Search Results (266)

Nanoparticle superlattices—periodic assemblies of uniformly spaced nanocrystals—bridge the nanoscale precision of individual particles with emergent collective properties akin to those of bulk materials. Recent advances demonstrate that multivalent ions and charged polymers can guide the co-assembly of nanoparticles, imparting electrostatic gating and enabling semiconductor-like behavior. However, the specific roles of anion geometry, valency, and charge density in mediating ion transport remain unclear. Here, we employ coarse-grained molecular dynamics simulations to investigate how applied electric fields (0–0.40 V/nm) modulate ionic conductivity and spatial distribution in trimethylammonium-functionalized gold nanoparticle superlattices assembled with four phosphate anions of distinct geometries and charges. Our results reveal that linear anions outperform ring-shaped analogues in conductivity due to higher charge densities and weaker interfacial binding. Notably, charge density exerts a greater influence on ion mobility than size alone. Under strong fields, anions accumulate at nanoparticle interfaces, where interfacial adsorption and steric constraints suppress transport. In contrast, local migration is governed by geometrical confinement and field strength. Analyses of transition probability and residence time further indicate that the rigidity and delocalized charge of cyclic anions act as mobility barriers. These findings provide mechanistic insights into the structure–function relationship governing ion transport in superlattices, offering guidance for designing next-generation ion conductors, electrochemical sensors, and energy storage materials through anion engineering. Full article

The enhancement of drug delivery into the lung surfactant is facilitated by research on the interaction between drugs and the lung surfactant. Drug designers must have a thorough theoretical understanding of a drug before performing clinical tests to reduce the experimental cost. The current study uses a coarse-grained molecular dynamics (MD) approach with the MARTINI force field to parameterize the corticosteroid drug mometasone furoate, which is used to treat lung inflammation. Here, we investigate the accurate parametrization of drug molecules and validate the parameters with the help of umbrella sampling simulations. A collection of thermodynamic parameters was studied during the parametrization procedure. The Gibbs free energy gradient was used to calculate the partition coefficient value of mometasone furoate, which was approximately 10.49 based on our umbrella sampling simulation. The value was then matched with the experimental and predicted the partition coefficient of the drug, showing good agreement. The drug molecule was then delivered into the lung surfactant monolayer membrane at the alveolar air–water interface, resulting a concentration-dependent drop in surface tension while controlling the underlying continual compression–expansion of alveoli that maintains the exhalation–inhalation respiratory cycle. The dynamical properties of the monolayer demonstrate that the drug’s capacity to diffuse into the monolayer is considerably diminished in larger clusters, and this effect is intensified when there are more drug molecules present in the monolayer. The monolayer microstructure analysis shows that the drug concentration controls monolayer morphology. The results of this investigation may be helpful for corticosteroid drug delivery into the lung alveoli, which can be applied to comprehend how the drug interacts with lung surfactant monolayers or bilayers. Full article

This study employs coarse-grained molecular dynamics simulations to investigate how the overlap distance between graphene nanosheets influences the mechanical properties of “brick-mortar”-structured graphene–polyethylene nanocomposites. Simulations are conducted in a fixed box size while varying the overlap distance from 2.4 to 24 nm. The stress–strain response exhibits three distinct stages: elastic increase, plastic plateau, and slow decrease. The yield strength increases nearly linearly from 115.3 ± 3.8 to 347.9 ± 33.0 MPa with increasing overlap distance, a trend well captured by an extended shear-lag model incorporating polymer stretch. The critical failure strain, marking the onset of strain localization, first increases and then decreases, peaking at an overlap distance of 4.8 nm. This non-monotonic behavior is attributed to a competition between polymer stretch and polymer shear in interfacial stress transfer. Similarly, the plateau stress and toughness show two-stage evolution: the plateau stress remains constant (~100 MPa) up to 4.8 nm before increasing significantly, while toughness rises from 16.9 ± 0.2 to 51.0 ± 4.0 MJ/m³ across the range. These findings reveal the nanoscale mechanisms behind strength and toughness in bioinspired nanocomposites and provide guidelines for optimizing performance through overlap distance tuning. Full article

