Directed cell migration requires a spatially polarized distribution of polymerized actin. We develop and treat a mechanical model of cell polarization based on polymerization and depolymerization of actin filaments at the two ends of a cell, modulated by forces at either end that are coupled by the cell membrane. We solve this model using both a simulation approach that treats filament nucleation, polymerization, and depolymerization stochastically, and a rate-equation approach based on key properties such as the number of filaments N and the number of polymerized subunits F at either end of the cell. The rate-equation approach agrees closely with the stochastic approach at steady state and, when appropriately generalized, also predicts the dynamic behavior accurately. The calculated transitions from symmetric to polarized states show that polarization is enhanced by a high free-actin concentration, a large pointed-end off-rate, a small barbed-end off-rate, and a small spontaneous nucleation rate. The rate-equation approach allows us to perform a linear-stability analysis to pin down the key interactions that drive the polarization. The polarization is driven by a positive-feedback loop having two interactions. First, an increase in F at one side of the cell lengthens the filaments and thus reduces the decay rate of N (increasing N); second, increasing N enhances F because the force per growing filament tip is reduced. We find that the transitions induced by changing system properties result from supercritical pitchfork bifurcations. The filament lifetime depends strongly on the average filament length, and this effect is crucial for obtaining polarization correctly.
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http://dx.doi.org/10.1088/1478-3975/11/6/066002 | DOI Listing |
ACS Omega
November 2024
Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States.
Although methods to derive the rate equation from a kinetic model have been known for over a century, it remains mathematically challenging to derive the rate equation for complex reactions involving multiple steps, as the derivation requires a solution for simultaneous differential equations. Furthermore, the derived kinetic equations are often difficult to intuitively understand. Here, we report a radically different approach to analyze chemical kinetics using the mean reaction time, the average of the time required for the completion of a chemical reaction.
View Article and Find Full Text PDFJ Chem Theory Comput
November 2024
High Performance Artificial Intelligence Systems Research Team, RIKEN Center for Computational Science, 7 Chome-1-26 Minatojima Minamimachi, Kobe, Hyogo 650-0047, Japan.
Radical pairs (electron-hole pairs, polaron pairs) are transient reaction intermediates that are found and exploited in all areas of science, from the hard realm of physics in the form of organic semiconductors, spintronics, quantum computing, and solar cells to the soft domain of chemistry and biology under the guise of chemical reactions in solution, biomimetic systems, and quantum biology. Quantitative analysis of radical pair phenomena has historically been successful by a few select groups. With this in mind, we present an intuitive open-source framework in the Python programming language that provides classical, semiclassical, and quantum simulation methodologies.
View Article and Find Full Text PDFDalton Trans
October 2024
School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.
The development of hydrogen energy is widely recognized as a key approach to addressing the energy and carbon emission challenges. Methanol steam reforming is a promising hydrogen production scheme that can provide high-purity hydrogen. In this work, we studied the primary reaction mechanisms of methanol steam reforming over the Cu(111) and Cu(211) surfaces using density functional theory (DFT) calculations and microkinetic simulations.
View Article and Find Full Text PDFACS Omega
September 2024
Department of Chemistry, National Changhua University of Education, 1 Jin-De Road, Changhua City 50007, Taiwan.
This study introduces a novel one-pot method employing tannic acid (TA) to synthesize stable gold nanoparticles (TA-AuNPs), which are characterized using transmission electron microscopy, X-ray powder diffraction, and Fourier transform infrared spectroscopy. We apply these TA-AuNPs in a newly developed colorimetric assay for hydrogen peroxide (HO) detection that utilizes the oxidation of iodide (I) on TA-AuNPs, leading to a detectable yellow color change in the solution. The reaction kinetics are captured by the rate equation R = 0.
View Article and Find Full Text PDFEur J Pharm Biopharm
November 2024
Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. Electronic address:
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