Nucleation Pathway Research Articles

The inhibitory action of the chaperone BRICHOS against the α-Synuclein secondary nucleation pathway.

The complex kinetics of disease-related amyloid aggregation of proteins such as α-Synuclein (α-Syn) in Parkinson's disease and Aβ42 in Alzheimer's disease include primary nucleation, amyloid fibril elongation and secondary nucleation. The latter can be a key accelerator of the aggregation process. It has been demonstrated that the chaperone domain BRICHOS can interfere with the secondary nucleation process of Aβ42. Here, we explore the mechanism of secondary nucleation inhibition of the BRICHOS domain of the lung surfactant protein (proSP-C) against α-Syn aggregation and amyloid formation. We determine the 3D NMR structure of an inactive trimer of proSP-C BRICHOS and its active monomer using a designed mutant. Furthermore, the interaction between the proSP-C BRICHOS chaperone and a substrate peptide has been studied. NMR-based interaction studies of proSP-C BRICHOS with α-Syn fibrils show that proSP-C BRICHOS binds to the C-terminal flexible fuzzy coat of the fibrils, which is the secondary nucleation site on the fibrils. Super-resolution fluorescence microscopy demonstrates that proSP-C BRICHOS runs along the fibrillar axis diffusion-dependently sweeping off monomeric α-Syn from the fibrils. The observed mechanism explains how a weakly binding chaperone can inhibit the α-Syn secondary nucleation pathway via avidity where a single proSP-C BRICHOS molecule is sufficient against up to ~7-40 α-Syn molecules embedded within the fibrils.

Unconventional Near‐equilibrium Nucleation of Graphene on Si‐terminated SiC(0001) Surface

The transfer‐free character of graphene growth on Silicon Carbide (SiC) makes it compatible with state‐of‐the‐art Si semi‐conductor technologies for directly fabricating high‐end electronics. Although significant progress has been achieved in epitaxial growth of graphene on SiC recently, the underlying nucleation mechanism remains elusive. Here, we present a theoretical study to elucidate graphene near‐equilibrium nucleation on Si‐terminated hexagonal‐SiC(0001) surface. It is found that the ultra‐large lattice mismatch between SiC(0001) surface and graphene and the highly localized electron distribution on SiC(0001) surface lead to a distinctive nucleation process: (i) Most of the magic carbon clusters on SiC(0001) show only C1 symmetry and are mainly composed of pentagonal rings; (ii) Two possible nucleation pathways are revealed, i.e, longitudinal and circular modes; (iii) Carbon clusters are more stable on flat terraces than near atomic step edges. Based on above findings, a graphene nucleation diagram on SiC(0001) is established and experimentally observed contradictories for graphene growth on SiC(0001) are answered. Our in‐depth understanding on graphene nucleation on SiC(0001) extends nucleation mechanisms of 2D crystals and will benefit high‐quality graphene growth on SiC(0001).

Unconventional Near-equilibriumNucleation of Graphene on Si-terminated SiC(0001) Surface.

The transfer-free character of graphene growth on Silicon Carbide (SiC) makes it compatible with state-of-the-art Si semi-conductor technologies for directly fabricating high-end electronics. Although significant progress has been achieved in epitaxial growth of graphene on SiC recently, the underlying nucleation mechanism remains elusive. Here, we present a theoretical study to elucidate graphene near-equilibrium nucleation on Si-terminated hexagonal-SiC(0001) surface. It is found that the ultra-large lattice mismatch between SiC(0001) surface and graphene and the highly localized electron distribution on SiC(0001) surface lead to a distinctive nucleation process: (i) Most of the magic carbon clusters on SiC(0001) show only C1 symmetry and are mainly composed of pentagonal rings; (ii) Two possible nucleation pathways are revealed, i.e, longitudinal and circular modes; (iii) Carbon clusters are more stable on flat terraces than near atomic step edges. Based on above findings, a graphene nucleation diagram on SiC(0001) is established and experimentally observed contradictories for graphene growth on SiC(0001) are answered. Our in-depth understanding on graphene nucleation on SiC(0001) extends nucleation mechanisms of 2D crystals and will benefit high-quality graphene growth on SiC(0001).

