Search results for "MOLECULAR-DYNAMICS SIMULATION"
showing 8 items of 8 documents
Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters
2018
Lipophilic neurotransmitters (NTs) such as dopamine are chemical messengers enabling neurotransmission by adhering onto the extracellular surface of the post-synaptic membrane in a synapse, followed by binding to their receptors. Previous studies have shown that the strength of the NT-membrane association is dependent on the lipid composition of the membrane. Negatively charged lipids such as phosphatidylserine, phosphatidylglycerol, and phosphatidic acid have been indicated to promote NT-membrane binding, however these anionic lipids reside almost exclusively in the intracellular leaflet of the post-synaptic membrane instead of the extracellular leaflet facing the synaptic cleft. Meanwhile…
Chemical Identification at the Solid–Liquid Interface
2017
Solid-liquid interfaces are decisive for a wide range of natural and technological processes, including fields as diverse as geochemistry and environmental science as well as catalysis and corrosion protection. Dynamic atomic force microscopy nowadays provides unparalleled structural insights into solid-liquid interfaces, including the solvation structure above the surface. In contrast, chemical identification of individual interfacial atoms still remains a considerable challenge. So far, an identification of chemically alike atoms in a surface alloy has only been demonstrated under well-controlled ultrahigh vacuum conditions. In liquids, the recent advent of three-dimensional force mapping…
Static Properties of a Simulated Supercooled Polymer Melt: Structure Factors, Monomer Distributions Relative to the Center of Mass, and Triple Correl…
2004
We analyze structural and conformational properties in a simulated bead-spring model of a non-entangled, supercooled polymer melt. We explore the statics of the model via various structure factors, involving not only the monomers, but also the center of mass (CM). We find that the conformation of the chains and the CM-CM structure factor, which is well described by a recently proposed approximation [Krakoviack et al., Europhys. Lett. 58, 53 (2002)], remain essentially unchanged on cooling toward the critical glass transition temperature of mode-coupling theory. Spatial correlations between monomers on different chains, however, depend on temperature, albeit smoothly. This implies that the g…
Study of the Density and Temperature Dependences of the Vibrational Raman Transition in Compressed Liquid N2
1991
0021-9606; Accurate values of linewidth and line shift in the isotropic vibrational Raman spectrum of compressed liquid N2 have been obtained by using inverse Raman spectroscopy. Experiments have been performed for eight isotherms, from the normal boiling point to the critical point temperatures of N2, the number density varying between the value on the coexistence line, and the maximum value of 2.1 x 10^22 cm-3. Minima of the linewidth have been observed above 86 K, showing the increasing influence of vibration-rotation coupling (motional narrowing) competing with the broadening due to pure vibrational dephasing. Moreover, for the first time, maxima of the red line shifts have been found, …
Water-Hydrophobic Zeolite Systems
2012
Water intrusion-extrusion in hydrophobic microporous AFI, IFR, MTW and TON pure silica zeolites (zeosils) has been investigated through molecular dynamics (MD) simulations. It was found that intruded water volumes correlate with the free volume of the zeosil unit cells. Calculated adsorption isotherms allowed us to estimate the amounts of water intruded, and deviations from experiments (lower experimental with respect to calculated intrusion pressures) have been;explained in terms of connectivity defects in the synthesized materials. Water phase transitions in defectless zeosils occur in a narrow range at high pressure. On the basis of a simple model, we derived a thermodynamic equation tha…
Myoglobin embedded in saccharide amorphous matrices: water-dependent domains evidenced by small angle X-ray scattering
2010
We report Small Angle X-ray Scattering (SAXS) measurements performed on samples of carboxy-myoglobin (MbCO) embedded in low-water trehalose glasses. Results showed that, in such samples, "low-protein" trehalose-water domains are present, surrounded by a protein-trehalose-water background; such finding is supported by Infrared Spectroscopy (FTIR) measurements. These domains, which do not appear in the absence of the protein and in analogous sucrose systems, preferentially incorporate the incoming water at the onset of rehydration, and disappear following large hydration. This observation suggests that, in organisms under anhydrobiosis, analogous domains could play a buffering role against th…
Elastic neutron scattering of dry and rehydrated trehalose coated carboxy-myoglobin
2008
We report here a comparison between the hydrogen atoms mean square displacements measured by elastic neutron scattering on trehalose coated carboxy-myoglobin, at ILL on the backscattering spectrometers IN13 and IN16. An inconsistency is observed when comparing the mean square displacements measured on the two spectrometer, on samples of identical composition, since they resulted of larger amplitude on IN13 (either in condition of drought or after overnight rehydration under 75% D2O atmosphere), notwithstanding the lower time window accessible on this instrument with respect to IN16. Such inconsistency disappears when the data obtained on this last spectrometer are analyzed in two separate r…
Anomalous surface diffusion of protons on lipid membranes.
2014
AbstractThe cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive re…