Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field

Insight into black phosphorus interactions with supported lipid bilayers

HYPOTHESIS

Nanomaterials have gained significant attention due to their unique properties and potential applications in various biomedical fields, including immediate or targeted drug delivery for wound treatment, cancers, and microbial infections, as well as advancements in diagnostic techniques and tissue engineering. They can also penetrate biological barriers, such as lipid bilayers, offering potential for enhanced drug delivery systems. However, understanding nanomaterial-biomembrane interactions is critical to optimize their design for efficient and safe therapeutic applications. We hypothesize that liquid exfoliated black phosphorus (BP) disrupts lipid bilayers, leading to altered membrane integrity and dynamics, which could influence its potential as an antimicrobial agent or drug delivery vehicle.

EXPERIMENTS

To test this hypothesis, we investigated the interaction between BP flakes and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayers using atomic force microscopy (AFM), force spectroscopy, and molecular dynamics (MD) simulations. AFM provided topographical and force measurements, while MD simulations offered atomistic insights into the interaction mechanisms.

FINDINGS

AFM imaging and force measurements revealed significant destabilization of the lipid bilayer, with a reduction in rupture force by more than half upon interaction with BP flakes. MD simulations corroborated these results, showing penetration and disruption of the lipid bilayer by BP. These findings enhance our understanding of nanomaterial-membrane interactions and demonstrate BP's potential for developing advanced nanomaterial-based drug delivery systems and antimicrobial therapies.

Coarse-grained simulation of colloidal self-assembly, cation exchange, and rheology in Na/Ca smectite clay gels

KNOWLEDGE GAP

The aggregation of clay minerals-layered silicate nanoparticles-strongly impacts fluid flow, solute migration, and solid mechanics in soils, sediments, and sedimentary rocks. Experimental and computational characterization of clay aggregation is inhibited by the delicate water-mediated nature of clay colloidal interactions and by the range of spatial scales involved, from 1 nm thick platelets to flocs with dimensions up to micrometers or more.

SIMULATIONS

Using a new coarse-grained molecular dynamics (CGMD) approach, we predicted the microstructure, dynamics, and rheology of hydrated smectite (more precisely, montmorillonite) clay gels containing up to 2,000 clay platelets on length scales up to 0.1 μm. Simulations investigated the impact of simulation time, platelet diameters (6 to 25 nm), and the ratio of Na to Ca exchangeable cations on the assembly of tactoids (i.e., stacks of parallel clay platelets) and larger aggregates (i.e., assemblages of tactoids). We analyzed structural features including tactoid size and size distribution, basal spacing, counterion distribution in the electrical double layer, clay association modes, and the rheological properties of smectite gels.

FINDINGS

Our results demonstrate new potential to characterize and understand clay aggregation in dilute suspensions and gels on a scale of thousands of particles with explicit representation of counterion clouds and with accuracy approaching that of all-atom molecular dynamics (MD) simulations. For example, our simulations predict the strong impact of Na/Ca ratio on clay tactoid formation and the shear-thinning rheology of clay gels.

Molecular interactions of surfactants with other chemicals in chemical flooding processes: A comprehensive review on molecular dynamics simulation studies

Due to the growing demand for fossil fuels and the transition of many oil fields into a high water-cut stage, enhanced oil recovery (EOR) techniques have become more prevalent to meet this rising demand. Among these techniques, chemical flooding stands out as an effective method, supported by numerous experimental and simulation studies. However, the complexity of a chemical slug composition under harsh reservoir conditions makes the physicochemical phenomena involved in a chemical flooding process highly intricate. To comprehensively understand the microscopic mechanisms governing the phase behavior of complex fluid systems underground, molecular dynamics (MD) simulations have been increasingly employed in recent years to investigate the molecular interactions between various chemicals involved in chemical flooding processes. In this work, we have comprehensively reviewed the recent MD studies focusing on the molecular interactions between surfactants and other chemicals in the chemical flooding processes. Based on the molecular interactions within different chemicals, various nanoscale mechanisms have been proposed to shed light on the physicochemical flow in porous media. Additionally, the MD techniques used in these studies have been summarized, and challenges in the application of MD simulations in the field of chemical flooding have been identified for improving the quality of future MD studies.

Estimating fluid-solid interfacial free energies for wettabilities: A review of molecular simulation methods

Fluid-solid interfacial free energy (IFE) is a fundamental parameter influencing wetting behaviors, which play a crucial role across a broad range of industrial applications. Obtaining reliable data for fluid-solid IFE remains challenging with experimental and semi-empirical methods, and the applicability of first-principle theoretical methods is constrained by a lack of accessible computational tools. In recent years, a variety of molecular simulation methods have been developed for determining the fluid-solid IFE. This review provides a comprehensive summary and critical evaluation of these techniques. The developments, fundamental principles, and implementations of various simulation methods are presented from mechanical routes, such as the contact angle approach, the technique using Bakker's equation, and the Wilhelmy simulation method, as well as thermodynamic routes, including the cleaving wall method, the Frenkel-Ladd technique, and the test-volume/area methods. These approaches can be applied to compute various fluid-solid interfacial properties, including IFE, relative IFE, surface stress, and superficial tension, although these properties are often used without differentiation in the literature. Additionally, selected applications of these methods are reviewed to provide insight into the behavior of fluid-solid interfacial energies in diverse systems. We also illustrate two interpretations of the fluid-solid IFE based on the theory of Navascués and Berry and Bakker's equation. It is shown that the simulation methods developed from these two interpretations are identical. This review advocates for the broader adoption of molecular simulation methods in estimating fluid-solid IFE, which is essential for advancing our understanding of wetting behaviors in various chemical systems.

Mechanism of wetting by anionic surfactants with different polar groups on hydrophilic and hydrophobic nano-silica

CONTEXT

With advancing technology, the hazards of hydrophilic and hydrophobic nano-silica dust have become increasingly apparent. Surfactants are widely used in dust control; however, their performance is primarily determined by their polar groups. To investigate the effect of various polar groups of anionic surfactants on the wettability of hydrophilic and hydrophobic nanosilica. The results indicate that the electronegativity of the electrostatic potential on the hydroxylated silica surface is relatively strong, the larger the electrostatic potential difference (ΔESP) between the surface binding sites and the polar groups of the surfactant, the less favorable the surface is for hydrophobic modification. Additionally, C and O atoms tend to form smaller negative electrostatic potentials compared to S and O atoms, with polar group activity ranked as carboxylate > sulfonate > benzene sulfonate > sulfate. The interaction between SiO2-OH surfaces and water molecules is approximately 3.4 times stronger than that of SiO2-CH3 surfaces. The interaction between water molecules and the SiO2-OH surface is primarily governed by van der Waals forces, whereas the interaction between water molecules and the SiO2-CH3 surface is mainly driven by electrostatic forces. The polar groups of the surfactant are distributed in the aqueous phase, while the nonpolar groups interact with the surface through electrostatic interactions. The hydration layer surrounding the polar groups of hydrophilic surfaces is primarily stabilized by strong hydrogen bonding with water molecules. In contrast, for hydrophobic nano-silica surfaces, the hydration layer is influenced by both van der Waals forces and weaker hydrogen bonding interactions. The SiO2-CH3 surface cannot form hydrogen bonds, while the SiO2-OH surface has a strong capacity to stably form hydrogen bonds with carboxylate and sulfate groups. Hydrogen bonding is an essential factor in wetting. The polar group COO- is suitable for controlling hydrophilic and hydrophobic nano-silica dust. These findings provide theoretical and technical references for the selection, application, and design of surfactants in nano-silica dust control.

METHODS

To elucidate the effects of various polar groups of anionic surfactants on the wetting of hydrophilic and hydrophobic nano-silica, quantum chemical calculations and molecular dynamics simulations were used to investigate the interfacial adsorption and wetting behavior of anionic surfactants with identical chain lengths but different polar groups on these surfaces.

Quantitative Nanometrology of Binary Particle Systems Using Fluorescence Recovery after Photobleaching: Application to Colloidal Silica

We present an application of fluorescence recovery after photobleaching (FRAP) to measure the size of the individual nanoparticles in binary systems. The presence of nanoparticles with varying sizes was successfully demonstrated using a straightforward biexponential model and their sizes were accurately determined. Furthermore, we have demonstrated the benefits of preprocessing the data using a simple machine learning algorithm based on the gradient boosting machine and fitting the resulting curves to a triexponential model. This approach allows the accurate recovery of the sizes of each of the three components in a binary particle system, namely, the 6 nm LUDOX HS40, 11 nm LUDOX AS40, and the free R6G labeling dye. Lastly, it has been demonstrated using molecular dynamics simulations that R6G adsorption to silica nanoparticles (SNPs) is indeed size-dependent, with larger constructs as the preferred target because of their higher charge and smaller curvature. The theoretical and experimental results were therefore consistent with one another.

