SAMP: Identifying Antimicrobial Peptides by an Ensemble Learning Model Based on Proportionalized Split Amino Acid Composition.

It is projected that 10 million deaths could be attributed to drug-resistant bacteria infections in 2050. To address this concern, identifying new-generation antibiotics is an effective way. Antimicrobial peptides (AMPs), a class of innate immune effectors, have received significant attention for their capacity to eliminate drug-resistant pathogens, including viruses, bacteria, and fungi. Recent years have witnessed widespread applications of computational methods especially machine learning (ML) and deep learning (DL) for discovering AMPs. However, existing methods only use features including compositional, physiochemical, and structural properties of peptides, which cannot fully capture sequence information from AMPs. Here, we present SAMP, an ensemble random projection (RP) based computational model that leverages a new type of features called Proportionalized Split Amino Acid Composition (PSAAC) in addition to conventional sequence-based features for AMP prediction. With this new feature set, SAMP captures the residue patterns like sorting signals at around both the N-terminus and the C-terminus, while also retaining the sequence order information from the middle peptide fragments. Benchmarking tests on different balanced and imbalanced datasets demonstrate that SAMP consistently outperforms existing state-of-the-art methods, such as iAMPpred and AMPScanner V2, in terms of accuracy, MCC, G-measure and F1-score. In addition, by leveraging an ensemble RP architecture, SAMP is scalable to processing large-scale AMP identification with further performance improvement, compared to those models without RP. To facilitate the use of SAMP, we have developed a Python package freely available at https://github.com/wan-mlab/SAMP.

Surface Plasmonic Core-Shell Nanostructures in Surface Enhanced Raman Scattering and Photocatalysis.

Core-shell nanostructures are a typical material design. Usually, it consists of a core wrapped in a shell. It has attracted much attention due to its tunable structure and composition, high surface area, and high programmability. The properties and resonance frequency of their surface plasmons can be adjusted by regulating the shape, size, and composition of metal core-shell nanostructures. This interaction makes core-shell nanostructures an excellent platform for plasmon-enhanced optical effects. This Perspective explores the categories of core-shell nanostructures, their exchanges with excitons in two-dimensional materials, their spectrum-enhanced aspects, and prospects for future applications of core-shell nanostructures.

Charge transfer excitons and directional fluorescence of in-plane lateral MoSe2-WSe2 heterostructures.

In this article, the linear and nonlinear optical properties of in-plane lateral MoSe2-WSe2 heterostructures are theoretically investigated. The polarization-dependent strongest optical absorption in one-photon absorption occurs in charge transfer excited states, where electrons transfer from WSe2 to MoSe2. This phenomenon is supported by the LUMO (lowest unoccupied molecular orbital) and HUMO (highest occupied molecular orbital) imaging obtained through scanning tunneling microscopy. The charge difference density and transition density matrix are used to interpret the electronic transitions, and these interpretations rely on the concept of transition density. The optical properties of two-photon absorption in its nonlinear optical process are significantly different from the excitation in one-photon absorption, where the strongest optical absorption is contributed from direct transition from the ground state to the final state without going through an intermediate excited state, due to the very large difference of permanent dipole moments between the excited and ground states. Our results also reveal directional fluorescence and physical mechanism of in-plane lateral MoSe2-WSe2 heterostructures. Our work can provide insights into the physical mechanism of the optical properties of in-plane lateral MoSe2-WSe2 heterostructures.

Co-application of straw incorporation and biochar addition stimulated soil N2O and NH3 productions.