Three Distinctive Steps for Heterogeneous Nucleation of Tunnel-Structured Mn Oxide on Quartz under Light Exposure.

Natural manganese (Mn) oxide coatings, resulting from the heterogeneous nucleation on foreign substances, have garnered interest based on their importance in the reaction with organic substances and in environmental systems. However, the heterogeneous nucleation of the natural Mn oxide coatings still remains elusive. Here, via fast photochemical oxidation of Mn2+(aq), we show that Mn(IV) oxide nuclei form and aggregate on quartz in three distinct successive stages: (i) a nanocrystalline film of unaligned grain forms, (ii) nanoislands develop on the film, and (iii) nanorods form on the nanoislands. Each stage has different crystalline structures and forms by aligned attachment of nanoscale precursors on the preceding surface. Crystal lattice analyses confirm the crystalline development, from the short-range order of the Mn oxide film to the long-range order of the nanorods. Also, the heterogeneous nucleation observed in this work produced groutellite-like tunnel structures of Mn oxide on quartz. This revealed pathway of the heterogeneous nucleation can offer a new perspective on the variety of poorly crystalline structures of natural Mn oxides found in the environment, which can affect elemental redox cycles, contaminant sequestration and removal, and soil carbon storage.

Explicit description of viral capsid subunit shapes by unfolding dihedrons.

Viral capsid assembly and the design of capsid-based nanocontainers critically depend on understanding the shapes and interfaces of constituent protein subunits. However, a comprehensive framework for characterizing these features is still lacking. Here, we introduce a novel approach based on spherical tiling theory that explicitly describes the 2D shapes and interfaces of subunits in icosahedral capsids. Our method unfolds spherical dihedrons defined by icosahedral symmetry axes, enabling systematic characterization of all possible subunit geometries. Applying this framework to real T = 1 capsid structures reveals distinct interface groups within this single classification, with variations in interaction patterns around 3-fold and 5-fold symmetry axes. We validate our classification through molecular docking simulations, demonstrating its consistency with physical subunit interactions. This analysis suggests different assembly pathways for capsid nucleation. Our general framework is applicable to other triangular numbers, paving the way for broader studies in structural virology and nanomaterial design.

Monomers Versus Prenucleation Clusters En Route to Polymorphism of Supramolecular Polymers.

Polymorphism in supramolecular polymers is strongly correlated with the polymerization pathways underlying their formation. To effectively control emerging polymorphs, a comprehensive understanding of nucleation pathways and mechanisms is essential. Herein, a coronene-dipeptide conjugate (Cr-o-FFOEt) is introduced and its self-assembly into two different stable 1D supramolecular polymorphs (Agg 1 and 2f) is observed in the same solvent composition (water/THF, 7:3 v/v) and same concentration at room temperature, following two competitive self-assembly pathways. The difference in the mode of solvent addition triggers the two self-assembly pathways. Furthermore, the isolated intermediate Agg 2i is found to transform into Agg 1 or Agg 2f under controlled experimental conditions. The supramolecular aggregates of Cr-o-FFOEt are thoroughly examined with the help of optical, chiroptical, and morphological techniques to understand the subtle difference in choosing the self-assembling pathways. The studies reveal that the nanotube formation of Agg 1 follows a classical nucleation-elongation supramolecular polymerization mechanism (involving monomers). In contrast, the helical fibers of Agg 2f are formed by the involvement of preorganized oligomers (nonclassical process). The observation highlights the underappreciated role of prenucleation clusters in pathway complexity and polymorphism of supramolecular 1D polymers.

Repercussion of Primary Nucleation Pathway: Dementia and Cognitive Impairment.

Neurodegenerative diseases, such as Alzheimer's, Parkinson's, and prion disease, are characterized by the conversion of normally soluble proteins or peptides into aggregated amyloidal fibrils. These diseases result in the permanent loss of specific types of neurons, making them incurable and devastating. Research on animal models of memory problems mentioned in this article contributes to our knowledge of brain health and functionality. Neurodegenerative disorders, which often lead to cognitive impairment and dementia, are becoming more prevalent as global life expectancy increases. These diseases cause severe neurological impairment and neuronal death, making them highly debilitating. Exploring and understanding these complex diseases offer significant insights into the fundamental processes essential for maintaining brain health. Exploring the intricate mechanisms underlying neurodegenerative diseases not only holds promise for potential treatments but also enhances our understanding of fundamental brain health and functionality. By unraveling the complexities of these disorders, researchers can pave the way for advancements in diagnosis, treatment, and ultimately, improving the lives of individuals affected by neurodegenerative diseases.

