Model System Research Articles

Applying Machine Learning in Numerical Weather and Climate Modeling Systems

Applying Machine Learning in Numerical Weather and Climate Modeling Systems

The reference genome of Macropodus opercularis (the paradise fish)

Amongst fishes, zebrafish (Danio rerio) has gained popularity as a model system over most other species and while their value as a model is well documented, their usefulness is limited in certain fields of research such as behavior. By embracing other, less conventional experimental organisms, opportunities arise to gain broader insights into evolution and development, as well as studying behavioral aspects not available in current popular model systems. The anabantoid paradise fish (Macropodus opercularis), an “air-breather” species has a highly complex behavioral repertoire and has been the subject of many ethological investigations but lacks genomic resources. Here we report the reference genome assembly of M. opercularis using long-read sequences at 150-fold coverage. The final assembly consisted of 483,077,705 base pairs (~483 Mb) on 152 contigs. Within the assembled genome we identified and annotated 20,157 protein coding genes and assigned ~90% of them to orthogroups.

A data-driven exploration of the complexity of the phosphorus-centered pnictogen bonds

Phosphorus-centered pnictogen bonds, similar to well-studied halogen bonds, play a vital role in molecular recognition and assembly. This study aims to explain how pnictogen bonds interact with other noncovalent interactions. A model system, phosphines (PH3), which is also present in phosphorus cycles and reduces planetary atmospheres, is examined. The investigation of the phosphorus trifluoride (PF3) molecule explores its substituent effects. To generate a broad spectrum of molecular configurations, a specially tailored protocol for sampling and optimisation was implemented. The configurations were refined to uncover primary interaction patterns, and a clustering algorithm revealed unique interaction patterns. This report presents the energy stability and distribution of all the clusters. Our findings verify the prevalent presence of pnictogen bonds, identified by their geometric characteristics and co-occurrence with hydrogen bonds, which show an almost linear correlation. Another significant discovery is the correlation between various energy decomposition elements, especially regarding the electrostatic energy and overall binding energy. These results are anticipated to significantly contribute towards our comprehension of non-covalent interactions among phosphorus-containing molecules and the formulation of empirical models having physical interpretations.

Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds III: QM/MM MD simulations of solid-state systems at the example of layered carbon structures.

The previously introduced workflow to achieve an energetically and structurally optimized description of frontier bonds in quantum mechanical/molecular mechanics (QM/MM)-type applications was extended into the regime of computational material sciences at the example of a layered carbon model systems. Optimized QM/MM link bond parameters at HSEsol/6-311G(d,p) and self-consistent density functional tight binding (SCC-DFTB) were derived for graphitic systems, enabling detailed investigation of specific structure motifs occurring in graphene-derived structures quantum-chemical calculations. Exemplary molecular dynamics (MD) simulations in the isochoric-isothermic (NVT) ensemble were carried out to study the intercalation of lithium and the properties of the Stone-Thrower-Wales defect. The diffusivity of lithium as well as hydrogen and proton adsorption on a defective graphene surface served as additional example. The results of the QM/MM MD simulations provide detailed insight into the applicability of the employed link-bond strategy when studying intercalation and adsorption properties of graphitic materials.

The adaptive value of density-dependent habitat specialization and social network centrality

Density dependence is a fundamental ecological process. In particular, animal habitat selection and social behavior often affect fitness in a density-dependent manner. The Ideal Free Distribution (IFD) and niche variation hypothesis (NVH) present distinct predictions associated with Optimal Foraging Theory about how the effect of habitat selection on fitness varies with population density. Using caribou (Rangifer tarandus) in Canada as a model system, we test competing hypotheses about how habitat specialization, social behavior, and annual reproductive success (co)vary across a population density gradient. Within a behavioral reaction norm framework, we estimate repeatability, behavioral plasticity, and covariance among social behavior and habitat selection to investigate the adaptive value of sociality and habitat selection. In support of NVH, but not the IFD, we find that at high density habitat specialists had higher annual reproductive success than generalists, but were also less social than generalists, suggesting the possibility that specialists were less social to avoid competition. Our study supports niche variation as a mechanism for density-dependent habitat specialization.