Microscopic Distribution of Quaternary Ammonium Salt Organic Modifiers in the Interlayer Space of Montmorillonite: Molecular Simulation Study

This study employs molecular dynamics simulations to construct designed unit cells of organic montmorillonite (OMMT) modified with four types of quaternary ammonium salts. The effects of modifier type and quantity on the basal spacing of montmorillonite (MMT) were analyzed. Molecular motion, morphology, interaction energy (Eint), and hydrogen bonding interactions were investigated to elucidate the molecular-level mechanisms between modifiers and MMT. The results indicate that the organic modification of MMT proceeds in three distinct stages: the filled stage, saturated stage, and supersaturated stage. During the filled stage, the basal spacing remains largely unchanged while Eint increases rapidly. In the saturated stage, the basal spacing expands as the growth rate of Eint slows. In the supersaturated stage, the basal spacing continues to increase while Eint stabilizes. The transition from the filled to saturated stage is governed by the van der Waals space occupied by the modifiers. Within the MMT interlayer, the modifiers adopt a bilayer morphology, with the nitrogen atom heads adhering to the MMT surfaces and the tails self-assembling. These findings provide theoretical insights into the basal spacing expansion and organic modification mechanisms of MMT, thereby facilitating improved material compatibility.

Revealing thermophysical and mechanical responses of graphene-reinforced polyvinyl alcohol nanocomposites using molecular dynamics simulations

The effects of graphene (G) nanofiller content on enhancing the mechanical and thermal resistance of the polyvinyl alcohol (PVA) matrix are disentangled by performing all-atom classical molecular dynamics (MD) simulations. The crux of the computational work is to assess several key performance-limiting factors of the functional hybrid material, including the strain rate, temperature, and the size and distribution of the graphene nanofiller. Adding graphene nanofiller to the polymer results in more compact polymer chains, with the most significant impact observed in the 2% graphene composite. Uniaxial compression MD simulations revealed that the yield strength of the material is impacted by the proportion of nanofiller present. Specifically, the calculated stress-strain responses at a strain rate of 1.5 × 108 s-1 show that incorporating 2% graphene nanofiller remarkably enhances the yield strength. Conversely, increasing the graphene content to 5-10% led to a reduction in yield stress, which is primarily attributed to the disruption of hydrogen bond networks and destabilization of non-covalent interactions. Further analysis shows that increasing the strain rate led to higher yield stress in the G-PVA composite, while elevated temperatures caused its yield stress to decrease. Additionally, the glass transition temperature of the PVA composite rises with the graphene content and strongly correlates with the polymer chain mobility. The proposed theoretical approach may serve as a quantitative framework for elucidating the crucial role of interfacial interaction between polymers and nanomaterials in modulating the conformational, thermodynamic, and macroscopic properties of the hybrid materials.

Adsorption, Structure, and Dynamics of DNA in Montmorillonite and Montmorillonite-Humic Acid: A Molecular-Level Insight

Extracellular DNA (eDNA) has become a focus in public health, with soil recognized as a key reservoir where eDNA's mobility and stability are primarily controlled by clay minerals and organic matter. Montmorillonite (MMT) often interacts with humic acids (HA), forming MMT-HA complexes, although the molecular mechanisms behind DNA adsorption in these complexes remain unclear. Here, molecular dynamics simulations were used to examine the adsorption, diffusion, interfacial structure, and dynamics of DNA on MMT and MMT-HA complexes, revealing critical molecular interactions. Interaction energy analysis showed that DNA adsorption is energetically more favorable on MMT than on MMT-HA, as HA reduces DNA's adsorption capacity on MMT. Diffusion coefficients indicated that DNA has lower mobility on MMT than on MMT-HA. Ca2+ cations and water molecules bridge MMT surfaces and DNA phosphate groups, enhancing DNA adsorption on MMT, while HA occupies MMT binding sites and forms limited hydrogen bonds with DNA, thereby inhibiting adsorption. These results provide insights into the adsorption, migration, and stability of eDNA on soil clay minerals.

Self-Assembled Multilayered Concentric Supraparticle Architecture

Supraparticles (SPs) with unique properties are emerging as versatile platforms for applications in catalysis, photonics, and medicine. However, the synthesis of novel SPs with complex internal structures remains a challenge. Self-Assembled Multilayered Supraparticles (SAMS) presented here are composed of concentric lamellar spherical structures made from metallic nanoparticles, formed from a synergistic three-way interaction phenomenon between gold nanoparticles, lipidoid, and gelatin, exhibiting interlayer spacing of 3.5  ± 0.2 nm within a self-limited 156.8  ± 56.6 nm diameter. The formation is critically influenced by both physical (including nanoparticle size, lipidoid chain length) and chemical factors (including elemental composition, nanoparticle cap, and organic material), which collectively modulate the surface chemistry and hydrophobicity, affecting interparticle interactions. SAMS can efficiently deliver labile payloads such as siRNA, achieving dose-dependent silencing in vivo, while also showing potential for complex payloads such as mRNA. This work not only advances the field of SP design by introducing a new structure and interaction phenomenon but also demonstrates its potential in nanomedicine.

Stomata biosilica and Equisetum photosynthesis: ionic tomography insight using a PDMPO silicaphilic probe

Confocal microscopy using silicaphilic molecular probes is a promising approach to identify the ionic character of silica interfaces. Using ab initio and density functional theory we model structural and electronic properties of the (2-(4-pyridyl)-5(4-(2-dimethyl-aminoethyl-aminocarbamoyl)-methoxy)phenyl)-oxazole (PDMPO) chromophore at different protonation states, in vacuum, and when next to silica of different ionicity. For protonated chromophores next to anionic silica sites, theory suggests strong emission in the visible spectral range from higher excited states and the probability of weaker near infrared fluorescence from a lower energy manifold. Using theory insights, we conduct single- and two-color confocal microscopy in the visible and in the near infrared, respectively, to study open and closed stomata of Equisetum arvense, a heavily silicified primitive plant. Three-dimensional ionic tomography resolves sub-micron neighbouring regions of high and low ionic charges of exo/endo-skeletal silica components according to whether they are open or closed. Considering the variance of methane and carbon dioxide levels prior to, during and after the Silurian, we discuss the observed high ionic contrast of stomatal apertures upon opening as a signature of bioinorganic machinery able to moderate methane and carbon dioxide transport for optimal growth under a range of atmospheric conditions.

Single-particle adsorption of ultra-small gold nanoparticles at the biomembrane phase boundary

Nanomaterials are revolutionizing biomedical research by enabling the development of novel therapies, with applications ranging from drug delivery and diagnostics to the modulation of specific biological processes. Current research focuses on tasks such as enhancing cellular uptake of materials while preserving their functionality. However, the mechanisms governing interactions between nanomaterials and biological systems-particularly cellular membranes-remain challenging to elucidate due to the complex, dynamic nature of the lipid bilayer environment. This complexity arises from factors such as coexisting lipid domains (conserved regions of lipids) or lipid rafts, as well as cellular behaviors that induce state changes. The heterogeneous membrane landscape may offer unique adsorption properties and other functional effects, making it crucial to understand these interactions for greater biological control in nanotherapeutics. In this work, we systematically expose a phase-separated phospholipid-supported lipid bilayer (SLB)-specifically, a fluid-gel DOPC:DPPC bilayer-to low concentrations of citrate-capped 5 nm gold nanoparticles (AuNPs) to observe the adsorption process of individual AuNPs at the molecular scale. Using atomic force microscopy (AFM), we experimentally detect the adsorption of some AuNPs at the phase boundary. Complementary molecular dynamics (MD) simulations further elucidate the mechanism of single AuNP adsorption at lipid phase boundaries. Our findings indicate that the AuNP preferentially incorporates into the fluid-phase DOPC lipids while maintaining partial association with the gel-phase DPPC lipids due to diffusion effects. During adsorption, the AuNP disrupts lipid organization by increasing lateral lipid mixing across the phase boundary. This disruption to lipid molecular ordering is further evident upon AuNP incorporation into the bilayer. The ability to modulate the spatial organization and structure of lipid molecules has significant implications for therapeutics that leverage lipid diffusion pathways for alternative drug delivery mechanisms or to induce specific lipid behaviors.

