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DOE OSTI2025

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory

The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC’s ability to adjust its diameter in response to the membrane tension, underscoring the importance of exploring how variations in pore size influence molecular transport through the NPC. In this study, we investigated the relationship between pore size and transport rate and proposed a mathematical model describing this connection. We began by theoretically analyzing how the pore size scales with the characteristic dimensions of the mesh-like structure within the pore. By introducing key assumptions about how the meshwork structure influences molecular diffusion, we derived a mathematical expression for the transport rate based on the size of the pore and the transported molecules. To validate our model, we conducted Brownian dynamics simulations using a coarse-grained representation of the NPC. These simulations, performed across a range of pore sizes, demonstrated strong agreement with our model’s predictions, confirming its accuracy and applicability. Our model is specifically tailored for small-to-medium-sized molecules, approximately 5 nanometers in size, making it relevant to a wide range of transcription factors and signaling molecules. It also extends to molecules with weak and transient interactions with FG-Nups, such as importin-β. By presenting this model formula, our study offers a quantitative framework for analyzing the effects of pore dilation on nucleocytoplasmic transport.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Functionalized Graphene via a One-Pot Reaction Enabling Exact Pore Sizes, Modifiable Pore Functionalization, and Precision Doping

Functionalizing graphene with exact pore size, specific functional groups, and precision doping poses many significant challenges. Current methods lack precision and produce random pore sizes, sites of attachment, and amounts of dopant, leading to compromised structural integrity and affecting graphene’s applications. In this work, we report a strategy for the synthesis of functionalized graphitic materials with modifiable nanometer-sized pores via a Pictet–Spengler polymerization reaction. This one-pot, four-step synthesis uses concepts based on covalent organic frameworks (COFs) synthesis to produce crystalline two-dimensional materials that were confirmed by PXRD, TEM measurements, and DFT studies. These new materials are structurally analogous to doped graphene and graphene oxide (GO) but, unlike GO, maintain their semiconductive properties when fully functionalized.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Multi‐Stage Optimization of Pore Size and Shape in Pore‐Space‐Partitioned Metal–Organic Frameworks for Highly Selective and Sensitive Benzene Capture

Abstract Compared to exploratory development of new structure types, pushing the limits of isoreticular synthesis on a high‐performance MOF platform may have higher probability of achieving targeted properties. Multi‐modular MOF platforms could offer even more opportunities by expanding the scope of isoreticular chemistry. However, navigating isoreticular chemistry towards best properties on a multi‐modular platform is challenging due to multiple interconnected pathways. Here on the multi‐modular pacs (partitioned acs) platform, we demonstrate accessibility to a new regime of pore geometry using two independently adjustable modules (framework‐forming module 1 and pore‐partitioning module 2). A series of new pacs materials have been made. Benzene/cyclohexane selectivity is tuned, progressively, from 4.5 to 15.6 to 195.4 and to 482.5 by pushing the boundary of the pacs platform towards the smallest modules known so far. The exceptional stability of these materials in retaining both porosity and single crystallinity enables single‐crystal diffraction studies of different crystal forms (as‐synthesized, activated, guest‐loaded) that help reveal the mechanistic aspects of adsorption in pacs materials.

Chen, Yichong↗

DOE OSTI2024

Multi–Stage Optimization of Pore Size and Shape in Pore–Space–Partitioned Metal–Organic Frameworks for Highly Selective and Sensitive Benzene Capture

Compared to exploratory development of new structure types, pushing the limits of isoreticular synthesis on a high-performance MOF platform may have higher probability of achieving targeted properties. Multi-modular MOF platforms could offer even more opportunities by expanding the scope of isoreticular chemistry. However, navigating isoreticular chemistry towards best properties on a multi-modular platform is challenging due to multiple interconnected pathways. Here on the multi-modular pacs (partitioned acs) platform, we demonstrate accessibility to a new regime of pore geometry using two independently adjustable modules (framework-forming module 1 and pore-partitioning module 2). A series of new pacs materials have been made. Benzene/cyclohexane selectivity is tuned, progressively, from 4.5 to 15.6 to 195.4 and to 482.5 by pushing the boundary of the pacs platform towards the smallest modules known so far. The exceptional stability of these materials in retaining both porosity and single crystallinity enables single-crystal diffraction studies of different crystal forms (as-synthesized, activated, guest-loaded) that help reveal the mechanistic aspects of adsorption in pacs materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Pore-Scale Study on the Positive Feedback Between Stress and Porosity Caused by Pressure Solution in Porous Media