Problems of recycling polystyrene plastics from waste electronic and electrical equipment (WEEE)

The problem of restoring the life cycle of polymers using the example of waste electronic and electrical equipment (WEEE) consists in carefully separating polymers by type and increasing the mechanical characteristics of polymers after their aging. It is shown that when separating polystyrene plastics based on impact-resistant polystyrene, the material also includes polyolefins, in particular, filled polypropylene. On this basis, a model system containing high-impact polystyrene and chalk-filled polypropylene was chosen. The effect of modifying additives such as SEBS, maleinated polystyrene and polypropylene on the physical and mechanical characteristics of impact-resistant polystyrene, including in the presence of filled polypropylene, has been studied. The influence of the composition of the composition on its thermal stability, as well as the thermal stability of industrial batches of secondary impact-resistant polystyrene from the WEEE has also been determined. As a result, using the example of a model system, ways of possible modifycation of the high-impact polystyrene from WEEE are shown in order to obtain a commercial product with improved characteristics.

Challenges and opportunities in piezoelectric polymers: Effect of oriented amorphous fraction in ferroelectric semicrystalline polymers

AbstractDespite extensive research on piezoelectric polymers since the discovery of piezoelectric poly(vinylidene fluoride) (PVDF) in 1969, the fundamental physics of polymer piezoelectricity has remained elusive. Based on the classic principle of piezoelectricity, polymer piezoelectricity should originate from the polar crystalline phase. Surprisingly, the crystal contribution to the piezoelectric strain coefficient d31 is determined to be less than 10%, primarily owing to the difficulty in changing the molecular bond lengths and bond angles. Instead, >85% contribution is from Poisson's ratio, which is closely related to the oriented amorphous fraction (OAF) in uniaxially stretched films of semicrystalline ferroelectric (FE) polymers. In this perspective, the semicrystalline structure–piezoelectric property relationship is revealed using PVDF‐based FE polymers as a model system. In melt‐processed FE polymers, the OAF is often present and links the crystalline lamellae to the isotropic amorphous fraction. Molecular dynamics simulations demonstrate that the electrostrictive conformation transformation of the OAF chains induces a polarization change upon the application of either a stress (the direct piezoelectric effect) or an electric field (the converse piezoelectric effect). Meanwhile, relaxor‐like secondary crystals in OAF (SCOAF), which are favored to grow in the extended‐chain crystal (ECC) structure, can further enhance the piezoelectricity. However, the ECC structure is difficult to achieve in PVDF homopolymers without high‐pressure crystallization. We have discovered that high‐power ultrasonication can effectively induce SCOAF in PVDF homopolymers to improve its piezoelectric performance. Finally, we envision that the electrostrictive OAF mechanism should also be applicable for other FE polymers such as odd‐numbered nylons and piezoelectric biopolymers.

Motion and mooring load responses of a novel 12 MW semi-submersible floating wind turbine: An experimental study

Abstract Due to the complexity of the integrated Floating Wind Turbine (FWT) system, obtaining reliable results necessitates extensive experiments. This paper conducts a comprehensive study on the motion performance and mooring load responses of a novel 12 MW semi-submersible FWT through model tests carried out in a wave basin. A multi-blade large-scale wind generation system, equipped with a rectifier network, was enhanced and constructed to provide a dependable wind field. And a flexible tower was designed and fabricated, achieving an accurate simulation of the tower's stiffness characteristic and its impact on the overall dynamic response. The marine environmental conditions encompass various combinations of wind, waves, and currents. Rigorous calibration and identification tests were undertaken to validate the environmental conditions and the model system. The findings reveal that, under mild wave parameters, the mooring load is primarily influenced by the resonance response with platform motions, particularly surge resonance. The load effect of wind and current induces mean surge and pitch motions, while their damping effect reduces the standard deviation of responses, notably suppressing the pitch response peak at its natural motion frequency. Wave loads predominantly dictate the vibration range of motion responses. When the current velocity reaches a sufficient magnitude, the coupling effect between current and wave in the wave-frequency region significantly amplifies the mooring response. Notably, motions and mooring loads in the 60° and 90° directions surpass those in the 0° direction, with the maximum responses occurring at 60°.

Long short-term memory (LSTM) neural networks for predicting dynamic responses and application in piezoelectric energy harvesting