Efficient remediation of cadmium and lead contaminated soil in coal mining areas by MICP application in hydrothermal carbon-based bacterial agents: Nucleation pathways and mineralization mechanisms

The development of industrial mining has resulted in a large amount of Cd and Pb polluting the soil in mining areas, and leads to adverse health effects on the life of both plants and animals. Here, a soft template method was conducted to prepare hydrothermal carbon (HC) with regular morphology, which assisted with Bacillus pasteurii to induce calcite precipitation for decontamination of mining soil. Soil remediation experiments over 30 days of remediation with an HC microbial agent (HCMA) resulted in 89.4% and 87.8% decrease in the amount of leached Cd and Pb, respectively. The content of exchangeable Cd and Pb decreased by 76.1% and 81.0%, respectively. At the same time, soil fertility significantly improved. The electrostatic potential and surface charge distribution of extracellular polymeric substances (EPS) and sodium citrate (NaCit) were analyzed using DFT simulations, their nucleophilic and electrophilic regions were determined, and the nucleation mechanism was determined. The DFT results indicated that the oxygen-containing groups of EPS and NaCit had strong negative electrostatic potential and electronegativity, which could cause Cd2+, Pb2+, and Ca2+ to aggregate on their surfaces. They also combined with CO32− produced by urease during the decomposition of urea, resulting in Cd2+ and Pb2+ being encapsulated by calcium carbonate to form a coprecipitate. X-ray diffraction analyses revealed that the precipitate was mainly calcite calcium carbonate, which is more stable and less prone to secondary leaching of HMs. The gathered data prove the significant role of HCMA in remediation of mining soil contaminated with Cd and Pb.

Synthesis pathways of (HfZrTiCe/La/Y)O2-x nanoparticles via benzyl alcohol route at critical temperature

The controllable synthesis of high-entropy fluorite oxide (HEO) having large ionic radius mismatch remains a challenging due to poor understanding on nucleation. The (HfZrTiLn)-5HEO nanoparticles with 15 % ionic radius mismatch were synthesized via benzyl alcohol route at 220 °C-5 min in presence of PtCl4 and Fe(acac)3, exhibiting novel optical, electrical and magnetic properties. Nucleation pathways of the 5HEO at the critical temperature were elucidated by using a comparison study of conventional heating and microwave irradiation heating. Consistency of XRD patterns and STEM-EDX observation indicate that the resultant Hf-OBn monomers acted as the nucleation center of the 5HEO, determined by diffusion kinetics. The nucleation rate depended on the metal monomers assembly and esterification reaction, which was accelerated by water vapor pressure produced in-situ by 0.5×10−4mol/l PtCl4 catalyst. The Fe-metal organic cages derived from 1.5×10−4mol/l Fe(acac)3 additive served as the structure stabilizer of Zr/Ti monomers, and prevented early hydrothermal reaction route.

A microscopic approach to crystallization: Challenging the classical/non-classical dichotomy.

We present a fundamental framework for the study of crystallization based on a combination of classical density functional theory and fluctuating hydrodynamics that is free of any assumptions regarding order parameters and that requires no input other than molecular interaction potentials. We use it to study the nucleation of both droplets and crystalline solids from a low-concentration solution of colloidal particles using two different interaction potentials. We find that the nucleation pathways of both droplets and crystals are remarkably similar at the early stages of nucleation until they diverge due to a rapid ordering along the solid pathways in line with the paradigm of "non-classical" crystallization. We compute the unstable modes at the critical clusters and find that despite the non-classical nature of solid nucleation, the size of the nucleating clusters remains the principle order parameter in all cases, supporting a "classical" description of the dynamics of crystallization. We show that nucleation rates can be extracted from our formalism in a systematic way. Our results suggest that in some cases, despite the non-classical nature of the nucleation pathways, classical nucleation theory can give reasonable results for solids but that there are circumstances where it may fail. This contributes a nuanced perspective to recent experimental and simulation work, suggesting that important aspects of crystal nucleation can be described within a classical framework.