Pressure solution is an important process in the evolution of sedimentary rocks, which provide storage space for most of our petroleum resources. It directly influences the generation, migration, and storage of petroleum fluids in subsurface sedimentary rocks. Here, in this paper, we develop a pore-scale, mechanochemical model to demonstrate a possible positive feedback between the local porosity and pore surface stress, in which a higher local porosity causes a higher local pore surface stress, thus enhancing pressure solution and consequently further increasing the local porosity. Pore surface stress represents stress on a solid grain adjacent to a pore. Specifically, the pore-scale, mechanochemical model directly simulates the stress distribution over solid and pore surfaces using a finite element model. The dissolution of solids at the solid-pore interfaces under a far-from-equilibrium condition is simulated using a first-order kinetics model that accounts for the local stress distribution. The updated pore geometry, caused by pore surface dissolution, is then used in the stress simulation in the next numerical iteration. Two types of porous media, the Oriskany sandstone and an artificial porous medium with spherical pores, were tested in the mechanochemical simulation. The positive stress-porosity feedback during pressure solution was observed in both samples. In addition, the model quantitatively illustrated the distribution of local mineral dissolution rates on all pore surfaces, as well as its relation to the effective mineral dissolution rate of the entire sample. Based on the comparison between the two porous media, the local mineral dissolution was regulated by pore space distribution, geometry, and coalescence during pressure solution. This work is the first that uses direct, pore-scale numerical simulation to demonstrate the positive stress-porosity feedback during pressure solution, which has the potential to advance the understanding of the mechanical-chemical (MC) coupling in many geological processes that are relevant to subsurface energy systems, such as the recovery of petroleum hydrocarbons and geothermal energy.

CT scanning↗

DOE OSTI2026

Mechanics of pore array collapse and interaction in shock-compressed polymethyl methacrylate (PMMA)

Recent studies on dynamic pore collapse have revealed significant development of shear localization, which can lead to material failure in porous structures and hot spot generation in energetic materials. These findings have dramatically improved the understanding of failure mechanisms during pore collapse but also prompt further investigation of realistic porous materials. In particular, porous media consist of many pores and porous networks. Even in low-porosity materials, pores can form in close proximity during the manufacturing process, leading to the critical question of pore–pore interaction during collapse under dynamic loading conditions. This study investigates, via plate impact experiments coupled with high-speed internal digital image correlation and shadowgraphy techniques, the collapse of two pores in shock-compressed PMMA at stresses between 0.4 and 1 GPa. The results of these experiments provide new insights into shear localization in pore collapse, in addition to distinct interactions between pores. Shadowgraphy measurements reveal novel, direct visualization of shear band development and crack evolution from pore surfaces. Spacing between adiabatic shear bands is measured over a range of impact stresses and is predicted accurately by the Grady–Kipp model. Pore interactions are found to effect a transition in the impact stress threshold at which different failure mechanisms initiate and are also found to possibly influence preferential sites for shear cracking. Throughout the study, numerical and theoretical models are leveraged to understand shear localization behavior. The role of baroclinicity and wave interactions between the pores is used to elucidate interaction mechanisms between pores.

