Assembly Behavior Research Articles

Entropy-Driven Phase Transition in Nanonucleation via Reciprocal Relations.

Depletion forces, commonly modeled with rigid body assumptions, inadequately describe nanoparticle behavior. This study introduces the roles of Soret and Dufour effects in nanoparticle systems, focusing on mass and energy gradient interchange. The Dufour effect drives energy flow through mass gradients, which implies the possibility of driving the energy flow near the nanoparticles to induce phase transitions via manipulating the monomer concentrations. Our experimental platform confirmed these theories, synthesizing HCP quantum dots from Au, Ag, Pd, and mixed halide perovskites under varied precursor concentrations. By analyzing energy flow and nucleation dynamics through the Dufour effect, we mapped phase transition thresholds, linking them to material entropy. This study provides insight into nanoparticle assembly and phase behavior, highlighting the significance of entropy in nucleation dynamics.

Maturation-dependent changes in the size, structure and seeding capacity of Aβ42 amyloid fibrils

Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile functional biomaterials. Thus, protein self-assembly has been widely studied to shed light on the properties of fibrils and their intermediates. A still open question in the field concerns the microscopic processes that underlie the long-time behaviour and properties of amyloid fibrillar assemblies. Here, we use atomic force microscopy with angstrom-sensitivity to observe that amyloid fibrils undergo a maturation process, associated with an increase in both fibril length and thickness, leading to a decrease of their density, and to a change in their cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein-based materials.

Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites.

Molecular simulations of biomacromolecules that assemble into multimeric complexes remain a challenge due to computationally inaccessible length and time scales. Low-resolution and implicit-solvent coarse-grained modeling approaches using traditional nonbonded interactions (both pairwise and spherically isotropic) have been able to partially address this gap. However, these models may fail to capture the complex anisotropic interactions present at macromolecular interfaces unless higher-order interaction potentials are incorporated at the expense of the computational cost. In this work, we introduce an alternate and systematic approach to represent directional interactions at protein-protein interfaces by using virtual sites restricted to pairwise interactions. We show that virtual site interaction parameters can be optimized within a relative entropy minimization framework by using only information from known statistics between coarse-grained sites. We compare our virtual site models to traditional coarse-grained models using two case studies of multimeric protein assemblies and find that the virtual site models predict pairwise correlations with higher fidelity and, more importantly, assembly behavior that is morphologically consistent with experiments. Our study underscores the importance of anisotropic interaction representations and paves the way for more accurate yet computationally efficient coarse-grained simulations of macromolecular assembly in future research.

Assessment of the assembly behaviour and physicochemical parameters for the tetradecyltrimethylammonium bromide and promazine hydrochloride mixture: Impact of monohydroxy organic compounds

Assessment of the assembly behaviour and physicochemical parameters for the tetradecyltrimethylammonium bromide and promazine hydrochloride mixture: Impact of monohydroxy organic compounds

Thiols Modulated Gold Nanorods Self-Assembly: Indirect Hydrophobic Effects Instead of Direct Electrostatic/Hydrogen Bonds Attraction.

For nanocrystals (NCs) self-assembly, understanding the chemical and supramolecular interactions among building blocks is significant for both fundamental scientific interests and rational nanosuperstructure construction. However, it has remained an extreme challenge for many self-assembly systems due to the lack of appropriately quantitative approaches for the corresponding exploration. Herein, by combination of the proposed colorimetric method for cationic surfactant quantitation and all-atom simulations, we manage to present a clear chemical picture for the thiol molecules modulated self-assembly of gold nanorods (GNRs), one of the earliest and most convenient methods for the fabrication of freestanding GNR self-assemblies. It is revealed that the self-assembly of GNRs is driven by the hydrophobic effects of the alkyl chains of the modified cationic surfactants, as their bilayer structure is destroyed by the added thiol molecules. In other words, the actual roles of the thiol molecules for causing GNRs assembly are indirectly inductive effects instead of the previously believed direct electrostatic attraction and/or hydrogen-bond linking effects of the binding thiol molecules. Furthermore, the GNRs exhibit diameter-dependent assembly behaviors: thicker GNRs tend to adopt the end-to-end assembly mode, while thin ones prefer the side-by-side assembly mode, further demonstrating that hydrophobic effects among the build blocks are the driving force for the GNRs assembly.

