A Computational Platform to Unravel the Mechanisms of Directed Self-Assembly of Nanoparticles on Surfaces

The development of miniaturization in semiconductor manufacturing is mainly driven by the continuous pursuit of extremely powerful performance and efficient energy consumption behind which requires more sophisticated design of devices in nanoscale, even beyond sub-10 nm dimension. Integration of nanomaterials with such patterned devices would further promote cooperative phenomenon with adjacent substrate materials, and demonstrate extraordinary physicochemical properties. However, the fabrication process of above-mentioned low-dimensional devices demands strict control on nanostructure positioning that incurs several difficulties. None of the conventional patterning techniques with top-down photolithography is able to adequately address the challenge due to physical restriction in resolution. Alternative techniques have been introduced to solve the problem, including ultra-violet lithography, nanoimprint lithography, and directed self-assembly, among which directed self-assembly presents a potential in producing structurally and functionally complex substrate-supported nanostructure in a well-tunable and cost-effective manner, in addition to its broad applicability and operational simplicity. Recent development in directed self-assembly on templated surfaces, while remains at a beginning stage, has presented the opportunity of assembling arrays of nanoparticles. Advanced control over the assembly process including the dynamics of advancing/receding contact line, optimization of con finement and template, nevertheless, requires accurate and complete understanding of the underlying mechanisms. In addition, the experimental study on the contact line behavior or further in directed self-assembly needs to create a thin lm of hundred nanometers thickness which remains a challenge in terms of efficiency and cost. Nevertheless, computational modeling provides with great feasibility and convenience to investigate a variety of parameters at specific conditions. We develop a 3D kinetic Monte Carlo model to understand the dynamics of the liquid film developed during dip coating process and the wetting behavior of a liquid lm rising along a vertical substrate. By varying gravitational acceleration and surface tension, we present explicit analysis of the effect of dynamics of solid-liquid interface on the interfacial displacement and contact line roughness. To further unravel the wetting mechanism of spontaneous rise of thin liquid lm, we present a coarse grained Molecular Dynamics simulation. We investigate the dynamics of a rising contact line by demonstrating its displacement and dynamic contact angle in single- and double-wall geometry, and different surface roughness. Lithographically-de ned substrates also play a signifi cant role in pinning, deformation, and contact line of a liquid lm receding over the substrate. Using a coarse grained Molecular Dynamics simulation, we show the pinning force and distortion of the pinned contact line varies across different nanocavity shapes and orientation. A rotational flow at the receding contact line is observed, and a localized clamping effect originated from the variation of dynamic contact angle is determined, and discussed. To explore the impact of confinement, nanoparticle density, and template geometry on the directed self-assembly of nanoparticles, we utilize a series of coarse grained Molecular Dynamics simulations. We develop a phase diagram for the directed self-assembly of nanoparticles. From the phase diagram, we show that high yield of nanoparticle deposition is obtained at specific combination of liquid film thickness (con finement) and nanoparticle density. We propose a new mechanism for the directed self-assembly by providing a series of analyses of nanoparticles trajectories. The new mechanism has roots in random hopping between the bulk liquid and nanocavity, which is shown to occur far from liquid-vapor meniscus. We also discuss the impact of template geometry on the yield by modifying the center-to-center distance and circular nanocavity radius. We then turn to the energetics of the directed self-assembly, and determine the free energy and entropic contributions to the self-assembly of nanoparticles, using Jarzynski's equality. Taking advantage of the Steered Molecular Dynamics simulations with both stagnant and receding liquid films, we discuss the impact of nanoparticle densities and receding contact line on the free energy contributions. We show that the directed self-assembly of nanoparticles is entropically prohibitive at low nanoparticle densities, and energetically unfavorable at high nanoparticle densities. Last but not least, we propose future directions, which can facilitate the template design, controlling non-equilibrium process of directed self-assembly of nanoparticles, and optimizing the yield during experiments, using machine learning with a continuous feedback loop linked to the experiments

A predictive model to probe the impact of gravity and surface tension on rising wetting thin films

Utilizing kinetic Monte Carlo simulations, we developed a three dimensional Ising lattice gas model to reveal the wetting mechanism of a liquid film rising along a vertical substrate. The model takes into account the impact of surface tension, gravity, interaction energy between liquid particles, and between liquid and substrate on the rise of the liquid film. We verify that in low gravitational acceleration regime, the growth of the liquid film follows the universal law of √ t. As gravitational acceleration and surface tension vary, the simulation results show the detailed dynamics of the solid-liquid interface. Explicit analysis of the interface displacement and roughness under different gravitational accelerations and surface tensions is also presented