Competing nucleation pathways in nanocrystal formation

Despite numerous efforts from numerical approaches to complement experimental measurements, several fundamental challenges have still hindered one’s ability to truly provide an atomistic picture of the nucleation process in nanocrystals. Among them, our study resolves three obstacles: (1) Machine-learning force fields including long-range interactions able to capture the finesse of the underlying atomic interactions, (2) Data-driven characterization of the local ordering in a complex structural landscape associated with several crystal polymorphs and (3) Comparing results from a large range of temperatures using both brute-force and rare-event sampling. Altogether, our simulation strategy has allowed us to study zinc oxide crystallization from nano-droplet melt. Remarkably, our results show that different nucleation pathways compete depending on the investigated degree of supercooling.

Nucleation Mechanism of Hexagonal Boron Nitride on Diamond (111) and Its Hydrogen-Terminated Surface: A DFT Study.

Hexagonal boron nitride (h-BN) has attracted significant attention due to its exceptional properties. Among various substrates used for h-BN growth, diamond emerges as a more promising substrate due to its high-temperature resistance and superior electrical properties. To reveal the nucleation mechanism of h-BN on the diamond (111) surface and the impact of hydrogenation treatment on this process, we explored the adsorption, diffusion, nucleation morphologies, and predicted nucleation pathways in this process using first-principles calculations based on density functional theory (DFT). Our results indicate that N positioned above the first layer of C and B positioned above the second layer of C enhance the stability of BN clusters. During the growth of BN clusters, there is a geometric transformation from chain-like structures to honeycomb-like structures. The proportion of unhybridized sp2 atoms within BN clusters and geometric symmetry significantly influence h-BN growth. Moreover, computational findings also suggest that to enhance the nucleation rate of h-BN it is essential to inhibit the formation of zigzag chain structures by BN clusters during the early stages of nucleation on a clean diamond surface. Additionally, hydrogenation treatment decreases the binding affinity of B and N on the substrate, facilitating atomic diffusion, and has been identified as an effective approach to facilitate nucleation. Furthermore, hydrogen-terminated diamond acts as an electron donor in the system, which profoundly affects the morphology of growing h-BN and the characteristics of the h-BN/diamond heterostructures. These conclusions are important to understanding and optimizing h-BN growth on diamond and provide a theoretical basis of the construction and application of the h-BN/diamond heterostructure.

Concentration effect of zinc ions on amyloid fibrillation of hen egg-white lysozyme with thermal treatment revealed by Raman spectroscopy

Accumulation of Zn2+ ions in protein aggregates has been suggested to be a key factor in Alzheimer’s disease etiology. However, the specific influence of Zn2+ ions on the formation of amyloid fibrils or amorphous aggregates is still much debated. Herein, we conducted a combined study of Raman spectroscopy, UV–vis absorption spectroscopy and ThT fluorescence assay on the concentration effects of Zn2+ ions on amyloid fibrillation of hen egg-white lysozyme with thermal treatment. The addition of Zn2+ ions showed a negligible effect on unfolding of the protein tertiary structures and nucleation pathways on amyloid fibrillation. In contrast, a distinct concentration-dependence was observed for the influence of Zn2+ ions on the transformation of lysozyme secondary structures. At low concentration, the metal ions do not affect the populations of major secondary structures in the final state after incubation, while they at high concentration exhibit a promotion effect on the transformation from α-helix to β-sheet-like structures. These findings provide insights into the multifaceted impact of Zn2+ ions on protein aggregation, shedding light on potential therapeutic strategies for neurodegenerative diseases.