Lawlor, Barry P. [California Institute of Technolo↗

DOE OSTI2025

A statistical and simulation-informed model for estimating permeability from pore size distribution in saturated geomaterials

Accurate permeability estimation is essential across subsurface engineering applications but remains challenging due to the complex pore structures of natural geomaterials. Traditional empirical methods and simplified theoretical models often inadequately capture the role of pore size distribution and connectivity. Here, this study develops a statistical and simulation-informed permeability model that collapses pore-scale complexity into a compact scaling of the form k = αϕμ d 2 , where ϕ is porosity, μ d is mean pore size, and α is a weakly varying coefficient. By combining pore network simulations with statistical analysis of unimodal and bimodal pore size distributions, we identify three key findings: (i) permeability is much more sensitive to mean pore size than to porosity; (ii) across extensive datasets, the ratio σ d /μ d (standard deviation to mean) clusters around a characteristic value ∼0.4, allowing the effects of the full pore size distribution to be represented by μ d and a narrowly varying α ≈ 0.05; and (iii) for bimodal systems, there exists a critical fraction of small pores ∼0.78 above which flow becomes small-pore dominated, enabling the definition of an effective flow-controlling pore population and facilitating simplified permeability estimation for such systems. The resulting model, which requires only porosity and a representative mean pore size as inputs, is validated against comprehensive experimental datasets (>1700 samples) spanning diverse soils and rocks and achieves good predictive accuracy. Overall, this work provides a physically grounded yet practically simple permeability estimator suitable for subsurface engineering, environmental protection, and resource management applications.

Permeability↗

DOE OSTI2024

Integrated experimental studies of pore structure and fluid uptake in the Bossier Shale in eastern Texas, USA

Within the Haynesville-Bossier Shale complex, the Bossier Shale has not been extensively studied by either industry and academia, despite it being an unconventional gas reservoir and a potential caprock for carbon storage in the underlaying Haynesville Shale. The lack of knowledge of the complex pore structures and fluid-rock interactions hinders the effective extraction of gas and the characterization of fluid reservoirs and sealing capacity. Integrated experimental studies of pore structure and fluid-rock interactions were conducted in seven Bossier Shale core samples collected in eastern Texas. Petrographic, geochemical, and petrophysical properties such as mineral composition, organic richness, thermal maturity, porosity, pore/pore throat diameter distribution, water-accessible pores, liquid water imbibition, and water vapor adsorption were characterized using complementary approaches of thin-section petrography, scanning electron microscopy, X-ray diffraction, total organic matter, pyrolysis, mercury intrusion porosimetry, nuclear magnetic resonance, (Ultra-) small angle X-rays scattering as well as small angle neutron scattering with deuterated liquids and contrast variation. Further, the results show that the thermally mature Bossier Shales are composed of mixed argillaceous mudstone, mixed mudstone, and mixed carbonate mudstone. The shale contains both organic and inorganic pores, with porosities of 3.24-9.37 %, pore-to-throat ratios of 1.65 to 19.4, and water-accessible pores accounting for 28.7-72.6 % of total pores. Approaches of liquid water imbibition and water vapor adsorption, with and without direct contact of water with shale samples, indicate that liquid water first enters the nano-sized pores under high capillary pressures, and water vapor adsorption is mainly controlled by both clay minerals and pores with diameters less than 10 nm. These findings contribute to a better understanding of pore structures and water-shale interactions and their controlling factors in the Bossier Shale.

58 GEOSCIENCES↗

DOE OSTI2025

Solvent Transport in Disordered and Dynamic Membrane Pores: Implications for Reverse Osmosis and Nanofiltration Membranes

Pressure-driven separations with nanoporous membranes, such as reverse osmosis and nanofiltration, play a vital role in addressing water scarcity and enabling resource recovery. Understanding water or solvent transport in membrane pores is essential for advancing membrane separation technologies. A key question in transport modeling is to establish a relationship between solvent permeability and membrane porous structure properties, such as porosity or pore size. The nano- and subnanometer pores in polymeric membranes such as reverse osmosis and nanofiltration membranes are highly tortuous and dynamically connected, which challenges the conventional methods of transport modeling. This study addresses this challenge by developing a theoretical framework to describe solvent transport through membranes with dynamic and disordered porous structure. Specifically, we propose a lattice model to describe the pore network, while preserving the viscous nature of solvent permeation. We further establish a relationship between solvent permeability and membrane porosity or pore size, which is validated by molecular dynamics simulations and experimental data. By integrating this relationship into the solution-friction model, we define pore connectivity and local friction coefficient to quantify the impact of pore structure on solvent permeability. Our analysis highlights the dominant influence of pore connectivity on the permeability of reverse osmosis and nanofiltration membranes, particularly when the pore size approaches the dimensions of solvent molecules. Overall, this study provides critical insights into water and solvent transport mechanisms in nanoporous membranes, opening the door for strategies to substantially enhance membrane performance.

