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. As a proof of concept, the self-assembly and structural evolution of plasmonic-fluorescent hybrid nanoparticles (PFNPs) from concentric circle to core shell and then to Janus structures is demonstrated by using alkane chain-modified AuNPs and AIEgens as building blocks. The spatial position of AuNPs in the signal nanocomposite is controlled by varying the alkane ligand length and density on the AuNP surface. The mechanism behind the formation of various PFNP nanostructures is also elucidated through experiments and theoretical simulation. The obtained PFNPs with diverse structures exhibit spatially tunable optical and photothermal properties for advanced applications in multicolor and multimode immunolabeling and photothermal sterilization. This work presents an innovative synthetic approach of constructing AIEgen-functionalized OINPs with diverse structures, compositions, and functionalities, thereby championing the progressive development of these OINPs.

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. Subsequently, macromolecules on silica NPs originating from the copolymerization of growing PS or PVBA chains with the surface-grafted MMS compatibilizer are engineered by fine-tuning of polymer compositions or adjustment of solvent qualities. Moreover, multistage silica regrowth of tripod and tetrapod allowed a fine control of the patch-to-particle size ratio ranging from 0.69 to 1.54. Intriguingly, patchy silica NPs (1-, 2-, 3-PSNs) rather than hybrid clusters are successfully used as templates for multistep regrowth experiments, leading to the formation of silica NPs with a new morphology and size controllable PVBA/PS patches. Last but not least, combined with mesoscale dynamics simulations, the self-assembly kinetics of 2-PSN and 3-PSN into linear colloidal polymers and honeycomb-like lattices are studied. This work paves a new avenue for constructing colloidal polymers with a well-defined sequence and colloidal crystals with a predetermined architecture.

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

The Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis) 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. GO and KEGG enrichment analysis showed that the up-regulated genes in the controlled environment population were significantly associated with glucose metabolism, amino acid metabolism, and the nervous system, while those up-regulated in the ex situ population were significantly associated with energy supply and biosynthesis. Further analysis showed that metabolic and hearing-related genes were significantly affected by changes in the environment, and key metabolic genes such as HK, PFK, IDH, and GLS and key hearing-related genes such as OTOA, OTOF, SLC38A1, and GABBR2 were identified. These results suggest that the controlled environment population may have enhanced glucose metabolic ability via activation of glycolysis/gluconeogenesis, the TCA cycle, and inositol phosphate metabolism, while the ex situ population may meet higher energy requirements via enhancement of the amino acid metabolism of the liver and muscle and oxidative phosphorylation. Additionally, the acoustic behavior and auditory-related genes of Yangtze finless porpoise may show responsive changes and differential expression under different environment conditions, and thus the auditory sensitivity may also show corresponding adaptive characteristics. This study provides a new perspective for further exploration of the responsive changes of the two populations to various environments and provides a theoretical reference for further improvements in conservation practices for the Yangtze finless porpoise.

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. Additionally, we introduce ProRefiner, a memory-efficient global graph attention model to fully utilize the denoised context. Our proposed method achieves state-of-the-art performance on multiple sequence design benchmarks in different design settings. Furthermore, we demonstrate the applicability of ProRefiner in redesigning Transposon-associated transposase B, where six out of the 20 variants we propose exhibit improved gene editing activity.

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 DddAtox homolog from Ruminococcus sp. AF17-6 (RsDddA). We engineered RsDddA for mitochondrial base editing in a mammalian cell line and demonstrated RsDddA-derived cytosine base editors (RsDdCBE) offered a broadened NC sequence compatibility and exhibited robust editing efficiency. Moreover, our results suggest the average frequencies of mitochondrial genome-wide off-target editing arising from RsDdCBE are comparable to canonical DdCBE and its variants.

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. By increasing the cylinder size, LCs exhibit a transition from multi-helical to layered structures. Notably, we observe two stable structures, namely the helical structure and the layered structure, at moderate cylinder size. We also investigate the effects of the arrangement of cylindrical wall particles (hexagonal or square array) and anchoring strength on the LC structure. Our findings reveal that both the hexagonal array and strong anchoring strength promote the formation of helical structures. Our study provides novel insights into the confinement physics of LCs and highlights the potential for achieving helical structures in achiral LCs, which will expand the future applications of LCs.

