Sökning: "GROMACS"

Visar resultat 1 - 5 av 9 avhandlingar innehållade ordet GROMACS.

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

   Författare :Guomin Yang; Göran Lindbergh; Ivars Neretnieks; Michael Holmboe; Jan Forsman; KTH; []
   Nyckelord :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;

   Sammanfattning : 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. LÄS MER

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

   Författare :Mohammad Mehdi Ghahremanpour; David Van der Spoel; Kresten Lindorff-Larsen; Uppsala universitet; []
   Nyckelord :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;

   Sammanfattning : 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. LÄS MER

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

   Författare :Christofer Östlin; Carl Caleman; Uppsala universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; XFEL; serial femtosecond x-ray crystallography; single particle imaging; radiation damage; GROMACS; Cretin; computer simulation;

   Sammanfattning : 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. LÄS MER

5. 4. Leveraging Intermediate Representations for High-Performance Portable Discrete Fourier Transform Frameworks : with Application to Molecular Dynamics

   Författare :Måns Andersson; Stefano Markidis; Artur Podobas; Niclas Jansson; Ivy Bo Peng; Hartwig Anzt; KTH; []
   Nyckelord :Intermediate Representation; Discrete Fourier Transform; Fast Fourier Transform; Molecular Dynamics; Mellankod; diskret Fouriertransform; snabb Fouriertransform; Molekyldynamik;

   Sammanfattning : The Discrete Fourier Transform (DFT) and its improved formulations, the Fast Fourier Transforms (FFTs), are vital for scientists and engineers in a range of domains from signal processing to the solution of partial differential equations.  A growing trend in Scientific Computing is heterogeneous computing, where accelerators are used instead or together with CPUs. LÄS MER

7. 5. Modeling of voltage-gated ion channels

   Författare :Pär Bjelkmar; Erik Lindahl; Toby W. Allen; Stockholms universitet; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Molecular modeling; Molecular dynamics; Voltage-gating; Ion channels; Protein structure prediction; Chemistry; Kemi; biokemi; inriktning teoretisk kemi; Biochemistry with Emphasis on Theoretical Chemistry;

   Sammanfattning : 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. LÄS MER