Nitrous oxide (N2O) and ammonia (NH3) volatilization (AV) are the major pathways of nitrogen (N) loss in soil, and recently, N2O and NH3 mitigation has become urgently needed in agricultural systems worldwide. However, the influence of straw incorporation (SI) and biochar addition (BC) on N2O and NH3 emissions are still unclear. To fill this knowledge gap, a soil column experiment was conducted with two management strategies using straw - straw incorporation (S1) and straw removal (S0) - and four biochar application rates (0 (C0), 15 (C1), 30 (C2), and 45 t ha-1 (C3)) to evaluate the impacts of their interactions on N2O and NH3 emissions. The results showed that NO3--N concentration and pH was the major contributors to affect the N2O and NH3 losses. Without biochar addition, N2O emissions was decreased by 59.6% (P<0.05) but AV was increased by 97.3% (P<0.05) under SI when compared to SR. Biochar was beneficial for N2O mitigation when straw was removed, but increased N2O emission by 39.4%-83.8% when straw was incorporated. Additionally, biochar stimulated AV by 27.9%-60.4% under S0 and 78.6%-170.3% under S1. Consequently, SI was found to significantly interact with BC in terms of affecting N2O (P<0.001) and NH3 (P<0.001) emissions; co-application of SI and BC promoted N2O emissions and offset the mitigation potential by SI or BC alone. The indirect N2O emissions caused by AV, however, might offset the reduction of direct N2O caused by SI or BC, thus leading to an increase in overall N2O emission. This paper recommended that SI combined BC at the amount of 8.2 t ha-1 for maintaining a lower overall N2O emission for future agriculture practices, but the long-term impacts of straw incorporation and biochar addition on the trade-off between N2O and NH3 emissions and reactive N losses should be further examined and assessed.

Recent progress of MXene as an energy storage material.

Thanks to its adjustable interlayer distance, large specific surface area, abundant active sites, and diverse surface functional groups, MXene has always been regarded as an excellent candidate for energy storage materials, including supercapacitors and ion batteries. Recent studies have also shown that MXene can serve as an efficient hydrogen storage catalyst. This review aims to summarize the latest research achievements in the field of MXene, especially its performance and application in energy storage. Different synthesis techniques have different effects on the energy storage performance of MXene. In this review, various common synthesis methods and the latest innovations in synthesis methods are discussed. MXene is prone to oxidation, and how to resist oxidation is also an important topic in MXene research. This article introduces the research results on improving the chemical stability of MXene through annealing. In addition, it aims to gain a deeper understanding of the future development and potential of MXene.

Modulating Thermoelectric Properties of the MoSe2/WSe2 Superlattice Heterostructure by Twist Angles.

In the current era of limited resources, the matter of energy conversion holds significant importance. Thermoelectric materials possess the ability to transform thermal energy into electric power. Achieving an impressive thermoelectric figure of merit (ZT) necessitates the presence of a high power factor alongside low thermal conductivity. Stimulated by recent experimental reports on the in-plane lateral MoSe2/WSe2 heterostructure in the application thermoelectric device [Zhang Y. et al., Simultaneous electrical and thermal rectification in a monolayer lateral heterojunction. Science 2022, 378, 169], in this study, the method of twisting angle is used to modulate the energy bands of van der Waals MoSe2/WSe2 superlattice heterostructures to optimize the carrier concentration, band gap, electric conductance, thermal conductivity, and ZT of the heterostructure. The 21.79° twisted heterostructures among different twisting-angle heterostructures benefit from both the high power factor and low thermal conductivity, ultimately leading to significantly improved ZT compared to the untwisted counterpart.

Spectral Analysis on Cuba-Lumacaftor: Cubane as Benzene Bioisosteres of Lumacaftor.

In this paper, we theoretically investigate the electronic structure and physical properties of cuba-lumacaftor, cubane as benzene bioisosteres of lumacaftor, stimulated by recent experimental reports [Wiesenfeldt M. P.; Nature2023, 618, 513-518]. The permanent electric dipole moments of cuba-lumacaftor in neutral, acidic, and alkaline environments are significantly enlarged than that of lumacaftor, significantly promoting the interaction between cuba-lumacaftor and surrounding polar solvent environments and resulting in pH-independent high solubility and pharmacological activity. Furthermore, electronic circular dichroism (ECD) spectra reveal that the chirality of cuba-lumacaftor is much decreased compared to that of lumacaftor. Raman spectra and resonance Raman spectra combined with polarizability also reveal the vibrational information on cuba-lumacaftor. Our results promote a deeper understanding of better pharmacological activity.

