Molecular dynamics model membrane

This coarse-grained molecular dynamics model helped consolidate the main features of microstructure formation in CLs of PEFCs. These showed that the final microstructure depends on carbon particle choices and ionomer-carbon interactions. While ionomer sidechains are buried inside hydrophilic domains with a weak contact to carbon domains, the ionomer backbones are attached to the surface of carbon agglomerates. The evolving structural characteristics of the catalyst layers (CL) are particularly important for further analysis of transport of protons, electrons, reactant molecules (O2) and water as well as the distribution of electrocatalytic activity at Pt/water interfaces. In principle, such meso-scale simulation studies allow relating of these properties to the selection of solvent, carbon (particle sizes and wettability), catalyst loading, and level of membrane hydration in the catalyst layer. There is still a lack of explicit experimental data with which these results could be compared. Versatile experimental techniques have to be employed to study particle-particle interactions, structural characteristics of phases and interfaces, and phase correlations of carbon, ionomer, and water in pores. 

Biomembranes are complex structures composed of various lipids and proteins. Different membrane compositions affect viscoelastic and hydrodynamic properties of membranes, which are critical to their functions. Cholesterol-rich vesicles are similar to cell membranes in structure and component. Therefore, cholesterol-rich vesicles can represent a typical model for studying membrane dynamics and functions. Nuclear magnetic relaxation dispersion was used to investigate the detailed molecular dynamics of membrane differences between vesicles and cholesterol vesicles in the temperature range of 278-298 K. Vesicles of two different sizes were prepared. The effect of cholesterol mainly affected the order fluctuation of membranes and the diffusional motion of lipid molecules. ... 

Stepaniants et al., 1997] Stepaniants, S., Izrailev, S., and Schulten, K. Extraction of lipids from phospholipid membranes by steered molecular dynamics. J. Mol. Model. 3 (1997) 473-475... 

The simulations to investigate electro-osmosis were carried out using the molecular dynamics method of Murad and Powles [22] described earher. For nonionic polar fluids the solvent molecule was modeled as a rigid homo-nuclear diatomic with charges q and —q on the two active LJ sites. The solute molecules were modeled as spherical LJ particles [26], as were the molecules that constituted the single molecular layer membrane. The effect of uniform external fields with directions either perpendicular to the membrane or along the diagonal direction (i.e. Ex = Ey = E ) was monitored. The simulation system is shown in Fig. 2. The density profiles, mean squared displacement, and movement of the solvent molecules across the membrane were examined, with and without an external held, to establish whether electro-osmosis can take place in polar systems. The results clearly estab-hshed that electro-osmosis can indeed take place in such solutions. 

For any even vaguely realistic atomically constituted membrane it is unlikely that any theory will become available in the near future which will properly or reasonably describe the dynamic properties of the membrane, the fluids near it, and their passage, or selective passage, through it. Nevertheless, one should continue trying with simple models and simple theories [39-43], which show the way forward and can, as usual, be tested by the virtually exact results of molecular dynamics simulation. 

Further progress in understanding membrane instability and nonlocality requires development of microscopic theory and modeling. Analysis of membrane thickness fluctuations derived from molecular dynamics simulations can serve such a purpose. A possible difficulty with such analysis must be mentioned. In a natural environment isolated membranes assume a stressless state. However, MD modeling requires imposition of special boundary conditions corresponding to a stressed state of the membrane (see Refs. 84,87,112). This stress can interfere with the fluctuations of membrane shape and thickness, an effect that must be accounted for in analyzing data extracted from computer experiments. 

Studies of the effect of permeant s size on the translational diffusion in membranes suggest that a free-volume model is appropriate for the description of diffusion processes in the bilayers [93]. The dynamic motion of the chains of the membrane lipids and proteins may result in the formation of transient pockets of free volume or cavities into which a permeant molecule can enter. Diffusion occurs when a permeant jumps from a donor to an acceptor cavity. Results from recent molecular dynamics simulations suggest that the free volume transport mechanism is more likely to be operative in the core of the bilayer [84]. In the more ordered region of the bilayer, a kink shift diffusion mechanism is more likely to occur [84,94]. Kinks may be pictured as dynamic structural defects representing small, mobile free volumes in the hydrocarbon phase of the membrane, i.e., conformational kink g tg ) isomers of the hydrocarbon chains resulting from thermal motion [52] (Fig. 8). Small molecules can enter the small free volumes of the kinks and migrate across the membrane together with the kinks. 