Creation of polystyrene nanoparticle patterns for structural color application

The ability to regulate the spatial distribution of nanoparticles to generate patterns/arrays makes them promising applications in various fields. Here, a versatile and potential method, based on the polymer brushes patterned surface with hydrophilic-hydrophobic contrast characteristic, was developed to create the nanoparticle patterns with complicated architectures and controllable structural colors on the silicon/glass substrate. Employing DMD-mediated Photo-ATRP process, the selective growth of hydrophilic poly (ethylene glycol) methyl acrylate (PEGMA) brushes on the surface functionalized with hydrophobic initiators was achieved. Subsequently, the as-obtained hydrophilic-hydrophobic patterned substrate was acted as a template for regulating the assembly behavior and spatial arrangement of polystyrene (PS) nanoparticles, leading to the generation of nanoparticle patterns with desired architectures. Especially, the assembly densities could be controlled via tuning the grafting density of patterned PEGMA brushes, which enabled the effective regulation of structural color on the patterned surface. On the basis of the spatiotemporal control of patterned hydrophilic region formation, the sequential assembly of different nanoparticles on the same substrate could be achieved, allowing for a multi-component nanoparticle pattern for structural color-based anticounterfeiting application. The presented technique for the creation of nanoparticle patterns/arrays exhibits a tremendous practical potential in various fields including high-throughput preparation of structural colors, anticounterfeiting/ information encryption, and optical hypersurfaces.

Understanding the interplay between particle shape, grading and sample density on the behaviour of granular assemblies: A DEM approach

This study investigates the interplay between particle shape, grading and initial sample density, three of the most important factors influencing the mechanical behaviour of sheared granular assemblies. Using the discrete element method (DEM), two-dimensional assemblies of varying initial sample density, particle aspect ratio, AR\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$AR$$\\end{document}, and coefficients of uniformity, Cu\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${C}_{u}$$\\end{document}, were prepared and subjected to drained biaxial shearing until the critical state was reached. We assessed the interplay between each of these parameters by evaluating whether the effect of any given parameter on a mechanical quantity is influenced by any other parameter. Our analyses show that the effect of some of these key parameters on mechanical response, can indeed be influenced by other key parameters. The effect of the particle AR\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$AR$$\\end{document} on the peak shear strength for the initially dense assemblies differs when compared with the medium-dense assemblies. The mechanical coordination number of the assemblies at the initial state correlates with the peak strength thereby explaining the interplay between particle AR\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$AR$$\\end{document} and initial sample density on the peak shear strength. The linear relationship established between strength and dilatancy for a combination of all assemblies studied suggests that the strength-dilatancy relationship is a unique characteristic of granular assemblies. The dilatancy of the assemblies correlates strongly with the amount of contacts lost during shearing. The interplays found between particle shape, grading and initial sample density in this study show that to develop robust constitutive models for the prediction of granular material behaviour, the effects of multiple factors must be considered.Graphic abstract

Divergent catalytic behaviors of assembled organogold(i) clusters derived from enyne cyclization.

Homogeneous gold catalysis has attracted much recent attention due to diverse activation modes of gold(i) towards unsaturated organic groups. Because of attractive aurophilic interaction, structural transformations of metalated species into high nuclear clusters are often proposed in gold catalysis, while to date little is known about their assembly behaviors and catalytic activity. In this work, based on stoichiometric Au(i)-mediated enyne cyclization reactions, we achieve a discrete vicinal dicarbanion-centered Au4 intermediate and three assembled Au11, Au28, and Au14 clusters held together by several aryl dicarbanions. Spectral monitoring, kinetic and theoretical investigations confirm that these discrete and assembled intermediates display four different pathways upon catalyzing the cyclization reaction of the same 1,5-enyne substrate. The discrete Au4 cluster undergoes a full protodeauration process to generate active [Au(PPh3)]+ species for catalytic use. In contrast, the net-like Au11 cluster experiences a substrate-induced dissociation to generate a semi-stable Au10 unit and an active [alkyne-Au(PPh3)]+ fragment for further transformation. The dumbbell-like Au28 cluster is prone to cleavage of the central Au-Au linkage and each Au14 moiety exposes a coordination unsaturated site to activate a substrate molecule. However, the synthetic closed-Au14 cluster with full ligand protection is no longer catalytically active.

