In-silico Modeling of Lipid-Water Complexes and Lipid Bilayers

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Title: In-silico Modeling of Lipid-Water Complexes and Lipid Bilayers
Authors: Jadidi, Tayebeh
Thesis advisor: Prof. Dr. Philipp Maass
Thesis referee: Prof. Dr. Mohammad Reza Rahimitabar
Abstract: In the first part of the thesis, the molecular structure and electronic properties of phospholipids at the single molecule level and also for a monolayer structure are investigated via ab initio calculations under different degrees of hydration. The focus of the study is on phosphatidylcholines, in particular dipalmitoylphosphatidylcholine (DPPC), which are the most abundant phospholipids in biological membranes. Upon hydration, the phospholipid shape into a sickle-like structure. The hydration dramatically alters the surface potential, dipole and quadrupole moments of the lipids, and probably guides the interactions of the lipids with other molecules and the communication between cells. The vibrational spectrum of DPPC and DPPC-water complexes are completely assigned and it is shown that water hydrating the lipid head groups enables efficient energy transfer across membrane leaflets on sub-picosecond time scales. Moreover, the vibrational modes and lifetimes of pure and hydrated DPPC lipids, at human body temperature, are estimated by performing ab initio molecular dynamics simulations. The vibrational modes of the water molecules close to the head group of DPPC are active in the frequency range between 0.5 - 55 THz, with a peak at 2.80 THz in the energy spectrum. The computed lifetimes for the high-frequency modes agree well with recent data measured at room temperature, where high-order phonon scattering is not negligible. The structure and auto-ionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation and generalized gradient approximation for the exchange-correlation energy functional. Depending on the lipid head group, strongly enhanced ionization is observed, leading to dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally. In the second part of the thesis, Monte Carlo simulations of the lipid bilayer, on the basis of a coarse grained model, are performed to gain insight into the mechanical properties of planar lipid bilayers. By using a rescaling method, the Poisson's ratio is calculated for different phases. Additional information on the bending rigidity, determined from height fluctuations on the basis of the Helfrich Hamiltonian, allows for calculation of the Young's modulus for each phase. In addition, the free energy barrier for lipid flip-flop process in the fluid and gel phases are estimated. The main rate-limiting step to complete a flip-flop process is related to a free energy barrier that has to be crossed in order to reach the center of the bilayer. The free energy cost for performing a lipid flip-flop in the gel phase is found to be five times greater than in the fluid phase, demonstrating the rarity of such events in the gel phase. Moreover, an energy barrier is estimated for formation of transient water pores that often precedes lipid translocation events and accounts for the rate-limiting step of these pore-associated lipid translocation processes.
Subject Keywords: Lipid; Lipid Bilayers; phospholipids; DPPC; DPPE; Electronic Structure; Water autoionization; Vibrational dynamics; Spectral energy density; Electronic density of state; Phonon density of state; Vibrational lifetime; AIMC; AIMD; Lipid-water coupling; Ab-initio modeling; Coarse-grained simulation; Poisson’s ratio; Young’s modulus; Lipid flip flop; Pore formation; Free energy estimation; Electric dipole moment; Electric quadrupole moment
Issue Date: 21-Oct-2013
License name: Namensnennung - Nicht-kommerziell - Weitergabe unter gleichen Bedingungen 3.0 Unported
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Type of publication: Dissertation oder Habilitation [doctoralThesis]
Appears in Collections:FB04 - E-Dissertationen

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