Abstract Long Short-Time Memory (LSTM) deep neural networks are capable of learning order dependence in sequence problems and capturing long-term, non-linear temporal dependencies between the input and out of a system. With the long-term vision to model dynamical systems to which analytical or numerical methods are impossible or difficult to apply, this paper presents a study of modeling system dynamics and predicting responses using the LSTM networks, which have demonstrated excellent capability in predicting single-mode responses in a prior study. However, the LSTM network exhibits difficulties in modeling and predicting multi-mode responses accurately. To resolve the multi-mode issue, this paper presents an approach that obtains an equivalent network consisting of a set of sub-networks learned on isolated modes, and demonstrates its effectiveness on a simulated 2-degree-of-freedom (2DOF) mass-spring-damper system of nonlinear Duffing springs. The second part of the paper is focused on the application of the proposed approach in piezoelectric energy harvesting. Experiments are conducted on a harvester subjected to random base-motion excitation and exhibiting nonlinearity in its multi-mode response. Both the direct and mode-separation LSTM modeling approaches are applied to predict the output voltage given a random base-motion excitation. The mode-separation approach outperforms the direct approach significantly, and yields an excellent match between the actual and predicted responses. Specifically, for a test electrical voltage response of RMS value 0.2241 V, the difference between the actual test and predicted responses by using the mode-separation approach has an RMS value of 0.0504 V, compared to 0.1645 V obtained by using the direct LSTM approach. It is also much lower than the RMS value of 0.1835 V obtained by using the attention-based LSTM network, another comparison method. Leveraging a deep learning strategy, the validated approach opens up opportunities for accurately modeling energy harvesting systems of high complexities and/or strong nonlinearities.

Light‐Induced Dynamic Activation of Copper/Silicon Interface for Highly Selective Carbon Dioxide Reduction

Numerous studies have shown a fact that phase transformation and/or reconstruction are likely to occur and play crucial roles in electrochemical scenarios. Nevertheless, a decisive factor (such as facet, phase etc.) behind the diverse photoelectrochemical activity and selectivity of various copper/silicon photoelectrodes is still largely debated and missing in the community, especially for possibly dynamic behaviors of metal catalyst/semiconductor interface. Herein, through in situ X‐ray absorption spectroscopy and transmission electron microscope, a model system of Cu nanocrystals with well‐defined facets on black p‐type silicon (BSi) is demonstrated to unprecedentedly reveal the dynamic phase transformation of forming irreversible silicide at Cu nanocrystal‐BSi interface, which is validated to originate from the atomic interdiffusion between Cu and Si driven by light‐induced dynamic activation process. The presence of in situ formed silicide can significantly enhance photovoltage and deliver a record‐high onset potential above ‐0.4 V versus reversible reference electrode (RHE) for photoelectrochemical CH4 production. Significantly, the adaptive junction at Cu/Si interface is activated by an expansion of interatomic Cu‐Cu distance, which efficiently restricts the C‐C coupling pathway but strengthens the bonding with key intermediate of *CHO for CH4 yield, resulting in a remarkable 16‐fold improvement in the product ratio of CH4/C2 products.

Identification and Characterization of microRNAs in Morphological Color Change of Polychromatic Midas Cichlids (Amphilophus citrinellus)

As a representative genetic and economic trait, pigmentation has a strong impact on speciation and adaptation. However, information and reports on microRNAs (miRNAs) associated with pigmentation remain limited. The Midas cichlid fish, with three typical distinct stages of body color pattern, “black-gray-gold”, is an ideal model system for investigating pigmentation traits. In this study, miRNA libraries from scale tissues with the attached epidermis of Midas cichlids at three distinct stages of color transformation, black (B), transition (T), and gold (G), were sequenced using Illumina sequencing technology. In total, 53 (B vs. G), 88 (B vs. T), and 57 (T vs. G) miRNAs were differentially expressed between the respective groups. Target genes of the identified miRNAs were predicted, and the results showed that multiple target genes were related to pigmentation and pigment–cell differentiation. The miRNA–mRNA regulatory network suggests that miR-183-x and miR-133-x were predicted to be involved in regulating morphological color changes in Midas cichlids. The results advance our understanding of potential functions of miRNAs in skin pigment differentiation and early skin color fading of fishes.

Light-Induced Dynamic Activation of Copper/Silicon Interface for Highly Selective Carbon Dioxide Reduction.

Numerous studies have shown a fact that phase transformation and/or reconstruction are likely to occur and play crucial roles in electrochemical scenarios. Nevertheless, a decisive factor (such as facet, phase etc.) behind the diverse photoelectrochemical activity and selectivity of various copper/silicon photoelectrodes is still largely debated and missing in the community, especially for possibly dynamic behaviors of metal catalyst/semiconductor interface. Herein, through in situ X-ray absorption spectroscopy and transmission electron microscope, a model system of Cu nanocrystals with well-defined facets on black p-type silicon (BSi) is demonstrated to unprecedentedly reveal the dynamic phase transformation of forming irreversible silicide at Cu nanocrystal-BSi interface, which is validated to originate from the atomic interdiffusion between Cu and Si driven by light-induced dynamic activation process. The presence of in situ formed silicide can significantly enhance photovoltage and deliver a record-high onset potential above -0.4 V versus reversible reference electrode (RHE) for photoelectrochemical CH4 production. Significantly, the adaptive junction at Cu/Si interface is activated by an expansion of interatomic Cu-Cu distance, which efficiently restricts the C-C coupling pathway but strengthens the bonding with key intermediate of *CHO for CH4 yield, resulting in a remarkable 16-fold improvement in the product ratio of CH4/C2 products.

