Discovery of CRISPR-Cas12a clades using a large language model.

CRISPR-Cas systems revolutionize life science. Metagenomes contain millions of unknown Cas proteins. Traditional mining relies on protein sequence alignments.

Engineered Cas12j-8 is a Versatile Platform for Multiplexed Genome Modulation in Mammalian Cells.

Cas12j-8 is a compact Cas nuclease discovered from the metagenome of giant bacteriophages, consisting of only 717 amino acids and recognizing the '5-TTN-3' protospacer adjacent motif (PAM) sequence. However, its low gene editing efficiency in mammalian cells limits its application in therapeutic gene editing. To address this limitation, structure-guided mutagenesis is employed to replace key negatively charged residues with arginine, strengthening DNA binding.

A new strategy for Cas protein recognition based on graph neural networks and SMILES encoding.

The CRISPR-Cas system, an adaptive immune mechanism found in bacteria and archaea, has evolved into a promising genomic editing tool, with various types of Cas proteins playing a crucial role. In this study, we developed a set of strategies for mining and identifying Cas1 proteins. Firstly, we analyzed the characteristic differences of 14 types of Cas proteins in the protein large language model embedding space in detail; then converted proteins into the Simplified Molecular Input Line Entry System (SMILES) format, thereby constructing graph data representing atom and bond features.

Nanohelix Arrays with Giant Circular Dichroism through Patch-Enthalpy-Driven Self-Confined Self-Assembly of Janus Nanoparticles.

Plasmonic nanohelix arrays, exhibiting strong circular dichroism, are among the most promising optical chiral metamaterials. However, achieving chiral plasmonic effects in the visible range remains challenging with current manufacturing techniques, as it requires structures small enough to resonate at visible wavelengths. Herein, we propose a novel strategy for constructing nanohelix arrays through patch-enthalpy-driven self-confined self-assembly of Janus nanoparticles.

Genesis and Accumulation Modes of Coalbed Methane at the Eastern Margin of Ordos Basin, China: Evidence from Its Geochemistry.

The genesis, occurrence, and accumulation of coalbed methane (CBM) are critical to the methane exploration and development. Combining the geological and geochemical data from CBM exploration wells and basin modeling, the genesis and accumulation characteristics of CBM in different regions and depths at the eastern margin of Ordos Basin were elucidated. Regional-scale gas content is controlled by depth and coal rank without turning depth occurs, but blocks perform variably.

Two-Step Chirality Transfer to Twisted Assemblies: Synergistic Interplay of Chiral and Aggregation Interactions.

Chirality plays a pivotal role in both the origin of life and the self-assembly of materials. However, the governing principles behind chirality transfer in hierarchical self-assembly across multiple length scales remain elusive. Here, we propose a concise and versatile simulation strategy using the patchy particle chain model to investigate the self-assembly of rods interacting through chiral and aggregation interactions.

Hydrogen Bond-Induced Flexible and Twisted Self-Assembly of Functionalized Carbon Dots with Customized-Color Circularly Polarized Luminescence.

Circularly polarized luminescence (CPL) has numerous applications in optical data storage, quantum computing, bioresponsive imaging, liquid crystal displays, and backlights in three-dimensional (3D) displays. In addition to their competitive optical properties, carbon dots (CDs) benefit from simple and low-cost preparation, facile post-modification, and excellent resistance to photo- and chemical bleaching after carbonization. Combining the superior optical performance with polarization peculiarities through hierarchical structure engineering is imperative for the development of CDs.

Relative kinetic stability of defect patterns in two-dimensional nematic liquid crystals with rectangular confinement.

Guiding and dynamically modulating topological defects are critical challenges in defect engineering of liquid crystals. Here, we employ molecular dynamics simulations to investigate the transition dynamics and relative kinetic stability of defect patterns in two-dimensional nematic Gay-Berne liquid crystals confined within rectangular geometries. We observe the formation of various defect patterns including long-axis, diagonal, X-shaped, composite, and bend configurations under different confinement conditions.

A Ligand-Directed Spatial Regulation to Structural and Functional Tunability in Aggregation-Induced Emission Luminogen-Functionalized Organic-Inorganic Nanoassemblies.

Aggregation-induced emission luminogen (AIEgen)-functionalized organic-inorganic hybrid nanoparticles (OINPs) are an emerging category of multifunctional nanomaterials with vast potential applications. The spatial arrangement and positioning of AIEgens and inorganic compounds in AIEgen-functionalized OINPs determine the structures, properties, and functionalities of the self-assembled nanomaterials. In this work, a facile and general emulsion self-assembly tactic for synthesizing well-defined AIEgen-functionalized OINPs is proposed by coassembling alkane chain-functionalized inorganic nanoparticles with hydrophobic organic AIEgens.

Surface Engineering and Programmed Self-Assembly of Silica Nanoparticles with Controllable Polystyrene/Poly(4-vinybenzyl azide) Patches.

The programmed self-assembly of patchy nanoparticles (NPs) through a bottom-up approach is an efficient strategy for producing highly organized materials with a predetermined architecture. Herein, we report the preparation of di- and trivalent silica NPs with polystyrene (PS)/poly(4-vinylbenzyl azide) (PVBA) patches and assemble them in a THF mixture by lowering the solvent quality. Silica-PS/PVBA colloidal hybrid clusters were synthesized through the seeded growth emulsion copolymerization of styrene and 4-vinylbenzyl azide (VBA) in varying ratios.

Comparative Blood Transcriptome Analysis of Semi-Natural and Controlled Environment Populations of Yangtze Finless Porpoise.

