Control of Target Molecular Recognition in a Small Pore Space with Biomolecule-Recognition Gating Membrane

Porous aluminophosphate zeotypes (AlPOs) are promising materials for heat transformation applications using water as a working fluid. Two “types” of adsorbed water molecules can be distinguished in hydrated AlPOs: Water molecules adsorbed in the direct proximity of framework aluminium atoms form bonds to these Al atoms, with the coordination number of Al increasing from four to five or six. The remaining water molecules that are adsorbed in other parts of the accessible pore space are not strongly bonded to any framework atom, they interact with their environment exclusively through hydrogen bonds. The APC-type small-pore aluminophosphate AlPO4-H3 contains both types of H2O molecules. In the present work, this prototypical hydrated AlPO is studied using dispersion-corrected density functional theory (DFT) calculations. After validating the computations against experimental crystal structure and Raman spectroscopy data, three interrelated aspects are addressed: First, calculations for various partially hydrated models are used to establish that such partially hydrated phases are not thermodynamically stable, as the interaction with the adsorbed water molecules is distinctly weaker than in fully hydrated AlPO4-H3. Second, IR and Raman spectra are computed and compared to those of the dehydrated analogue AlPO4-C, leading to the identification of a few “fingerprint” modes that could be used as indicators for the presence of Al-coordinated water molecules. Finally, DFT-based molecular dynamics calculations are employed to study the dynamics of the adsorbed water molecules. All in all, this in-depth computational study of AlPO4-H3 contributes to the fundamental understanding of hydrated AlPOs, and should therefore provide valuable information for future computational and experimental studies of these systems.

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Shale Gas-in-Place Calculations Part I: New Pore-Scale Considerations

SPE Journal ◽

10.2118/131772-pa ◽

2011 ◽

Vol 17 (01) ◽

pp. 219-229 ◽

Cited By ~ 289

Author(s):

Ray J. Ambrose ◽

Robert C. Hartman ◽

Mery Diaz-Campos ◽

I. Yucel Akkutlu ◽

Carl H. Sondergeld

Keyword(s):

Shale Gas ◽

Organic Material ◽

Storage Capacity ◽

Pore Space ◽

Ion Beam ◽

Gas Storage ◽

Organic Content ◽

Free Gas ◽

Adsorbed Phase ◽

Small Pore

Summary Using focused-ion-beam (FIB)/scanning-electron-microscope (SEM) imaging technology, a series of 2D and 3D submicroscale investigations revealed a finely dispersed porous organic (kerogen) material embedded within an inorganic matrix. The organic material has pores and capillaries having characteristic lengths typically less than 100 nm. A significant portion of total gas in place appears to be associated with interconnected large nanopores within the organic material. Thermodynamics (phase behavior) of fluids in these pores is quite different; gas residing in a small pore or capillary is rarefied under the influence of organic pore walls and shows a different density profile. This raises serious questions related to gas-in-place calculations: Under reservoir conditions, what fraction of the pore volume of the organic material can be considered available as free gas, and what fraction is taken up by the adsorbed phase? How accurately is the shale-gas storage capacity estimated using the conventional volumetric methods? And finally, do average densities exist for the free and the adsorbed phases? We combine the Langmuir adsorption isotherm with the volumetrics for free gas and formulate a new gas-in-place equation accounting for the pore space taken up by the sorbed phase. The method yields a total-gas-in-place prediction. Molecular dynamics simulations involving methane in small carbon slit-pores of varying size and temperature predict density profiles across the pores and show that (a) the adsorbed methane forms a 0.38-nm monolayer phase and (b) the adsorbed-phase density is 1.8–2.5 times larger than that of bulk methane. These findings could be a more important consideration with larger hydrocarbons and suggest that a significant adjustment is necessary in volume calculations, especially for gas shales high in total organic content. Finally, using typical values for the parameters, calculations show a 10–25% decrease in total gas-storage capacity compared with that using the conventional approach. The role of sorbed gas is more important than previously thought. The new methodology is recommended for estimating shale gas in place.

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Whole plant-environment microscopy reveals how Bacillus subtilis utilises the soil pore space to colonise plant roots

10.1101/2021.02.13.430456 ◽

2021 ◽

Author(s):

Yangminghao Liu ◽

Daniel Patko ◽

Ilonka Engelhardt ◽

Timothy S George ◽

Nicola Stanley-Wall ◽

...

