The aim of this paper is to develop a broadly-applicable and self-consistent thin-film biphasic modelling framework for the full crawling cycle of a single animal cell. A hierarchy of thin-film two-phase 'reactive flow' models is derived; between them these cover a wide range of biologically relevant parameter regimes. The mathematical properties and biological implications of the resulting systems of high-order nonlinear degenerate parabolic-elliptic evolution equations are investigated. Linear-stability arguments suggest the formation of highly localized regions of high or low network density associated with small irregular oscillations or 'ruffling' of the plasma membrane. Local analyses at the contact line identify the classes of admissible contact-line conditions, through which we study for the first time the effect on the cell-scale motion of the 'mesoscopic' contact-line physics, which consists of the chemical and mechanical mechanisms for protrusive and retractive force generation near the outer cell periphery. One of the formulations is used to develop a minimal model for cell body translocation over a thin pseudopod, which predicts that myosin-driven contraction is not essential for rapid translocation. An analytic prediction for the translocation speed is given in terms of the network viscosity and slip coefficient (a parameter measuring the adhesion strength), of the membrane tension and of the thicknesses of the pseudopod and actin cortex; this is in good agreement with the translocation speed of osteoblasts on biomaterial substrates commonly used for orthopaedic implants. Limitations of the modelling approach and directions for future work are outlined.
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http://dx.doi.org/10.1093/imammb/dqh022 | DOI Listing |
J Am Chem Soc
January 2025
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States.
Direct translocation of RNA with secondary structures using single-molecule electrophoresis through protein nanopores shows significant fluctuations in the measured ionic current, in contrast to unstructured single-stranded RNA or DNA. We developed a multiscale model combining the oxRNA model for RNA with the 3-dimensional Poisson-Nernst-Planck formalism for electric fields within protein pores, aiming to map RNA conformations to ionic currents as RNA translocates through three protein nanopores: α-hemolysin, CsgG, and MspA. Our findings reveal three distinct stages of translocation (pseudoknot, melting, and molten globule) based on contact maps and current values.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Institute of Quantitative Biology, College of Life Sciences, and School of Physics, Zhejiang University, Hangzhou, Zhejiang 310058, China.
The emergence of nanopores in two-dimensional (2D) nanomaterials offers an attractive solid-state platform for high-throughput and low-cost DNA sequencing. However, several challenges remain to be addressed before their wide application, including the too-fast DNA translocation speed (compared to state-of-the-art single nucleoside detection techniques) and too large noise/signal ratios due to DNA fluctuations inside the nanopores. Here, we use molecular dynamics (MD) simulations to demonstrate the feasibility of utilizing RNA-DNA interactions in modulating DNA translocations in 2D MoS nanopores.
View Article and Find Full Text PDFClin Exp Pharmacol Physiol
March 2025
School of Physical Education, Hangzhou Normal University, Hangzhou, China.
Exercise activates autophagy and lysosome system in skeletal muscle, which are known to play an important role in metabolic adaptation. However, the mechanism of exercise-activated autophagy and lysosome system in obese insulin resistance remains covert. In this study, we investigated the role of exercise-induced activation of autophagy and lysosome system in improving glucose metabolism of skeletal muscle.
View Article and Find Full Text PDFJ Phys Chem Lett
January 2025
School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, People's Republic of China.
Efficient capture of single-stranded DNA (ssDNA) is crucial for high-throughput sequencing, which influences the speed and accuracy of genetic analysis. Electrophoresis (EP) and electro-osmotic flow (EOF) have a significant impact on the translocation behavior of ssDNA through the nanopore. Experimentally, dynamically tracking these two effects remains challenging, and conventional numerical methods also struggle to capture their dynamic properties in the presence of DNA.
View Article and Find Full Text PDFProtein translocation across cellular membranes is an essential and nano-scale dynamic process. In the bacterial cytoplasmic membrane, the core proteins in this process are a membrane protein complex, SecYEG, corresponding to the eukaryotic Sec61 complex, and a cytoplasmic protein, SecA ATPase. Despite more than three decades of extensive research on Sec proteins, from genetic experiments to cutting-edge single-molecule analyses, no study has visually demonstrated protein translocation.
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