A new dynamical discrete/continuum solvation model was tested for NH(4)(+) and OH(-) ions in water solvent. The method is similar to continuum solvation models in a sense that the linear response approximation is used. However, different from pure continuum models, explicit solvent molecules are included in the inner shell, which allows adequate treatment of specific solute-solvent interactions present in the first solvation shell, the main drawback of continuum models. Molecular dynamics calculations coupled with SCC-DFTB method are used to generate the configurations of the solute in a box with 64 water molecules, while the interaction energies are calculated at the DFT level. We have tested the convergence of the method using a variable number of explicit water molecules and it was found that even a small number of waters (as low as 14) are able to produce converged values. Our results also point out that the Born model, often used for long-range correction, is not reliable and our method should be applied for more accurate calculations.
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Comput Biol Med
February 2025
Multiscale in Mechanical and Biological Engineering (M2BE), Engineering Research Institute of Aragon (I3A), Department of Mechanical Engineering, Universidad de Zaragoza, Zaragoza, 50018, Spain. Electronic address:
Mechanical signals are crucial in regulating the response of cells in a monolayer to both physiological and pathological stressors, including intracellular bacterial infections. In particular, during intracellular infection of epithelial cells in monolayer with the food-borne bacterial pathogen Listeria monocytogenes, cellular biomechanics dictates the degree of bacterial dissemination across the monolayer. This occurs through a process whereby surrounder uninfected cells mechanically compete and eventually extrude infected cells.
View Article and Find Full Text PDFMath Biosci Eng
July 2024
Stanford University Online High School, 415 Broadway Academy Hall, Floor 2, 8853,415 Broadway, Redwood City, CA 94063, USA.
Tumor growth dynamics serve as a critical aspect of understanding cancer progression and treatment response to mitigate one of the most pressing challenges in healthcare. The in silico approach to understanding tumor behavior computationally provides an efficient, cost-effective alternative to wet-lab examinations and are adaptable to different environmental conditions, time scales, and unique patient parameters. As a result, this paper explored modeling of free tumor growth in cancer, surveying contemporary literature on continuum, discrete, and hybrid approaches.
View Article and Find Full Text PDFJ Theor Biol
November 2023
Department of Mechanical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran.
One of the most commonly used approaches for treating solid tumors is the systemic delivery of chemotherapeutic drugs. However, our understanding of the factors influencing treatment efficacy through this method is still limited. This study presents a comprehensive and realistic mathematical model that incorporates the dynamics of tumor growth, capillary network extension, and drug delivery in a coupled and simultaneous manner.
View Article and Find Full Text PDFBiology (Basel)
June 2023
School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, IN 47907, USA.
Convective transport of drug solutes in biological tissues is regulated by the interstitial fluid pressure, which plays a crucial role in drug absorption into the lymphatic system through the subcutaneous (SC) injection. In this paper, an approximate continuum poroelasticity model is developed to simulate the pressure evolution in the soft porous tissue during an SC injection. This poroelastic model mimics the deformation of the tissue by introducing the time variation of the interstitial fluid pressure.
View Article and Find Full Text PDFPhotochem Photobiol
July 2023
Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Naples, Italy.
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