Seed-Assisted Reversible Dissolution/Deposition of MnO for Long-Cyclic and Green Aqueous Zinc-Ion Batteries.

Manganese oxide (MnO) based aqueous zinc-ion batteries (AZIBs) are considered to be a promising battery for grid-scale energy storage. However, they usually suffer from the great challenge of capacity attenuation due to Mn dissolution and irreversible structural transformation. Herein, full use of the shortcomings is made to design high-performance cathode-free AZIBs.

In Situ Fabrication of Hierarchical CuO@CoNi-LDH Composite Structures for High-Performance Supercapacitors.

Layered double hydroxide (LDH) materials, despite their high theoretical capacity, exhibit significant performance degradation with increasing load due to their low conductivity. Simultaneously achieving both high capacity and high rate performance is challenging. Herein, we fabricated vertically aligned CuO nanowires in situ on the copper foam (CF) substrate by alkali-etching combined with the annealing process.

Interlayer and Phase Engineering Modifications of K-MoS@C Nanoflowers for High-Performance Degradable Zn-Ion Batteries.

2D transition metal dichalcogenides (TMDs) have garnered significant interest as cathode materials for aqueous zinc-ion batteries (AZIBs) due to their open transport channels and abundant Zn intercalation sites. However, unmodified TMDs exhibit low electrochemical activity and poor kinetics owing to the high binding energy and large hydration radius of divalent Zn. To overcome these limitations, an interlayer engineering strategy is proposed where K is preintercalated into K-MoS nanosheets, which then undergo in situ growth on carbon nanospheres (denoted as K-MoS@C nanoflowers).

Compartmentalization with nuclear landmarks yields random, yet precise, genome organization.

The 3D organization of eukaryotic genomes plays an important role in genome function. While significant progress has been made in deciphering the folding mechanisms of individual chromosomes, the principles of the dynamic large-scale spatial arrangement of all chromosomes inside the nucleus are poorly understood. We use polymer simulations to model the diploid human genome compartmentalization relative to nuclear bodies such as nuclear lamina, nucleoli, and speckles.

Phase Separation and Correlated Motions in Motorized Genome.

The human genome is arranged in the cell nucleus nonrandomly, and phase separation has been proposed as an important driving force for genome organization. However, the cell nucleus is an active system, and the contribution of nonequilibrium activities to phase separation and genome structure and dynamics remains to be explored. We simulated the genome using an energy function parametrized with chromosome conformation capture (Hi-C) data with the presence of active, nondirectional forces that break the detailed balance.

STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming.

The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization, especially the long-range enhancer-promoter contacts and subsequent gene expression control in cancer, remains poorly understood.

Chromatin network retards nucleoli coalescence.

Nuclear bodies are membraneless condensates that may form via liquid-liquid phase separation. The viscoelastic chromatin network could impact their stability and may hold the key for understanding experimental observations that defy predictions of classical theories. However, quantitative studies on the role of the chromatin network in phase separation have remained challenging.

Multiscale modeling of genome organization with maximum entropy optimization.

Three-dimensional (3D) organization of the human genome plays an essential role in all DNA-templated processes, including gene transcription, gene regulation, and DNA replication. Computational modeling can be an effective way of building high-resolution genome structures and improving our understanding of these molecular processes. However, it faces significant challenges as the human genome consists of over 6 × 10 base pairs, a system size that exceeds the capacity of traditional modeling approaches.

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization.

Chromosomes are positioned nonrandomly inside the nucleus to coordinate with their transcriptional activity. The molecular mechanisms that dictate the global genome organization and the nuclear localization of individual chromosomes are not fully understood. We introduce a polymer model to study the organization of the diploid human genome.

Characterizing chromatin folding coordinate and landscape with deep learning.

Genome organization is critical for setting up the spatial environment of gene transcription, and substantial progress has been made towards its high-resolution characterization. The underlying molecular mechanism for its establishment is much less understood. We applied a deep-learning approach, variational autoencoder (VAE), to analyze the fluctuation and heterogeneity of chromatin structures revealed by single-cell imaging and to identify a reaction coordinate for chromatin folding.

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.

Widespread changes to DNA methylation and chromatin are well documented in cancer, but the fate of higher-order chromosomal structure remains obscure. Here we integrated topological maps for colon tumors and normal colons with epigenetic, transcriptional, and imaging data to characterize alterations to chromatin loops, topologically associated domains, and large-scale compartments. We found that spatial partitioning of the open and closed genome compartments is profoundly compromised in tumors.

3D ATAC-PALM: super-resolution imaging of the accessible genome.

To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA-fluorescence in situ hybridization (FISH), RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs.

Predicting three-dimensional genome organization with chromatin states.

We introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution. Simulated chromatin structures recapitulate known features of genome organization, including the formation of chromatin loops, topologically associating domains (TADs) and compartments, and are in quantitative agreement with chromosome conformation capture experiments and super-resolution microscopy measurements.

Catalytic Kinetics of Different Types of Surface Atoms on Shaped Pd Nanocrystals.

To understand the catalytic properties or roles of different types of surface atoms on metal nanocatalysts, the catalytic kinetics and dynamics of the different types of surface atoms (plane and edge) were revealed for the first time by a statistical quantitative deconvolution of observables obtained from traditional single-molecule nanocatalysis of Pd nanocrystals.It was found that the edge and plane of Pd nanocubes show similar size-dependent product formation processes, but inverse product dissociation processes. This work helps push the traditional single-molecule nanocatalysis method towards the sub-particle level.