membranes↗

DOE OSTI2024

Exploratory Studies of Mechanical Properties, Residual Stress, and Grain Evolution at the Local Regions near Pores in Additively Manufactured Metals

Directed energy deposition (DED) is gaining widespread acceptance in various industrial applications since its unique manufacturing features allow the DED to print metallic parts with very complex geometries. However, DED inevitably generates a lot of internal pores which can limit the widespread applications of the DED technique. The current studies on DED porosity are mostly focused on analyzing pores’ bulk-scale influences on mechanical properties and performances. Since DED pores have a micro-scale existence, with dimensions ranging from a few microns to several hundred microns, it is fundamental to explore the pores’ influences on the micro-scale, including local mechanical properties, residual stress, and grains near pores. However, this important research direction has been neglected. The objective of this work is to fill the above gap in DED porosity research and acquire a fundamental understanding of the role of porosity on a microscopic scale. The authors used nanoindentation approaches to investigate internal pores’ effects on mechanical properties and residual stress in local regions surrounding the pores. In addition, the grains near pores were observed through EBSD, and simulated with the Kinetic Monte Carlo model. The research findings can be provided for DED researchers and industrial practitioners as technical guidance. Most importantly, the research results can work as a good reference for tracing the source of bulk-scale mechanical performances and properties of DED parts with internal pores.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Pore Structures in Detritusphere of Soils Under Switchgrass and Restored Prairie Vegetation Community

Root detritusphere, that is, the soil in the vicinity of decomposing root residues, plays an important role in soil microbial activity and C sequestration. Pore structure (size distributions and connectivity of soil pores) in the detritusphere serves as a major driver for these processes and, in turn, is influenced by the physical characteristics of both soil and roots. This study compared pore structure characteristics in the root detritusphere of soils of contrasting texture and mineralogy subjected to > 6 years of contrasting vegetation: monoculture switchgrass and polyculture prairie systems. Soil samples were collected from five experimental sites in the US Midwest representing three soil types. Soil texture and mineralogy were measured using a hydrometer and x-ray powder diffraction, respectively. The intact cores were scanned with x-ray computed micro-tomography to identify visible soil pores, biopores, and particulate organic matter (POM). We specifically focused on pore structure within the detritusphere around the POM of root origin. Results showed that the detritusphere of coarser textured soils, characterized by high sand and quartz contents, had lower porosity in the vicinity of POM compared with finer textured soils. POM vicinities in finer textured soils had high proportions of large (> 300 μm diameter) pores, and their pores were better connected than in the coarser soils. Lower porosity in the outer (> 1 mm) parts of the detritusphere of switchgrass than of prairie suggested soil compaction by roots, with the effect especially pronounced in the coarser soils. Here, the results demonstrated that soil texture and mineralogy played a major, while vegetation played a more modest, role in defining the pore structure in the root detritusphere.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Pore-Scale Transport Effects in Electrochemical CO 2 Reduction on Gold via Coupled Microkinetic-Transport Modeling

A pore-resolved modeling framework is developed to quantify how pore-scale transport affects the intrinsic microkinetics of CO 2 -to-CO on Au. A DFT-informed microkinetic model is coupled self-consistently to a Generalized-Modified Poisson–Nernst–Planck (GMPNP) transport description in a single, electrolyte-filled cylindrical pore, allowing local concentrations and potential to feed back into site-specific reaction rates. FIB-SEM is used to determine pore sizes within realistic electrode materials. Across pore diameters, d p = 10–6000 nm, the surface-averaged CO 2 reduction rate is systematically reduced relative to the ideal microkinetic baseline where mass transport is not accounted for; the effectiveness factor 𝜂 𝑠,CO 2 , which quantifies this ratio, decreases rapidly at more negative potentials and is about 1% near −1.0 V vs SHE due to reactant depletion. Spatial maps reveal pore-bulk alkalization that emerges at higher cathodic bias, with a small, near-wall pH dip due to electrostatic repulsion of hydroxide at the cathode interface. For a fixed aspect ratio L p /d p , narrower pores exhibit larger 𝜂 𝑠,CO 2 by shortening diffusion paths, whereas variations in the aspect ratio L p /d p play a secondary role. A dimensionless analysis (surface/bulk Damköhler numbers) delineates operating regimes. In conclusion, this work offers a concept for incorporating microkinetic models into homogenized porous-electrode models through effectiveness factors and pore-size distribution.

