Green synthesis (GS), which utilizes natural products as precursors, is steadily gaining attention as a sustainable alternative to conventional chemical synthesis (CS). However, a proper and comprehensive interpretation of various synthesis parameters has not yet been established. This research aims to construct consistent and explainable GS results while highlighting the benefits of choosing GS over CS.
Natural precursor utilization
Alternative synthesis methods
Atom economy optimization
Toxicity assessment
Comparative lifecycle analysis (benchmarking)
Real-time monitoring
Scalability design
Phytochemistry
Sustainable design
GS exhibits better antibacterial activity (MIC) than CS against S. aureus.
Membrane disruption and ROS accumulation are more pronounced with GS due to the contribution of phytochemicals, which act as effective capping agents for AgNPs.
Both GS and CS show similar trends in AgNP size versus MIC; however, GS achieves a lower MIC for comparable particle sizes.
For CS, antibacterial efficacy against S. aureus declines significantly beyond 10 nm, whereas GS maintains effectiveness up to 30 nm.
The proposed silver precursor-to-extract dry weight ratio serves as an explainable synthesis parameter.
AgNP size exhibits a weak negative correlation with this parameter. It can be correlated to the fact that abundant phenolic compounds can affect AgNP size from the aggregation.
A strong correlation is observed between AgNP size and antibacterial activity (MIC value) against S. aureus, with efficacy dropping significantly for particle sizes above 30 nm.
The rise of organic electronics still faced many challenges to compete with inorganic counterparts. To advance the progress, computational simulation and modelling can help give insight to working principles and its design principle. However, structural diversity of molecular configuration such as orientation or distances can make traditional modelling difficult. It is due to the fact that intermolecular and intramolecular factors can critically influence electronic charge-transfer coupling. Although machine learning can be one of the solution, existing ML models still struggle with accuracy for complex structural variation and often trained with crystalline systems. This research aim to solve the problem using two-step machine learning; combining a model to predicts molecular orbitals of individual molecule fragments and second model to predict electronic coupling from MO overlap integrals.
Molecular orbital prediction
Machine learning framework development
Applications of physics-based metrics
Incorporates ab initio-level accuracy without direct quantum calculations for every new structure.
Accuracy improvement with 14- and 3-times lower (for ethylene dimers and naphthalene pairs) than previous methods.
Successfully handles amorphous-phase configurations.
Reducing reliance on large coupling-specific datasets by decoupling MO prediction from coupling calculation.
Demonstrate the feasibility of combining ML with physics based-metrics (e.g., overlap integral)
The G protein-coupled receptor (GPCR) superfamily is one of the largest and most diverse groups of proteins in the human genome. It plays a crucial role in cellular signaling and response to external stimuli. Unfortunately, existing databases like UniProt or GPCRdb still lack panoramic and interactive views of GPCR sequence-structure-function relationships. Moreover, due to the complex relationship within the GPCR family, it is difficult to classify new GPCR sequences and understand their roles within the superfamily network. Here, we provide a web-based graphical database: SeQuery; with multiple resolutions (individual, sequences, clusters, and families). The tools provide integrated GPCR sequences, structures, and functional annotations from various databases. Network analysis is calculated using BLASTp for similarity and distance, and minimum span clustering (MSC) to obtain cluster hierarchy at three resolution levels. Interactive visualization built with Cytoscape.js and centrality metrics used to identify key nodes in the network.
Database integration and management
Graph database development
Sequence similarity analysis
Bioinformatics tool development
Application of computational biology techniques
Correctly identified 99% GPCR sequences in validation test.
Constructed a network of 2841 GPCRs from >300 species, including receptors from all major classes.
Revealed hierarchical clustering of GPCRs into functional families (e.g., rhodopsin-like, taste receptor).
Quantified network centralities to identify "hub" which is critical for information flow.
Visualization can be viewed as bottom-up or top-down exploration.
Rapidly classify novel GPCR sequences.
Potential impact in investigating GPCR roles in diseases via network centrality analysis; accelerate drug discovery by mapping relationships between GPCR structure, function, and therapeutic potential; and applicable framework to other biological networks beyond GPCR.
Point-of-care detection can be important in an emergency or when an outbreak occurs. However, most high-end detection facilities require complex and relatively large devices with additional sample preparation that limits access to remote places. Using the surface plasmon resonance (SPR) principle, the research aims to build a portable, easy-to-use biosensor. Real-time detection can be achieved thanks to the output signal that can be interpreted directly with high detection sensitivity.
Biosensor development
Nanomaterials and surface chemistry
Optical engineering
Data analysis and modelling
Point-of-care diagnostics
Microfluidics
Significant time reduction for detection, from days in viral plaque assay to just a few minutes.
High sensitivity with EV71 and VP1 detection limit ~67 viral particles per mL in culture medium and ~4.8 pg per mL in PBS buffer.
Portable design of SPR system for more accessible and emergency settings.
Real-time monitoring without complex analysis of SPR signal output.
Improve practicality where additional assay or labeling is needed.