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Several factors affect the passive membrane permeation of small molecules, including size, charge, pH, or the presence of specific chemical groups. Understanding these features is paramount to identifying or designing drug candidates with optimal ADMET properties and this can be achieved through experimental/knowledge-based methodologies or using computational approaches. Empirical methods often lack detailed information about the underlying molecular mechanism. In contrast, Molecular Dynamics-based approaches are a powerful strategy, providing an atomistic description of this process. This technique is continuously growing, featuring new related methodologies. In this work, the recent advances in this research area will be discussed.
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http://dx.doi.org/10.1016/j.bbadva.2023.100099 | DOI Listing |
Pest Manag Sci
September 2025
Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
Background: Elucidating the species selectivity mechanism of succinate dehydrogenase (SDH) inhibitors (SDHIs) is crucial for the discovery novel eco-friendly SDHI fungicides. Fluxapyroxad (FLX), a representative SDHI, was investigated through in silico study to identify species-specific differences in its binding modes with SDH.
Results: SDH structure models of six species were constructed, and the model predicted by Discovery Studio 3.
Nat Biomed Eng
September 2025
Developmental, Stem Cell and Cancer Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
Biofluid flow generates fluid shear stress (FSS), a mechanical force widely present in the tissue microenvironment. How brain tumour growth alters the conduit of biofluid and impacts FSS-regulated cancer progression is unknown. Dissemination of medulloblastoma (MB) cells into the cerebrospinal fluid initiates metastasis within the central nervous system.
View Article and Find Full Text PDFGlycobiology
August 2025
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
Glycans are complex carbohydrates that exhibit extraordinary structural complexity and stereochemical diversity while playing essential roles in many biological processes, including immune regulation, pathogen recognition, and cell communication. In humans, more than half of all proteins are glycosylated, particularly those in secretory and membrane-associated pathways, highlighting the importance of glycans in health and disease. The recent release of the AlphaFold 3 source code enables customizable modeling not only of proteins but also glycan-containing biomolecular complexes.
View Article and Find Full Text PDFPhys Chem Chem Phys
August 2025
Institute of Theoretical and Computational Chemistry, Heinrich-Heine University, Düsseldorf, Germany.
Quasiclassical methods for nonadiabatic molecular dynamics, based on Mayer-Miller-Stock-Thoss mapping, are implemented in the open source computer package PySurf. This complements the implementation of surface hopping approaches performed in previous studies, and leads to a unified code that allows nonadiabatic dynamics simulations using various mapping approaches (Ehrenfest dynamics, the linearised semiclassical initial value representation, the Poisson-bracket mapping equation, the "unity" approach for the identity operator, the spin mapping, and the symmetrical quasiclassical windowing method) as well as different flavours of surface hopping (fewest-switches, Landau-Zener, and a mapping-inspired scheme). Furthermore, a plugin is developed to provide diabatic vibronic models as input in a sum-of-products form.
View Article and Find Full Text PDFPhys Rev E
July 2025
Georgia Institute of Technology, George W. Woodruff School of Mechanical Engineering, Atlanta, Georgia 30332, USA.
In this work, the conformational dynamics of the von Willebrand Factor (vWF) are investigated as it encounters localized regions of high shear and extensional forces in a converging/diverging channel. Using direct numerical simulations that employ two-way coupling between a lattice Boltzmann fluid solver and a Langevin dynamics-based bead-spring model for vWF, we study how flow-induced forces influence the spatiotemporal evolution of molecular unfolding. Unlike studies that rely on statistical models or averaged behavior, our approach captures transient and configuration-specific unfolding events that arise from the interplay between molecular conformation and flow-field structure.
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