffness of the coating material reduced the susceptibility of aggregate breakage producing a more stable inter-aggregated pore network during the drainage process. This study confirmed that coating material present in biopore surface increases the horizontal soil hydro structural stability. The microscale hydro-mechanic modelling can be useful for finding flow exchange parameters inputs for upscaled models and correlating pore-scale parameters to experimentally determined stress–strain macro parameters.

A 3D hybrid DFPM-DFM Model for gas production from fractured shale reservoirs

Hydraulic fracturing as a key technology has been applied to improve gas productivity from shale reservoirs. Both induced hydraulic fractures (HFs) and inherent natural fractures (NFs) delineate a shale reservoir into matrix and fracture domains. Accurate characterizations of matrix and fracture are critical in evaluating gas production. In this work, an in-house built 3D discrete fracture model (DFM) was proposed to explicitly represent the distribution of the NFs network. Gas flow in shale matrix containing multiscale pores in inorganic matters (IOM) and organic matters (OM) was represented by a dual-fractal permeability model (DFPM). Consequentially, a hybrid DFPM–DFM model was proposed to couple gas flow and geomechanics the model was solved by commercial software based on the finite element method. The proposed model was verified using field data from a shale reservoir. The model was further employed to investigate the impacts of fractally-distributed pore size and fracture attributes on the evolutions of permeability and the associated gas production. The results showed that the fractally distributed pore size of IOM accounts for the diverse profiles of permeability evolution that exhibits a downward trend before rebounding. The impacts of pore diameter and tortuosity index on cumulative gas production were quantitatively analysed. We also highlighted the remarkable effects of fracture patterns (fracture connectivity, aperture and number) on cumulative gas production. This work provides a framework to explore the multiscale structural heterogeneities on hydrocarbon recovery and shale deformation.

HIV-1 Gag specificity for PIP2 is regulated by macromolecular electric properties of both protein and membrane local environments

HIV-1 assembly occurs at the plasma membrane, with the Gag polyprotein playing a crucial role. Gag association with the membrane is directed by the matrix domain (MA), which is myristoylated and has a highly basic region that interacts with anionic lipids. Several pieces of evidence suggest that the presence of phosphatidylinositol-(4,5)-bisphosphate (PIP2) highly influences this binding. Furthermore, MA also interacts with nucleic acids, which is proposed to be important for the specificity of GAG for PIP2-containing membranes. It is hypothesized that RNA has a chaperone function by interacting with the MA domain, preventing Gag from associating with unspecific lipid interfaces. Here, we study the interaction of MA with monolayer and bilayer membrane systems, focusing on the specificity for PIP2 and on the possible effects of a Gag N-terminal peptide on impairing the binding for either RNA or membrane. We found that RNA decreases the kinetics of the protein association with lipid monolayers but has no effect on the selectivity for PIP2. Interestingly, for bilayer systems, this selectivity increases in presence of both the peptide and RNA, even for highly negatively charged compositions, where MA alone does not discriminate between membranes with or without PIP2. Therefore, we propose that the specificity of MA for PIP2-containing membranes might be related to the electrostatic properties of both membrane and protein local environments, rather than a simple difference in molecular affinities. This scenario provides a new understanding of the regulation mechanism, with a macromolecular view, rather than considering molecular interactions within a ligand-receptor model.