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Physics-Based and Data-Driven Mulitiscale Modeling of the Structural Formation in Macromolecular Systems

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Physics-Based and Data-Driven Mulitiscale Modeling of the Structural Formation in Macromolecular Systems (Volume 25) (English shop)

Philipp Nicolas Depta (Author)


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Table of Contents, PDF (51 KB)

ISBN-13 (Hard Copy) 9783736979727
ISBN-13 (eBook) 9783736969728
Language English
Page Number 296
Lamination of Cover matt
Edition 1.
Book Series SPE-Schriftenreihe
Volume 25
Publication Place Göttingen
Place of Dissertation TU Hamburg
Publication Date 2024-02-27
General Categorization Dissertation
Departments Biochemistry, molecular biology, gene technology
Mechanical and process engineering
Keywords multiscale modeling, molecular modeling, Molecular Discrete Element Method, MDEM, Discrete Element Method, DEM, coarse-graining, Molecular Dynamics, MD, Langevin dynamics, machine learning, ML, supervised learning, Kriging, macromolecular self-assembly, structural formation simulation, anisotropic macromolecules, assembly pathways, assembly kinetics, molecular collisions, 6D intermolecular interaction potentials, specialized force-fields, molecular binding, bonded interaction, hepatitis B core antigen, HBcAg, capsid formation, virus-like particles, VLP, pyruvate dehydrogenase complex, PDC, alginate, alginic acid, biopolymer, gelation, gel, aerogel, porous nanomaterial, anisotropic diffusion, ion binding model, calcium, proteins, enzymes, multi-enzymatic biocatalysis, metabolic channeling, high performance computing, HLRS, GPU implementation, MUSEN

In order to improve knowledge on macromolecular structural formation and self-assembly, this work proposes a physics-based and data-driven multiscale modeling framework capable of describing structural formation on micro-meter and milli-second scales near molecular-level precision. The framework abstracts macromolecules as anisotropic unit objects and models the interactions and environment using data-driven approaches. The models are parameterized in a bottom-up fashion and validated top-down by comparison with literature and collaborator data for self-assembly of three model system: alginate gelation, hepatitis B virus capsids, and the pyruvate dehydrogenase complex.