315 research outputs found
Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces
No full textWe study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes; it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in case of charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo, as the two plates are brought together
Effect of the treatment of long-range forces on the dynamics of ions in aqueous solutions
No full textThe goal of the present work is to study the dependence of the limiting ionic mobility of such anions as fluoride, chloride, and bromide in water on the way the long-range forces are treated in the computer simulations. With this in mind we have performed molecular dynamics computer simulations where the long-range electrostatic forces were treated using: (a) simple truncation procedure, (b) energy switching procedure, (c) reaction field method, and (d) Ewald summation technique. Our analysis shows that the switching procedure with the short-range switching function introduces artifacts into the simulations. These artifacts are responsible for the faster decay and oscillations in the velocity autocorrelation function of the ions and therefore for the lower value of the diffusion coefficients
Detailed molecular dynamics simulations of model biological membranes containing cholesterol
No full textAbstractDetailed molecular dynamics simulations performed to study the nature of lipid raft domains that appear in model membranes are reviewed in this paper. The described simulations were performed on hydrated bilayers containing binary mixtures of cholesterol with phospholipids and also on ternary mixtures containing cholesterol, a phospholipid with a high main transition temperature Tm, and a phospholipid with a low transition temperature Tm. These simulations provide qualitative and semi-quantitative information about cholesterol–lipid interactions and also a testing ground for major assumptions made to explain the nature of lipid rafts in model membranes
Stretch-Induced Cavitation: How Critical Cavity Radius and Barrier Energy, Radius, and Energy of a Stable Cavity Depend on the Stretching Factor
No full textFree Energy Barrier for Melittin Reorientation from a Membrane-Bound State to a Transmembrane State
No full textAn important step in a phospholipid membrane pore formation by melittin antimicrobial peptide is a reorientation of the peptide from a surface into a transmembrane conformation. In this work we perform umbrella sampling simulations to calculate the potential of mean force (PMF) for the reorientation of melittin from a surface-bound state to a transmembrane state and provide a molecular level insight into understanding peptide and lipid properties that influence the existence of the free energy barrier. The PMFs were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We observe that the free energy barrier is reduced when the P/L ratio increased. In addition, we study the cooperative effect; specifically we investigate if the barrier is smaller for a second melittin reorientation, given that another neighboring melittin was already in the transmembrane state. We observe that indeed the barrier of the PMF curve is reduced in this case, thus confirming the presence of a cooperative effect
“THE SON OF SAM” IN THE NEW YORK TIMES: CONTENT ANALYSIS RESULTS
No full textThe article aims at the study of the representation of serial killer David Berkowitz (The Son of Sam) in The New York Times using content analysis. The research includes all newspaper articles that have been published from the time of the first murder and until the judgment of the court. During the research the author analyzes not only exterior characteristics of the articles (genre, photographs, comments, etc.) but also interior characteristics created by the author (evaluative and descriptive elements, character properties). The author assumes that the newspaper intentionally or unintentionally creates an appealing image of the killer using different methods and linguistic techniques. Statistical data that we have obtained allow us to assert that the author`s hypothesis is confirmed. In particular, the author finds out that The New York Times journalists depict David Berkowitz as a worldwide celebrity and a mystic monster and endow him with supernatural properties and outstanding abilities. Such depiction has a great influence on the audience`s perception of the killer. Many examples of the killer`s psychological aggression in the newspaper allow us to assert that The New York Times is partly responsible for the panic in New York City during a yearlong Son of Sam shooting spree
Stabilization energies of Cl − , Br − , and I − ions in water clusters
No full textMolecular dynamics computer simulations were performed on clusters of Cl-(H20)n (n =2, ... ,15). From the simulations we calculated the stabilization energies of the anion in the cluster. These energies were compared with the values of stabilization energies obtained from the photodetachment spectra of X-(H20)n clusters (X=CI-, Br-, or 1-). The comparison confirms the hypothesis that the anion is attached to the water cluster
The Implementation of Slab Geometry for Membrane-Channel Molecular Dynamics Simulations
No full textAbstractSlab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties
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