Au-catalyst↗

DOE OSTI2024

Deep learning with mixup augmentation for improved pore detection during additive manufacturing

In additive manufacturing (AM), process defects such as keyhole pores are difficult to anticipate, affecting the quality and integrity of the AM-produced materials. Hence, considerable efforts have aimed to predict these process defects by training machine learning (ML) models using passive measurements such as acoustic emissions. This work considered a dataset in which keyhole pores of a laser powder bed fusion (LPBF) experiment were identified using X-ray radiography and then registered both in space and time to acoustic measurements recorded during the LPBF experiment. Due to AM’s intrinsic process controls, where a pore-forming event is relatively rare, the acoustic datasets collected during monitoring include more non-pores than pores. In other words, the dataset for ML model development is imbalanced. Moreover, this imbalanced and sparse data phenomenon remains ubiquitous across many AM monitoring schemes since training data is nontrivial to collect. Hence, we propose a machine learning approach to improve this dataset imbalance and enhance the prediction accuracy of pore-labeled data. Specifically, we investigate how data augmentation helps predict pores and non-pores better. This imbalance is improved using recent advances in data augmentation called Mixup, a weak-supervised learning method. Convolutional neural networks (CNNs) are trained on original and augmented datasets, and an appreciable increase in performance is reported when testing on five different experimental trials. When ML models are trained on original and augmented datasets, they achieve an accuracy of 95% and 99% on test datasets, respectively. We also provide information on how dataset size affects model performance. Lastly, we investigate the optimal Mixup parameters for augmentation in the context of CNN performance.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Deep learning with mixup augmentation for improved pore detection during additive manufacturing

42 ENGINEERING↗

DOE OSTI2024

Hydrogen Diffusion in Slit Pores: Role of Temperature, Pressure, Confinement, and Roughness

Diffusion of hydrogen (H 2 ) is important to understand the leakage risk and transport behavior for H 2 geologic storage. We applied molecular dynamics simulations to investigate the influencing factors of H2 diffusion in the slit pores of calcite, hematite, and quartz, owing to their abundance. It is revealed that the H2 self-diffusion coefficient increases with the temperature, regardless of the type of pore minerals. The diffusion of H 2 in the 20 nm slit pores falls into the bulk diffusion regime when the pressure is 10 MPa. The self-diffusion of H 2 decreases with pressure in all three types of slit pores, following a power law model with the exponents ranging from -0.825 to -0.964. Furthermore, the impact of confinement on H 2 diffusion is more pronounced for the slit pores with stronger interactions with H 2 -like calcite. The role of surface roughness in H 2 diffusion depends on the slit aperture. The rough surface enhances H 2 diffusion in the larger slit pores due to the enlarged effective pore space, whereas it weakens H 2 diffusion in the small slit pores due to stronger adsorption. These findings will fill the knowledge gap on the coupling effect of different factors influencing H 2 diffusion.

08 HYDROGEN↗

DOE OSTI2025

Probing Carbon Mineralization Mechanisms in Pore and Bulk Fluids by Harnessing Architected Calcium Silicates

