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  • 1
    Electronic Resource
    Electronic Resource
    Liquid benzene confined between graphite surfaces. A constant pressure molecular dynamics study (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 5405-5417 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We derive expressions for the internal and external stress tensor for a molecular system which is periodic in two dimensions and confined by an external potential along the third dimension. Based on the external pressure, we propose an extended-phase-space constant pressure molecular dynamics simulation method. We apply this method to simulations of liquid benzene confined between two graphite surfaces. The intramolecular interactions are thereby adopted from the amber force field, whereas the liquid-surface interaction is described in terms of a static external potential acting on the benzene molecules. Our results test the method and provide a molecular picture of the surface induced structure of the liquid as well as its dynamical behavior near the surface. We find that the surface affects the structure of the liquid on a length scale significantly larger than the direct range of the liquid-surface potential. Additionally, we observe a fast exchange of benzene molecules between the first and second liquid layer adjacent to the surface.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466223
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  • 2
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation study of the adsorption of chain alkanes from solution onto graphite (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 5528-5534 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We use the molecular dynamics simulation method to study the adsorption of an n alkane from a benzene solution onto the basal plane of graphite. We show that it is possible to simulate the entire adsorption process, i.e., the diffusion of the alkanes to the surface, the penetration of the highly structured solvent layers near the surface, and the physisorption of the chains on the graphite. Specifically, we consider a solution of C14H30 in benzene confined between two graphite surfaces. The alkane chains are initially dispersed near the center of the slit where the solvent is bulklike. During the simulation, the chains are attracted by the surfaces where they adsorb replacing benzene molecules in the structured liquid near the surfaces. The alkane chains adsorb parallel to the graphite plane assuming predominately stretched conformations without tails extending into the solution. The simulation also shows evidence for the onset of self-organization due to strong lateral interactions between the adsorbed molecules.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465971
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  • 3
    Electronic Resource
    Electronic Resource
    Comparative molecular dynamics simulation study of the benzene–graphite and the benzene–1,12-dodecanediol–graphite interface (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 3930-3939 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using the molecular dynamics simulation technique, we study the effect of a highly ordered physisorbed alkyl monolayer on the surface induced liquid structure near a smooth solid–liquid interface. The system considered here is 1,12-dodecanediol adsorbed at the benzene–graphite interface. We compare the results on the graphite–1,12-dodecanediol–benzene interface to previous simulations on the bare graphite–benzene interface. We find that the surface induced liquid structure near the adsorbate covered interface differs from the structure induced by the bare interface only within the first solvation shell. Beyond the first solvation shell, there is no discernible difference, even though the surface induced structure is still pronounced. In addition, we study the structure of the hydrogen bond stabilized molecular adsorbate network. Here we find that the hydrogen bonds link the 1,12-dodecanediol molecules in a chain-like fashion across the boundaries of the herringbone structure formed by the adsorbate.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466328
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  • 4
    Electronic Resource
    Electronic Resource
    Dynamic properties of molecular chains with variable stiffness (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 7750-7757 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dynamics of a free-draining chain of variable stiffness in a dilute solution is investigated. The chain is considered as a differentiable space curve with stretching and bending elasticity. Second moments, like the mean square end-to-end distance, the radius of gyration, and the pair correlation function of the equilibrium distribution exactly agree with those of the well-known Kratky–Porod wormlike chain. The equation of motion of the chain is derived and solved by a normal mode analysis. In the limit of a flexible chain the model exhibits the well-known Rouse dynamics, whereas in the rod limit the eigenfunctions correspond to bending motion only. In addition, the rotational motion in the latter limit is naturally obtained within the model. The relaxation times obtained by the model are compared with experimental transient birefringence and dynamic light scattering data. In addition, electric dichroism measurements are interpreted in terms of the model. All of these experiments are in good agreement with the theoretical predictions. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469027
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  • 5
    Electronic Resource
    Electronic Resource
    Time reversible and phase-space conserving molecular dynamics at constant temperature (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 9018-9025 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Algorithms for constant temperature molecular dynamics simulations are presented. The basic equations of motion, keeping the temperature constant, are derived by an extension of phase space. Time reversible integration algorithms are obtained for these equations of motion by a factorization of the classical Liouville propagator. In particular an algorithm is derived which includes the phase-space conservation property of the equations of motion. This algorithm is compared with the Nosé–Hoover approach for systems of a single degree of freedom. It is demonstrated that the derived equations of motion generate canonical distributions. In addition, a comparison with various isothermal integration algorithms for the Nosé–Hoover equations is presented for a system of Lennard-Jones particles. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468850