Exploring the Mechanism of Microstructural Changes in Ultra-High-Performance Concrete Under Microwave Influence: Experiments and Molecular Dynamics Simulation

To elucidate the mechanisms of microstructural changes in ultra-high-performance concrete (UHPC) under microwave exposure, this study characterizes the microstructure at multiple scales using a combination of microscopic experiments and molecular dynamics simulations. The hydration products, pore structure, morphology, and interface transition zone (ITZ) of UHPC specimens were analyzed using mercury intrusion porosimetry (MIP), X-ray diffraction (XRD), and scanning electron microscopy (SEM). Molecular dynamics simulations were employed to investigate the uniaxial tensile behavior, free volume, and radial distribution of calcium silicate hydrate (C-S-H) gel, the primary hydration product. The results indicate that microwave curing significantly reduces the pore volume of specimens, with a daily average reduction of 0.15% in the early stages. This accelerated reduction in porosity effectively diminishes the number of high-risk pores. The hydration products formed under microwave curing exhibit higher density and enhanced internal pore optimization. Simulation findings suggest that the non-thermal effects of microwaves play a more significant role in the structural evolution. The molecular orientation of C-S-H changes after oscillation, leading to more ordered molecular arrangements. Mechanical oscillation also expels free volume from the crystal cells, promoting a more compact overall structure and increasing the tensile strength by up to 1 GPa.

Neural Network Atomistic Potential for Pyrophyllite Clay Simulations

In this study, a high-dimensional neural network potential for the smectite pyrophyllite clay has been developed from density functional theory (DFT) data, including correction for dispersion interactions. The data set has been built from the adaptive learning approach, resulting in a diverse and very concise set of selected structures comprising only representative ones. Two neural network potential (NNP) data sets have been constituted from sets of energies and forces computed at two different levels of DFT accuracy. Validation tests show very good accuracy for the computed energies and forces of various systems differing by their size and simulation conditions. The developed potentials are able to reproduce structural parameters with excellent agreement with DFT values as well as experimental data and are the first NNPS able to reproduce clay layers' properties held together via van der Waals interactions. The NNP constructed from data of higher DFT levels shows better results for extreme condition simulations. In addition, elastic properties, exfoliation energies, and vibrational density of state are also well reproduced, showing better performances than standard force fields at a fraction of DFT computation time.

Adsorption of Per- and Polyfluoroalkyl Substances by Edible Nutraceutical-Amended Montmorillonite Clays: In Vitro, In Vivo and In Silico Enterosorption Strategies

Exposure of animals and humans to PFAS through contaminated water and foods pose significant threats to public health. To tackle this challenge, this study aimed to develop edible clays that might enhance the binding, detoxification, and elimination of PFAS in the gastrointestinal tract. Montmorillonite clays (CM) were amended with caffeine (CMCAF), curcumin (CMCUR), and riboflavin (CMRIB), and the binding efficacy for a mixture of four PFAS (PFOS, GenX, PFOA and PFBS) was determined. In vitro studies were used to explore adsorption isotherms while computational simulations investigate PFAS mixture, delineate the contribution of each PFAS molecule to clays and determine if amended clays can contribute to enhanced binding of different PFAS in the mixture. In vivo models (Lemna minor and Hydra vulgaris) were used to validate in vitro and in silico studies and establish the safety and effectiveness of these amended clays. The resulting Qmax and Kd values along with the curved shape of the Langmuir plot indicated saturable binding of GenX, PFOA and PFOS to active surfaces of CM and the amended clays. All three clays demonstrated a slightly higher binding capacity for GenX than the parent clay. Furthermore, the simulations elucidated the binding contribution of each PFAS molecule to parent and amended clays as well as predicting how amended clays can contribute to mechanisms of binding of different PFAS in the mixture. The proof-of-concept for the efficacy of the clays was established in Caenorhabditis elegans, Lemna minor and Hydra vulgaris, where the clays (at 1% w/v inclusion) protected against toxicities of the four PFAS controls. This protection could be attributed to PFAS binding to the amended clays and the biological activities of these nutraceuticals (caffeine, riboflavin, and curcumin) including antioxidative, anti-inflammatory and modulatory activities which mitigate the oxidative stress and inflammatory effects of PFAS. These edible toxin binders may be delivered in mixtures as additives in flavored drinking water and food to decrease PFAS exposure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11270-025-07930-2.

Carbocation charge as an interpretable descriptor for the catalytic activity of hydrolytic nanozymes

A universal theory for predicting the catalytic activity of hydrolytic nanozymes has yet to be developed. Herein, by investigating the polarization and hydrolysis mechanisms of nanomaterials towards amide bonds, carbocation charge was identified as a key electronic descriptor for predicting catalytic activity in amide hydrolysis. Through machine learning correlation analysis and the Sure Independence Screening and Sparsifying Operator (SISSO) algorithm, this descriptor was interpreted to associate with the d-band center and Lewis acidity on the nanomaterial surface. On this basis, copper nanoparticles (Cu NPs) were discovered to exhibit significant hydrolytic activity. Further, peptidomic analysis and molecular dynamics simulations showed that Cu NPs demonstrated substrate selectivity. In the presence of water molecules, hydrophobic amino acid residues were driven towards the nanomaterial surface by hydrophobic groups of proteins, leading to the preferential hydrolysis of peptide bonds linked to these residues. This study provided a theoretic framework for predicting highly efficient hydrolytic nanozymes with broad potential applications.

Insight on the biomimetic of lysozyme interaction with functionalized iron oxide nanoparticles

INTRODUCTION

Lysozyme is a globular hydrolytic enzyme whose tissue level is imperative for various clinical diagnostics. High levels of lysozyme are related to several inflammatory disorders, that breakdown cartilaginous tissues. Recently nanostructures have become widely used as modulators for enzyme activity.

AREAS COVERED

This study delves into the influential role played by surface-modified iron oxide nanoparticles (IONPs) as novel lysozyme nano-inhibitors. Stern-Volmer plots results for lysozyme interaction with Cit-IONPs and Thy-IONPs reveal dynamic quenching constant (KSV) of 40.075 and 65.714 ml/mg, binding constant (Kb) of 1.539 × 103 and 4.418 × 103 ml/mg, and binding free energy (∆G°binding) of -43.563 KJ. mol-1 and -49.821 KJ. mol-1, respectively. Upon interaction with IONPs, the catalytic activity of lysozyme decreases due to conjugation with Thy-IONPs and Cit-IONPs compared to the free form of the enzyme. Computational approaches show that the citrate and thymoquinone molecules have binding affinities with lysozyme active residues of about -4.3 and -4.7 kcal/mol, respectively.

EXPERT OPINION/COMMENTARY

Both formulations of IONPs demonstrate high affinity toward lysozyme proteins. This work shows a higher binding affinity between lysozyme and Thy-IONPs than with Cit-IONPs. These findings suggest that Thy-IONPs represent a promising class of nano-inhibitors for lysozyme, opening new avenues for treating disorders associated with lysozyme overexpression.

Phonon interference in single-molecule junctions

Wave interference allows unprecedented coherent control of various physical properties and has been widely studied in electronic and photonic materials. However, the interference of phonons, or thermal vibrations, central to understanding coherent thermal transport in all electrically insulating materials, has been poorly characterized due to experimental challenges. Here we report the observation of phonon interference at room temperature in molecular-scale junctions. This is enabled by custom-developed scanning thermal probes with combined high stability and sensitivity, allowing quantification of heat flow through molecular junctions one molecule at a time. Using isomers of oligo(phenylene ethynylene)3 with either para- or meta-connected centre rings, our experiments revealed a remarkable reduction in thermal conductance in meta-conformations. Quantum-mechanically accurate molecular dynamics simulations show that this difference arises from the destructive interference of phonons through the molecular backbone. This work opens opportunities for studying numerous wave-driven material properties of phonons down to the single-molecule level that have remained experimentally inaccessible.