Spectral Physics of Stable Cu(III) Produced by Oxidative Addition of an Alkyl Halide.

In this paper, we theoretically investigated spectral physics on Cu(III) complexes formed by the oxidative addition of α-haloacetonitrile to ionic and neutral Cu(I) complexes, stimulated by recent experimental reports. Firstly, the electronic structures of reactants of α-haloacetonitrile and neutral Cu(I) and two kinds of products of Cu(III) complexes are visualized with the density of state (DOS) and orbital energy levels of HOMO and LUMO. The visually manifested static and dynamic polarizability as well as the first hyperpolarizability are employed to reveal the vibrational modes of the normal and resonance Raman spectra of two Cu(III) complexes. The nuclear magnetic resonance (NMR) spectra are not only used to identify the reactants and products but also to distinguish between two Cu(III) complexes. The charge difference density (CDD) reveals intramolecular charge transfer in electronic transitions in optical absorption spectra. The CDDs in fluorescence visually reveal electron-hole recombination. Our results promote a deeper understanding of the physical mechanism of stable Cu(III) produced by the oxidative addition of an alkyl halide.

Electronic, optoelectronic, and thermoelectric properties of single molecular devices of 2D fullerenes with zigzag graphene nanoribbons as electrodes.

Zigzag graphene nanoribbons (GNRs) were selected as electrodes, and the electron transport properties, optical properties, and thermoelectric properties of four fullerene cluster-based molecular devices were studied. By applying different voltages on them, their I-V curves exhibited the multiple negative differential resistance (NDR) effect and the platform effect, which are described in more detail using their density of states (DOS) and projected density of states (PDOS). The results of rotating two types of (C60)4 molecules verify that both the NDR and the platform effects are essential characteristics of them. Furthermore, an examination is conducted on the photocurrent of the devices at the point of maximum light absorption, revealing that α-(C60)4 connected by a [2+2] ring addition bond in the transport direction exhibits superior optical properties and works better as a photoelectric device than ß-(C60)4 connected via a C-C single bond in the transport direction. Finally, the thermoelectric current of the devices was studied. Our results contribute to the understanding and the potential application of single devices based on fullerene clusters in the area of molecular electronics.

Emerging Characteristics and Properties of Moiré Materials.

In recent years, scientists have conducted extensive research on Moiré materials and have discovered some compelling properties. The Moiré superlattice allows superconductivity through flat-band and strong correlation effects. The presence of flat bands causes the Moiré material to exhibit topological properties as well. Modulating electronic interactions with magnetic fields in Moiré materials enables the fractional quantum Hall effect. In addition, Moiré materials have ferromagnetic and antiferromagnetic properties. By tuning the interlayer coupling and spin interactions of the Moiré superlattice, different magnetic properties can be achieved. Finally, this review also discusses the applications of Moiré materials in the fields of photocurrent, superconductivity, and thermoelectricity. Overall, Moiré superlattices provide a new dimension in the development of two-dimensional materials.

Mechanisms of chiral plasmonics-Scattering, absorption, and photoluminescence.

Chirality is a concept that one object is not superimposable on its mirror image by translation and rotation. In particular, chiral plasmonics have been widely investigated due to their excellent optical chiral properties, and have led to numerous applications such as optical polarizing element etc. In this study, we develop a model based on the concept of the interaction between harmonic oscillators to investigate and explain the optical chiral mechanisms of strongly coupled metal nanoparticles (MNPs). The chirality of the scattering, absorption, and photoluminescence spectra are carefully discussed in detail. The results show that the chirality of the system originates not only from the orientations of the MNPs, but also from the different eigen parameters between them. Specifically, the derived three factors contribute to the chirality: the symmetry, the coupling strength, and the coherent superposition of the emitted electric field. This work provides a deeper understanding on the chiral plasmonics and may guide relevant applications in theory.

Construction and characterization of microsatellite markers for the Schistosoma japonicum isolate from a hilly area of China based on whole genome sequencing.

