| dc.contributor.advisor | Risselada, Herre Jelger Prof. Dr. | |
| dc.contributor.author | Stroh, Kai Steffen | |
| dc.date.accessioned | 2023-12-11T10:36:19Z | |
| dc.date.available | 2023-12-18T00:54:52Z | |
| dc.date.issued | 2023-12-11 | |
| dc.identifier.uri | http://resolver.sub.uni-goettingen.de/purl?ediss-11858/15024 | |
| dc.identifier.uri | http://dx.doi.org/10.53846/goediss-10236 | |
| dc.format.extent | 113 | de |
| dc.language.iso | eng | de |
| dc.subject.ddc | 530 | de |
| dc.title | Biomolecular space exploration - Phase space and parameter space sampling in realistic protein-lipid environments | de |
| dc.type | cumulativeThesis | de |
| dc.contributor.referee | Risselada, Herre Jelger Prof. Dr. | |
| dc.date.examination | 2023-01-23 | de |
| dc.subject.gok | Physik (PPN621336750) | de |
| dc.description.abstracteng | Lipid composition affects membrane properties and specifically adapted compositions allow biomembranes to fulfill their functions. By altering membrane properties lipids regulate biological processes. Specifically, membrane curvature and the related lipid packing defects, i.e., hydrophobic regions exposed to the environment, play an essential role in the organization and trafficking of membrane associated proteins. In Chapter 2 a free-energy calculation method is presented that allows the direct quantification of the relative partitioning free energy of proteins as a function of membrane curvature from molecular dynamics simulations.
As lipid diversity profoundly affects biological processes, a broad range of computational studies, where membrane-related effects play a role, rely on a large variety of lipid models to accurately recreate specific types of membranes. The endeavor for more realistic membrane models has received significant attention in recent years, but molecule parameterization can be a time consuming task when done by human labor. In Chapter 3 a framework for automated molecule parameterization in building-block force fields is presented. This framework, termed CGCompiler, utilizes mixed-variable particle swarm optimization in conjunction with molecular dynamics simulations to optimally select force field parameters. As a demonstration of the algorithm, the lipid sphingomyelin is parameterized within the Martini 3 coarse-grained force field, matching both structural as well as thermodynamic target data. | de |
| dc.contributor.coReferee | Klumpp, Stefan Prof. Dr. | |
| dc.subject.eng | simulations | de |
| dc.subject.eng | optimization | de |
| dc.subject.eng | lipids | de |
| dc.subject.eng | free energy | de |
| dc.subject.eng | proteins | de |
| dc.subject.eng | membranes | de |
| dc.identifier.urn | urn:nbn:de:gbv:7-ediss-15024-6 | |
| dc.affiliation.institute | Fakultät für Physik | de |
| dc.description.embargoed | 2023-12-18 | de |
| dc.identifier.ppn | 1873100302 | |
| dc.notes.confirmationsent | Confirmation sent 2023-12-11T11:15:01 | de |