Understanding the atomistic basis of multi-layer mechanisms employed by broadly reactive neutralizing antibodies of the SARS-CoV-2 spike protein without directly blocking receptor engagement remains an important challenge in coronavirus immunology. Class 4 antibodies represent an intriguing case: they target a deeply conserved, cryptic epitope on the receptor-binding domain yet exhibit variable neutralization potency across subgroups F1 (CR3022, EY6A, COVA1-16), F2 (DH1047), and F3 (S2X259). The molecular basis for this variability is not fully understood. Here, we employed a multi-modal computational approach integrating atomistic and coarse-grained molecular dynamics simulations, binding free energy calculations, mutational scanning, and dynamic network analysis to elucidate how these antibodies engage the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and influence its function. Our results reveal that neutralization efficacy arises from the interplay of direct interfacial interactions and allosteric effects. Group F1 antibodies (CR3022, EY6A, COVA1-16) primarily operate via classic allostery, modulating flexibility in RBD loop regions to indirectly interfere with the ACE2 receptor binding through long-range effects. Group F2 antibody DH1047 represents an intermediate mechanism, combining partial steric hindrance—through engagement of ACE2-critical residues T376, R408, V503, and Y508—with significant allosteric influence, facilitated by localized communication pathways linking the epitope to the receptor interface. Group F3 antibody S2X259 achieves potent neutralization through a synergistic mechanism involving direct competition with ACE2 and localized allosteric stabilization, albeit with potentially increased escape vulnerability. Dynamic network analysis identified a conserved “allosteric ring” within the RBD core that serves as a structural scaffold for long-range signal propagation, with antibody-specific extensions modulating communication to the ACE2 interface. These findings support a model where Class 4 neutralization strategies evolve through the refinement of peripheral allosteric connections rather than epitope redesign. This study establishes a robust computational framework for understanding the atomistic basis of neutralization activity and immune escape for Class 4 antibodies, highlighting how the interplay of binding energetics, conformational dynamics, and allosteric modulation governs their effectiveness against SARS-CoV-2. Full article

We explored the pharmacology of the P-glycoprotein (P-gp) efflux pump and its role in multidrug resistance. We used Protein Data Bank (PDB) database mining and the artificial intelligence (AI) model Boltz-2.1.1, developed for simultaneous structure and affinity prediction, to explore the multimeric nature of recent P-gp inhibitors. We construct a MARTINI coarse-grained (CG) force field description of P-gp embedded in a model of the endothelial blood–brain barrier. We found that recent P-gp inhibitors have been captured in either monomeric, dimeric, or trimeric states. Our CG model demonstrates the ability of P-gp substrates to permeate and transition across the BBB bilayer. We report a multimodal binding model of P-gp inhibition in which later generations of inhibitors are found in dimeric and trimeric states. We report analyses of P-gp substrates that point to an extended binding surface that explains how P-gp can bind over 300 substrates non-selectively. Our coarse-grained model of substrate permeation into membranes expressing P-gp shows benchmarking similarities to prior atomistic models and provide new insights on far longer timescales. Full article

The melting behavior of alkanes plays a critical role in a wide field of applications. While experimental studies have established the occurrence of premelting phenomena in both short- and long-chain alkanes, molecular-level insights remain limited. In this work, we employ coarse-grained molecular dynamics simulations to investigate the melting behavior of high-molecular-weight alkanes, with a particular focus on continuous premelting dynamics in the transition regime toward polymer-like systems. By simulating alkane chains of varying lengths and analyzing temperature-dependent structural changes, we identify a crossover from discrete phase transitions to a gradual premelting process beyond chain lengths of $N\approx 40$ coarse-grained beads. The extrapolation of melting temperatures to zero heating rate yields values that agree well with the experimental data for the longest simulated chains. Compared to previous simulation studies, the slower heating rates used here offer enhanced quantitative agreement. Overall, the results provide new molecular-level insights into the melting of long-chain alkanes and highlight the utility of coarse-grained models in capturing complex phase behavior. Full article