Basement Membranes, Brittlestar Tendons, and Their Mechanical Adaptability

Basement membranes (BMs) are thin layers of extracellular matrix that separate epithelia, endothelia, muscle cells, and nerve cells from adjacent interstitial connective tissue. BMs are ubiquitous in almost all multicellular animals, and their composition is highly conserved across the Metazoa. There is increasing interest in the mechanical functioning of BMs, including the involvement of altered BM stiffness in development and pathology, particularly cancer metastasis, which can be facilitated by BM destabilization. Such BM weakening has been assumed to occur primarily through enzymatic degradation by matrix metalloproteinases. However, emerging evidence indicates that non-enzymatic mechanisms may also contribute. In brittlestars (Echinodermata, Ophiuroidea), the tendons linking the musculature to the endoskeleton consist of extensions of muscle cell BMs. During the process of brittlestar autotomy, in which arms are detached for the purpose of self-defense, muscles break away from the endoskeleton as a consequence of the rapid destabilization and rupture of their BM-derived tendons. This contribution provides a broad overview of current knowledge of the structural organization and biomechanics of non-echinoderm BMs, compares this with the equivalent information on brittlestar tendons, and discusses the possible relationship between the weakening phenomena exhibited by BMs and brittlestar tendons, and the potential translational value of the latter as a model system of BM destabilization.

Proteomic reference map for sarcopenia research: mass spectrometric identification of key muscle proteins of organelles, cellular signaling, bioenergetic metabolism and molecular chaperoning.

During the natural aging process, frailty is often associated with abnormal muscular performance. Although inter-individual differences exit, in most elderly the tissue mass and physiological functionality of voluntary muscles drastically decreases. In order to study age-related contractile decline, animal model research is of central importance in the field of biogerontology. Here we have analyzed wild type mouse muscle to establish a proteomic map of crude tissue extracts. Proteomics is an advanced and large-scale biochemical method that attempts to identify all accessible proteins in a given biological sample. It is a technology-driven approach that uses mass spectrometry for the characterization of individual protein species. Total protein extracts were used in this study in order to minimize the potential introduction of artefacts due to excess subcellular fractionation procedures. In this report, the proteomic survey of aged muscles has focused on organellar marker proteins, as well as proteins that are involved in cellular signaling, the regulation of ion homeostasis, bioenergetic metabolism and molecular chaperoning. Hence, this study has establish a proteomic reference map of a highly suitable model system for future aging research.

Metal-induced Enhancement of Tetrel Bonding. The Case of C···X-IrIII (X = Cl, Br) Tetrel Bond Involving a Methyl Group.

In X-ray structures of the isomorphic mer-[IrX3(THT)(CNXyl)2] (X = Cl 1, Br 2; THT = tetrahydrothiophene; Xyl = 2,6-Me2C6H3-) complexes, we revealed short intermolecular contacts between the C-atom of an isocyanide methyl group and halide ligands of another molecule. Geometrical consideration of the X-ray data and analysis of appropriate DFT studies allowed the attribution of these contacts to CMe···X-IrIII (X = Cl, Br) tetrel bond. Specifically, through the application of DFT calculations and various theoretical models, the presence of tetrel bonding interactions was validated, and the contribution of the CMe···X-IrIII interaction was assessed. The reinforcement of the tetrel bond upon the isocyanide coordination to iridium(III) is substantiated by molecular electrostatic potential (MEP) surface calculations. To distinguish the tetrel bonding characteristics of CMe···X-IrIII (X = Cl, Br) interactions from conventional hydrogen bonding, we employed multiple computational methodologies, including Natural Bond Orbital (NBO) analysis and Electron Localization Function (ELF) analysis. Additionally, Energy Decomposition Analysis (EDA) was applied to selected model systems to explore the underlying physical nature of these interactions.

Diversity, evolution, and emergence of fish viruses.

The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission.

Pathogen-microbiome interactions and the virulence of an entomopathogenic fungus.