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  • 6
    Electronic Resource
    Electronic Resource
    Models and equilibrium properties of stiff molecular chains (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 8119-8129 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The partition functions of discrete as well as continuous stiff molecular chains are calculated using the maximum entropy principle. The chain is described by mass points, and their connectivity is taken into account by harmonic constraints (flexible segments) in addition to the bending restrictions. For comparison and as a test of the formalism the freely rotating chain as well as the Kratky–Porod wormlike chain (rigid segments) are reexamined treating the bending restrictions as constraints. It is shown that the second moments for the chain of flexible segments agree exactly with those known from the freely rotating chain for the discrete as well as the continuous chain and for all stiffnesses. Moreover, the Green's function for the continuous chain is determined, which allows to obtain any desired two point distribution function. The influence of various bending restrictions on equilibrium properties is discussed. Furthermore, a comparison to other existing models, especially the Harris and Hearst model, is given and the validity of the various models is examined.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468239
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  • 7
    Electronic Resource
    Electronic Resource
    Dynamic structure factor of semiflexible macromolecules in dilute solution (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 6355-6368 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dynamic structure factor for molecular chains with variable stiffness in a dilute solution is investigated. In the limit of small scattering vectors q only the overall translational motion of the macromolecules contributes to the dynamic structure factor. The translational diffusion coefficient D exhibits a chain length dependence D∼1/(square root of)L for flexible chains and D∼ln L/L+const/L for rodlike chains. For flexible chains there is an intermediate scattering vector regime in which the decay rate or spectral linewidth of the dynamic structure factor is proportional to q3 indicating that stretching modes are dominant. Such an intermediate scattering vector regime cannot be observed for semiflexible or rodlike chains. At large scattering vectors q/2p(approximately-greater-than)1.5, where 1/2p is the persistence length of the macromolecules, the chain stiffness becomes important for any kind of molecules, i.e., even for very flexible ones. The dynamic structure factor and the decay rate are compared with experimental results of quasielastic neutron and light scattering experiments on different natural and synthetic macromolecules. These experimental results are in good agreement with the theoretical predictions. Furthermore, we determine the persistence length of F-actin from a dynamic light scattering experiment. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.471297
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  • 8
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation study of the dynamics of fluids in thin films (1996)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 8103-8111 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The structure and dynamics of fluids in thin films are investigated by molecular dynamics simulations. Particularly the influence of surface attraction or repulsion on the structure of hexadecane melts (C16H34) is investigated. We find that for a strongly attractive surface, well ordered, crystalline like monolayers are the most stable configuration. In addition, the dynamics perpendicular to solid surfaces of the hexadecane molecules as well as of a simple Lennard-Jones fluid is investigated. For the Lennard-Jones fluid, the numerical results are compared with analytical calculations based on the diffusion equation, which shows that the numerical results can very well be described by the solution of the diffusion equation for reflecting surfaces. The diffusion coefficient is practically independent of the position within the film, although the fluid is inhomogeneous perpendicular to the surfaces. However, we observe a slight influence of the finite size of the fluid particles on their dynamics in the layer adjacent to a surface. In contrast, the dynamics of the centers of mass of hexadecane molecules perpendicular to repulsive surfaces is severely slowed down due to their extended and anisotropic nature and cannot be described by a single particle diffusion equation. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.471497
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  • 9
    Electronic Resource
    Electronic Resource
    Influence of stiffness on the dynamics of macromolecules in a melt (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 2469-2476 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Analytical expressions are derived for the incoherent and coherent dynamic structure factor of macromolecules in a melt. In particular, the influence of chain stiffness on these quantities is investigated. For scattering vectors q〈πp/2, where 1/2p is the persistence length of the macromolecules, the well known results for the Rouse model are reproduced. However, in the scattering vector range q〉πp/2 the incoherent dynamic structure factor is shown to be a universal function of only the combination q8/3tp1/3, reflecting the strong influence of the local chain stiffness on dynamical properties at small length scales. Moreover, the q dependence of both the full width at half maximum of the Fourier transformed incoherent dynamic structure factor and the initial decay rate of the coherent dynamic structure factor are calculated. The comparison of the theoretical results with quasielastic neutron scattering experiments of different polymers exhibits good agreement. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.473154
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  • 10
    Electronic Resource
    Electronic Resource
    Initial decay rate of the dynamic structure factor of polymer molecules in solution (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 5160-5161 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The initial decay rate of the dynamic structure factor of macromolecules in solution is briefly discussed. In particular, the theoretical calculations are compared with experimental data of polystyrene both in carbon disulfide and in benzene-d6. Our theoretical calculations agree very well with the experimental data. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.477130
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