This study investigated the coupling mechanism between interlayer twist angle and projectile size on the ballistic performance of bilayer phosphorene membranes, a topic essential for designing efficient nano-protective materials, yet still poorly understood. Using coarse-grained molecular dynamic simulations, we systematically explored how twist angles (0–90°) and projectile radii (2–10 nm) jointly influence impact response for membranes with a radius equal to 48 nm. We found that the effect of twist angle becomes significant only beyond a critical projectile size (~8 nm). Below this threshold, deformation remains local and twist-independent. However, for larger projectiles, the twist angle drastically alters wave propagation and failure modes. Specifically, a 90° twist induces severe wave reflection and interference, leading to a dramatic force amplification (up to 82%) and a 28% reduction in ballistic limit velocity, making it the most susceptible configuration. These results underline the critical role of twist–boundary–wave interaction in governing impact resistance and provide practical insights for the design of phosphorene-based nano-armor systems tailored to specific impact conditions. Full article

Liposomes are nanoscale, spherical vesicles composed of phospholipid bilayers, typically ranging from 50 to 200 nm in diameter. Their unique ability to encapsulate both hydrophilic and hydrophobic molecules makes them powerful nanocarriers for drug delivery, diagnostics, and vaccine formulations. Several FDA-approved formulations such as Doxil^® (Baxter Healthcare Corporation, Deerfield, IL, USA), AmBisome^® (Gilead Sciences, Inc., Foster City, CA, USA), and Onivyde^® (Ipsen Biopharmaceuticals, Inc., Basking Ridge, NJ, USA) highlight their clinical significance. This review provides a comprehensive synthesis of how molecular dynamics (MD) simulations, particularly coarse-grained (CG) and atomistic approaches, advance our understanding of liposomal membranes. We explore key membrane biophysical properties, including area per lipid (APL), bilayer thickness, segmental order parameter ($S_{CD}$), radial distribution functions (RDFs), bending modulus, and flip-flop dynamics, and examine how these are modulated by cholesterol concentration, PEGylation, and curvature. Special attention is given to curvature-induced effects in spherical vesicles, such as lipid asymmetry, interleaflet coupling, and stress gradients across the leaflets. We discuss recent developments in vesicle modeling using tools such as TS2CG, CHARMM-GUI Martini Maker, and Packmol, which have enabled the simulation of large-scale, compositionally heterogeneous systems. The review also highlights simulation-guided strategies for designing stealth liposomes, tuning membrane permeability, and enhancing structural stability under physiological conditions. A range of CG force fields, MARTINI, SPICA, SIRAH, ELBA, SDK, as well as emerging machine learning (ML)-based models, are critically assessed for their strengths and limitations. Despite the efficiency of CG models, challenges remain in capturing long-timescale events and atomistic-level interactions, driving the development of hybrid multiscale frameworks and AI-integrated techniques. By bridging experimental findings with in silico insights, MD simulations continue to play a pivotal role in the rational design of next-generation liposomal therapeutics. Full article

Cholesterol plays an essential role in biological membranes and is crucial for maintaining their stability and functionality. In addition to biological membranes, cholesterol is also used in various synthetic lipid-based structures such as liposomes, proteoliposomes, and nanodiscs. Cholesterol regulates membrane properties by influencing the density of lipids, phase separation into liquid-ordered (Lo) and liquid-disordered (Ld) areas, and stability of protein–membrane interactions. For planar bilayers, cholesterol thickens the membrane, decreases permeability, and brings lipids into well-ordered domains, thereby increasing membrane rigidity by condensing lipid packing, while maintaining lateral lipid mobility in disordered regions to preserve overall membrane fluidity. It modulates membrane curvature in curved bilayers and vesicles, and stabilizes low-curvature regions, which are important for structural integrity. In liposomes, cholesterol facilitates drug encapsulation and release by controlling bilayer flexibility and stability. In nanodiscs, cholesterol enhances structural integrity and protein compatibility, which enables the investigation of protein–lipid interactions under physiological conditions. In proteoliposomes, cholesterol regulates the conformational stability of embedded proteins that have implications for protein–lipid interaction. Developments in molecular dynamics (MD) techniques, from coarse-grained to all-atom simulations, have shown how cholesterol modulates lipid tail ordering, membrane curvature, and flip-flop behavior in response to concentration. Such simulations provide insights into the mechanisms underlying membrane-associated diseases, aiding in the design of efficient drug delivery systems. In this review, we combine results from MD simulations to provide a synoptic explanation of cholesterol’s complex function in regulating membrane behavior. This synthesis combines fundamental biophysical information with practical membrane engineering, underscoring cholesterol’s important role in membrane structure, dynamics, and performance, and paving the way for rational design of stable and functional lipid-based systems to be used in medicine. In this review, we gather evidence from MD simulations to provide an overview of cholesterol’s complex function regulating membrane behavior. This synthesis connects the fundamental biophysical science with practical membrane engineering, which highlights cholesterol’s important role in membrane structure, dynamics, and function and helps us rationally design stable and functional lipid-based systems for therapeutic purposes. Full article

