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http://cimat.repositorioinstitucional.mx/jspui/handle/1008/983| General methodology to generate atomic-based volumetric meshes of the capsid of icosahedral viruses and its application to study their mechanical properties | |
| JOSE LUIS ALONZO VELAZQUEZ | |
| Acceso Abierto | |
| Atribución-NoComercial | |
| Motivated by the studies of mechanical properties of viral capsids by nanoindentation, using both biophysical and computational approximations, here we propose an alternative methodology to generate robust viral capsid meshes suitable for numerical simulations of the nanoindentation process. Our proposal takes advantage of the intrinsic symmetry of icosahedral viral capsids. Nanoindentation is the most common test to study macromolecular mechanical properties. A powerful experimental technique is the atomic force microscopy (AFM). It allows to probe a single viral particle and measure the deformation produced by a given force. AFM consists of a cantilever with a sharp tip (probe) at its end, that typically is used to scan the specimen's surface. When the tip is brought into proximity of a sample surface, forces between the tip and the sample lead to a de ection of the cantilever (according to Hooke's law for small deformations). Depending on the situation, forces that are measured in AFM include mechanical contact force, van der Waals forces, capillary forces, etc. Typically, the de ection is measured using a laser spot re ected from the top surface of the cantilever into an array of photodiodes. Structural insights of viral particles have been provided by experiments using the AFM technique. Nanoindentation results show the relation between the applied force and the resulting deformation of viral capsids, which provide an appropriate framework to validate theoretical predictions, e. g., numerical simulations. From such theoretical standpoint, it has become possible in recent years to study whole viruses by Molecular Dynamics (MD) methods, employing all-atom models. In particular, the nanoindentation experiments performed on the Cowpea Chlorotic Mottle Virus (CCMV), a T=3 phytopathogen, have been partially reproduced computationally using coarse-grain models and elastic network approximations. However, such models have a very high computational cost. As an alternative, the Finite Element Method (FEM) is a promising and less costly approach, but requires meshes with specic properties of regularity. While there are various algorithms that generate molecular surfaces, the triangular meshes they generate are optimized for visualization, but are not suitable for FEM. Other procedures to generate molecular volumetric meshes use surface meshes which are then lled up as non-structured meshes using third-party software. Building the viral capsid mesh for an icosa | |
| 10-05-2018 | |
| Tesis de doctorado | |
| INFORMÁTICA | |
| Versión aceptada | |
| acceptedVersion - Versión aceptada | |
| Aparece en las colecciones: | Tesis del CIMAT |
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| Fichero | Descripción | Tamaño | Formato | |
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| TE 708.pdf | 23.31 MB | Adobe PDF | Visualizar/Abrir |