Unveiling the nucleation and growth of Zr oxide precipitates in internally oxidized Nb3Sn superconductors

We report on atomic-scale analyses of nucleation and growth of Zr oxide precipitates and the microstructural evolution of internally oxidized Nb3Sn wires for high-field superconducting magnet applications, utilizing atom probe tomography (APT), transmission electron microscopy (TEM), and first-principles calculations. APT analyses reveal that oxygen and zirconium are already segregated at grain boundaries (GBs) in the unreacted Nb-1Zr-4Ta (at%) alloy prior to forming Nb3Sn through reacting the Nb alloy with Sn and SnO2. After forming Nb3Sn, Zr oxide precipitates nucleate both at the Nb3Sn/Nb heterophase interfaces and in the Nb3Sn grains, driven by the small solubilities of Zr and O in Nb3Sn compared to their value in Nb. A high number density (Nv) of Zr oxide nanoprecipitates is observed in the Nb3Sn layers, ∼1023 m−3, with a mean diameter <10 nm for a heat treatment at 625 °C. Quantitative APT and TEM analyses of the Zr oxide precipitates in the reacted Nb3Sn layers elucidate details of the nucleation, growth, and coarsening processes of the Zr oxide precipitates in Nb3Sn. First-principles calculations and classical nucleation theory are employed to study the nucleation of Zr oxide precipitates in Nb3Sn and to estimate the maximum energy barrier and critical radius for nucleation. Our research unveils the kinetic pathways for nucleation and growth of Zr oxide precipitates and the microstructural evolution of Nb3Sn layers, which helps to understand and improve the superconducting properties of internally oxidized Nb3Sn wires for use in high-field superconducting magnets.

Unveiling the Factors Influencing Different Nucleation Pathways and Liquid-Liquid Phase Separation.

Exploring nucleation pathways has been a research hot spot in the fields of crystal engineering. In this work, vanillin as a model compound was utilized to explore the factors influencing different nucleation pathways with or without liquid-liquid phase separation (LLPS). A thermodynamic phase diagram of vanillin in the mixed solvent system of water and acetone from 10 to 55 °C was determined. It was found that the occurrence of LLPS might be related to different nucleation pathways. Under the guidance of a thermodynamic phase diagram, Raman spectroscopy and molecular simulation were applied to investigate the influencing factors of different nucleation paths. It was found that the degree of solvation is a key factor determining the nucleation path, and strong solvation could lead to LLPS. Additionally, the molecular self-assembly evolution during the crystallization process was further investigated by using small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS). The findings indicate that larger clusters with a diffuse transition layer may lead to LLPS during the nucleation process.

Multi-condensate state as a functional strategy to optimize the cell signaling output

The existence of multiple biomolecular condensates inside living cells is a peculiar phenomenon not compatible with the predictions of equilibrium statistical mechanics. In this work, we address the problem of multiple condensates state (MCS) from a functional perspective. We combine Langevin dynamics, reaction-diffusion simulation, and dynamical systems theory to demonstrate that MCS can indeed be a function optimization strategy. Using Arp2/3 mediated actin nucleation pathway as an example, we show that actin polymerization is maximum at an optimal number of condensates. For a fixed amount of Arp2/3, MCS produces a greater response compared to its single condensate counterpart. Our analysis reveals the functional significance of the condensate size distribution which can be mapped to the recent experimental findings. Given the spatial heterogeneity within condensates and non-linear nature of intracellular networks, we envision MCS to be a generic functional solution, so that structures of network motifs may have evolved to accommodate such configurations.

Combining fast scanning chip calorimetry and nanoindentation: Young's modulus and hardness of poly (l-lactic acid) containing α′- and α-crystals

Fast scanning chip calorimetry (FSC) allows subjecting polymer melts to well-defined vitrification, crystal nucleation, and crystal growth pathways and, therefore, precise control of morphologies, from fully amorphous glassy states to semicrystalline structures containing perfect crystals. Due to the required use of nanogram-sized samples, needed to achieve high cooling rates, their mechanical properties, in order to establish structure-property relations, are difficult to assess. In this work, indentation modulus and indentation hardness of FSC samples are successfully determined on example of semicrystalline poly (ʟ-lactic acid) (PLLA) containing spherulitically grown disorder α′- or rather perfect α-crystals, with the correctness of the applied preparation and analyses routes confirmed by nanoindentation measurements on milligram-sized samples prepared through hotstage microscopy, and by applying both static single-step and quasi-continuous stiffness measurements. Modulus and hardness data are consistent with prior analyses of bulk samples, confirming that semicrystalline PLLA containing α-crystals exhibits around 10–20 % higher values of these properties compared to PLLA containing α′-crystals, related to the different molecular-chain packing in the crystal lattice. This work demonstrates that combination of FSC and nanoindentation techniques is an effective tool for determining mechanical properties of samples solidified at specific thermal pathways which otherwise cannot be realized.

