Metal–Metal Binary Nanoparticle Superlattices: A Case Study of Mixing Co and Ag Nanoparticles

Here, Co/Ag binary nanoparticle superlattices were engineered. It is demonstrated that the Ag/Co nanoparticle size ratio is the dominating factor in the formation of binary nanoparticle superlattices. However, regardless of the relative ratio concentration of Co and Ag nanoparticles, the deposition temperature, <i>T</i>_d markedly changes the crystalline structure of binary superlattices. A systematic study of these parameters is presented in order to shed light on the driving force in the formation of binary metallic nanoparticle superlattices. For metal Co and Ag nanoparticles, the interparticle potential pairs are considered to be strong, but entropy is still the main driving force for the assembling into binary nanoparticle superlattices, rather than the energy arising from the interparticle interactions

Unusual Effect of an Electron Beam on the Formation of Core/Shell (Co/CoO) Nanoparticles Differing by Their Crystalline Structures

In this study, an unusual effect of the electron beam in transmission electron microscopy (TEM) on the formation of Co/CoO core/shell structures is developed through careful in situ TEM/scanning TEM (STEM) analysis. By feature of the nanoscale precision of this approach, the electron beam-irradiated Co nanoparticles reveals remarkable resistance to oxidation compared to those without irradiation treatment. Moreover, the irradiated hcp single domain Co nanocrystals result in Co/CoO core/shell nanoparticles after oxidation, instead of the CoO hollow nanoparticles without irradiation treatment. This study highlights the electron beam can also play a role in nanoscale Kirkendall effect, in addition to the nanocrystallinity and 2D ordering effect that we have recently demonstrated. By careful in situ STEM-EELS (electron energy-loss spectroscopy) studies of the Co nanoparticles, it was found that the deliberately irradiated nanoparticles undergo an outward diffusion process of Co ions, forming an oxide layer with O species produced by the carboxylic group covalently bound to the Co atoms of the surface

Nanocrystallinity and the Ordering of Nanoparticles in Two-Dimensional Superlattices: Controlled Formation of Either Core/Shell (Co/CoO) or Hollow CoO Nanocrystals

Here it is demonstrated that the diffusion process of oxygen in Co nanoparticles is controlled by their 2D ordering and crystallinity. The crystallinity of isolated Co nanoparticles deposited on a substrate does not play any role in the oxide formation. When they are self-assembled in 2D superlattices, the oxidation process is slowed and produces either core/shell (Co/CoO) nanoparticles or hollow CoO nanocrystals. This is attributed to the decrease in the oxygen diffusion rate when the nanoparticles are interdigitated. Initially, polycrystalline nanoparticles form core/shell (Co/CoO) structures, while for single-domain hexagonal close-packed Co nanocrystals, the outward diffusion of Co ions is favored over the inward diffusion of oxygen, producing hollow CoO single-domain nanocrystals

Beyond Entropy: Magnetic Forces Induce Formation of Quasicrystalline Structure in Binary Nanocrystal Superlattices

Here, it is shown that binary superlattices of Co/Ag nanocrystals with the same size, surface coating, differing by their type of crystallinity are governed by Co–Co magnetic interactions. By using 9 nm amorphous-phase Co nanocrystals and 4 nm polycrystalline Ag nanocrystals at 25 °C, triangle-shaped NaCl-type binary nanocrystal superlattices are produced driven by the entropic force, maximizing the packing density. By contrast, using ferromagnetic 9 nm single domain (<i>hcp</i>) Co nanocrystals instead of amorphous-phase Co, dodecagonal quasicrystalline order is obtained, together with less-packed phases such as the CoAg₁₃ (NaZn₁₃-type), CoAg (AuCu-type), and CoAg₃ (AuCu₃-type) structures. On increasing temperature to 65 °C, 9 nm <i>hcp</i> Co nanocrystals become superparamagnetic, and the system yields the CoAg₃ (AuCu₃-type) and CoAg₂ (AlB₂-type) structures, as observed with 9 nm amorphous Co nanocrystals. Furthermore, by decreasing the Co nanocrystal size from 9 to 7 nm, stable AlB₂-type binary nanocrystal superlattices are produced, which remain independent of the crystallinity of Co nanocrystals with the superparamagnetic state

Do Binary Supracrystals Enhance the Crystal Stability?

