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Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting up and using membrane simulations can come with barriers due to the multidisciplinary effort involved and the vast choice of existing simulations models. In this review, we introduce the non-expert reader to coarse-grained membrane simulations at the mesoscale. Firstly, we give a concise overview of the modelling approaches to study fluid membranes, together with guidance to more specialized references. Secondly, we provide a conceptual guide on how to develop mesoscale membrane simulations. Lastly, we construct a hands-on tutorial on how to apply mesoscale membrane simulations, by providing a pedagogical examination of membrane tether pulling, shape and mechanics of membrane tubes, and membrane fluctuations with three different membrane models, and discussing them in terms of their scope and how resource-intensive they are. To ease the reader's venture into the field, we provide a repository with ready-to-run tutorials.
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http://dx.doi.org/10.1039/d5sm00148j | DOI Listing |
Medicine (Baltimore)
September 2025
Department of Thoracic Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu, P.R. China.
Resveratrol is a natural polyphenol known for its antioxidant and anti-inflammatory effects, but its role in lung adenocarcinoma (LUAD) remains unclear. Our study integrated network pharmacology, molecular docking, and bioinformatics to investigate the molecular mechanisms by which resveratrol suppresses LUAD through the identification of key targets and pathways. We identified 100 resveratrol-related targets and 50,000 LUAD-related genes from databases, finding 98 overlapping targets.
View Article and Find Full Text PDFFood Res Int
November 2025
School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China; Shaanxi Research Institute of Agricultural Products Processing Technology, Xi'an 710021, China. Electronic address:
Goat milk is prized for its nutritional value, but the illegal addition of δ-decanolactone to enhance flavor poses risks to product integrity and safety. This study employed a tripartite multi-omics framework integrating metabolomics, lipidomics, and proteomics, combined with FTIR and CLSM to systematically elucidate the multifaceted effects of δ-decanolactone on goat milk. Chemometric and bioinformatic pipelines identified dysregulated molecules and pathways, while molecular docking validated interactions with key targets.
View Article and Find Full Text PDFFood Res Int
November 2025
State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China. Electronic address:
Osteopontin (OPN), a multifunctional milk protein essential for bioactive functions, remains challenging to isolate efficiently due to the limited specificity of conventional methods. We developed hydrogel-based molecularly imprinted membranes (MIMs) for selective OPN recognition. Dimethylaminopropyl methacrylamide (DMAPMA) and N-isopropylacrylamide (NIPAM) were selected as functional monomers based on molecular docking and molecular dynamics (MD) simulations, ensuring optimized binding interactions.
View Article and Find Full Text PDFJ Phys Chem B
September 2025
School of Science, RMIT University, Melbourne 3000, Australia.
Pentameric ligand-gated ion channels control synaptic neurotransmission via an allosteric mechanism, whereby agonist binding induces global protein conformational changes that open an ion-conducting pore. For the proton-activated bacterial () ligand-gated ion channel (GLIC), high-resolution structures are available in multiple conformational states. We used a library of atomistic molecular dynamics (MD) simulations to study conformational changes and to perform dynamic network analysis to elucidate the communication pathways underlying the gating process.
View Article and Find Full Text PDFNano Lett
September 2025
State Key Laboratory of Materials Low-Carbon Recycling, College of Materials Science and Engineering, Beijing University of Technology, Beijing 100124, P. R. China.
Two-dimensional (2D) nanofluidic architectures with nanoconfined interlayer channels and excess surface charges have revolutionized membrane-based reverse electrodialysis systems, demonstrating highly efficient osmotic energy collection through strong electrostatic screening of electric double layer (EDL). However, the ion-transport dynamics in 2D nanofluidic anion-selective membranes (2D-NAMs) still remain unexplored. Here, we combine density functional theory and molecular dynamics (MD) simulations to systematically explore ion transport in the 2D-NAMs.
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