Diffusion Properties of C9 Petroleum Resin in Porous γ-Al2O3: A Molecular Dynamics Study

C9 petroleum resin hydrogenation is a classic macromolecular heterogeneous catalyzed reaction that can markedly improve the material's thermal stability and compatibility. The diffusion of these macromolecules within the catalyst pores significantly influences the mass transfer there and the overall hydrogenation process. However, due to experimental limitations, the diffusivity of reactants in the pores remains challenging to determine, which affects the accurate design and operation of the catalytic reaction process. A more realistic model of γ-Al2O3 was developed by incorporating atomic charge considerations, and a more precise interaction between the guest molecule and γ-Al2O3 was described using the INTERFACE force field. The model was characterized by calculating the accessible surface area, total pore volume, hydroxyl group density, wide-angle X-ray diffraction patterns, and benzene adsorption. The calculated results were validated and compared with the corresponding laboratory data. Molecular dynamics simulations were further employed to evaluate the diffusion behavior of C9 petroleum resin within the generated γ-Al2O3. The effects of temperature, the kinetic diameter of C9 petroleum resin, pore size, and pore window size of γ-Al2O3 on diffusion performance were examined. It was found that an increase in temperature can accelerate molecular diffusion, with larger molecules being more sensitive to temperature variations. A linear relationship between the diffusion coefficient and the kinetic diameter of C9 petroleum resin was observed for a given γ-Al2O3 pore structure. Additionally, the diffusion coefficient exhibited a parabolic dependence on pore size at a constant kinetic diameter, while the pore window size had a crucial influence on the diffusion of C9 petroleum resin. These results provide optimized operating conditions and valuable guidance for the preparation of feasible porous γ-Al2O3 catalysts for C9 petroleum resin hydrogenation.

Chemical control of colloidal self-assembly driven by the electrosolvation force

Self-assembly of matter in solution generally relies on attractive interactions that overcome entropy and drive the formation of higher-order molecular and particulate structures. Such interactions are central to a variety of molecular processes, e.g., crystallisation, biomolecular folding and condensation, pathological protein aggregation and biofouling. The electrosolvation force introduces a distinct conceptual paradigm to the existing palette of interactions that govern the spontaneous accretion and organisation of matter. However, an understanding of the underlying physical chemistry, and therefore the ability to exert control over and tune the interaction, remains incomplete. Here we provide further evidence that this force arises from the structure of the interfacial electrolyte. Neutral molecules such as a different solvent, osmolytes or surfactants, may - even at very low concentrations in the medium - disrupt or reinforce pre-existing interfacial solvent structure, thereby delivering unanticipated chemical tuning of the ability of matter to self-assemble. The observations present unexpected mechanistic elements that may explain the impact of co-solvents and osmolytes on protein structure, stability and biomolecular condensation. Our findings thus furnish insight into the microscopic mechanisms that drive the emergence of order and structure from molecular to macroscopic scales in the solution phase.

The Effect of Spacer Chain Length on Foam Stability of Mixed Amine Gemini Surfactant/NaOl by Molecular Dynamic Simulations

Foam stability critically determines the efficiency of the mineral flotation process. Although the mixed amine Gemini surfactant/anionic surfactants exhibit excellent flotation performance, atomic-level investigations of the mechanism of their impact on foam stability remain limited. This study employs molecular dynamics simulations to investigate the self-aggregation behavior of mixed amine Gemini surfactant/sodium oleate (NaOl) systems with varying spacer chain lengths at the air/water interface. The structural parameters of self-aggregation, surface tension, synergistic energy, and diffusion coefficient of water molecules were calculated in detail. The results of molecular dynamics simulations indicated that synergistic adsorption between surfactants occurred. Compared with single amine Gemini surfactant systems, the mixed surfactant systems exhibited an enhanced interfacial activity. The spacer chain length significantly affected the adsorption configurations of the mixed surfactant at the air/water interface. For spacer chains containing fewer than five methylene groups, carboxyl groups preferentially adsorbed between two intramolecular amine groups, forming independently clustered aggregates. Conversely, longer spacer chains promoted adsorption between carboxyl groups and intermolecular amine groups, forming interconnected network-like aggregates. Both structural configurations constrained interfacial water mobility, thereby reducing the liquid flow rate between foam films, suppressing water loss and enhancing the mechanical stability of flotation foams.

Green-Engineered Montmorillonite Clays for the Adsorption, Detoxification, and Mitigation of Aflatoxin B1 Toxicity

Dietary and environmental exposure to aflatoxins via contaminated food items can pose major health challenges to both humans and animals. Studies have reported the coexistence of aflatoxins and other environmental toxins. This emphasizes the urgent need for efficient and effective mitigation strategies for aflatoxins. Previous reports from our laboratory have demonstrated the potency of the green-engineered clays (GECs) on ochratoxin and other toxic chemicals. Therefore, this study sought to investigate the binding and detoxification potential of chlorophyll (CMCH and SMCH) and chlorophyllin (CMCHin and SMCHin)-amended montmorillonite clays for aflatoxin B1 (AFB1). In addition to analyzing binding metrics including affinity, capacity, free energy, and enthalpy, the sorption mechanisms of AFB1 onto the surfaces of engineered clays were also investigated. Computational and experimental studies were performed to validate the efficacy and safety of the clays. CMCH showed the highest binding capacity (Qmax) of 0.43 mol/kg compared to the parent clays CM (0.34 mol/kg) and SM (0.32 mol/kg). Interestingly, there were no significant changes in the binding capacity of the clays at pH2 and pH6, suggesting that the clays can bind to AFB1 throughout the gastrointestinal track. In silico investigations employing molecular dynamics simulations also demonstrated that CMCH enhanced AFB1 binding as compared to parent clay and predicted hydrophobic interactions as the main mode of interaction between the AFB1 and CMCH. This was corroborated by the kinetic results which indicated that the interaction was best defined by chemosorption with favorable thermodynamics and Gibbs free energy (∆G) being negative. In vitro experiments in Hep G2 cells showed that clay treatment mitigated AFB1-induced cytotoxicity, with the exception of 0.5% (w/v) SMCH. Finally, the in vivo results validated the protection of all the clays against AFB1-induced toxicities in Hydra vulgaris. This study showed that these clays significantly detoxified AFB1 (86% to 100%) and provided complete protection at levels as low as 0.1%, suggesting that they may be used as AFB1 binders in feed and food.

Prediction of carbon nanostructure mechanical properties and the role of defects using machine learning

Graphene-based nanostructures hold immense potential as strong and lightweight materials, however, their mechanical properties such as modulus and strength are difficult to fully exploit due to challenges in atomic-scale engineering. This study presents a database of over 2,000 pristine and defective nanoscale CNT bundles and other graphitic assemblies, inspired by microscopy, with associated stress-strain curves from reactive molecular dynamics (MD) simulations using the reactive INTERFACE force field (IFF-R). These 3D structures, containing up to 80,000 atoms, enable detailed analyses of structure-stiffness-failure relationships. By leveraging the database and physics- and chemistry-informed machine learning (ML), accurate predictions of elastic moduli and tensile strength are demonstrated at speeds 1,000 to 10,000 times faster than efficient MD simulations. Hierarchical Graph Neural Networks with Spatial Information (HS-GNNs) are introduced, which integrate chemistry knowledge. HS-GNNs as well as extreme gradient boosted trees (XGBoost) achieve forecasts of mechanical properties of arbitrary carbon nanostructures with only 3 to 6% mean relative error. The reliability equals experimental accuracy and is up to 20 times higher than other ML methods. Predictions maintain 8 to 18% accuracy for large CNT bundles, CNT junctions, and carbon fiber cross-sections outside the training distribution. The physics- and chemistry-informed HS-GNN works remarkably well for data outside the training range while XGBoost works well with limited training data inside the training range. The carbon nanostructure database is designed for integration with multimodal experimental and simulation data, scalable beyond 100 nm size, and extendable to chemically similar compounds and broader property ranges. The ML approaches have potential for applications in structural materials, nanoelectronics, and carbon-based catalysts.

Coating Nanowires with Straw Carbon Enhances Their Bactericidal Performance and Enables Efficient Water Disinfection

Bacterial contamination in water remains a significant public health threat, and it is crucial to develop disinfection methods that are both safe and effective. In this study, we developed straw carbon-coated nanowires (SC/NWs) as an effective bactericidal material for water disinfection. The thermal decomposition of rice straw produced an sp2-structured, amorphous carbon layer with oxygen-containing functional groups and hetero atoms on its surface. The SC coating enhanced the bactericidal performance of Cu(OH)2 NWs by more than 3-log, achieving >6-log inactivation of Escherichia coli at a flux of 2000 L m-2 h-1. The bacteria exposed to SC/NWs suffered extensive membrane disruption and lost cellular integrity. In contrast, the uncoated NWs caused limited damage to the bacteria. Molecular dynamics simulations revealed that the SC coating had strong van der Waals and electrostatic interactions with bacterial membranes, and these attractive forces led to efficient rupture of bacteria during water flow. The SC/NWs were used to disinfect real water samples, including tap water and reclaimed water, with >6-log reductions in bacterial counts during storage. Importantly, no bacterial reactivation was observed after 24 h of storage, which indicated that the SC/NWs caused irreversible membrane damage to the bacteria. This work presents a cost-effective, sustainable solution for developing mechano-bactericidal materials tailored to water disinfection.