Aerobic Oxidation of Formaldehyde Catalyzed by Polyvanadotungstates

Three tetra-<i>n</i>-butylammonium (TBA) salts of polyvanadotungstates, [<i>n</i>-Bu₄N]₆[PW₉V₃O₄₀] (<b>PW</b>_<b>9</b><b>V</b>_<b>3</b>), [<i>n</i>-Bu₄N]₅H₂PW₈V₄O₄₀ (<b>PW</b>_<b>8</b><b>V</b>_<b>4</b>), and [<i>n</i>-Bu₄N]₄H₅PW₆V₆O₄₀·20H₂O (<b>PW</b>_<b>6</b><b>V</b>_<b>6</b>), have been synthesized and shown to be effective catalysts for the aerobic oxidation of formaldehyde to formic acid under ambient conditions. These complexes, characterized by elemental analysis, Fourier transform infrared spectroscopy, UV–vis spectroscopy, and thermogravimetric analysis, exhibit a catalytic activity for this reaction comparable to those of other polyoxometalates. Importantly, they are more effective in the presence of water than the metal oxide-supported Pt and/or Au nanoparticles traditionally used as catalysts for formaldehyde oxidation in the gas phase. The polyvanadotungstate-catalyzed oxidation reactions are first-order in formaldehyde, parabolic-order (slow, fast, and slow again) in catalyst, and zero-order in O₂. Under optimized conditions, a turnover number of ∼57 has been obtained. These catalysts can be recycled and reused without a significant loss of catalytic activity

Efficient Reconstruction of CAS-CI-Type Wave Functions for a DMRG State Using Quantum Information Theory and a Genetic Algorithm

We improve the methodology to construct a complete active space-configuration interaction (CAS-CI) expansion for density-matrix renormalization group (DMRG) wave functions using a matrix-product state representation, inspired by the sampling-reconstructed CAS [SR-CAS; Boguslawski, K.; J. Chem. Phys. 2011, 134, 224101] algorithm. In our scheme, the genetic algorithm, in which the “crossover” and “mutation” processes can be optimized based on quantum information theory, is employed when reconstructing a CAS-CI-type wave function in the Hilbert space. Analysis of results for ground and excited state wave functions of conjugated molecules, transition metal compounds, and a lanthanide complex illustrate that our scheme is very efficient for searching the most important CI expansions in large active spaces

Additional file 1 of The innovative checkpoint inhibitors of lung adenocarcinoma, cg09897064 methylation and ZBP1 expression reduction, have implications for macrophage polarization and tumor growth in lung cancer

Additional file 1: Table S3. PCR primers. Table S4. Patients’ basic information. Figure S1. The immunofluorescence staining for validation of CD14+ cell. Figure S2. The body weight of the each mice. Figure S3. The Ethics approval and consent for investigation on human CD14+ cells. Figure S4. The Ethics approval and consent for animal experiments

Microprecision Delivery of Oligonucleotides in a 3D Tissue Model and Its Characterization Using Optical Imaging

Despite significant potential of oligonucleotides (ONs) for therapeutic and diagnostic applications, rapid and widespread intracellular delivery of ONs in cells situated in tissues such as skin, head and neck cavity, and eye has not been achieved. This study was aimed at evaluating the synergistic combination of microneedle (MN) arrays and biochemical approaches for localized intratissue delivery of oligonucleotides in living cells in 3D tissue models. This synergistic combination was based on the ability of MNs to precisely deliver ONs into tissues to achieve widespread distribution, and the ability of biochemical agents (streptolysin O (SLO) and cholesterol conjugation to ONs) to enhance intracellular ON delivery. The results of this study demonstrate that ON probes were uniformly coated on microneedle arrays and were efficiently released from the microneedle surface upon insertion in tissue phantoms. Co-insertion of microneedles coated with ONs and SLO into 3D tissue models resulted in delivery of ONs into both the cytoplasm and nucleus of cells. Within a short incubation time (35 min), ONs were observed both laterally and along the depth of a 3D tissue up to a distance of 500 μm from the microneedle insertion point. Similar widespread intratissue distribution of ONs was achieved upon delivery of ON–cholesterol conjugates. Uniformity of ON delivery in tissues improved with longer incubation times (24 h) postinsertion. Using cholesterol-conjugated ONs, delivery of ON probes was limited to the cytoplasm of cells within a tissue. Finally, delivery of cholesterol-conjugated anti-GFP ON resulted in reduction of GFP expression in HeLa cells. In summary, the results of this study provide a novel approach for efficient intracellular delivery of ONs in tissues

Ultrashort Single-Walled Carbon Nanotubes Insert into a Pulmonary Surfactant Monolayer via Self-Rotation: Poration and Mechanical Inhibition

