Bridging multiscale modeling of biomolecules and experiments through a user-friendly computational platform
Year: 2024
Type: dissertation
Abstract: Note: This version of the thesis is a revised edition of the original deposited at the Universidad Autónoma de Madrid's institutional repository, available at: http://hdl.handle.net/10486/716305.The present version includes improved formatting for better readability, minor typo corrections, and slight clarifications in some sections. For the official version, please refer to the university repository.Abstract: In this thesis, theoretical and computational physics are combined with experimental disciplines to study phenomena not only pertaining to physics but also to other sciences such as biology or chemistry. Any experimental technique can be understood as a process from which limited information is extracted from a complex system. This information, that integrates contributions from many degrees of freedom, is encrypted in a few experimental signals. This thesis offers computational and theoretical tools to reproduce experiments, which allow the inclusion of the degrees of freedom of the system at mesoscopic scales so that this information can be decrypted and the experimental signal can be related to the "microscopic" details and properties of the system. In particular, the thesis focuses on phenomena involving biological structures such as proteins, DNA, or viruses. Additionally, these tools are applied to the analysis of the atomic force microscope (AFM) and secondarily to other techniques such as optical tweezers (OT) or quartz crystal microbalance (QCM). The thesis is divided into four parts. In the first part, an introduction to the different theoretical tools employed is provided; specifically, we will discuss a list of models that allow various simplified representations of complex processes and structures. In the second part, we will introduce a set of computational tools designed to describe various types of interactions between mesoscopic (coarse-grained) entities with different degrees of resolution. This part of the thesis is organized with a hierarchy of decreasing complexity for the user, so that it shows i) how to efficiently implement new types of interactions on GPU architectures, ii) how to use the tools with a Python environment, and iii) how to use the tools from a web interface, introducing the essential information of each experimental system. Next, we show through a series of applied projects how to combine computational and theoretical tools with experiments to enhance our understanding and perform measurements of microscopic properties of certain biological structures. In particular, we will focus on how these systems achieve complex behaviors by modifying their mechanical properties. Finally, we list how these tools are currently being used in new projects by various research groups and present the conclusions.
Source: Hispana
Author: Ibáñez-Freire, Pablo
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6949451714
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