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. We further find the change of LC structure from bipolar to watermelon-striped during the phase transition from smectic-A (SmA) to smectic-B (SmB) phases. Our results reveal the transition from bipolar defects to the inhomogeneous structures with the coexistence of nematic and smectic phases in smectic liquid-crystal droplets. We also study the influence of the sphere size in the range of 10σ0 ≤ Rsphere ≤ 50σ0 on the structural inhomogeneities. It shows a weak dependence on the sphere size. We further focus on how the structures can be affected by the interaction strength εGB-LJ. Interestingly, we find the watermelon-striped structure can be changed into a configuration with four defects at the vertices of a tetrahedron upon increasing the interaction strength. The liquid crystals at a strong interaction strength of εGB-LJ = 10.0ε0 show the two-dimensional nematic phase at the surface. We further present an explanation for the origin of the striped-pattern formation. Our results highlight the potential for using confinement to control these defects and their associated nanostructural heterogeneity.

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. However, it is considered difficult for small aspect ratio liquid crystals to generate all these four types of defects. In this study, we use molecular dynamics simulation to investigate the defect formed in Gay-Berne, ellipsoidal liquid crystals, with small aspect ratios confined in a circular cavity. As expected, we only find two types of defects (inside the circle and at the boundary) in circular, confined, Gay-Berne ellipsoids under static conditions at various densities, aspect ratios, and interactions between the wall and liquid crystals. However, when introducing an external field to the system, four types of defects can be observed. With increasing the strength of the external field, the singularities in the circular, confined system change from the inside to the boundary and the outside, and the farthest position that the singularities can reach depends on the strength of the external field. We further introduce an alternating, triangular wave, external field to the system to check if we can observe the transformation of different defects within an oscillating period. We find that the position of the singularities greatly depends on the oscillating intensity and oscillating period. By changing the oscillating intensity and oscillating period of the external field, the defect types can be adjusted, and the transformation between different defects can be easily observed. This provides a feasible way to modulate liquid crystal defects and investigate the transformation between different defects.

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. In self-assembly, cooperativity is achieved by tuning the interaction and particle size ratio of colloidal building blocks. The pyrochlore lattice formed by self-assembly of triblock Janus colloids acts as a soft template to direct the packing of colloidal spheres into cubic diamond lattices. Numerical simulations show that this cooperative self-assembly strategy works well in a large range of particle size ratio of these two species. Moreover, photonic band structure calculations reveal that the resulting cubic diamond lattices exhibit wide and complete photonic bandgaps and the width and frequency of the bandgaps can also be easily adjusted by tuning the particle size ratio. Our work will open up a promising avenue toward photonic bandgap materials by cooperative self-assembly employing surface-anisotropic Janus or patchy colloids as a soft template.

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. In addition, we find that the pitch and tilt angle of the helix structure can also be adjusted by changing the strength and oscillation period of the applied alternating external field. This may provide a feasible route for the regulation of chiral liquid crystal phases by an alternating external field.

Multiple 2D crystal structures in bilayered lamellae from the direct self-assembly of 3D systems of soft Janus particles.

Numerous crystals and Frank-Kasper phases in two-dimensional (2D) systems of soft particles have been presented by theoretical investigations. How to realize 2D crystals or Frank-Kasper phases via the direct self-assembly of three-dimensional (3D) systems remains an important issue. Here, through numerical simulations, we report the surprising finding of multiple 2D crystal structures in bilayered lamellae from the direct self-assembly of 3D systems of soft Janus particles. With varying the patch size and particle density, soft Janus particles, which exhibit very similar self-assembly behavior to giant amphiphiles, spontaneously form ordered bilayered lamellae. Within each layer of the bilayered lamellae, we find abundant highly-ordered 2D crystals including the Frank-Kasper σ phase and open kagome lattice. The kinetic mechanisms of the formation of these 2D crystals within the layers are revealed, and include a classical one-step nucleation mechanism and a two-step nucleation mechanism. Our findings suggest a simple route towards 2D crystals via the direct self-assembly of 3D systems of amphiphilic Janus building blocks.

