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Molecular Dynamics Simulations of Fluid Lipid MembranesBrandt, Erik G. January 2011 (has links)
Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales. Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy. Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted. / QC 20111014 / Modelling of biological membranes
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Towards In Situ Studies of Polymer Dynamics and Entanglement under Shear through Neutron Spin Echo SpectroscopyKawecki, Maciej January 2015 (has links)
Entangled polymeric fluids subjected to shear display a stress plateau through a range of shear rates. The formation of this plateau is often attributed to an entanglement-disentanglement transition in scientific literature. However, to our best knowledge in situ studies recovering the intermediate scattering function of polymer dynamics under shear have until now never been performed. This thesis documents the successful development of a high viscosity shear device whose interaction with polarized neutrons is small enough to allow use for Neutron Spin Echo spectroscopy. Further, first measurements towards the direct observation of the variation of the degree of entanglement throughout increasing shear are documented, albeit yet for too short Fourier times to measure beyond Rouse dynamics.
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Temperature-dependent structure and dynamics of highly-branched poly(N -isopropylacrylamide) in aqueous solutionAl-Baradi, A.M., Rimmer, Stephen, Carter, Steven, de Silva, J.P., King, S.M., Maccarini, M., Farago, B., Noirez, L., Geoghegan, M. 28 May 2019 (has links)
Yes / Small-angle neutron scattering (SANS) and neutron spin-echo (NSE) have been used to investigate the temperature-dependent solution behaviour of highly-branched poly(N-isopropylacrylamide) (HB-PNIPAM). SANS experiments have shown that water is a good solvent for both HB-PNIPAM and a linear PNIPAM control at low temperatures where the small angle scattering is described by a single correlation length model. Increasing the temperature leads to a gradual collapse of HB-PNIPAM until above the lower critical solution temperature (LCST), at which point aggregation occurs, forming disperse spherical particles of up to 60 nm in diameter, independent of the degree of branching. However, SANS from linear PNIPAM above the LCST is described by a model that combines particulate structure and a contribution from solvated chains. NSE was used to study the internal and translational solution dynamics of HB-PNIPAM chains below the LCST. Internal HB-PNIPAM dynamics is described well by the Rouse model for non-entangled chains.
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