Assembly of multilayer phthalocyanine vanadium oxide molecules on Ag<sub>2</sub>Sb alloy monolayer

Fabricating ordered molecular films and further tuning their assembly behavior is important for constructing organic devices with diverse performances. By using high-resolution scanning tunneling microscopy, in this work, we demonstrate that well-organized vanadyl phthalocyanine (VOPc) films can be formed <i>via</i> ‘bottom-up’ molecular self-assembly on a binary alloy Ag<sub>2</sub>Sb/Ag(111). The Ag<sub>2</sub>Sb monolayer is prepared by evaporating Sb atoms on clean Ag(111) and followed by annealing. The VOPc molecules are deposited on the Ag<sub>2</sub>Sb layer <i>via</i> thermal evaporation. The molecular configuration, structural and orbital characteristics of VOPc are clearly clarified at a submolecular level. It is found that initially the ordered VOPc membrane only exhibits the O-up adsorption configuration. Its square-shaped unit cell consists of five VOPc molecules where two adsorption orientations coexist with the horizontal axis of VOPc which is rotated by about 11° or 21° relative to the side of the unit cell. Due to the molecular dipole-dipole interaction, further-deposited molecules result in the assembly of the second-layer VOPc films with the O-down configuration and the square-shaped unit cell that contains only one VOPc molecule. Subsequently, due to the dipole-dipole interaction between layered molecules, following VOPc molecular layers adopt alternating O-up and O-down configurations as well as the square-shaped unit cell, similar to the case of the second layer. In addition, we find that the molecular orbitals overlap in each assembled molecular layer due to the π-π interaction which could facilitate the charge transport along the π stacking direction of VOPc. This research provides possibility to regulate the adsorption configuration and assembly behavior of functional organic molecules on metal surfaces by forming surface alloys.

Engineered assemblies from isomeric pentapeptides augment dry eye treatment

Changing positions of amino acid residues in the peptide sequence alters the peptide’ s assembly behaviors, affording various nanostructures. However, it remains elusive that how subtle changes in the peptide sequence influence the in vivo bioactivity of peptide-based nanocarriers, further impacting the efficacy of the encapsulated drugs. We report here a class of isomeric pentapeptide amphiphiles that associate into filaments with different dimensions, which were further used as carriers of Diquafosol tetrasodium (DQS), for the treatment of dry eye disease. Our results suggest that subtle changes in peptide sequences resulted in dramatically different molecular packings and distinct morphologies, which were verified by molecular dynamics simulations. In vivo results show that the drug retention time could be prolonged by the peptidic nanostructures on the ocular surface but were highly morphological-dependent. The longer retention time promised better therapeutic efficacy. In terms of facile synthesis and good biocompatibility, we believe that these peptides could be used for eye disease treatments or other related areas.

Supramolecular assembly of isomeric SN-38 prodrugs regulated by conjugation sites.

Supramolecular polymers (SPs) are an emerging class of drug transporters employed to improve drug therapy. Through the rational design of self-assembling monomers, one can optimize the properties of the resulting supramolecular nanostructures, such as size, shape, surface chemistry, release, and, therefore, biological fates. This study highlights the design of isomeric SN38 prodrugs through the conjugation of hydrophilic oligo(ethylene glycol) (OEG) with hydroxyls at positions 10 and 20 on hydrophobic SN-38. Self-assembling prodrug (SAPD) isomers 10-OEG-SN38 and 20-OEG-SN38 can self-assemble into giant nanotubes and filamentous assemblies, respectively, via aromatic associations that dominate self-assembly. Our study reveales the influence of modification sites on the assembly behavior and ability of the SN38 SAPDs, as well as drug release and subsequent in vitro and in vivo antitumor effects. The SAPD modified at position 20 exhibits stronger π-π interactions among SN38 units, leading to more compact packing and enhanced assembly capability, whereas OEG at position 10 poses steric hindrance for aromatic associations. Importantly, owing to its higher chemical and supramolecular stability, 20-OEG-SN38 outperforms 10-OEG-SN38 and irinotecan, a clinically used prodrug of SN38, in a CT26 tumor model, demonstrating enhanced tumor growth inhibition and prolonged animal survival. This study presents a new strategy of using interactions among drug molecules as dominating features to create supramolecular assemblies. It also brings some insights into creating effective supramolecular drug assemblies via the engineering of self-assembling building blocks, which could contribute to the optimization of design principles for supramolecular drug delivery systems.

Tuning molecular assembly behavior to amplify the sonodynamic activity of porphyrins for efficient antibacterial therapy.

