Quantifying topological transformation in lipid self-assemblies

Endter, Laura Josefine

Free-Energy Calculations in Complex Systems

dc.contributor.advisor	Risselada, Herre Jelger Dr.
dc.contributor.author	Endter, Laura Josefine
dc.date.accessioned	2021-06-03T09:29:13Z
dc.date.available	2021-06-09T00:50:09Z
dc.date.issued	2021-06-03
dc.identifier.uri	http://hdl.handle.net/21.11130/00-1735-0000-0008-5841-C
dc.identifier.uri	http://dx.doi.org/10.53846/goediss-8636
dc.language.iso	eng	de
dc.relation.uri	http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject.ddc	571.4	de
dc.title	Quantifying topological transformation in lipid self-assemblies	de
dc.title.alternative	Free-Energy Calculations in Complex Systems	de
dc.type	cumulativeThesis	de
dc.contributor.referee	Risselada, Herre Jelger Dr.
dc.date.examination	2021-05-21
dc.description.abstracteng	Surfactant assemblies are characterized by soft intermolecular interactions and can be deformed or topologically altered by thermal or mechanical stress of the magnitude of thermal fluctuations. In biology, the protein mediated remodeling of the lipid membrane is essential for many cellular processes such as membrane fission, fusion, formation of lipid droplets or cell lysis. Quantifying the free-energy differences between end states of formed intermediates can provide valuable insights into the potential roles and mechanisms of cellular remodeling proteins. The aim of this project was to develop and apply a versatile free-energy calculation protocol to enable the estimation of free-energy differences between meta-stable states of lipid assemblies. We propose a novel method coined ‘Density Field Thermodynamic Integration’ (DFTI) which adopts the universality and transferability of alchemical methods while simultaneously exploiting the soft excess interactions between surfactant molecules. DFTI is designed for a rapid quantification of the free energy differences between different metastable structures in soft, fluid materials. Combining thermodynamic integration, one of the most established free-energy methods with a density-based external potential, offers the possibility to outline morphologies along a reversible path connecting two meta-stable states. The same holds true for the string method adaptation used in this work, which was first used in this combination by Smirnova et al. to calculate the minimum free energy path (MFEP) for stalk formation between two apposing membranes and the influence of the presence of SNARE transmembrane domains. Both methods were tested on three example systems: the breaking of a worm-like micelle and a toroidal micelle and the formation of a stalk. In all cases DFTI and string method yielded comparable results. This work explores the usage of density field based free energy methods in its predictive power and limitations. In addition, lipid droplets, as an example for membranes as active players in biological processes, are investigated with a focus on their emergence and the role of the related protein seipin.	de
dc.contributor.coReferee	Steinem, Claudia Prof. Dr.
dc.subject.eng	free energy	de
dc.subject.eng	string method	de
dc.subject.eng	lipid droplets	de
dc.subject.eng	Molecular Dynamics Simulations	de
dc.subject.eng	Computer Simulations	de
dc.subject.eng	bola lipids	de
dc.subject.eng	density-field	de
dc.subject.eng	thermodynamic integration	de
dc.identifier.urn	urn:nbn:de:gbv:7-21.11130/00-1735-0000-0008-5841-C-9
dc.affiliation.institute	Göttinger Graduiertenschule für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB)	de
dc.subject.gokfull	Biologie (PPN619462639)	de
dc.description.embargoed	2021-06-09
dc.identifier.ppn	1759780979

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GGNB - Göttinger Graduiertenzentrum für Neurowissenschaften, Biophysik und molekulare Biowissenschaften [1016]
GGNB - Göttingen Graduate Center for Neurosciences, Biophysics and Molecular Biosciences

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