Modelling components of nacre structure in silico: Interactions of a nacre peptide with chitin and an aragonite surface

The nacre formation process is a fascinating phenomenon involving mineral phase transformations, self-assembly processes, and protein-mineral interactions, resulting in a hierarchical structure that exhibits outstanding mechanical properties. However, this process is only partially known, and many aspects of nacre structure are not well understood, especially at the molecular scale. To understand the interplay between components-aragonite, protein and chitin-of the structure of nacre observed experimentally, we investigate the interactions of a peptide that is part of the protein lustrin A, identified in the nacreous layer of the shell of the abalone Haliotis rufescens, with the (001) crystal surface of aragonite and the chitin molecule. We report the results of atomistic molecular-modelling calculations and molecular-dynamics simulations of the peptide interacting with both the aragonite surface and the chitin polymer. The peptide shows an energetically favourable binding to the aragonite surface. The interaction of the carboxylic groups of the glutamic unit with the crystalline surface is essential to reproduce the characteristic elastomeric properties of this peptide in nacre.

High-performance, multi-component epoxy resin simulation for predicting thermo-mechanical property evolution during curing

High-performance epoxy systems are extensively used in structural polymer‒matrix composites for aerospace vehicles. The evolution of the thermomechanical properties of these epoxies significantly impacts the evolution of process-induced residual stresses. The corresponding process parameters need to be optimized via multiscale process modeling to minimize the residual stresses and maximize the composite strength and durability. In this study, the thermomechanical properties of a multicomponent epoxy system are predicted via molecular dynamics (MD) simulation as a function of the degree of cure to provide critical property evolution data for process modeling. In addition, the experimentally validated results of this study provide critical insight into MD modeling protocols. Among these insights, harmonic- and Morse-bond-based force fields predict similar mechanical properties. However, simulations with the Morse-bond potential fail at intermediate strain values because of cross-term energy dominance. Additionally, crosslinking simulations should be conducted at the corresponding processing temperature, because the simulation temperature impacts shrinkage evolution significantly. Multiple analysis methods are utilized to process MD heating/cooling data for glass transition temperature prediction, and the results indicate that neither method has a significant advantage. These results are important for effective and comprehensive process modeling within the ICME (Integrated Computational Materials Engineering) and Materials Genome Initiative frameworks.

Probing Impact of Support Pore Diameter on Three-phase Interfaces of Pt/C Catalysts by Molecular Dynamic Simulation

Investigating how the size of carbon support pores influences the three-phase interface of platinum (Pt) particles in fuel cells is essential for enhancing catalyst utilization. This study employed molecular dynamics simulations and density functional theory calculation to examine the effects of mesoporous carbon support size, specifically its pore diameter, on Nafion ionomer distribution, as well as on proton and gas/liquid transport channels, and the utilization of Pt active sites. The findings show that when Pt particles are located within the pores of carbon support (Pt/PC), there is a significant enhancement in the spatial distribution of Nafion ionomer, along with a reduction in encapsulation around the Pt particles, compared to when Pt particles are positioned on the surface or in excessively large pores of the carbon support. While increasing pore diameter improves the construction of proton transport channels formed by sulfonate groups of Nafion ionomer and water molecules, it also raises the risk of obstructing oxygen diffusion. To achieve maximum Pt utilization and exchange current density, it is essential to balance the proton and gas/liquid transport channels. Among the models investigated, the Pt/PC-8 nm system demonstrates the highest Pt utilization. This work offers valuable insights for designing carbon support materials to optimize three-phase interfaces in the catalytic layer of fuel cells.

Molecular Simulation Study of All-Silica Zeolites for the Adsorptive Removal of Airborne Chloroethenes

Chloroethenes (C2H4-xClx with x = 1, 2, 3, 4) are produced and consumed in various industrial processes. As the release of these compounds into air, water, and soils can pose significant risks to human health and the environment, different techniques have been exploited to prevent or remediate chloroethene pollution. Although several previous experimental and computational studies investigated the removal of chloroethenes using zeolite adsorbents, their structural diversity in terms of pore size and pore topology has hardly been explored so far. In this work, molecular simulations using validated empirical force field parameters were used to study the gas-phase adsorption of chloroethenes in 16 structurally distinct zeolite frameworks. As all of these frameworks are synthetically accessible in high-silica form, the simulations used purely siliceous zeolite models. In the most relevant concentration range (0.1 to 10 ppm by volume), substantial uptakes of tri- and tetrachloroethene were computed for several zeolite frameworks, prominently EUO, IFR, MTW, MOR, and BEA. In contrast, vinyl chloride uptakes were always too low to be of practical relevance for adsorptive removal. For selected frameworks, simulation snapshots were analyzed to investigate the impact of pore shape and, at higher uptakes, guest-guest interactions on the adsorption behavior. Hence, this study not only identifies zeolites that should be prioritized in future investigations but also contributes to the microscopic understanding of chloroethene adsorption in crystalline microporous materials.

Investigating the structure-property correlations of pyrolyzed phenolic resin as a function of degree of carbonization

Carbon-carbon (C/C) composites are attractive materials for high-speed flights and terrestrial atmospheric reentry applications due to their insulating thermal properties, thermal resistance, and high strength-to-weight ratio. It is important to understand the evolving structure-property correlations in these materials during pyrolysis, but the extreme laboratory conditions required to produce C/C composites make it difficult to quantify the properties in situ. This work presents an atomistic modeling methodology to pyrolyze a crosslinked phenolic resin network and track the evolving thermomechanical properties of the skeletal matrix during simulated pyrolysis. First, the crosslinked resin is pyrolyzed and the resulting char yield and mass density are verified to match experimental values, establishing the model's powerful predictive capabilities. Young's modulus, yield stress, Poisson's ratio, and thermal conductivity are calculated for the polymerized structure, intermediate pyrolyzed structures, and fully pyrolyzed structure to reveal structure-property correlations, and the evolution of properties are linked to observed structural features. It is determined that reduction in fractional free volume and densification of the resin during pyrolysis contribute significantly to the increase in thermomechanical properties of the skeletal phenolic matrix. A complex interplay of the formation of six-membered carbon rings at the expense of five and seven-membered carbon rings is revealed to affect thermal conductivity. Increased anisotropy was observed in the latter stages of pyrolysis due to the development of aligned aromatic structures. Experimentally validated predictive atomistic models are a key first step to multiscale process modeling of C/C composites to optimize next-generation materials.

Macro-Superlubricity Induced by Tribocatalysis of High-Entropy Ceramics

Macroscale superlubricity has attracted considerable attention as a promising strategy to minimize frictional energy dissipation and achieve near-zero wear. However, realizing macroscale superlubricity with prolonged durability remains an immense challenge, particularly on engineering steels. Current superlubricants render steel surfaces susceptible to corrosion, causing severe wear and superlubrication failure. Herein, high-entropy ceramics (HEC) with catalytic properties are innovatively introduced to prevent corrosion of engineering steels and achieve macro-superlubricity through tribo-catalytic effect. Furthermore, this catalytically induced superlubricity system exhibits an ultra-low friction coefficient of 0.0037 under contact pressure up to 1.47 GPa, an ultra-long cycle lifetime of 1.25 × 106 cycles (corresponding sliding distance up to 5 km), and an extremely low wear rate of 3.032 × 10-10 mm3·N-1·m-1 on the HEC surface. Based on the experimental analysis and theoretical simulation, the in situ formed HEC nanocrystals reduce the Gibbs free energy of hydrolysis of PA molecules into inositol and phosphoric acid molecules in the lubricant. Notably, the hydrolysis products favorably contributed to the reduction of shear force in the lubrication system, which is essential for achieving macroscale superlubricity over a long time. This study provides a new perspective for designing robust superlubricity systems by harnessing the tribocatalytic effect of high-entropy materials.