Sonodynamic therapy (SDT) is a promising strategy to treat deep-seated bacterial infections with good tissue penetration and spatiotemporal controllability. However, the low ROS generation efficiency of current sonosensitizers limits the development of SDT. Herein, we report a porphyrin derivative, TAPyPP-2, the sonodynamic activity of which is enhanced with less oxygen dependence by tuning its molecular assembly behavior. TAPyPP-2 can spontaneously form an ultra-small nano-assembly with a diameter of 6 nm in water by conjugation with primary amine salt-decorated pyridinium via π-π staking. The ultra-small assembly behavior can lower the energy gap between singlet and triplet states to 0.01 eV and promote the separation of holes and electrons, which facilitates ROS generation under ultrasound irradiation, in particular type I ROS. The unique hydrophilic ratio and positive charges endow TAPyPP-2 with superior abilities to interact with Staphylococcus aureus, resulting in extremely high sonodynamic antibacterial activity. Therefore, TAPyPP-2 successfully kills Staphylococcus aureus bacteria in the enclosed cavity of synovial joint and achieves effective SDT of septic arthritis. This work is anticipated to motivate enormous interest in the development of efficient SDT.

Percolation of nonequilibrium assemblies of colloidal particles in active chiral liquids.

The growing interest in the non-equilibrium assembly of colloidal particles in active liquids is driven by the motivation to create novel structures endowed with tunable properties unattainable within the confines of equilibrium systems. Here, we present an experimental investigation of the structural features of colloidal assemblies in active liquids of chiral E. coli. The colloidal particles form dynamic clusters due to the effective interaction mediated by active media. The activity and chirality of the swimmers strongly influence the dynamics and local ordering of colloidal particles, resulting in clusters with persistent rotation, whose structure differs significantly from those in equilibrium systems with attractive interactions, such as colloid-polymer mixtures. Our colloid-bacteria mixture displays several hallmark features of a percolation transition at a critical density, where the clusters span the system size. A closer examination of the critical exponents associated with cluster size distribution, the average cluster size, and the correlation length in the vicinity of the critical density shows deviations from the prediction of the standard continuum percolation model. Therefore, our experiments reveal a richer phase behavior of colloidal assemblies in active liquids.

Screening of oxidative behavior in catalytic amyloid assemblies.

Once considered a thermodynamic minimum of the protein fold or as simply by-products of a misfolding process, amyloids are increasingly showing remarkable potential for promoting enzyme-like catalysis. Recent studies have demonstrated a diverse range of catalytic behaviors that amyloids can promote way beyond the hydrolytic behaviors originally reported. We and others have demonstrated the strong propensity of catalytic amyloids to facilitate redox reactions both in the presence and in the absence of metal cofactors. Here, we present a detailed protocol for measuring the oxidative ability of supramolecular peptide assemblies.

Liquefaction behaviour of aluminium and plastic rod assemblies using bi-axial apparatus with application of image analysis

It has recently been shown that the overall deformation characteristics of granular materials during liquefaction seems to be governed by local void ratio characteristics. The aim of this study is to investigate the relationship between mechanical properties and local void ratio changes during liquefaction in two materials of different weights (aluminium-type and plastic-type rod assemblies). A series of constant-volume cyclic bi-axial loading tests was conducted together with the image analysis obtaining local void behaviour. The experimental results demonstrate that the first liquefaction resistance of the plastic sample is higher than the aluminium one, corresponding to its smaller initial void ratio and less contractive behaviour observed in the early stage of drained monotonic compression. However, after experiencing the first liquefaction and subsequent re-consolidation histories, a liquefiable assembly of aluminium and plastic rods both became either denser (densification) or more homogenous (homogenization) in terms of local void ratio, suggesting an increase in liquefaction resistance in the next liquefaction stage. This work also includes a preliminary analogous study using a semi-3D discrete element method (DEM) with one single layer of spherical particles to simulate the similar liquefaction behaviour observed in the laboratory tests.

Phospholipid Epitaxial Assembly Behavior on a Hydrophobic Highly Ordered Pyrolytic Graphite Surface.

Supported lipid bilayers (SLBs) are excellent models of cell membranes. However, most SLBs exist in the form of phospholipid molecules standing on a substrate, making it difficult to have a side view of the phospholipid membranes. In this study, the phospholipid striped lamella with the arrangement of their alkane tails lying on highly ordered pyrolytic graphite (HOPG) was constructed by a spin coating method. Atomic force microscopy and molecular dynamics simulations are utilized to study the self-assembly of phospholipids on HOPG. Results show that various phospholipids with different packing parameters and electrical property are able to epitaxially adsorb on HOPG. 0.1 mg/mL Plasm PC (0.1 mg/mL) could form a striped monolayer with a width of 5.93 ± 0.21 nm and form relatively stable four striped layers with the concentration increasing to 1 mg/mL. The width of the DOPS multilayer is more than that of electroneutral lipids due to the static electrical repulsion force. This universal strategy sheds light on direct observation of the membrane structure from the side view and modification of 2D materials with amphiphilic biomolecules.