Entomopathogenic fungi play important roles in the population dynamics of many insect species. Understanding the factors shaping entomopathogen virulence is critical for agricultural management and for the use of fungi in pest biocontrol. We show that heritable bacteria in aphids, which confer protection to their hosts against fungal entomopathogens, influence virulence against subsequent hosts. Aphids reproduce asexually and are typically surrounded by genetically identical offspring, and thus these effects likely shape the dynamics of fungal disease in aphid populations. Furthermore, fungal entomopathogens are known to rapidly lose virulence in lab culture, complicating their laboratory use. We show that this phenomenon is not driven by changes in the associated bacterial microbiome. These results contribute to our broader understanding of the aphid model system and shed light on the biology of the Entomophthorales-an important but understudied group of fungi.

Electronic-grade epitaxial (111) KTaO3 heterostructures.

KTaO3 heterostructures have recently attracted attention as model systems to study the interplay of quantum paraelectricity, spin-orbit coupling, and superconductivity. However, the high and low vapor pressures of potassium and tantalum present processing challenges to creating heterostructure interfaces clean enough to reveal the intrinsic quantum properties. Here, we report superconducting heterostructures based on high-quality epitaxial (111) KTaO3 thin films using an adsorption-controlled hybrid PLD to overcome the vapor pressure mismatch. Electrical and structural characterizations reveal that the higher-quality heterostructure interface between amorphous LaAlO3 and KTaO3 thin films supports a two-dimensional electron gas with substantially higher electron mobility, superconducting transition temperature, and critical current density than that in bulk single-crystal KTaO3-based heterostructures. Our hybrid approach may enable epitaxial growth of other alkali metal-based oxides that lie beyond the capabilities of conventional methods.

Campylobacter jejuni and casein hydrolysate addition: Impact on poultry in vitro cecal microbiota and metabolome.

This study investigates the impact of casein hydrolysates on the poultry ceca inoculated with Campylobacter focusing on microbial molecular preferences for different protein sources in the presence of Campylobacter jejuni. Three casein sources (intact casein (IN), casein enzyme hydrolysate (EH), and casein acid hydrolysate (AH)) were introduced to cecal contents in combination with inoculated C. jejuni in an in vitro model system incubated for 48 h at 42°C under microaerophilic conditions. Samples were collected at 0, 24, and 48 h. Genomic DNA was extracted and amplified using custom dual-indexed primers, followed by sequencing on an Illumina MiSeq platform. The obtained sequencing data were then analyzed via QIIME2-2021.11. Metabolite extracts were analyzed with ultra-high-performance liquid orbitrap chromatography-mass spectrometry (UHPLC-MS). Statistical analysis of metabolites was conducted using MetaboAnalyst 5.0, while functional analysis was performed using Mummichog 2.0 with a significance threshold set at P < 0.00001. DNA sequencing and metabolomic analyses revealed that C. jejuni was most abundant in the EH group. Microbial diversity and richness improved in casein supplemented groups, with core microbial differences observed, compared to non-supplemented groups. Vitamin B-associated metabolites significantly increased in the supplemented groups, displaying distinct patterns in vitamin B6 and B9 metabolism between EH and AH groups (P < 0.05). Faecalibacterium and Phascolarctobacterium were associated with AH and EH groups, respectively. These findings suggest microbial interactions in the presence of C. jejuni and casein supplementation are influenced by microbial community preferences for casein hydrolysates impacting B vitamin production and shaping competitive dynamics within the cecal microbial community. These findings underscore the potential of nutritional interventions to modulate the poultry GIT microbiota for improved health outcomes.

Lower-Temperature Nucleation and Growth of Colloidal CdTe Quantum Dots Enabled by Prenucleation Clusters with Cd-Te Bond Conservation.

The reason why heating is required remains elusive for the traditional synthesis of colloidal semiconductor quantum dots (QDs) of II-VI metal chalcogenide (ME). Using CdTe as a model system, we show that the formation of Cd-Te covalent bonds with individual Cd- and Te-containing compounds can be decoupled from the nucleation and growth of CdTe QDs. Prepared at an elevated temperature, a prenucleation-stage sample contains clusters that are the precursor compound (PC) of magic-size clusters (MSCs); the Cd-Te bond formation occurs at temperatures higher than 120 °C in the reaction. Afterward, the PC-to-QD transformation appears via monomers at lower temperatures in dispersion. Our findings suggest that the number of Cd-Te bonds broken in the PC reactant is similar to that of Cd-Te bonds formed in the QD product. For the traditional synthesis of ME QDs, heating is responsible for the M-E bond formation rather than for nucleation.