Keyword(s):

Bacillus Subtilis ◽

Pore Space ◽

Light Sheet ◽

Root Surface ◽

Plant Roots ◽

Soil Particles ◽

Transparent Soil ◽

Plant Environment ◽

Small Pore ◽

Soil Pore Space

AbstractPlant growth is supported by complex interactions with many biophysical elements of their environment including microorganisms, geochemicals, water and gas, all within the otherwise complex and heterogeneous soils’ physical environment. Our understanding of plant-environment interactions in soil are limited by the difficulty of observing such interactions at the microscopic scale which occur throughout the large volume of influence of the plant. Here, we present the development of 3D live microscopy approaches for resolving plant-microbe interactions across the environment of an entire seedling root growing in a transparent soil in tailor-made mesocosms, maintaining physical conditions for the culture of both plants and microorganisms. A dual-illumination light-sheet system was used to acquire scattering signals from the plant whilst fluorescence signals were captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm3 in size with as good as 5 μm resolution at a rate of up to one scan every 30 minutes. The system can track the movement of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time, revealing previously unseen patterns of activity. Motile bacteria favoured small pore spaces over the surface of soil particles, colonising the root in a pulsatile manner. Migrations appeared to be directed first towards the root cap as the point “first contact”, before subsequent colonisation of mature epidermis cells. Our findings show that microscopes dedicated to live environmental studies present an invaluable tool to understand life in soils.SignificanceBetter knowledge of microbial movement and interaction with plant roots is essential to understanding soil ecosystems. However, the lack of a suitable approach for observing biological activity in such environments severely impedes advances in this field of research. Here, we overcome this major limitation by combining the use of transparent soil with cutting edge live microscopy techniques. We performed a detailed analysis of the movements of Bacillus subtilis and revealed how the soil pore structure influences the behaviour of the bacteria, both before and during the formation of biofilms on the root surface. This work sheds light on previously unseen phenomenon, and accelerates our understanding of soil dwelling organisms which were, before now, unobserved in their native environment.

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Microbially Induced Calcium Carbonate Plugging for Enhanced Oil Recovery

Geofluids ◽

10.1155/2020/5921789 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Chenpeng Song ◽

Derek Elsworth

Keyword(s):

Calcium Carbonate ◽

Oil Recovery ◽

Extracellular Polymeric Substances ◽

Pore Space ◽

Pore Wall ◽

Ion Source ◽

Sweep Efficiency ◽

Small Pore ◽

Lower Permeability ◽

Enhance Oil Recovery

Plugging high-permeability zones within oil reservoirs is a straightforward approach to enhance oil recovery by diverting waterflooding fluids through the lower-permeability oil-saturated zones and thereby increase hydrocarbon displacement by improvements in sweep efficiency. Sporosarcina pasteurii (ATCC 11859) is a nitrogen-circulating bacterium capable of precipitating calcium carbonate given a calcium ion source and urea. This microbially induced carbonate precipitation (MICP) is able to infill the pore spaces of the porous medium and thus can act as a potential microbial plugging agent for enhancing sweep efficiency. The following explores the microscopic characteristics of MICP-plugging and its effectiveness in permeability reduction. We fabricate artificial rock cores composed of Ottawa sand with three separate grain-size fractions which represent large (40/60 mesh sand), intermediate (60/80 mesh sand), and small (80/120 mesh sand) pore sizes. The results indicate a significant reduction in permeability after only short periods of MICP treatment. Specifically, after eight cycles of microbial treatment (about four days), the permeability for the artificial cores representing large, intermediate, and small pore size maximally drop to 47%, 32%, and 16% of individual initial permeabilities. X-ray diffraction (XRD) indicates that most of the generated calcium carbonate crystals occur as vaterite with only a small amount of calcite. Imaging by SEM indicates that the pore wall is coated by a calcium carbonate film with crystals of vaterite and calcite scattered on the pore wall and acting to effectively plug the pore space. The distribution pattern and morphology of microbially mediated CaCO3 indicate that MICP has a higher efficiency in plugging pores compared with extracellular polymeric substances (EPSs) which are currently the primary microbial plugging agent used to enhance sweep efficiency.

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Pore Structure Characteristics of Tight Carbonate Reservoir in Qingxi Sag, Jiuquan Basin

Lithosphere ◽

10.2113/2021/5524247 ◽

2021 ◽

Vol 2021 (Special 1) ◽

Author(s):

Xiangye Kong ◽

Jianhui Zeng ◽

Xianfeng Tan ◽

Xianglu Gao ◽

Yu Peng ◽

...