We study the oxygen thermal stability of two binary systems. The larger particles are magnetic amorphous Co (7.2 nm) or Fe₃O₄ (7.5 nm) nanocrystals, whereas the smaller ones (3.7 nm) are Au nanocrystals. The nanocrystal ordering as well as the choice of the magnetic nanoparticles very much influence the stability of the binary system. A perfect crystalline structure is obtained with the Fe₃O₄/Au binary supracrystals. For the Co/Au binary system, oxidation of Co results in the chemical transformation from Co to CoO, where the size of the amorphous Co nanoparticles increases from 7.2 to 9.8 nm in diameter. During the volume expansion of the Co nanoparticles, Au nanoparticles within the binary assemblies coalesce and are at the origin of the instability of the binary nanoparticle supracrystals. On the other hand, for the Fe₃O₄/Au binary system, the oxidation of Fe₃O₄ to γ-Fe₂O₃ does not lead to a size change of the nanoparticles, which maintains the stability of the binary nanoparticle supracrystals. A similar behavior is observed for an AlB₂-type Co–Ag binary system: The crystalline structure is maintained, whereas in disordered assemblies, coalescence of Ag nanocrystals is observed

DataSheet_1_Machine learning and experimental validation identified autophagy signature in hepatic fibrosis.docx

BackgroundThe molecular mechanisms of hepatic fibrosis (HF), closely related to autophagy, remain unclear. This study aimed to investigate autophagy characteristics in HF.MethodsGene expression profiles (GSE6764, GSE49541 and GSE84044) were downloaded, normalized, and merged. Autophagy-related differentially expressed genes (ARDEGs) were determined using the limma R package and the Wilcoxon rank sum test and then analyzed by GO, KEGG, GSEA and GSVA. The infiltration of immune cells, molecular subtypes and immune types of healthy control (HC) and HF were analyzed. Machine learning was carried out with two methods, by which, core genes were obtained. Models of liver fibrosis in vivo and in vitro were constructed to verify the expression of core genes and corresponding immune cells.ResultsA total of 69 ARDEGs were identified. Series functional cluster analysis showed that ARDEGs were significantly enriched in autophagy and immunity. Activated CD4 T cells, CD56bright natural killer cells, CD56dim natural killer cells, eosinophils, macrophages, mast cells, neutrophils, and type 17 T helper (Th17) cells showed significant differences in infiltration between HC and HF groups. Among ARDEGs, three core genes were identified, that were ATG5, RB1CC1, and PARK2. Considerable changes in the infiltration of immune cells were observed at different expression levels of the three core genes, among which the expression of RB1CC1 was significantly associated with the infiltration of macrophage, Th17 cell, natural killer cell and CD56dim natural killer cell. In the mouse liver fibrosis experiment, ATG5, RB1CC1, and PARK2 were at higher levels in HF group than those in HC group. Compared with HC group, HF group showed low positive area in F4/80, IL-17 and CD56, indicating decreased expression of macrophage, Th17 cell, natural killer cell and CD56dim natural killer cell. Meanwhile, knocking down RB1CC1 was found to inhibit the activation of hepatic stellate cells and alleviate liver fibrosis.ConclusionATG5, RB1CC1, and PARK2 are promising autophagy-related therapeutic biomarkers for HF. This is the first study to identify RB1CC1 in HF, which may promote the progression of liver fibrosis by regulating macrophage, Th17 cell, natural killer cell and CD56dim natural killer cell.</p

DataSheet_2_Machine learning and experimental validation identified autophagy signature in hepatic fibrosis.docx