The favourable properties which mark out vesicles as protocell models were confirmed by computer simulation (Pohorill and Wilson, 1995). These researchers studied the molecular dynamics of simple membrane/water boundary layers the bilayer surface fluctuated in time and space. The model membrane consisted of glycerine-1-monooleate defects were present which allowed ion transport to occur, whereby negative ions passed through the bilayer more easily than positive ions. The membrane-water boundary layer should be particularly suited to reactions which are accelerated by heterogeneous catalysis. Thus, the authors believe that these vesicles fulfil almost all the conditions required for the first protocells on earth ... 

Membrane-Interaction (MI)-QSAR approach developed by Iyer et al. was used to develop predictive models of some organic compounds through BBB, and to simulate the interaction of a solute with the phospholipide-rich regions of cellular membranes surrounded by a layer of water. Molecular dynamics simulations were used to determine the explicit interaction of each test compound with the DMPC-water model (a model of dimyristoylphosphatidylcholine membrane monolayer, constructed using the software Material Studio according to the work done by van der Ploeg and Berendsen). Six MI-QSAR equations were constructed (Eqs. 74-79) ... 

An alternative mesoscale approach for high-level molecular modeling of hydrated ionomer membranes is coarse-grained molecular dynamics (CGMD) simulations. One should notice an important difference between CGMD and DPD techniques. CGMD is essentially a multiscale technique (parameters are directly extracted from classical atomistic MD) and it... 

Fig. 8 Proposed model for gramicidin S in a membrane according to the orientational constraints obtained from and N-NMR. The upright backbone alignment (r 80°) and slant of the /3-sheets (p -45°) are compatible with the formation of an oligomeric /3-barrel that is stabilized by hydrogen bonds (dotted lines). A The oligomer is depicted sideways from within the lipid bilayer interior (showing only backbone atoms for clarity, but with hydrophobic side chains added to one of the monomers). Atomic coordinates of GS were taken from a monomeric structure [4], and the two DMPC lipid molecules are drawn to scale (from a molecular dynamics simulation coordinate file). The bilayer cross-section is coloured yellow in its hydrophobic core, red in the amphiphilic regions, and light blue near the aqueous surface. B Illustrates a top view of the putative pore, although the number of monomers remains speculative...

MD simulations of model membrane systems have provided a unique view of lipid interactions at a molecular level of resolution [21], Due to the inherent fluidity and heterogeneity in lipid membranes, computer simulation is an attractive tool. MD simulations allow us to obtain structural, dynamic, and energetic information about model lipid membranes. Comparing calculated structural properties from our simulations to experimental values, such as areas and volumes per lipid, and electron density profiles, allows validation of our models. With molecular resolution, we are able to probe lipid-lipid interactions at a level difficult to achieve experimentally. 

Berkowitz, M.L. Detailed molecular dynamics simulations of model biological membranes containing cholesterol. Biochim. Biophys. Acta 2009, 1788, 86-96. 

G-Protein-coupled receptors do not lend themselves to analysis by either NMR or x-ray crystallography due to their structural dependence on an intact cell membrane. In our laboratories we pursued this valuable structural information by utilizing a combination of structural homology modeling, molecular dynamics, systematic conformational searching methods, and mutagenesis experiments. The combination of these techniques led to a proposed model of bradykinin bound to the agonist site on its receptor [41]. 

Because of the complexity of hydrated PEMs, a full atomistic modeling of proton transport is impractical. The generic problem is a disparity of time and space scales. While elementary molecular dynamics events occur on a femtosecond time scale, the time interval between consecutive transfer events is usually 3 orders of magnitude greater. The smallest pore may be a few tenth of nanometer while the largest may be a few tens of nanometers. The molecular dynamics events that protons transfer between the water filled pores may have a timescale of 100-1000 ns. This combination of time and spatial scales are far out of the domain for AIMD but in the domain of MD and KMC as shown in Fig. 2. Because of this difficulty, in the models the complexity of the systems is restricted. In fact in many models the dynamics of excess protons in liquid water is considered as an approximation for proton conduction in a hydrated Nation membrane. The conformations and energetics of proton dissociation in acid/water clusters were also evaluated as approximations for those in a Nation membrane.16,19 20 22 24 25... 

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