Molecular Dynamics Simulations of Phospholipid Bilayers with Cholesterol

AbstractTo investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0–40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations—corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols

How to Apply Assignment Methods that were Developed for Vehicular Traffic to Pedestrian Microsimulations

Applying assignment methods to compute user-equilibrium route choice is very common in traffic planning. It is common sense that vehicular traffic arranges in a user-equilibrium based on generalized costs in which travel time is a major factor. Surprisingly travel time has not received much attention for the route choice of pedestrians. In microscopic simulations of pedestrians the vastly dominating paradigm for the computation of the preferred walking direction is set into the direction of the (spatially) shortest path. For situations where pedestrians have travel time as primary determinant for their walking behavior it would be desirable to also have an assignment method in pedestrian simulations. To apply existing (road traffic) assignment methods with simulations of pedestrians one has to reduce the nondenumerably many possible pedestrian trajectories to a small subset of routes which represent the main, relevant, and significantly distinguished routing alternatives. All except one of these routes will mark detours, i.e. not the shortest connection between origin and destination. The proposed assignment method is intended to work with common operational models of pedestrian dynamics. These - as mentioned before - usually send pedestrians into the direction of the spatially shortest path. Thus, all detouring routes have to be equipped with intermediate destinations, such that pedestrians can do a detour as a piecewise connection of segments on which they walk into the direction of the shortest path. One has then to take care that the transgression from one segment to the following one no artifacts are introduced into the pedestrian trajectory.Comment: contribution to PANAM 2014 conferenc

Grid based energy system setup optimisation with Rivus in dedicated regions

Within the project IDEE (Integrated Design Efficient Energy systems in urban regions) the expertise of four cross-border (Italia & Austria) research centres and one public authority is bundled up to support the planning of new setups or the extension of existing setups in grid based sustainable energy systems for pilot regions inside the project areas. A special focus within the project is the optimization of network topologies in district heating setups. First scenarios on possible system setups for the pilot regions have been calculated outlining the topology of optimal pipe setups as well as the load of (Heat-) pipes at different time steps with the objective to minimise overall system costs. Keywords: District heating, Optimization, Network calculation, MIL

Microscale CFD Simulations of a Wind Energy Test Site in the Swabian Alps with Mesoscale Based Inflow Data

The current study describes analyses of the WINSENT wind energy test site located in complex terrain in Southern Germany by highly resolved numerical simulations. The resolved atmospheric turbulence is simulated with Delayed Detached Eddy Simulations by the flow solver FLOWer without consideration of the research wind turbines. The mean inflow and wind direction of the analysed time period is provided by precursor simulations of project partners. The simulation model chain consists of three codes with different time scales and resolutions. The model chain provides a data transfer from mesoscale WRF simulations to OpenFOAM. As a next step OpenFOAM provides inflow data in the valley of the terrain site for the present FLOWer simulations, the code with the highest resolution in space and time. The mean velocity field provided by OpenFOAM is superimposed with fluctuations that are based on measurements to obtain the small turbulent scales within the FLOWer simulations, which the previous tools of the model chain can not resolve. Comparisons with the two already installed met masts clarify that the current FLOWer simulations provide an adequate agreement with measured data. The results are verified with the application of a second simulation, in which a homogeneous velocity profile is superimposed with turbulence. Thus, comparisons with measured data showed that the benefit of using the inflow data of this model chain is especially evident near the ground

Subdiffusion and lateral diffusion coefficient of lipid atoms and molecules in phospholipid bilayers

We use a long, all-atom molecular dynamics (MD) simulation combined with theoretical modeling to investigate the dynamics of selected lipid atoms and lipid molecules in a hydrated diyristoyl-phosphatidylcholine (DMPC) lipid bilayer. From the analysis of a 0.1 $\mu$s MD trajectory we find that the time evolution of the mean square displacement, [\delta{r}(t)]^2, of lipid atoms and molecules exhibits three well separated dynamical regions: (i) ballistic, with [\delta{r}(t)]^2 ~ t^2 for t < 10 fs; (ii) subdiffusive, with [\delta{r}(t)]^2 ~ t^{\beta} with \beta<1, for 10 ps < t < 10 ns; and (iii) Fickian diffusion, with [\delta{r}(t)]^2 ~ t for t > 30 ns. We propose a memory function approach for calculating [\delta{r}(t)]^2 over the entire time range extending from the ballistic to the Fickian diffusion regimes. The results are in very good agreement with the ones from the MD simulations. We also examine the implications of the presence of the subdiffusive dynamics of lipids on the self-intermediate scattering function and the incoherent dynamics structure factor measured in neutron scattering experiments.Comment: Submitted to Phys. Rev.

Control of helical chirality in supramolecular chromophore-DNA architectures

Four different D- and L-configured chromophore–20-deoxyuridine conjugates were applied to elucidate the helical chirality of their non-covalent assemblies along the D- and L-configured DNA templates by optical spectroscopy. There is no configuration-selective recognition between these nucleosides and the DNA templates. The helicity of the DNA assemblies is either controlled by the configuration of the DNA template or by the nucleoside configuration