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. The transition usually starts from the line or point defect regions, and the competition between neighboring and opposite boundary effects induces the continuous realignments of the smectic layers to connect the neighboring or opposite walls. The relative stability of these two defect patterns can be controlled by changing the confinement conditions. These results deepen our understanding of transition kinetics of defect patterns in confined liquid crystals.

Intercluster Exchange-Stabilized Novel Complex Colloidal χc 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 (χc) phase, which resembles the essential structural features of α-manganese but at a larger length scale, is obtained through molecular dynamics simulations. The formation of the χc phase undergoes a remarkable two-step self-assembly process, that is, the self-assembly of clusters with specific size dispersity from Janus colloids, followed by the highly ordered organization of these clusters. More importantly, the dynamic exchange of particles between these clusters plays a critical role in stabilizing the χc phase. Such a conceptual design framework based on intercluster exchange has the potential to effectively construct novel complex cluster crystals by hierarchical self-assembly of colloidal building blocks.

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. Photonic calculations show that the direct pyrochlore lattices formed from overlapping soft triblock Janus particles exhibit even larger photonic bandgaps than the ideal nonoverlapping pyrochlore lattice, and proper overlap arising from softness can also dramatically improve the photonic properties of the inverse pyrochlore and perovskite lattices. Our study offers a new and feasible self-assembly path toward three-dimensional photonic crystals with large and robust photonic bandgaps.

Highly Controlled Janus Organic-Inorganic Nanocomposite as a Versatile Photoacoustic Platform.

Controlling the structural order of nanoparticles (NPs), morphology, and composition is of paramount significance in tailoring the physical properties of nanoassembly. However, the commonly reported symmetrical nanocomposites often suffer an interference or sacrifice of the photophysical properties of the original components. To address this challenge, we developed a novel type of organic-inorganic Janus nanocomposite (JNCP) with an asymmetric architecture, offering unique features such as the precisely controlled localization of components, combined modular optical properties, and independent stimuli. As a proof of concept, JNCPs were prepared by incorporating two photoacoustic (PA) imaging agents, namely an organic semiconducting dye and responsive gold nanoparticles (AuNP) assembly in separate compartments of JNCP. Theoretical simulation results confirmed that the formation mechanism of JNCPs arises from the entropy equilibrium in the system. The AuNP assembly generated a PA images with the variation of pH, while the semiconducting molecule served as an internal PA standard agent, leading to ratiometric PA imaging of pH. JNCP based probe holds great potential for real-time and accurate detection of diverse biological targets in living systems.

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. By virtue of the Arrhenius two-state model describing reversible reactions, we figured out the conditions in terms of active energy and binding energy for different products. Specifically, the ultraslow growth of COFs under high reversibility of reactions corresponding to low binding energies resulted in a single crystal by inhibiting the emergence of nuclei as well as correcting defects through continually dropping small defective fragments off at crystal boundaries. High bonding energies responsible for the high nucleation rate and rapid growth that incorporated defects in crystals and caused the division of crystals through defect correcting processes led to small crystallites or polycrystals. The insights into the mechanisms help us to understand and further control the growth kinetics by exploiting reversible conditions to synthesize COFs of higher quality.

A controlling parameter of topological defects in two-dimensional covalent organic frameworks.

