Doctoral thesis 'Simulation of processes in cellular membranes' written!

I have just handed four copies of my doctoral thesis with the title ‘Simulation of processes in cellular membranes’ to the faculty. From today’s point of view, it was not such an easy task as it had looked like in the beginning. Collecting your work from the whole PhD study and summarize it in a compact and comprehensive way – easy, right? To me, the most complicated part was weaving it together so that it makes a single solid story. You can check yourself how much I have succeeded in that – the thesis is available here.

The contents of the thesis are well summarized in the preface:

My work is motivated by processes, which involve interactions of biologically relevant ions with cellular membranes. For instance in neurons, the fusion of synaptic vesicles containing neurotransmitter with neuronal cell membranes is controlled by a divalent cation calcium. This process is triggered by a change in the transmembrane potential across the neuronal plasma membrane, which is modulated by the exchange of the monovalent cations sodium and potassium. The transmembrane potential in atomistic simulations can be modeled by two approaches, the constant electric field method, and the ion-imbalance method. The methodological differences between them raise the following questions: Do they provide the same results? Can they be used interchangeably? What happens to the membrane under voltage?

Until recently, there was no consensus on the binding of sodium, potassium and calcium cations to biological membranes – simulations and some experiments do not reproduce other experiments From the point of simulations, all currently available models require improvements to reproduce quantitatively structures and interactions with cations. Here, the following questions arise: Is the missing electronic polarization in standard non-polarizable simulations responsible for the discrepancy? If yes, how crucial is it for the interactions of phospholipid bilayers with biologically relevant cations, and can it be effectively accounted for by rescaling charges? Can we obtain in this way realistic structures of phospholipid bilayers with interacting cations at atomistic resolution?

– PhD thesis ‘Simulation of processes in cellular membranes’.