An in Silico Investigation into Polyester Adsorption onto Alumina toward an Improved Understanding of Hydrogenolysis Catalysts

Chemical recycling of end-of-life plastic wastes through hydrogenolysis is a promising pathway for achieving a circular plastics economy and reducing overall energy costs. Understanding molecular interactions at the inorganic-organic depolymerization interface is crucial for enhancing catalyst performance and overcoming challenges posed by mixed plastic waste streams. We investigated a fundamental step in the depolymerization process: physisorption of polymers onto the metal oxide support preceding diffusion to and reaction at the catalyst-support junction. Molecular dynamics simulations, augmented with well-tempered metadynamics, were conducted to explore the adsorption of polylactic acid (PLA) and polyethylene terephthalate (PET) oligomers onto a hydroxylated alumina support surface. Our findings revealed multiple layers of highly oriented solvent molecules (1,4-dioxane) above the surface, creating significant barriers to polyester adsorption. Disrupting and displacing these solvent layers led PET oligomers to adsorb closer to and interact stronger with the surface than PLA oligomers, possibly contributing to the higher reaction temperatures needed to achieve full conversion in PET versus PLA hydrogenolysis. We further suggest an experimental approach to validate our results of solvent layering behavior through predictions of X-ray reflectivity that are consistent with our initial experiments. The insights gained in this study can be leveraged to refine our understanding of catalytic mechanisms to predict depolymerization reactivity and selectivity and improve future hydrogenolysis catalyst designs.

pH-Dependent Conformational Plasticity of Monoclonal Antibodies at the SiO2/Water Interface: Insights from Neutron Reflectivity and Molecular Dynamics

Investigating the molecular conformations of monoclonal antibodies (mAbs) adsorbed at the solid/liquid interface is crucial for understanding mAb solution stability and advancing the development of mAb-based biosensors. This study examines the pH-dependent conformational plasticity of a human IgG1k mAb, COE-3, at the SiO2/water interface under varying pH conditions (pH 5.5 and 9). By integrating neutron reflectivity (NR) and molecular dynamics (MD) simulations, we reveal that the mAb irreversibly deposits onto the interface at pH 5.5, with surface density saturation reached at 20 ppm bulk concentration. At pH 5.5, the adsorbed mAb adopts a stable "flat-on" orientation, while at pH 9, it assumes a more flexible conformation and a "tilted" orientation. This pH-dependent orientation shift is reversible and influenced by the distinct surface charge properties of the Fab and Fc fragments, with the Fc fragment more prone to desorption at higher pH. The root-mean-square deviation (RMSD) analysis further shows that COE-3 maintains structural stability upon adsorption across both pH levels, showing minimal unfolding or denaturation. These findings highlight how pH-dependent electrostatic interactions between mAb fragments and the SiO2 interface drive conformational adjustments in the intact mAb, offering insights into adsorption-induced aggregation and suggesting pH modulation as a mechanism for controlling biosensor efficiency.

Molecular Dynamics Study of Chitosan Adsorption at a Silica Surface

Chitosan is a nontoxic biopolymer with many potential biomedical and material applications due to its biodegradability, biocompatibility, and antimicrobial properties. Here, fully atomistic molecular dynamics simulations and enhanced sampling methods have been used to study the adsorption mechanism of chitosan oligomers on a silica surface from an aqueous solution. The free energy of adsorption of chitosan on a silica surface was calculated to be 0.6 kcal mol-1 per monomer in 0.15 mol L-1 aqueous solution, which is comparable to k B T at room temperature. The loading capacity of chitosan on the silica surface was found to be 0.094 mg m-2, and it is dominated by charge compensation. Furthermore, the hydrogen bonding between chitosan and silica was analyzed. The nitrogen and hydroxyl group oxygen chitosan atoms were found to be the main contributors to the hydrogen bonding between chitosan and silica. These findings have the potential to guide the experimental design of chitosan-coated silica nanoparticles for applications such as drug delivery or additives for biopolymer food packaging.

Electrified Nanogaps under an AC Field: A Molecular Dynamics Study

The organization and dynamics of ions and water molecules at electrified solid-liquid interfaces are generally well understood under static fields, especially for macroscopic electrochemical systems. In contrast, studies involving alternating (AC) fields tend to be more challenging. In nanoscale systems, added complexity can arise from interfacial interactions and the need to consider ions and molecules explicitly. Here we use molecular dynamics (MD) simulations to investigate the behavior of NaCl aqueous solutions at different concentrations confined in nanogaps under AC fields ranging from 10 MHz to 10 GHz. We explore the impact of the gap size (2-60 nm) and of the solid material composing the electrode (silica, charged silica, or gold). Analysis of the transient and stable responses of the system shows that the total transverse dipole M z,total formed by the water molecules and the ions across the gap is always able to counter the applied field regardless of AC frequency, NaCl concentration, or electrode material. As expected, the ions lag at higher frequencies, leading to a capacitive behavior. This effect is fully compensated by water dipoles that lead the field, reaching a maximum lead at a specific frequency which depends on salt concentration and gap size. Changing the gap size affects the magnitude of M z,total. Finally, the electrode material is shown to affect the electrolyte behavior in the gap region. We anticipate these results to be useful for nanoscale dielectric spectroscopy, including scanning probes.

The Influence of Ionic Environment on Nucleosome-Mica Interactions Revealed via Molecular Dynamics Simulations

Nucleosomes are the fundamental units of DNA compaction, playing a key role in modulating gene expression. As such, they are widely studied through both experimental and computational methods. While atomic force microscopy (AFM) is a powerful tool for visualizing and characterizing both canonical and modified nucleosomes, it relies on nucleosome interactions with mica surfaces. These interactions occur through cations adsorbed on the negatively charged mica, but the specific influences of monovalent and divalent cations on nucleosome adsorption remain unclear. In this study, we used molecular dynamics simulations to investigate how monovalent potassium ions and divalent magnesium ions affect nucleosome binding to mica surfaces. We also explored the impact of pretreated mica surfaces on nucleosome binding and structure. Our findings reveal that nucleosome-mica interactions depend on the type of cations present, which leads to distinct effects on nucleosome structure. Notably, nucleosomes bind effectively to mica surfaces in the presence of potassium ions with minimal structural perturbations.

Intercalation of the anticancer drug lenalidomide into montmorillonite for bioavailability improvement: a computational study

CONTEXT

Lenalidomide (LEN) is used for the treatment of myeloma blood cancer disease. It has become one of the most efficient drugs to halt this disease. LEN is a low-soluble drug in aqueous media. The search of a pharmaceutical preparation to improve the bioavailability and, therefore, to optimize its efficiency is an important issue for pharmaceutical industries and health care. The use of natural excipients such as montmorillonite (MNT) can provide changes in the physical-chemical properties for improving the bioavailability of this drug. We present the first computational study at the atomic scale of the periodic crystal forms of the polymorphs for this anticancer drug, highly demanded in the pharmacy market. In addition, we propose a pharmaceutical preparation by intercalation of LEN in natural MNT. So, our calculations predict that LEN can be intercalated in the interlayer space of MNT, and be released in aqueous media, and physiological aqueous media in consequence. This release process is a more exothermic reaction than the unpacking energy of any of its polymorphs. Besides, the infrared spectra of the LEN molecule and its crystal polymorphs, and LEN intercalated in the confined space of MNT, have been calculated at different levels of theory. The band frequencies have been assigned, matching with the experimental bands, predicting the use of this technique for experimental studies.

METHOD

In this work, the method is aimed to explore this research at the atomic and molecular level by using computational modelling methods including INTERFACE FF and other FF along with quantum mechanical calculations (Dmol3 and CASTEP) of 3-D periodical systems applying periodical boundary conditions. Models of the isolated molecule and two polymorphs of the crystal structures, with the model of bulk water and LEN intercalated in the MNT model, have been considered. An analysis of the intermolecular interactions is accomplished.

Molecular structure data and modelling roadmap for optimized oxidized graphene quantum dot and epoxy interface and mechanical properties

Hybrid epoxy composites are highly considered for low-density applications due to the excellent specific strength and specific stiffness. Enhancements made to the epoxy matrix by addition of nanofillers like carbon nanotubes (CNTs) and graphene (GNPs) have been studied in detail over the course of few decades. These enhancements not only help elevate the material properties of the matrix but also activate different failure mitigating mechanisms in the composite. Although highly beneficial, there are few shortcomings due to the challenging fabrication process of integrating such. Common problems like filler agglomeration, formation of voids, wrinkling and more can result in poor load transfer within the composite. Graphene quantum dots (GQDs), on the other hand are the smallest carbon-based filler which are known to promote more intimate contact with the matrix. Their small size enables simultaneous enhancement of stiffness, strength and toughness. In addition, functionalization of these materials enables other supramolecular interactions like hydrogen bonding which improve the interfacial interaction with the epoxy. This study provides a molecular dynamics (MD) workflow to model a single functionalized GQD embedded in an epoxy matrix and the effective mechanical response of the nanocomposite. Ten chemistries were developed with different oxygen-based functional groups which capture the effect of GQD on the mechanical properties of the nanocomposite. Uniaxial strain simulations revealed that a maximum strength gain of 56 % and stiffness gain of 18 % was computed by the oxidized GQD-epoxy nanocomposite.

