Sökning: "polarizable force fields"

Hittade 5 avhandlingar innehållade orden polarizable force fields.

  1. 1. 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

  3. 2. A first-principles approach to protein–ligand interaction

    Författare :Pär Söderhjelm; Beräkningskemi; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; solvation; exchange repulsion; polarizable force fields; polarization; molecular mechanics; quantum chemistry; intermolecular interactions; protein–ligand interaction;

    Sammanfattning : It is still impossible to make an accurate, purely theoretical prediction of the free energy of a ligand binding to a protein in aqueous environment. The two main problems are the immense number of nuclear configurations contributing to the binding free energy and the impossibility to apply accurate quantum-chemical methods to such a large system, even for a single configuration. LÄS MER

  4. 3. Light interactions in flexible conjugated dyes

    Författare :Jonas Sjöqvist; Patrick Norman; Per-Olof Åstrand; Linköpings universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; force field; molecular dynamics; QM MM; solvation effects; absorption spectroscopy; fluorescence spectrosocopy; infrared spectroscopy; Raman spectroscopy; stokes shift; conjugated polyelectrolytes;

    Sammanfattning : In this thesis methodological developments have been made for the description of flexible conjugated dyes in room temperature spectrum calculations.The methods in question target increased accuracy and efficiency by combining classical molecular dynamics (MD) simulations with time-dependent response theory spectrum calculations. LÄS MER

  5. 4. Tales from the Sweet Side of Life : Structure and dynamics of carbohydrate-based systems

    Författare :Alessandro Ruda; Göran Widmalm; Jesús Jiménez Barbero; Stockholms universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; carbohydrates; nuclear magnetic resonance; molecular dynamics; glycans; conformational analysis; structure elucidation; protein-glycan interactions; Organic Chemistry; organisk kemi;

    Sammanfattning : The field of glycomics has experienced significant developments in the last few decades, revealing a profound and elaborate language behind the intrinsic complexity of the glycans structures. This ‘sugar code’ is at the basis of intercellular interaction and recognition. For this language to be understood, its chemical basis must be unveiled. LÄS MER

  7. 5. Atomic decomposition of molecular properties

    Författare :Ignat Harczuk; Hans Ågren; Olav Vahtras; Per-Olof Åstrand; KTH; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Teoretisk kemi och biologi; Theoretical Chemistry and Biology;

    Sammanfattning : In this thesis, new methodology of computing properties aimed for multipleapplications is developed. We use quantum mechanics to compute propertiesof molecules, and having these properties as a basis, we set up equations basedon a classical reasoning. LÄS MER