Keyword(s):

Pore Structure ◽

Tube Bundle ◽

Pore Space ◽

Carbonate Reservoir ◽

Reservoir Rock ◽

Tight Oil ◽

Type I ◽

Structure Characteristics ◽

Small Pore ◽

Tight Carbonate

Abstract The Xiagou Formation is the main tight oil reservoir in Qingxi Sag of Jiuquan Basin. Given the poor physical properties and other factors restricting tight oil exploitation and production in this area, studies should focus on microscopic pore structure characteristics. In this study, a nano-CT scanner, a SEM, and an NMR were used to study the pore structure characteristics of a tight carbonate reservoir in Qingxi Sag, Jiuquan Basin. The Xiagou Formation reservoir mainly consists of gray argillaceous dolomite and dolomitic mudstone. The pore categories are mainly elliptic, irregular, intergranular, and intragranular and mostly filled with clay and carbonate cement. Pore space is small, the intergranular or organic pores are mostly separated, and pore-throat is weakly connected. The throats mostly develop with lamellar and tube bundle-like characteristics and with poor seepage ability. The pore-throats mostly span from nanometer to micrometer sizes, and pore diameters are mainly concentrated in the range of 0.01–0.1 and 1–10 μm. It is a unimodal pattern mainly composed of micropores, or a bimodal regular allocation dominated by micropores supplemented by macropores. The relationship between micropore (<0.1 μm) and macropore (>1 μm) content allocation and mean pore diameter strongly controls the permeability of reservoir rocks. When macropore content reaches more than 85%, or when pore content totals less than 3%, the permeability of a reservoir remarkably increases. At a higher ratio of the average finest throat sectional area and throat-pore of reservoir rock, the throat radius lies closer to the connecting pore radius, pore and throat connectivity improves, and reservoir seepage ability becomes stronger. Based on reservoir capacity and seepage ability, pore structures of the tight carbonate reservoirs in study area are classified into type I (small-pore–thin-throat), type II (thin-pore–thin-throat), and type III (microporous-microthroat) with rock permeability>0.1 mD, 0.05–0.1 mD, and <0.05 mD, respectively. The type I pore structure reservoir should be regarded as an indicator of tight oil “sweet spots” reservoir in the study area.

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First-Principles Study of AlPO4-H3, a Hydrated Aluminophosphate Zeotype Containing Two Different Types of Adsorbed Water Molecules

10.26434/chemrxiv.7701044.v1 ◽

2019 ◽

Author(s):

Michael Fischer

Keyword(s):

Crystal Structure ◽

Density Functional ◽

Computational Study ◽

Pore Space ◽

Experimental Studies ◽

Adsorbed Water ◽

Working Fluid ◽

Water Molecules ◽

Small Pore ◽

Experimental Crystal

<div>Porous aluminophosphate zeotypes (AlPOs) are promising materials for heat transformation applications using water as a working fluid. Two "types" of adsorbed water molecules can be distinguished in hydrated AlPOs: Water molecules adsorbed in the direct proximity of framework aluminium atoms form bonds to these Al atoms, with the coordination number of Al increasing from four to five or six. The remaining water molecules that are adsorbed in other parts of the accessible pore space are not strongly bonded to any framework atom, they interact with their environment exclusively through hydrogen bonds. The APC-type AlPO4-H3, a small-pore aluminophosphate, contains both types of H2O molecules, and the locations of the water molecules in the crystal structure have been determined previously using single-crystal X-ray diffraction. In the present work, this prototypical hydrated AlPO is studied using dispersion-corrected density functional theory (DFT) calculations. After validating the computations against experimental crystal structure and Raman spectroscopy data, three interrelated aspects are addressed: First, calculations for various partially hydrated models are used to establish that such partially hydrated phases are not thermodynamically stable, as the interaction with the adsorbed water molecules is distinctly weaker than in fully hydrated AlPO4-H3. Second, IR and Raman spectra are computed and compared to those of the dehydrated analogue AlPO4-C, leading to the identification of a few "fingerprint" modes that could be used as indicators for the presence of Al-coordinated water molecules. Finally, DFT-based molecular dynamics calculations are employed to study the dynamics of the adsorbed water molecules. All in all, this in-depth computational study of AlPO4-H3 contributes to the fundamental understanding of hydrated AlPOs, and should therefore provide valuable information for future computational and experimental studies of these systems.</div>

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Physical Rock Matrix Characterization: Structural and Mineralogical Heterogeneities in Granite

MRS Proceedings ◽

10.1557/proc-1124-q07-03 ◽

2008 ◽

Vol 1124 ◽

Author(s):

Mikko Voutilainen ◽

Suvi Lamminmäki ◽

Jussi Timonen ◽

Marja Siitari-kauppi ◽

Daniel Breitner

Keyword(s):

Pore Space ◽

3D Structure ◽

Rock Matrix ◽

X Ray ◽

Small Pore ◽

Waste Repositories ◽

Granite Samples ◽

Space Characterization ◽

Physical Rock

AbstractEvaluation of the transport and retardation properties of rock matrices that serve as host rock for nuclear waste repositories necessitates their thorough pore-space characterization. Relevant properties to be quantified include the diffusion depth and volume adjacent to water conducting features. The bulk values of these quantities are not sufficient due to the heterogeneity of mineral structure on the scale of the expected transport/interaction distances. In this work the 3D pore structure of altered granite samples with porosities of 5 to 15%, taken next to water conducting fractures at 180 200 m depth in Sievi, Finland, was studied. Characterization of diffusion pathways and porosity were based on quantitative autoradiography of rock sections impregnated with C14-labelled polymethylmethacrylate (PMMA). Construction of 3D structure from PMMA autoradiographs was tested. The PMMA method was augmented by field emission scanning electron microscopy and energy-dispersive X-ray analyses (FESEM/EDAX) in order to study small pore-aperture regions in more detail and to identify the corresponding minerals. The 3D distribution of minerals and their abundances were determined by X-ray microtomography. Combining the mineral specific porosity found by the PMMA method with these distributions provided us with a 3D porosity distribution in the rock matrix.