Synthesis of covalent organic frameworks with long-range molecular ordering is an outstanding challenge due to the fact that defects against predesigned topological symmetries are prone to form and break crystallization. The physical origins and controlling parameters of topological defects remain scarcely understood. By virtue of molecular dynamics simulations, we found that pentagons for combination [C4 + C4] and [C4 + C2] and heptagons for [C3 + C3] and [C3 + C2] were initial defects for growth dynamics with both uncontrolled and suppressed nucleation, further inducing more complex defects. The defects can be significantly reduced by achieving the growth with monomers added to a single nucleus, agreeing well with previous simulations and experiments. To understand the nature of defects, we proposed a parameter φ to describe the range of biased rotational angle between two monomers, within which chemical reactions are allowed. The parameter φ shows a monotonic relationship with defect population, which is demonstrated to be highly computable by using density functional theory calculations. When φ < 20, we can even observe defect-free growth for the four combinations, irrespective of growth dynamics. The results are essential for screening and designing condensation reactions for the synthesis of single crystals of high quality.

Biologically Responsive Plasmonic Assemblies for Second Near-Infrared Window Photoacoustic Imaging-Guided Concurrent Chemo-Immunotherapy.

We developed dual biologically responsive nanogapped gold nanoparticle vesicles loaded with immune inhibitor and carrying an anticancer polymeric prodrug for synergistic concurrent chemo-immunotherapy against primary and metastatic tumors, along with guided cargo release by photoacoustic (PA) imaging in the second near-infrared (NIR-II) window. The responsive vesicle was prepared by self-assembly of nanogapped gold nanoparticles (AuNNPs) grafted with poly(ethylene glycol) (PEG) and dual pH/GSH-responsive polyprodug poly(SN38-co-4-vinylpyridine) (termed AuNNP@PEG/PSN38VP), showing intense PA signal in the NIR-II window. The effect of the rigidity of hydrophobic polymer PSN38VP on the assembled structures and the formation mechanism of AuNNP@SN38 Ve were elucidated by computational simulations. The immune inhibitor BLZ-945 was encapsulated into the vesicles, resulting in pH-responsive release of BLZ-945 for targeted immunotherapy, followed by the dissociation of the vesicles into single AuNNP@PEG/PSN38VP. The hydrophilic AuNNP@PEG/PSN38VP nanoparticles could penetrate deep into the tumor tissues and release the anticancer drug SN38 under the reductive environment. A PA signal in the NIR-II window in the deep tumor region was obtained. The BLZ-945-loaded vesicle enabled enhanced PA imaging-guided concurrent chemo-immunotherapy efficacy, inhibiting the growth of both primary tumors and metastatic tumors.

Kinetics-controlled design principles for two-dimensional open lattices using atom-mimicking patchy particles.

The design and discovery of new two-dimensional materials with desired structures and properties are always one of the most fundamental goals in materials science. Here we present an atom-mimicking design concept to achieve direct self-assembly of two-dimensional low-coordinated open lattices using three-dimensional patchy particle systems. Besides honeycomb lattices, a new type of two-dimensional square-octagon lattice is obtained through rational design of the patch configuration of soft three-patch particles. However, unexpectedly the building blocks with thermodynamically favoured patch configuration cannot form square-octagon lattices in our simulations. We further reveal the kinetic mechanisms controlling the formation of the honeycomb and square-octagon lattices. The results indicate that the kinetically favoured intermediates play a critical role in determining the structure of obtained open lattices. This kinetics-controlled design principle provides a particularly effective and extendable framework to construct other novel open lattice structures.

Building Block Design for Minimizing Defects in the Construction of Two-Dimensional Covalent Organic Frameworks.

Polymerization of monomers into two-dimensional covalent organic frameworks with precise porous structures exhibits desired catalytic, gas separation, and optoelectronic properties. However, the defects arising from covalent bonding in a polymerization process always result in amorphous films with small crystalline domains or polycrystalline powders. It is still a tremendous challenge to synthesize high-quality crystalline products, even single crystals with a large size over the micrometer scale. In this work, we propose a general strategy of building block design to reduce the defects during growth of two-dimensional covalent organic frameworks. We demonstrate that the building block with a hexagonal pore unit, i.e., a hexamer, could greatly decrease defects by directional uniform growth in polymerization, while monomer, dimer, and trimer building blocks form more defects due to linear growth. Our work provides a new strategy to construct superlarge single crystals in practical applications by combining building block design and growing dynamics control.