It has been widely accepted that longer single-walled carbon nanotubes (SWCNTs) exhibit higher toxicity by causing severe pneumonia once inhaled, yet relatively little is known regarding the potential toxicity of ultrashort SWCNTs, which are of central importance to the development of suitable vehicles for biomedical applications. Here, by combining coarse-grained molecular dynamics (CGMD), pulling simulations, and scaling analysis, we demonstrate that the inhalation toxicity of ultrashort SWCNTs (1.5 nm < <i>l</i> < 5.5 nm) can be derived from the unique behaviors on interaction with the pulmonary surfactant monolayer (PSM), which is located at the air–water interface of alveoli and forms the frontline of the lung host defense. Molecular dynamics (MD) simulations suggest that ultrashort SWCNTs spontaneously insert into the PSM via fast self-rotation. Further translocation toward the water or air phase involves overcoming a high free-energy barrier, indicating that removal of inhaled ultrashort SWCNTs from the PSM is difficult, possibly leading to the accumulation of SWCNTs in the PSM, with prolonged retention and increased inflammation potentials. Under certain conditions, the inserted SWCNTs are found to open hydrophilic pores in the PSM via a mechanism that mimics that of the antimicrobial peptide. Besides, the mechanical property of the PSM is inhibited by the deposited ultrashort SWCNTs through segregation of the inner lipid molecules from the outer phase. Our results bring to the forefront the concern of the inhalation toxicity of ultrashort SWCNTs and provide guidelines for future design of inhaled nanodrug carriers with minimized side effects

Gene Expression Profiles Deciphering Leaf Senescence Variation between Early- and Late-Senescence Cotton Lines

<div><p>Leaf senescence varies greatly among genotypes of cotton (<i>Gossypium hirsutium</i> L), possibly due to the different expression of senescence-related genes. To determine genes involved in leaf senescence, we performed genome-wide transcriptional profiling of the main-stem leaves of an early- (K1) and a late-senescence (K2) cotton line at 110 day after planting (DAP) using the Solexa technology. The profiling analysis indicated that 1132 genes were up-regulated and 455 genes down-regulated in K1 compared with K2 at 110 DAP. The Solexa data were highly consistent with, and thus were validated by those from real-time quantitative PCR (RT-PCR). Most of the genes related to photosynthesis, anabolism of carbohydrates and other biomolecules were down-regulated, but those for catabolism of proteins, nucleic acids, lipids and nutrient recycling were mostly up-regulated in K1 compared with K2. Fifty-one differently expressed hormone-related genes were identified, of which 5 ethylene, 3 brassinosteroid (BR), 5 JA, 18 auxin, 8 GA and 1 ABA related genes were up-regulated in K1 compared with K2, indicating that these hormone-related genes might play crucial roles in early senescence of K1 leaves. Many differently expressed transcription factor (TF) genes were identified and 11 <i>NAC</i> and 8 <i>WRKY</i> TF genes were up-regulated in K1 compared with K2, suggesting that TF genes, especially <i>NAC</i> and <i>WRKY</i> genes were involved in early senescence of K1 leaves. Genotypic variation in leaf senescence was attributed to differently expressed genes, particularly hormone-related and TF genes.</p></div

Senescence-dependent changes in gene expression determined by quantitative RT-PCR in the main-stem leaves of K1 and K2 cotton lines at 65, 80, 95 and 110 DAP.

<p>A, Chlorophyll binding protein (<i>LHCB</i>; gene ID: EX169337). B, Large subunit of Rubisco, ribulose- 1,5-bisphosphate carboxylase/oxygenase (<i>RBCL</i>; gene ID: ES820978). C, Superoxide dismutase (<i>SOD</i>; gene ID: ES824305). D, Autophagy (<i>ATG</i>; gene ID: CO493577). E, Isopentenyltransferase (<i>IPT</i>; gene ID: DW494123). F, 9-cis-epoxycarotenoid dioxygenase (<i>GhNCED2</i>; gene ID: HM014161); G, 9-cis-epoxycarotenoid dioxygenase (<i>NCED1</i>; gene ID: EX168449). H, NAC domain protein (<i>NAC</i>; gene ID: CA992724). I, NAC domain protein (<i>GhNAC6</i>; gene ID: Dw517699). Expression ratios are presented relative to K2 values at 65 DAP. Data are means of three biological replicates ± SE.</p

Comparison of the expression ratios of some selected genes using Solexa sequencing and qRT-PCR.

<p>Comparison of the expression ratios of some selected genes using Solexa sequencing and qRT-PCR.</p