Schistosoma japonicum had once caused the greatest disease burden in China and has still been transmitted in some hilly areas, for example, in Shitai of Anhui province, where rodents are projected to be the main reservoir. This may lead to a critical need of molecular tools with high efficiency in monitoring the dynamic of the rodent-associated S. japonicum, as an appropriate amount of schistosome input can re-establish its life cycle in a place with snails and then result in the re-emergence of schistosomiasis. Therefore, the goal of this study was to develop high polymorphic microsatellites from the whole genome of rodent-associated S. japonicum strain to monitor its transmission dynamic. We sampled the hilly schistosome isolate from Shitai of Anhui in China and sequenced the parasite with the next-generation sequencing technology. The whole genome was assembled with four different approaches. We then developed 71 microsatellite markers at a genome-wide scale throughout two best assembled genomes. Based on their chromosome mapping and the expected length of targeted sequences, we selected 24 markers for the development of multiplex reactions. Two multiplexes composed of 10 loci were finally developed, and their potential was revealed by their successful application on and capturing the genetic diversity of three schistosome populations. The selected 10 markers, each with clear chromosome location and characteristics, will be greatly useful in tracing the dispersal pathways or/and dynamics of the rodent-associated S. japonicum or others in the hilly area of China or elsewhere.

Spectral analysis of oxidation on localized surface plasmon resonance of copper nanoparticles thin film.

Copper nanoparticles (CuNPs) possess localized surface plasmon resonance (LSPR) effect. Cu thin films composed of individual CuNPs exhibit stronger LSPR than the individual CuNPs due to the LSPR coupling among CuNPs. However, CuNPs are easy to be oxidized, which results in the rapid LSPR damping of the CuNPs thin films. Simulation of the variations of the coupled LSPR of two adjacent CuNPs with the thickness of oxide shells formed during oxidation is of great importance for understanding the mechanisms of the strong LSPR of CuNPs thin films and its rapid attenuation. In this paper, Discrete-dipole approximation method is used to simulate the extinction spectra of two adjacent spherical CuNPs as a function of the shell thickness (t), the ambient refractive index (n), the diameter (D) of the CuNPs, and the inter-nanoparticle spacing (L). The calculation is validated by experimental results. According to our model, for a definite CuNPs thin films, the oxide shell thickness of CuNPs can be calculated only if the extinction spectra and the morphology are provided. Further, it is found when the oxide shell thickness is small (t/R< 0.3), increasing n and decreasing L/D have an obvious synergistic effect on enhancing the coupled LSPR, but this synergistic effect weakens with the deepening of oxidation, and disappeared when t/R > 0.5. This study provides a calculation method for coupled core-shell nanoparticles and throws light on the role of oxidation on the rapid damped LSPR of CuNPs thin films.

Preparation of a Three-Dimensional Composite Structure Based on a Periodic Au@Ag Core-Shell Nanocube with Ultrasensitive Surface-Enhanced Raman Scattering for Rapid Detection.

The absorption and scattering frequencies of surface plasmon resonance can be selectively adjusted by changing the morphology, size, structure, arrangement, and gap between noble metal nanoparticles so that the local electromagnetic field on the substrate surface can be further enhanced. This change will promote and popularize surface-enhanced Raman spectroscopy. This paper reports the research results and improvement scheme of surface enhanced Raman scattering (SERS) activity of silver-coated gold nanocubed/organism (Au@Ag/CW NCs) prepared by three-phase self-assembly. In the experiment, the uppermost oil phase in the three-phase self-assembly process was optimized as ethanol and n-hexane solution containing a specific concentration of a probe molecule rhodamine 6G or aspartame. The probe molecules were directly self-assembled on the surface of the composite substrate to avoid the possible loss and pollution during immersion and preservation and achieve the purpose of rapid detection. The results show that the Au@Ag/CW NC array substrate is a periodic cubic ring structure. The sensitivity, uniformity, reproducibility, and stability of composite Au@Ag/CW NC array substrates are verified by comparing the Raman activities of various substrates. The feasibility of using the substrate to realize rapid SERS detection, compared with the advantages and disadvantages of the traditional soaking method, proved that the prepared substrate and improvement direction have excellent potential for application and development prospects in the field of rapid food additive detection.