Iodine Clusters in the Atmosphere I: Computational Benchmark and Dimer Formation of Oxyacids and Oxides.

The contribution of iodine-containing compounds to atmospheric new particle formation is still not fully understood, but iodic acid and iodous acid are thought to be significant contributors. While several quantum chemical studies have been carried out on clusters containing iodine, there is no comprehensive benchmark study quantifying the accuracy of the applied methods. Here, we present the first study in a series that investigate the role of iodine species in atmospheric cluster formation. In this work, we have studied the iodic acid, iodous acid, iodine tetroxide, and iodine pentoxide monomers and their dimers formed with common atmospheric precursors. We have tested the accuracy of commonly applied methods for calculating the geometry of the monomers, thermal corrections of monomers and dimers, the contribution of spin-orbit coupling to monomers and dimers, and finally, the accuracy of the electronic energy correction calculated at different levels of theory. We find that optimizing the structures either at the ωB97X-D3BJ/aug-cc-pVTZ-PP or the M06-2X/aug-cc-pVTZ-PP level achieves the best thermal contribution to the binding free energy. The electronic energy correction can then be calculated at the ZORA-DLPNO-CCSD(T0) level with the SARC-ZORA-TZVPP basis for iodine and ma-ZORA-def2-TZVPP for non-iodine atoms. We applied this methodology to calculate the binding free energies of iodine-containing dimer clusters, where we confirm the qualitative trends observed in previous studies. However, we identify that previous studies overestimate the stability of the clusters by several kcal/mol due to the neglect of relativistic effects. This means that their contributions to the currently studied nucleation pathways of new particle formation are likely overestimated.

Interrogation of 3d Transition Bimetallic Nanocrystal Nucleation and Growth Using In Situ Electron Microscope and Synchrotron X-ray Techniques.

Understanding the nucleation and growth mechanism of 3d transition bimetallic nanocrystals (NCs) is crucial to developing NCs with tailored nanostructures and properties. However, it remains a significant challenge due to the complexity of 3d bimetallic NCs formation and their sensitivity to oxygen. Here, by combining in situ electron microscopy and synchrotron X-ray techniques, we elucidate the nucleation and growth pathways of Fe-Ni NCs. Interestingly, the formation of Fe-Ni NCs emerges from the assimilation of Fe into Ni clusters together with the reduction of Fe-Ni oxides. Subsequently, these NCs undergo solid-state phase transitions, resulting in two distinct solid solutions, ultimately dominated by γ-Fe3Ni2. Furthermore, we deconvolve the interplays between local coordination and electronic state concerning the growth temperature. We directly visualize the oxidation-state distributions of Fe and Ni at the nanoscale and investigate their changes. This work may reshape and enhance the understanding of nucleation and growth in atomic crystallization.

Resolving the early-stage nucleus structure and evolution in atomic systems

Nucleation underpins a vast range of phase-transition phenomena in many disciplines. Critical to revealing nucleation thermodynamics and kinetics is the understanding of the nucleus structure at its early stage. Typically, it is assumed that nucleation is a sudden local structural transition from one phase to another. Here, we are able to access fundamental steps in the nucleation from amorphous phase by a combination of molecular simulations and experimental observation. We discover a surprising pathway of semicrystalline nucleation where one of the materials components crystallizes and another remains amorphous between the crystalline planes in the nuclei. The early-stage crystallization nucleus is robustly evidenced to undergo a gradual ordering and densification, originating from the presence of diffuse interfaces, and renders an ultralow interfacial energy that is orders of magnitude lower than those typically used in various formulations of nucleation. Our study provides critical information and insight for the early stages of nucleation that determine how crystallization is initiated and benefits controllable synthesis of materials.