Nanomedicine is rapidly evolving, with tailored nanoparticles enabling precise cellular-level interventions. Despite significant advances, challenges, such as rapid clearance and off-target effects, hinder the clinical translation of many nanosystems. Among the available nanoplatforms, gold nanoparticles (AuNPs) stand out due to their unique surface chemistry, low toxicity, and excellent biocompatibility. In this work, we present a multi-level computational investigation of ultra-small AuNPs coated with non-conventional amphiphilic polymer chains via atomistic and coarse-grained molecular dynamics. Through high-level-resolution atomistic simulations, we investigate how variations in grafting density impact the collective behaviors of these amphiphilic polymer chains within the coating by quantifying relevant conformational, structural, and energetic descriptors, such as the radius of gyration, terminal group presentation, polymer coating thickness, brush height, and solvation energy. Our results reveal a conformational shift of polymer chains from coiled to stretched as grafting density increases, with a direct effect on the polymer conformational regime, terminal group presentation, and coating thickness. In parallel, we further benchmark low-level coarse-grained models using the atomistic data as a reference, demonstrating their ability to correctly reproduce the atomistic trends. This computational investigation reveals how key descriptors vary with grafting density and provides the tools for conducting similar studies on broader time and length scales, thereby advancing the rational design of nanosystems for nanomedicine. Full article

The effects of proline co-solvent on helix folding are explored through the single discrete coordinate of the number of helical hydrogen bonds. The analysis is based on multi-microsecond length molecular dynamics simulations of alanine-based helix-forming peptides, (ALA)n, of length n = 4, 8, 15 and 21 residues, in an aqueous solution with 2 M concentration of proline. The effects of addition of proline on the free energy landscape for helix folding were analyzed using the graph-based Dijkstra algorithm, Optimal Dimensionality Reduction kinetic coarse graining, committor functions, as well as through the diffusion of the helix boundary. Viewed at a sufficiently long time-scale, helix folding in the coarse-grained hydrogen bond space follows a consecutive mechanism, with well-defined initiation and propagation phases, and an interesting set of intermediates. Proline addition slows down the folding relaxation of all four peptides, increases helix content and induces subtle mechanistic changes compared to pure water solvation. A general trend is for transition state shift towards earlier stages of folding in proline relative to water. For ALA5 and ALA8 direct folding is dominant. In ALA8 and ALA15 multiple pathways appear possible. For ALA21 a simple mechanism emerges, with a single path from helix to coil through a set of intermediates. Overall, this work provides new insights into effects of proline co-solvent on helix folding, complementary to more standard approaches based on three-dimensional molecular structures. Full article

