Search for dissertations about: "GROMACS"

Showing result 1 - 5 of 7 swedish dissertations containing the word GROMACS.

  1. 1. Interfacial properties of calcium montmorillonite in aqueous solutions Density functional theory and classical molecular dynamics studies on the electric double layer

    University dissertation from Stockholm : KTH Royal Institute of Technology

    Author : Guomin Yang; KTH.; [2017]
    Keywords : TEKNIK OCH TEKNOLOGIER; ENGINEERING AND TECHNOLOGY; Clay minerals; Bentonite; density functional theory; molecular dynamics; GROMACS; electric double layer; electrolytes; ionic liquids; primitive model; CLAYFF forcefield.; Chemical Engineering; Kemiteknik;

    Abstract : The swelling properties of Bentonite are highly affected by clay content and the clay-water interactions that arise from the ion distribution in the diffuse double layer formed near the charged montmorillonite (or smectite) surfaces. Existing continuum models describing the electric double layers, such as classical Poisson-Boltzmann and DLVO theory, ignore the ion-ion correlations, which are especially important for multivalent ions at high surface charge and ionic strength. READ MORE

  2. 2. Alexandria: A General Drude Polarizable Force Field with Spherical Charge Density

    University dissertation from Uppsala : Acta Universitatis Upsaliensis

    Author : Mohammad Mehdi Ghahremanpour; David Van der Spoel; Kresten Lindorff-Larsen; [2019]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Molecular mechanics; Force field; Drude oscillator model; Alexandria library; GROMACS; Physics with specialization in Biophysics; Fysik med inriktning mot biofysik;

    Abstract : Molecular-mechanical (MM) force fields are mathematical functions that map the geometry of a molecule to its associated energy. MM force fields have been extensively used for an atomistic view into the dynamic and thermodynamics of large molecular systems in their condensed phase. READ MORE

  3. 3. Advances in Biomolecular Imaging with X-ray Free-Electron Lasers

    University dissertation from Uppsala University

    Author : Christofer Östlin; Uppsala universitet.; [2017]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; XFEL; serial femtosecond x-ray crystallography; single particle imaging; radiation damage; GROMACS; Cretin; computer simulation;

    Abstract : Utilizing X-rays to solve molecular structures has proven to be an immensely powerful and im- portant scientific technique. The invention of X-ray crystallography has allowed for countless breakthroughs in chemistry, biology and material science and remains the number one method used for structural determination today. READ MORE

  4. 4. Modeling of voltage-gated ion channels

    University dissertation from Stockholm : Department of Biochemistry and Biophysics. Stockholm University

    Author : Pär Bjelkmar; Stockholms universitet.; [2011]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Molecular modeling; Molecular dynamics; Voltage-gating; Ion channels; Protein structure prediction; NATURAL SCIENCES Chemistry; NATURVETENSKAP Kemi; biokemi; inriktning teoretisk kemi; Biochemistry with Emphasis on Theoretical Chemistry;

    Abstract : The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity. Starting from the open crystal structures, we have studied the gating mechanism of these channels by molecular modeling techniques. READ MORE

  5. 5. Crystalline cellulose in bulk and at interfaces as studied by atomistic computer simulations

    University dissertation from Stockholm : KTH

    Author : Malin Bergenstråhle; KTH.; [2008]
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Cellulose; molecular dynamics simulation; interfaces; NATURAL SCIENCES Chemistry; NATURVETENSKAP Kemi;

    Abstract : Cellulose is a linear polysaccharide, serving as reinforcement in plant cell walls.Understanding its structure and properties is of importance in the developmentof nanostructured cellulose materials. READ MORE