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  • 1
    Electronic Resource
    Electronic Resource
    Inertial effects in butane stochastic dynamics (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 211-218 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The range of validity of diffusive algorithms is studied by comparing the isomerization rates and rotational reorientation times from a series of Langevin dynamics trajectories of butane with the results of a Brownian dynamics (diffusive) trajectory, as well as with analytic approximations. It is found that inertial effects may be ignored for rotation at most liquid densities and contribute approximately 10% to the isomerization rate at water viscosities. For neat butane, or other short-chain alkane solvents at room temperature, the effect of inertial terms on isomerization rates is significant.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457508
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  • 2
    Electronic Resource
    Electronic Resource
    Anisotropic bead models for molecular hydrodynamics (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 90 (1989), S. 5729-5734 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Some qualitative effects of slip hydrodynamic boundary conditions can be incorporated into bead models by replacing the scalar friction constant of a bead with a friction tensor. Translational and rotational diffusion coefficients are calculated analytically and exactly for polygons, analytically but approximately for spherical shells, and numerically by the method of Bloomfield and de la Torre. The calculated diffusion constants of benzene agree with experiment; such agreement is not possible using scalar friction constants. Some comments are made about the transition from overall slip to stick hydrodynamic behavior when tensor friction constants are used.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456429
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  • 3
    Electronic Resource
    Electronic Resource
    Brownian dynamics simulation of a lipid chain in a membrane bilayer (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 1112-1127 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A Brownian dynamics simulation of a lipid chain is used to model the motional properties of a dipalmitoyl phosphatidylcholine bilayer. The effects of the bilayer environment on the chain are represented by a mean field derived from an extension of the Marcelja model. The simulation was run 44 million steps, the equivalent of approximately 0.66 μs for a viscosity of 2.2 cp. The results are compared with those of a 30 million step simulation of the chain in the absence of the mean field. Deuterium order parameters for the methylene groups along the chain and the average chain length calculated from the mean field trajectory are shown to converge to the experimentally determined values for DPPC with an appropriate choice of parameters. An analysis of the torsional dynamics of the chain, including transition rates and kink probabilities, is carried out. It is demonstrated that kink formation is sometimes, though not always, concerted. A comparison of the membrane and free chain simulations implies that the internal dynamics of a hydrocarbon chain in a bilayer is very similar to that of a neat alkane. Thus, the significant limits on the orientational freedom of the chain, as expected by the nonzero order parameters, are induced by a potential that has only a small effect on the local motions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455218
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  • 4
    Electronic Resource
    Electronic Resource
    A simulation based model of NMR T1 relaxation in lipid bilayer vesicles (1988)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 89 (1988), S. 1128-1140 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The results of the Brownian dynamics simulation of a hydrocarbon chain in a membrane bilayer described in the preceding paper are used to analyze the 13C NMR T1 relaxation in lipid bilayer vesicles. The analysis shows that the frequency dependence of the relaxation does not arise from gauche–trans isomerization or from axial rotation of the entire lipid molecule. However, a model in which fast axial rotation (D(parallel)≈2×1010 s−1) and slow noncollective diffusive director fluctuations (D⊥≈1–2×108 s−1) are superimposed on the internal motions quantitatively accounts for both the magnitude and frequency dependence of the T1 data. An effective viscosity for the interior of the bilayer in the range of 1 cp, and a director order parameter of 0.5–0.7 are required to fit the NMR data. Collective effects do not appear necessary for explaining the NMR T1 data in vesicles, although they may be important for multilamellar dispersions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.455219
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  • 5
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulations of water wires in a lipid bilayer and water/octane model systems (2002)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 116 (2002), S. 2663-2664 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A series of classical molecular dynamics simulations of a water wire in a DPPC bilayer yielded lifetimes τ of up to 90 ps, with τ¯=37±8 ps (not including a significant fraction wires that broke during equilibration). This is sufficiently long to conduct protons across the bilayer through a quantum mechanical hopping mechanism, similar to proton conduction in ice. Lifetimes of wires in the octane region of a water/octane/water "sandwich" were qualitatively similar (τ¯=36±3 ps) though wires were rarely lost during equilibration. Hence, the utility of the water/octane system as a membrane surrogate depends on the application.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1434952
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  • 6
    Electronic Resource
    Electronic Resource
    Constant pressure molecular dynamics simulation: The Langevin piston method (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 4613-4621 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical "ringing'' of the volume associated with the piston mass. In this way it is similar to the "weak coupling algorithm'' developed by Berendsen and co-workers to perform molecular dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aqueous biopolymers or liquid/liquid interfaces.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470648