Molecular modeling calculations for the design and improvement of next-generation additives for motor oils have reached a level that can support and improve experimental results. The regulation of insoluble sludge nanoparticle aggregations within oil and on engine pistons is a critical performance metric for lubricant oil additives. There is a general agreement regarding the mechanism of deposit formation which is attributed to the self-aggregation of nano-sized carbon rich insoluble structures. Dispersants are a primary category of additives employed to inhibit aggregation in lubricant formulations. Along with the base oil, they are crucial in dispersing and stabilizing insoluble particles to manage the formation of deposits. In this study, multiscale modeling methods were used to elucidate molecular mechanism of deposit control via polyisobutylene-bis-succinimide (PIBSI) dispersants by using density functional theory (DFT), molecular dynamics (MD) simulations of cells constructed by statistical sampling of molecular configurations, and coarse-grained (CG) simulations. The aim of this study was to understand the role of different groups such as succinimide, amine center, and two polyisobutylene (PIB) tails in PIBSI dispersants. It was demonstrated that the mechanism of deposit control by the polymer-based PIBSI dispersant can be elucidated through the interactions among various constituents, including hydrogen bonding and hydrophilic–hydrophobic interactions. We showed that sludge type nanoparticle aggregation is mitigated by intercalation of polar amine central groups of dispersant between the nanoparticles followed by the extension of two hydrophobic PIB chains into the oil phase that decreases coalesce further by forming a hydrophobic repulsive layer. Full article

This study employs molecular dynamics simulations to unravel the interplay between twin spacing, temperature, and mechanical response in nanotwinned AgPd alloys. For fine-grained systems, a dual strengthening–softening transition emerges as twin spacing decreases, driven by a shift in dislocation behavior from inclined-to-twin-boundary slip to parallel-to-twin-boundary glide. In contrast, coarse-grained configurations exhibit monotonic strengthening with reduced twin spacing, governed by strain localization at grain boundaries and suppressed dislocation activity. Notably, cryogenic conditions stabilize pre-existing and nascent twins, whereas elevated temperatures intensify atomic mobility and boundary migration, accelerating twin boundary annihilation (“detwinning”). Full article

Epoxy resins are critical materials in aerospace applications, yet their mechanical properties, specifically the tensile modulus, can be significantly compromised when exposed to electron irradiation in space environments. To thoroughly examine this degradation, we developed an integrated research approach combining vacuum electron irradiation experiments with multi-scale simulations. Coarse-grained (CG) and Monte Carlo (MC) methods were employed to generate the necessary models and primary knock-on atom (PKA) data, while molecular dynamics (MD) simulations were conducted to model the irradiation and tensile processes. Our findings reveal that the tensile modulus percentage loss of epoxy resin stabilizes as the irradiation dose approaches 1.0×10¹⁵ eV/cm². The strong agreement between experimental and simulation results validates the accuracy of this methodology. In the epoxy resin systems studied with different degrees of cross-linking, irradiation leads to an increase in the tensile modulus of the low cross-linked structures with a maximum increase of 21.46%, and it leads to a decrease in the tensile modulus of the high cross-linked structures with a maximum decrease of 8.03%. This multi-scale approach has been successfully applied to investigate the trends and causes of tensile modulus changes in epoxy resins after electron irradiation. It can be used to explore the changes in the properties of a wider range of polymers after irradiation. Full article

Advanced nanocomposite membranes incorporate nanomaterials within a polymer matrix to augment the mechanical strength of the resultant product. Characterizing these membranes through molecular modeling necessitates specialized approaches to accurately capture the length scales, time scales, and structural complexities inherent in polymers. To address these requirements, an efficient simulation protocol is proposed, utilizing coarse-grained (CG) molecular dynamics simulations to examine the mechanical properties of polyethylene/single-walled carbon nanotube (PE/SWCNT) composites. This methodology integrates CG potentials derived from the statistical associating fluid theory (SAFT-$\gamma$ Mie) equation of state and a modified Tersoff potential as a model for SWCNTs. A qualitative correspondence with benchmark classical all-atom models, as well as available experimental data, is observed, alongside enhanced computational efficiency. Employing this CG model, the focus is directed at exploring the mechanical properties of PE/SWCNT composites under both tensile and compressive loading conditions. The investigation covered the influence of SWCNT size, dispersion, and weight fraction. The findings indicate that although SWCNTs enhance the mechanical strength of PE, the extent of enhancement marginally depends on the dispersion, filler size, and weight fraction. Fracture strengths may be elevated by 20% with a minor incorporation of SWCNTs. Under compression, the incorporation of SWCNTs into the composites results in a transformation from brittle to tough materials. These insights contribute to the optimization of PE/SWCNT composites, emphasizing the importance of considering multiple factors to fine-tune the desired mechanical performance. Full article