OPA, TPA and ECD spectra of π-conjugated interlocked chiral nanocarbons.

This paper presents a theoretical investigation of the optical absorption and molecular chirality of π-conjugated mechanically interlocked nanocarbons, using one photon absorption (OPA) and two photon absorption (TPA) as well as electronic circular dichroism (ECD) spectra. Our findings reveal the optical excitation properties of mechanically interlocked molecules (MIMs) and chirality resulting from interlocked mechanical bonds. While OPA spectra are unable to distinguish interlocked molecules from non-interlocked molecules, we demonstrate that TPA and ECD can effectively discriminate between them, and can also differentiate [2]catenanes from [3]catenanes. Thus, we propose new methods to identify interlocked mechanical bonds. Our results provide physical insight into the optical properties and absolute configuration of π-conjugated interlocked chiral nanocarbons.

Plexcitonics: plasmon-exciton coupling for enhancing spectroscopy, optical chirality, and nonlinearity.

Plexcitonics is a rapidly developing interdisciplinary field that holds immense potential for the creation of innovative optical technologies and devices. This field focuses on investigating the interactions between plasmons and excitons in hybrid systems. In this review, we provide an overview of the fundamental principles of plasmonics and plexcitonics and discuss the latest advancements in plexcitonics. Specifically, we highlight the ability to manipulate plasmon-exciton interactions, the emerging field of tip-enhanced spectroscopy, and advancements in optical chirality and nonlinearity. These recent developments have spurred further research in the field of plexcitonics and offer inspiration for the design of advanced materials and devices with enhanced optical properties and functionalities.

Planar π-extended all-armchair edge topological cycloparaphenylenes.

It is important to reveal the optical properties and physical mechanisms of electron transitions within planar π-extended cycloparaphenylenes (CPPs) with full armchair edge topology in nanoscience and nanotechnology. The optical properties of the planar π-extended ring stripped from the Au(111) surface are theoretically studied, based on the latest experimental synthesis [Nat. Chem. 2022, 14, 871]. Our calculation results indicate that there is a blue-shift of absorption peaks in non-planar systems compared with planar systems. For non-planar systems, we proved that there is no fluorescence in the closed loop while the open loop exhibits fluorescence, using charge density differences and transition densities as evidence. And we realized the transition from the weak excited state to the strong excited state by the two photon absorption (TPA) method. The resonance Raman spectrum confirmed that the S1 excited state of the non-planar closed loop is a dark excited state. Moreover, there is a red-shift of absorption peaks in non-planar charged systems compared with non-planar uncharged systems. We also investigated the visualization of charge transfer using absorption and fluorescence spectroscopy. Our results can provide more insights into the optical properties and potential design of optical nanodevices.

Fluorescence origin and chirality mechanism of graphene quantum Dots: Twist or Non-Twist?

In this paper, we theoretically investigate the fluorescence origin and chirality mechanism of graphene quantum dots with non-twist and twist geometries, respectively. It is revealed that twist is not necessary for fluorescence; but twist is must for the chirality, which can significantly enhance the intensity of chirality, demonstrated by ECD spectra. Our results provide deeper understanding on the physical mechanism of fluorescence and chirality of graphene quantum dot influenced by geometric twist.

Electronic band structure and anisotropic optical properties of bulk and monolayer fullerene networks.

We theoretically investigate the local electron density, electronic band structure, density of state, dielectric function, and optical absorption of the bulk and monolayer C60 network structures, based on the latest experimental synthesis [Nature, 2022, 606, 507]. The results show that the ground state electrons are concentrated on the bridge bonds between clusters, the bulk and monolayer C60 network structures have strong absorption peaks in the visible and near infrared regions, and the monolayer quasi-tetragonal phase C60 network structure shows strong polarization dependence. Our results not only provide insights into the physical mechanism of optical absorption of the monolayer C60 network structure, but also reveal potential applications of the C60 network structure in photoelectric devices.