BackgroundThe molecular mechanisms of hepatic fibrosis (HF), closely related to autophagy, remain unclear. This study aimed to investigate autophagy characteristics in HF.MethodsGene expression profiles (GSE6764, GSE49541 and GSE84044) were downloaded, normalized, and merged. Autophagy-related differentially expressed genes (ARDEGs) were determined using the limma R package and the Wilcoxon rank sum test and then analyzed by GO, KEGG, GSEA and GSVA. The infiltration of immune cells, molecular subtypes and immune types of healthy control (HC) and HF were analyzed. Machine learning was carried out with two methods, by which, core genes were obtained. Models of liver fibrosis in vivo and in vitro were constructed to verify the expression of core genes and corresponding immune cells.ResultsA total of 69 ARDEGs were identified. Series functional cluster analysis showed that ARDEGs were significantly enriched in autophagy and immunity. Activated CD4 T cells, CD56bright natural killer cells, CD56dim natural killer cells, eosinophils, macrophages, mast cells, neutrophils, and type 17 T helper (Th17) cells showed significant differences in infiltration between HC and HF groups. Among ARDEGs, three core genes were identified, that were ATG5, RB1CC1, and PARK2. Considerable changes in the infiltration of immune cells were observed at different expression levels of the three core genes, among which the expression of RB1CC1 was significantly associated with the infiltration of macrophage, Th17 cell, natural killer cell and CD56dim natural killer cell. In the mouse liver fibrosis experiment, ATG5, RB1CC1, and PARK2 were at higher levels in HF group than those in HC group. Compared with HC group, HF group showed low positive area in F4/80, IL-17 and CD56, indicating decreased expression of macrophage, Th17 cell, natural killer cell and CD56dim natural killer cell. Meanwhile, knocking down RB1CC1 was found to inhibit the activation of hepatic stellate cells and alleviate liver fibrosis.ConclusionATG5, RB1CC1, and PARK2 are promising autophagy-related therapeutic biomarkers for HF. This is the first study to identify RB1CC1 in HF, which may promote the progression of liver fibrosis by regulating macrophage, Th17 cell, natural killer cell and CD56dim natural killer cell.</p

Supracrystalline Colloidal Eggs: Epitaxial Growth and Freestanding Three-Dimensional Supracrystals in Nanoscaled Colloidosomes

The concept of template-confined chemical reactions allows the synthesis of complex molecules that would hardly be producible through conventional method. This idea was developed to produce high quality nanocrystals more than 20 years ago. However, template-mediated assembly of colloidal nanocrystals is still at an elementary level, not only because of the limited templates suitable for colloidal assemblies, but also because of the poor control over the assembly of nanocrystals within a confined space. Here, we report the design of a new system called “supracrystalline colloidal eggs” formed by controlled assembly of nanocrystals into complex colloidal supracrystals through superlattice-matched epitaxial overgrowth along the existing colloidosomes. Then, with this concept, we extend the supracrystalline growth to lattice-mismatched binary nanocrystal superlattices, in order to reach anisotropic superlattice growths, yielding freestanding binary nanocrystal supracrystals that could not be produced previously

Dispersion of Hydrophobic Co Supracrystal in Aqueous Solution

Assembly of nanoparticles into supracrystals provides a class of materials with interesting optical and magnetic properties. However, supracrystals are mostly obtained from hydrophobic particles and therefore cannot be manipulated in aqueous systems, limiting their range of applications. Here, we show that hydrophobic-shaped supracrystals self-assembled from 8.2 nm cobalt nanoparticles can be dispersed in water by coating the supracrystals with lipid vesicles. A careful characterization of these composite objects provides insights into their structure at different length scales. This composite, suspended in water, retains the crystalline structure and paramagnetic properties of the starting material, which can be moved with an applied magnetic field

Molecular dynamics simulation study on the inhibitory mechanism of RIPK1 by 4,5-dihydropyrazole derivatives

The receptor-interacting serine/threonine protein kinase 1 (RIPK1) is tightly related to Digestive System Neoplasms genesis. Therefore, inhibitors that target RIPK1 have gained popularity in today's anti-cancer therapy. Molecular docking, molecular dynamics simulations, and molecular mechanics/Poisson-Boltzmann surface area calculations were used to investigate the binding mode and inhibition mechanism of five 4,5-dihydropyrazole derivatives with RIPK1 in the present work. The results showed that the five inhibitors mainly interacted with RIPK1 through van der Waals interaction and were stably present in the hydrophobic pocket next to the ATP-binding pocket. During the simulation, the inhibitor 2R with opposite chirality displayed a significant flip-flop in the binding pose, causing the key residue Asp156 to not easily maintain the inactive conformation, affecting its inhibitory ability. Inhibitors with identical chirality but different 1-substituents could exert non-competitive inhibition via three pathways. First of all, the inhibitor interacted directly with ATP, influencing its γ-phosphate position. Second, it altered the conformation of Lys45, which was crucial for both ATP binding and γ-phosphate transfer. And then it affected the conformation of the P-loop and β1 sheet, resulting in differences in substrate peptide recognition. The results can provide a theoretical basis for the design of such inhibitors in the future.</p