The Yangtze finless porpoises () living in different environments display significant differences in behavior and physiology. To compare and analyze gene expression differences between an ex situ population and a controlled environment population of the Yangtze finless porpoise, we sequenced the transcriptome of blood tissues living in a semi-natural reserve and an artificial facility, respectively. We identified 6860 differentially expressed genes (DEGs), of which 6603 were up-regulated and 257 were down-regulated in the controlled environment vs ex situ comparison.

ProRefiner: an entropy-based refining strategy for inverse protein folding with global graph attention.

Inverse Protein Folding (IPF) is an important task of protein design, which aims to design sequences compatible with a given backbone structure. Despite the prosperous development of algorithms for this task, existing methods tend to rely on noisy predicted residues located in the local neighborhood when generating sequences. To address this limitation, we propose an entropy-based residue selection method to remove noise in the input residue context.

Engineering RsDddA as mitochondrial base editor with wide target compatibility and enhanced activity.

Double-stranded DNA-specific cytidine deaminase (DddA) base editors hold great promise for applications in bio-medical research, medicine, and biotechnology. Strict sequence preference on spacing region presents a challenge for DddA editors to reach their full potential. To overcome this sequence-context constraint, we analyzed a protein dataset and identified a novel DddA homolog from sp.

Helical structures of achiral liquid crystals under cylindrical confinement.

Confined liquid crystals (LCs) exhibit complex and intriguing structures, which are fascinating fundamental problems in soft matter. The helical structure of cylindrical cavities is of great importance in LC studies, particularly for their application in optical devices. In this study, we employ molecular dynamics simulations to explore the behavior of achiral smectic-B LCs confined in narrow cylindrical cavities, where geometric frustration plays an important role.

Defect transition of smectic liquid crystals confined in spherical cavities.

The formation and transformation of defects in confined liquid crystals are fascinating fundamental problems in soft matter. Here, we use molecular dynamics (MD) simulations to study ellipsoidal liquid crystals (LCs) confined in a spherical cavity, which significantly affects the orientation and translation of LC molecules near the surface. The liquid-crystal droplet can present the isotropic to smectic-B phase transition through the smectic-A phase, as the number density of the LC molecules increases.

External field induced defect transformation in circular confined Gay-Berne liquid crystals.

Normally, defects in two-dimensional, circular, confined liquid crystals can be classified into four types based on the position of singularities formed by liquid crystal molecules, i.e., the singularities located inside the circle, at the boundary, outside the circle, and outside the circle at infinity.

Colloidal cubic diamond photonic crystals through cooperative self-assembly.

Colloidal cubic diamond crystals with low-coordinated and staggered structures could display a wide photonic bandgap at low refractive index contrasts, which makes them extremely valuable for photonic applications. However, self-assembly of cubic diamond crystals using simple colloidal building blocks is still considerably challenging, due to their low packing fraction and mechanical instability. Here we propose a new strategy for constructing colloidal cubic diamond crystals through cooperative self-assembly of surface-anisotropic triblock Janus colloids and isotropic colloidal spheres into superlattices.

A chiral smectic phase induced by an alternating external field.

Using simple achiral building blocks modulated by an external field to achieve chiral liquid crystal phases remains a challenge. In this study, a chiral helix liquid crystal phase is obtained for a simple Gay-Berne ellipsoid model under an alternating external field by using molecular dynamics simulations. Our results show that the chiral helix liquid crystal phase can be observed in a wide range of external field strengths when the oscillation period is smaller than the rotational characteristic diffusion timescale of ellipsoids.

Transition kinetics of defect patterns in confined two-dimensional smectic liquid crystals.

Topological defects in liquid crystals under confined geometries have attracted extensive research interests. Here, we perform molecular dynamics simulations to investigate the formation and transition of defect patterns in two-dimensional smectic Gay-Berne liquid crystals with a simple rectangular confinement boundary. Two typical types of defect patterns, bridge and diagonal defect patterns, are observed, which can be transformable continuously between each other over time.

Intercluster Exchange-Stabilized Novel Complex Colloidal χ Phase.

Designing complex cluster crystals with a specific function using simple colloidal building blocks remains a challenge in materials science. Herein, we propose a conceptually new design strategy for constructing complex cluster crystals via hierarchical self-assembly of simple soft Janus colloids. A novel and previously unreported colloidal cluster-χ (χ) phase, which resembles the essential structural features of α-manganese but at a larger length scale, is obtained through molecular dynamics simulations.

Softness-Enhanced Self-Assembly of Pyrochlore- and Perovskite-like Colloidal Photonic Crystals from Triblock Janus Particles.

It remains extremely challenging to build three-dimensional photonic crystals with complete photonic bandgaps by simple and experimentally realizable colloidal building blocks. Here, we demonstrate that particle softness can enhance both the self-assembly of pyrochlore- and perovskite-like lattice structures from simple deformable triblock Janus colloids and their photonic bandgap performances. Dynamics simulation results show that the region of stability of pyrochlore lattices can be greatly expanded by appropriately increasing softness, and the perovskite lattices are unexpectedly obtained at enough high softness.

Mechanisms of Defect Correction by Reversible Chemistries in Covalent Organic Frameworks.

Reversible chemistries have been extensively explored to construct highly crystalline covalent organic frameworks (COFs) via defect correction. However, the mechanisms of defect correction that can explain the formation of products as single crystals, polycrystal/crystallites, or amorphous solids remain unknown. Herein, we employed molecular dynamics simulations combined with a polymerization model to investigate the growth kinetics of two-dimensional COFs.