Structure, Properties, and Applications of Silica Nanoparticles: Recent Theoretical Modeling Advances, Challenges, and Future Directions

Silica nanoparticles (SNPs), one of the most widely researched materials in modern science, are now commonly exploited in surface coatings, biomedicine, catalysis, and engineering of novel self-assembling materials. Theoretical approaches are invaluable to enhancing fundamental understanding of SNP properties and behavior. Tremendous research attention is dedicated to modeling silica structure, the silica-water interface, and functionalization of silica surfaces for tailored applications. In this review, the range of theoretical methodologies are discussed that have been employed to model bare silica and functionalized silica. The evolution of silica modeling approaches is detailed, including classical, quantum mechanical, and hybrid methods and highlight in particular the last decade of theoretical simulation advances. It is started with discussing investigations of bare silica systems, focusing on the fundamental interactions at the silica-water interface, following with a comprehensively review of the modeling studies that examine the interaction of silica with functional ligands, peptides, ions, surfactants, polymers, and carbonaceous species. The review is concluded with the perspective on existing challenges in the field and promising future directions that will further enhance the utility and importance of the theoretical approaches in guiding the rational design of SNPs for applications in engineering and biomedicine.

Dimerization of the Aβ42 under the Influence of the Gold Nanoparticle: A REMD Study

Advances in Alzheimer's disease (AD) are related to the oligomerization of Amyloid β (Aβ) peptides. Therefore, alteration of the process can prevent AD. We investigated the Aβ42 dimerization under the effects of gold nanoparticles using temperature replica-exchange molecular dynamics (REMD) simulations. The structural change of dimers in the presence and absence of the gold nanoparticle, Au55, was monitored over stable intervals. Physical insights into the oligomerization of Aβ were thus clarified. The computed metrics indicate that Au55 affects the progress of oligomerization. Specifically, the presence of the gold nanoparticle significantly modifies the structure of dimeric Aβ42. The β-content experienced a substantial decrease with the induction of Au55. The turn and coil-contents are also decreased under the effects of the gold nanoparticle. However, the α-content of the dimer exhibited a rigid increase. The influence of gold nanoparticles on the dimeric Aβ42 differs significantly from that of silver nanoparticles, which reduce β-content but increase coil-, turn-, and α-contents. The nature of inhibition will be discussed, in which the vdW interaction plays a driving force for the interaction between the Aβ42 dimer and the gold nanoparticle.

Advances in Molecular Dynamics-Based Characterization of Water and Ion Adsorption and Transport in C-S-H Gels

Cementitious material durability is affected by the transport and adsorption of water molecules and ions in the nanopore channels of cement hydration products. Hydrated calcium silicate (C-S-H) accounts for about 70% of the hydration product. It determines the mechanical properties of cementitious materials and their internal transport properties. The molecular dynamics method provides a complementary understanding of experimental and theoretical results. It can further reveal water molecules and ions' adsorption and transport mechanisms in C-S-H gel pores. This review article provides an overview of the current state of research on the structure of C-S-H gels and the adsorption and transport properties of water molecules and ions within C-S-H gels, as studied through molecular dynamics simulations. This paper summarizes the results of the molecular dynamics-based adsorption transport properties of water molecules and ions in C-S-H gels. The deficiencies in the current study were analyzed, and the fundamental problems to be solved and further research directions were clarified to provide scientific references for revealing the structural properties of C-S-H gels using molecular dynamics.

Modeling Realistic Clay Systems with ClayCode

Clays are a broad class of ubiquitous layered materials. Their specific chemophysical properties are intimately connected to their molecular structure, featuring repeating patterns broken by substitutions. Molecular dynamics simulations can provide insight into the mechanisms leading to the emergent properties of these layered materials; however, up to now, idealized clay structures have been simulated to make the modeling process tractable. We present ClayCode, a software facilitating the modeling of clay systems closely resembling experimentally determined structures. By comparing a realistic model to a commonly used montmorillonite clay model, we demonstrate that idealized models feature noticeably different ionic adsorption patterns. We then present an application of ClayCode to the study the competitive barium and sodium adsorption on Wyoming montmorillonite, Georgia kaolinite, and Montana Illite, of interest in the context of nuclear waste disposal.

Photoaging-induced variations in heteroaggregation of nanoplastics and suspended sediments in aquatic environments: A case study on nanopolystyrene

Photoaging of nanoplastics (NPs) and heteroaggregate with suspended sediments (SS) determines transport processes and ecological risks of NPs in aquatic environments. This study investigated the disruption of photoaging on the heteroaggregation behavior of polystyrene NPs (PSNPs) and SS in different valence electrolyte solutions and deduced the interaction mechanisms by integrating aggregation kinetics and molecular dynamics (MD) simulation. Increasing the electrolyte concentration significantly enhanced the heteroaggregation between PSNPs and SS, and the divalent electrolytes induced the heteroaggregation more efficiently. MD simulation at the molecular level revealed that PS and SS could spontaneously form clusters, and photoaged PS has a stronger potential to fold into a dense state with SS. Photoaging for 30 d retarded heteroaggregation due to the steric hindrance produced by the leached organic matter in NaCl solutions, and the critical coagulation concentration (CCC) increased by >85.44 %. Contrarily, photoaging caused more oxygen-containing functional groups produced on the surface of PSNPs through Ca2+ bridging promoting heteroaggregation and thus destabilizing in CaCl2 solutions, the CCC decreased by 23.53 % ∼ 35.29 %. These findings provide mechanistic insight into the environmental process of NPs and SS and are crucial for a comprehensive understanding of the environmental fate and transport of NPs in aquatic environments.

Chlorophyll-Amended Organoclays for the Detoxification of Ochratoxin A

Climate change has been associated with outbreaks of mycotoxicosis following periods of drought, enhanced fungal growth, and increased exposure to mycotoxins. For detoxification, the inclusion of clay-based materials in food and drinking water has resulted in a very promising strategy to reduce mycotoxin exposure. In this strategy, mycotoxins are tightly sorbed to high-affinity clay particles in the gastrointestinal tract, thus decreasing bioavailability, uptake to blood, and potential toxicity. This study investigated the ability of chlorophyll and chlorophyllin-amended montmorillonite clays to decrease the toxicity of ochratoxin A (OTA). The sorption mechanisms of OTA binding to surfaces of sorbents, as well as binding parameters such as capacity, affinity, enthalpy, and free energy, were examined. Chlorophyll-amended organoclay (CMCH) demonstrated the highest binding (72%) and was better than the chlorophyllin-amended hydrophilic clay (59%), possibly due to the hydrophobicity of OTA (LogP 4.7). In silico studies using molecular dynamics simulations showed that CMCH improves OTA binding in comparison to parent clay in line with experiments. Simulations depicted that chlorophyll amendments on clay facilitated OTA molecules binding both directly, through enhancing OTA binding on the clay, or predominantly indirectly, through OTA molecules interacting with bound chlorophyll amendments. Simulations uncovered the key role of calcium ions in OTA binding, particularly in neutral conditions, and demonstrated that CMCH binding to OTA is enhanced under both neutral and acidic conditions. Furthermore, the protection of various sorbents against OTA-induced toxicity was carried out using two living organisms (Hydra vulgaris and Caenorhabditis elegans) which are susceptible to OTA toxicity. This study showed the significant detoxification of OTA (33% to 100%) by inclusion of sorbents. Organoclay (CMCH) at 0.5% offered complete protection. These findings suggest that the chlorophyll-amended organoclays described in this study could be included in food and feed as OTA binders and as potential filter materials for water and beverages to protect against OTA contaminants during outbreaks and emergencies.

Aspartic Acid Binding on Hydroxyapatite Nanoparticles with Varying Morphologies Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulation

Hydroxyapatite (HAP) exhibits a highly oriented hierarchical structure in biological hard tissues. The formation and selective crystalline orientation of HAP is a process that involves functional biomineralization proteins abundant in acidic residues. To obtain insights into the process of HAP mineralization and acidic residue binding, synthesized HAP with specific lattice planes including (001), (100), and (011) are structurally characterized following the adsorption of aspartic acid (Asp). The adsorption affinity of Asp on HAP surfaces is evaluated quantitatively and demonstrates a high dependency on the HAP morphological form. Among the synthesized HAP nanoparticles (NPs), Asp exhibits the strongest adsorption affinity to short HAP nanorods, which are composed of (100) and (011) lattice planes, followed by nanosheets with a preferential expression of the (001) facet, to which Asp displays a similar but slightly lower binding affinity. HAP nanowires, with the (100) lattice plane preferentially developed, show significantly lower affinity to Asp and evidence of multilayer adsorption compared to the previous two types of HAP NPs. A combination of solid-state NMR (SSNMR) techniques including 13C and 15N CP-MAS, relaxation measurements and 13C-31P Rotational Echo DOuble Resonance (REDOR) is utilized to characterize the molecular structure and dynamics of Asp-HAP bionano interfaces with 13C- and 15N-enriched Asp. REDOR is used to determine 13C-31P internuclear distances, providing insight into the Asp binding geometry where stronger 13C-31P dipolar couplings correlate with binding affinity determined from Langmuir isotherms. The carboxyl sites are identified as the primary binding groups, facilitated by their interaction with surface calcium sites. The Asp chelation conformations revealed by SSNMR are further refined with molecular dynamics (MD) simulation where specific models strongly agree between the SSNMR and MD models for the various surfaces.

