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  • 51.
    Wohlert, Jakob
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Edholm, Olof
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion2006Ingår i: Journal of chemical physics, ISSN 0021-9606, Vol. 125, s. 204703-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It is shown that a long, near microsecond, atomistic simulation can shed some light upon the dynamical processes occurring in a lipid bilayer. The analysis focuses on reorientational dynamics of the chains and lateral diffusion of lipids. It is shown that the reorientational correlation functions exhibits an algebraic decay (rather than exponential) for several orders of magnitude in time. The calculated nuclear magnetic resonance relaxation rates agree with experiments for carbons at the C7 position while there are some differences for C3. Lateral diffusion can be divided into two stages. In a first stage occurring at short times, t < 5 ns, the center of mass of the lipid moves due to conformational changes of the chains while the headgroup position remains relatively fixed. In this stage, the center of mass can move up to similar to 0.8 nm. The fitted short-time diffusion coefficient is D-1=13x10(-7) cm(2) s(-1) On a longer time scale, the diffusion coefficient becomes D-2=0.79x10(-7) cm(2) s(-1).

  • 52.
    Wohlert, Jakob
    et al.
    KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Schnupf, Udo
    Brady, John W.
    Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution2010Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 133, nr 15, s. 155103-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Multidimensional potentials of mean force for the interactions in aqueous solution of both anomers of D-glucopyranose with two planar aromatic molecules, indole and para-methyl-phenol, have been calculated using molecular dynamics simulations with umbrella sampling and were subsequently used to estimate binding free energies. Indole and para-methyl-phenol serve as models for the side chains of the amino acids tryptophan and tyrosine, respectively. In all cases, a weak affinity between the glucose molecules and the flat aromatic surfaces was found. The global minimum for these interactions was found to be for the case when the pseudoplanar face of beta-D-glucopyranose is stacked against the planar surfaces of the aromatic residues. The calculated binding free energies are in good agreement with both experiment and previous simulations. The multidimensional free energy maps suggest a mechanism that could lend kinetic stability to the complexes formed by sugars bound to sugar-binding proteins. (C) 2010 American Institute of Physics.

  • 53.
    Wohlert, Jakob
    et al.
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi.
    Tolonen, Lasse K.
    Bergenstråhle-Wohlert, Malin
    KTH, Skolan för kemivetenskap (CHE), Fiber- och polymerteknologi.
    A simple model for cellulose solubility in supercritical water2015Ingår i: Nordic Pulp & Paper Research Journal, ISSN 0283-2631, E-ISSN 2000-0669, Vol. 30, nr 1, s. 14-19Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A simple model for the hydration of a polar molecule is developed in order to provide a description of cellulose solubility in water under ambient and supercritical conditions. The change in free energy upon hydration is regarded as the sum of the energy cost of forming a cavity and a polar contribution. The model is able to predict the existence of an optimal density for dissolution of polar solutes in supercritical water. Those results are in line with earlier experiments and simulations showing that water at high temperature and pressure dissolves cellulose, and that an optimal density for dissolution exists. The present study shows that the density dependence comes from the fact that both the cavity formation energy and the polar energy are highly density dependent but with opposing behaviour. The cavity formation energy increases with density, whereas the polar energy decreases. Based on the present model, it is possible to rationalize a few basic strategies regarding cellulose dissolution in aqueous media. To increase solubility, one can either increase the polar/electrostatic contribution, or more importantly, one can decrease the cost of cavity formation, e.g. by introducing co-solvents, changing temperature and/or pressure.

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