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  • 7
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation of methyl group relaxation in water (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 94 (1991), S. 4097-4098 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Recent theoretical studies of stochastic classical and quantum dynamics suggest that quantum effects may be significant in the nuclear magnetic resonance (NMR) relaxation of a methyl group attached to intermediate and large sized molecules at normal temperatures. The magnitude of the effects depends on the reorientational correlation time of the molecule, τ0, the barrier to internal rotation, V, and the correlation time for the collision induced randomization of the internal angular momentum, τω. This note reports the results of molecular dynamics simulations used to estimate τω for a methyl group in water. The simulations indicate that extended diffusion, rather than Fokker–Planck–Langevin, dynamics are appropriate for this system. Using τω determined in the simulation and V=13 KJ/mol (3 Kcal/mol), predictions of the classical and quantum models differ by 40% for the 13C relaxation of a methyl on an intermediate sized molecule, such as a disaccharide. In larger molecules, the differences are smaller due to smaller contributions from the internal dynamics to the NMR relaxation process, unless τω and/or V are larger. Experimental evidence suggests that τω is an order of magnitude or more larger in a hydrocarbon environment than in water. With the larger τω, a plausible example is given where the models' predictions differ by 80%. More work is needed, however, to better define τω in hydrophobic regions of macromolecules.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.460641
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  • 8
    Electronic Resource
    Electronic Resource
    Diffusion limited first contact of the ends of a polymer: Comparison of theory with simulation (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 105 (1996), S. 3878-3882 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The mean first passage time for the close approach of the ends of a polymer is investigated by computer simulation of the Brownian dynamics of a Rouse model. There are N bonds, of length b, and the contact distance is a. The results for N=50, 75, and 100 are compared with theoretical predictions by Wilemski and Fixman (WF), and by Szabo, Schulten, and Schulten (SSS). Theory differs from simulation by a factor of 1.3 to 3 when a is comparable to b but improves considerably when a is reduced. Closest agreement is obtained at a/b=0.1 for WF with a δ function sink, where theory is within the statistical error (≈5%) of the simulation for each case.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.472208
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  • 9
    Electronic Resource
    Electronic Resource
    Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 10252-10266 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Statistical ensembles for simulating liquid interfaces at constant pressure and/or surface tension are examined, and equations of motion for molecular dynamics are obtained by various extensions of the Andersen extended system approach. Valid ensembles include: constant normal pressure and surface area; constant tangential pressure and length normal to the interface; constant volume and surface tension; and constant normal pressure and surface tension. Simulations at 293 K and 1 atm normal pressure show consistent results with each other and with a simulation carried out at constant volume and energy. Calculated surface tensions for octane/water (61.5 dyn/cm), octane/vacuum (20.4 dyn/cm) and water/vacuum (70.2 dyn/cm) are in very good agreement with experiment (51.6, 21.7, and 72.8 dyn/cm, respectively). The practical consequences of simulating with two other approaches commonly used for isotropic systems are demonstrated on octane/water: applying equal normal and tangential pressures leads to an instability; and applying a constant isotropic pressure of 1 atm leads to a large positive normal pressure. Both results are expected for a system of nonzero surface tension. Mass density and water polarization profiles in the liquid/liquid and liquid/vapor interfaces are also compared.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469927
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  • 10
    Electronic Resource
    Electronic Resource
    Computer simulation of liquid/liquid interfaces. II. Surface tension-area dependence of a bilayer and monolayer (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 10267-10276 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A constant normal pressure-surface tension algorithm for molecular dynamics simulation, developed in the preceding paper, was used to laterally expand and compress the surface area of a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer. Then, from simulations carried out at constant normal pressure and surface area, values of the surface tension and other thermodynamic variables such as the internal energy and system volume were determined at four different values of the surface area per lipid, 60.0, 65.1, 68.1, and 72.1 A(ring)2. The surface tension shows dramatic variations with area, going from 6 to 60 dyn/cm at areas per molecule of 65.1 and 68.1 A(ring)2, respectively. An approximate thermodynamic analysis indicates that an area of 68.1 A(ring)2/lipid is the closest of the four to the free energy minimum for this system, in agreement with experimental measurements. The effect of surface area changes on the calculated deuterium order parameters, which can be compared with those obtained from nuclear magnetic resonance experiments, is found to be quite large. Additionally, simulations of lipid monolayers were performed at the same surface areas and, though the dependence of the surface tension with area shows qualitative agreement with experiment, the simulation results are more sensitive to area changes than is observed experimentally. The variation in surface tension with area is much greater for the bilayer than the monolayer, suggesting that monolayers are a good model of bilayers only in a narrow range of surface areas.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469928
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