Mechanistic Insights of Amino Acid Binding to Hydroxyapatite: Molecular Dynamics Charts Future Directions in Biomaterial Design

Extensive efforts have been made to improve the understanding of hard tissue regeneration, essential for advancing medical applications like bone graft materials. However, the mechanisms of bone biomineralization, particularly the regulation of hydroxyapatite growth by proteins/peptides, remain debated. Small biomolecules such as amino acids are ideal for studying these mechanisms due to their simplicity and relevance as protein/peptide building blocks. This study investigates the binding affinity of four amino acids including glycine (Gly), proline (Pro), lysine (Lys), and aspartic acid (Asp) to the hydroxyapatite (HAP) (100) surface through molecular dynamics simulations. Our findings reveal that aspartic acid exhibits the most energetically favorable binding affinity, attributed to its additional carboxylate group (-COO-), which facilitates stronger interactions with Ca2+ ions on the HAP surface compared to other amino acids with single carboxylate groups. This highlights the critical role of specific functional groups in modulating binding strength, emphasizing that the presence of multiple binding sites in amino acids enhances binding stability. Interestingly, the study also uncovers the significance of water-mediated interactions, as the compact water layer above the HAP surface acts as a barrier, complicating direct binding and underscoring the need to consider solvation effects in simulations. Glycine, due to its small size, demonstrates a unique ability to penetrate this tightly bound water monolayer, suggesting that molecular size influences binding dynamics. These simulations offer detailed insights into the atomic-level interactions, providing a deeper understanding of binding affinity and stability. These insights are pertinent for designing peptides or proteins with enhanced interactions with biomaterials, particularly in mimicking natural bone-binding processes.

Adenosine Triphosphate Inhibits Cold-Responsive Aggregation

Adenosine triphosphate (ATP), ubiquitous in all living organisms, is conventionally recognized as a fundamental energy currency essential for a myriad of cellular processes. While its traditional role in energy metabolism requires only micromolar concentrations, the cellular content of ATP has been found to be significantly higher at the millimolar level. Recent studies have attempted to correlate this higher concentration of ATP with its nonenergetic role in maintaining protein homeostasis, leaving the investigation of ATP's nontrivial activities in biology an open question. Here, by coupling computer simulations and experiments, we uncover new insights into ATP's role as a cryoprotectant against cold-salt stress, highlighting the necessity for higher cellular ATP concentrations. We present direct evidence at charged silica interfaces, demonstrating ATP's ability to restore native intersurface interactions disrupted by combined cold-salt stress, thereby inhibiting cold-responsive aggregation in high-salt conditions. ATP desorbs salt cations from negatively charged surfaces through predominant interactions between ATP and the salt cations. Although the mode of ATP's action remains unchanged with temperature, the extent of interaction scales with temperature, requiring less ATP activity at lower temperatures, justifying the reason for reduction in cellular ATP content due to the cold effect, reported in previous experimental studies. The trend observed in inorganic nanostructures is recurrent and robustly transferable to charged protein interfaces. A thorough comparison of ATP's cryoprotective activity with traditionally known biological cryoprotectants (glycine and betaine) reveals ATP's greater efficiency. In retrospect, our findings highlight ATP's additional biological role in cryopreservation, expanding its potential biomedical applications by offering effective protection of cells from cryoinjuries and avoiding the significant challenges associated with the toxicity of organic cryoprotectants.

NPCoronaPredict: A Computational Pipeline for the Prediction of the Nanoparticle-Biomolecule Corona

The corona of a nanoparticle immersed in a biological fluid is of key importance to its eventual fate and bioactivity in the environment or inside live tissues. It is critical to have insight into both the underlying bionano interactions and the corona composition to ensure biocompatibility of novel engineered nanomaterials. A prediction of these properties in silico requires the successful spanning of multiple orders of magnitude of both time and physical dimensions to produce results in a reasonable amount of time, necessitating the development of a multiscale modeling approach. Here, we present the NPCoronaPredict open-source software package: a suite of software tools to enable this prediction for complex multicomponent nanomaterials in essentially arbitrary biological fluids, or more generally any medium containing organic molecules. The package integrates several recent physics-based computational models and a library of both physics-based and data-driven parametrizations for nanomaterials and organic molecules. We describe the underlying theoretical background and the package functionality from the design of multicomponent NPs through to the evaluation of the corona.

On the Role of the Interlayer Interactions in Atomistic Simulations of Kaolinite Clay

A systematic simulation study was performed to investigate the interlayer interactions in a 1:1 layered phyllosilicate clay, kaolinite. Atomistic simulations with classical realistic force fields (INTERFACE and ClayFF) were used to examine the influence of the individual non-bonded interactions on the interlayer binding in the kaolinite model system. By switching off selected pairwise interactions in the applied force fields (leaving the intralayer interactions intact), it was confirmed that the tetrahedral-octahedral-type pairwise interactions held the kaolinite plates together and that interlayer hydrogen bonding, modeled by Coulombic forces, played a dominant role in this. Furthermore, it was observed that the number of hydrogen bonds formed had a significant influence on the basal spacing, and thus there was a striking change in the layer-layer interaction strength when there were only two kaolinite plates in the system, rather than several plates, as in real kaolinite particles. Contrary to expectations, the dispersion forces of the studied force fields alone were found to be strong enough to hold the kaolinite plates together.

Osmolyte-Induced Modulation of Hofmeister Series

Natural selection has driven the convergence toward a selected set of osmolytes, endowing them with the necessary efficiency to manage stress arising from salt diversity. This study combines atomistic simulations and experiments to investigate how two osmolytes, glycine and betaine, individually modulate the Hofmeister ion ordering of alkali metal salts (LiCl, KCl, and CsCl) near a charged silica interface. Both osmolytes are found to prevent salt-induced aggregation of the charged entities, yet their mode and degree of relative modulation depend on their intricate interplay with specific salt cations. Betaine's ion-mediated surface interaction maintains Hofmeister ion ordering, whereas glycine alters the relative Hofmeister order of the cation by salt-specific ion desorption from the surface. Experimental validation through surface-enhanced Raman spectroscopy supports these findings, elucidating osmolyte-mediated alterations in interfacial water structures. These observations based on an inorganic interface are reciprocated in amyloid beta 40 dimerization dynamics, highlighting osmolytes' efficacy in mitigating salt-induced aggregation. A molecular analysis suggests that the differential modes of interaction, as found here for glycine and betaine, are prevalent across classes of zwitterionic osmolytes.

Molecular Investigation of the Self-Assembly Mechanism Underlying Polydopamine Coatings: The Synergistic Effect of Typical Building Blocks Acting on Interfacial Adhesion

Polydopamine (PDA) is well known as a mussel-inspired adhesive material composed of oligomeric heteropolymers. However, the conventional eumelanin-like structural assumption of PDA seems deficient in explaining its interfacial adhesion. To determine the decisive mechanism of PDA coating formation, experiments and simulations were performed in this study. 5,6-Dihydroxyindole (DHI), the signature building block of eumelanin, was introduced as the control group. Various typical building blocks in PDA were quantified by physicochemical characterizations, and the polar-group-dominated interfacial interaction was evaluated by classic molecular dynamics and metadynamics methods. Aminoethyl has been proven to be the key functional group inducing the adsorption of PDA on the hydroxylated silica substrates, while DHI shows limited adhesion to the substrate due to the absence of aminoethyl as the catechol-indole structure of DHI exhibits poor affinity to the silica surface. Pyrrole carboxylic acid, as an oxidative product detected from PDA/DHI, is unfavorable for its adhesion to silica substrates. Overall, the coating formation and self-aggregating precipitation of PDA are two competitive aminoethyl-consuming paths; thus, the in situ oxidative coupling of dopamine is indispensable for the PDA coating preparation. The collected PDA precipitates can no longer present satisfactory coating forming behavior, resulting from a shortage of aminoethyl moieties.