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First-Principles Study of AlPO4-H3, a Hydrated Aluminophosphate Zeotype Containing Two Different Types of Adsorbed Water Molecules

10.26434/chemrxiv.7701044 ◽

2019 ◽

Author(s):

Michael Fischer

Keyword(s):

Density Functional ◽

Computational Study ◽

Pore Space ◽

Experimental Studies ◽

Adsorbed Water ◽

Working Fluid ◽

Water Molecules ◽

Small Pore ◽

Experimental Crystal ◽

Heat Transformation

<div>Porous aluminophosphate zeotypes (AlPOs) are promising materials for heat transformation applications using water as a working fluid. Two "types" of adsorbed water molecules can be distinguished in hydrated AlPOs: Water molecules adsorbed in the direct proximity of framework aluminium atoms form bonds to these Al atoms, with the coordination number of Al increasing from four to five or six. The remaining water molecules that are adsorbed in other parts of the accessible pore space are not strongly bonded to any framework atom, they interact with their environment exclusively through hydrogen bonds. The APC-type small-pore aluminophosphate AlPO4-H3 contains both types of H2O molecules. In the present work, this prototypical hydrated AlPO is studied using dispersion-corrected density functional theory (DFT) calculations. After validating the computations against experimental crystal structure and Raman spectroscopy data, three interrelated aspects are addressed: First, calculations for various partially hydrated models are used to establish that such partially hydrated phases are not thermodynamically stable, as the interaction with the adsorbed water molecules is distinctly weaker than in fully hydrated AlPO4-H3. Second, IR and Raman spectra are computed and compared to those of the dehydrated analogue AlPO4-C, leading to the identification of a few "fingerprint" modes that could be used as indicators for the presence of Al-coordinated water molecules. Finally, DFT-based molecular dynamics calculations are employed to study the dynamics of the adsorbed water molecules. All in all, this in-depth computational study of AlPO4-H3 contributes to the fundamental understanding of hydrated AlPOs, and should therefore provide valuable information for future computational and experimental studies of these systems.</div>

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First-Principles Study of AlPO4-H3, a Hydrated Aluminophosphate Zeotype Containing Two Different Types of Adsorbed Water Molecules

10.26434/chemrxiv.7701044.v2 ◽

2019 ◽

Author(s):

Michael Fischer

Keyword(s):

Density Functional ◽

Computational Study ◽

Pore Space ◽

Experimental Studies ◽

Adsorbed Water ◽

Working Fluid ◽

Water Molecules ◽

Small Pore ◽

Experimental Crystal ◽

Heat Transformation

<div>Porous aluminophosphate zeotypes (AlPOs) are promising materials for heat transformation applications using water as a working fluid. Two "types" of adsorbed water molecules can be distinguished in hydrated AlPOs: Water molecules adsorbed in the direct proximity of framework aluminium atoms form bonds to these Al atoms, with the coordination number of Al increasing from four to five or six. The remaining water molecules that are adsorbed in other parts of the accessible pore space are not strongly bonded to any framework atom, they interact with their environment exclusively through hydrogen bonds. The APC-type small-pore aluminophosphate AlPO4-H3 contains both types of H2O molecules. In the present work, this prototypical hydrated AlPO is studied using dispersion-corrected density functional theory (DFT) calculations. After validating the computations against experimental crystal structure and Raman spectroscopy data, three interrelated aspects are addressed: First, calculations for various partially hydrated models are used to establish that such partially hydrated phases are not thermodynamically stable, as the interaction with the adsorbed water molecules is distinctly weaker than in fully hydrated AlPO4-H3. Second, IR and Raman spectra are computed and compared to those of the dehydrated analogue AlPO4-C, leading to the identification of a few "fingerprint" modes that could be used as indicators for the presence of Al-coordinated water molecules. Finally, DFT-based molecular dynamics calculations are employed to study the dynamics of the adsorbed water molecules. All in all, this in-depth computational study of AlPO4-H3 contributes to the fundamental understanding of hydrated AlPOs, and should therefore provide valuable information for future computational and experimental studies of these systems.</div>

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