The ability to synthesize materials with well-controlled pore structures gives us unprecedented control over probing fluid interactions with reactive interfaces and advancing calibrated insights into coupled chemo-morphological interactions. One of the primary challenges in developing crystalline silicate materials lies in achieving ordered pore structures. Existing approaches of producing amorphous mesoporous metal silicates via sol–gel methods and heat-treatment of these materials to produce crystalline phases cause the pore structures in the amorphous phases to collapse. To overcome this challenge, carbon coating of amorphous mesoporous calcium silicate particles is carried out to retain the pore structure, while the material is heated to produce crystalline calcium silicate with calcium sulfate inclusions. The pore diameter in these materials is about 3.9 nm, with a surface area and a pore volume of 28.75 m 2 /g and 0.092 cm 2 /g, respectively. The mechanisms of carbon mineralization are investigated by reacting architected calcium silicate with 1 M Na 2 CO 3 and monitoring the evolution in the structural phases using operando wide-angle X-ray scattering (WAXS) measurements. Formation of stable calcium carbonate polymorph or calcite and metastable calcium carbonate polymorph or vaterite in pore and bulk fluids, respectively, resulting from the reaction between Na 2 CO 3 and CaSiO 3 , are noted. The mechanisms associated with carbon mineralization are delineated using ReaxFF molecular dynamics (MD) simulations. The surface dissolution reaction is initiated by 2H + ions that replace a Ca 2+ ion in the Ca–silicate matrix. Ca 2+ ions in the solution initially react with water to form calcium hydroxide and eventually form calcium (bi)carbonate. A slow and gradual increase in the formation of sodium silicate in the solution resulting from the reactions of silicic acid or the silicon dioxide reaction with sodium hydroxide is noted. When carbon mineralization occurs in environments bearing interfacial fluids, calcite is the dominant calcium carbonate polymorph, as determined using experiments with pore fluids and molecular-scale simulations. In conclusion, these studies provide fundamental insights into the mechanisms underlying the carbon mineralization of calcium silicate informed by experiments and molecular-scale simulations.

Calcium↗

DOE OSTI2024

Pore confinement enhances but surface adhesion reduces bacterial cell-to-cell conjugation

As the habitats of bacteria, soil pore network and surface properties control the distribution, adhesion, and motility of bacteria in soils. These physical processes in turn influence bacterial accesses to nutrients and bacterial interactions. Our understanding on the pore- and surface-mediated bacterial interactions is currently limited. In this research, we evaluated the effects of soil pore confinement and surface adhesion on conjugation-based bacterial interactions. The interaction was measured by plasmid transfer between donor and recipient cells within the population of soil bacterium Pseudomonas putida. We found that the presence of porous sand media led to a net increase in conjugation frequency compared to sand-free liquid control. The increase is attributed to the facilitated effect of pore confinement on the collision of bacteria within pores. In contrast, bacterial adhesion to sand surfaces under elevated ionic strength conditions decreased the conjugation frequency as a result of mobility reduction on the surface. Such collision and adhesion mechanisms jointly drive the conjugation as a function of pore and surface properties of porous media. Finally, these results provide valuable insights into the roles of soil pores and surfaces in regulating horizontal gene transfer, an essential cell-to-cell interaction sustaining key processes of soil ecology and health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Ion concentration polarization causes a nearly pore-length-independent conductance of nanopores

There has been a great amount of interest in nanopores as the basis for sensors and templates for preparation of biomimetic channels as well as model systems to understand transport properties at the nanoscale. The presence of surface charges on the pore walls has been shown to induce ion selectivity as well as enhance ionic conductance compared to uncharged pores. Here, using three-dimensional continuum modeling, we examine the role of the length of charged nanopores as well as applied voltage for controlling ion selectivity and ionic conductance of single nanopores and small nanopore arrays. First, we present conditions where the ion current and ion selectivity of nanopores with homogeneous surface charges remain unchanged, even if the pore length decreases by a factor of 6. This length-independent conductance is explained through the effect of ion concentration polarization (ICP), which modifies local ionic concentrations, not only at the pore entrances but also in the pore in a voltage-dependent manner. We describe how voltage controls the ion selectivity of nanopores with different lengths and present the conditions when charged nanopores conduct less current than uncharged pores of the same geometrical characteristics. The manuscript provides different measures of the extent of the depletion zone induced by ICP in single pores and nanopore arrays, including systems with ionic diodes. In conclusion, the modeling shown here will help design selective nanopores for a variety of applications where single nanopores and nanopore arrays are used.

Cain, DaVante↗