Challenges in the Virtual Geometry Assurance of Proton Exchange Membrane Fuel Cell Stacks

Hydrogen-powered fuel cells will play a vital role in the next generation of energy systems. In this regard, Proton Exchange Membrane Fuel Cells (PEMFC) represent a promising technical solution for all applications where direct electrification is not technically feasible or economically viable, such as the propulsion of heavy vehicles. However, robust production of high-quality fuel cell systems in scalable series production can only be achieved by an early assurance of the product quality considering the numerous variations on geometry element, part, and assembly level. This article presents the challenges and outlines the vision of a geometry assurance process capable of simulating the probabilistic assembly behavior of PEMFC stacks by multi-physics variation simulation, e.g., considering aspects of Finite Element Analysis and Computational Fluid Dynamics, under a realistic representation of the part manufacturing and assembly processes and their operation under variations. The findings reveal future research directions fostering the series production of robust, high-quality PEMFC stacks.

Transient cucurbit[7]uril-mediated host-guest complexes for time-dependent fluorescence and information-self-erasing hydrogel.

A non-equilibrium cucurbit[7]uril-mediated supramolecular host-guest system is fabricated by using urea/urease to control aqueous solution pH on time dimension, showing transient assembly behavior and time-dependent fluorescence. The dynamic assembly can be also achieved in hydrogel network, resulting in a time-dependent fluorescent hydrogel for information encryption.

Anisotropic functionalized platelets: percolation, porosity and network properties.

Anisotropic functionalized platelets are able to model the assembly behaviour of molecular systems in two dimensions thanks to the unique combination of steric and bonding constraints. The assembly scenarios can vary from open to close-packed crystals, finite clusters and chains, according to the features of the imposed constraints. In this work, we focus on the assembly of equilibrium networks. These networks can be seen as disordered, porous monolayers and can be of interest for instance in nano-filtration and optical applications. We investigate the formation and properties of two dimensional networks from shape anisotropic colloids functionalized with four patches. We characterize the connectivity properties, the typical local bonding motives, as well as the geometric features of the emerging networks for a large variety of different systems. Our results show that networks of shape anisotropic colloids assemble into highly versatile network topologies, that may be utilized for applications at the nanoscale.

Janus bottlebrush compatibilizers.

Bottlebrush random copolymers (BRCPs), consisting of a random distribution of two homopolymer chains along a backbone, can segregate to the interface between two immiscible homopolymers. BRCPs undergo a reconfiguration, where each block segregates to one of the homopolymer phases, adopting a Janus-type structure, reducing the interfacial tension and promoting adhesion between the two homopolymers, thereby serving as a Janus bottlebrush copolymer (JBCP) compatibilizer. We synthesized a series of JBCPs by copolymerizing deuterated or hydrogenated polystyrene (DPS/PS) and poly(tert-butyl acrylate) (PtBA) macromonomers using ruthenium benzylidene-initiated ring-opening metathesis polymerization (ROMP). Subsequent acid-catalyzed hydrolysis converted the PtBA brushes to poly(acrylic acid) (PAA). The JBCPs were then placed at the interface between DPS/PS homopolymers and poly(2-vinyl pyridine) (P2VP) homopolymers, where the degree of polymerization of the backbone (NBB) and the grafting density (GD) of the JBCPs were varied. Neutron reflectivity (NR) was used to determine the interfacial width and segmental density distributions (including PS homopolymer, PS block, PAA block and P2VP homopolymer) across the polymer-polymer interface. Our findings indicate that the star-like JBCP with NBB = 6 produces the largest interfacial broadening. Increasing NBB to 100 (rod-like shape) and 250 (worm-like shape) reduced the interfacial broadening due to a decrease in the interactions between blocks and homopolymers by stretching of blocks. Decreasing the GD from 100% to 80% at NBB = 100 caused an increase the interfacial width, yet further decreasing the GD to 50% and 20% reduced the interfacial width, as 80% of GD may efficiently increase the flexibility of blocks and promote interactions between homopolymers, while maintaining relatively high number of blocks attached to one molecule. The interfacial conformation of JBCPs was further translated into compatibilization efficiency. Thin film morphology studies showed that only the lower NBB values (NBB = 6 and NBB = 24) and the 80% GD of NBB = 100 had bicontinuous morphologies, due to a sufficient binding energy that arrested phase separation, supported by mechanical testing using asymmetric double cantilever beam (ADCB) tests. These provide fundamental insights into the assembly behavior of JBCPs compatibilizers at homopolymer interfaces, opening strategies for the design of new BCP compatibilizers.