Sökning: "GROMACS"

Visar resultat 1 - 5 av 19 uppsatser innehållade ordet GROMACS.

  1. 1. Simulations of anisotropic vibrations in ice induced by a laser

    Kandidat-uppsats, Uppsala universitet/Institutionen för fysik och astronomi

    Författare :Victor Freedman; [2022]
    Nyckelord :ice; anisotropy; laser; freedman; molecular dynamics; simulations;

    Sammanfattning : Systems of atoms have their kinetic energy distributed between three parts: translation, rotation and vibration. These are usually kept about the same following a Maxwell distribution, but under certain circumstances, this equilibrium might break. This would lead to, for example, ice melting anisotropically. LÄS MER

  3. 2. First principles DFT study of polyethylene insulation containing chemical impurities - implementing counterpoise correction

    Master-uppsats, KTH/Tillämpad fysik

    Författare :Max Pierre; [2022]
    Nyckelord :Applied physics; HVDC cable; Polymer physics; Polyethylene; Density functional theory; Molecular dynamics; CP2K; GROMAC; Electron traps; Band gaps; Density of states; Tillämpad fysik; HVDC kabel; Polymerfysik; Polyeten; Täthetsfunktionalteori; Molekulärdynamik; CP2K; GROMACS; Elektronfällor; Bandgap; Tillståndstäthet;

    Sammanfattning : Density functional theory (DFT) calculations of polyethylene (PE) HVDC cable insulation have been performed for systems containing four different chemical impurities: acetophenone, cumene, $\alpha$-methyl styrene and $\alpha$-cumyl alcohol. Systems were generated by molecular dynamics (MD) equilibration at four different temperatures relevant for cable insulation applications: 277 K, 293 K, 343 K and 363 K. LÄS MER

  4. 3. The effect of water on the orientation of a protein in an electric field

    Master-uppsats, Uppsala universitet/Institutionen för fysik och astronomi

    Författare :Gideon Elfrink; [2022]
    Nyckelord :Structure determination; Gromacs; tutorial; Molecular Dynamics; protein; ubiquitin;

    Sammanfattning : Structure determination of proteins is vital for the understanding of their function. It often relies on techniques that use intense X-ray pulses to create diffraction patterns of protein crystals, which then contain information on the three-dimensional structure of the crystallised protein. LÄS MER

  5. 4. Sustaining Orientation of Ubiquitin for Single Particle Imaging Using Electric Fields

    Kandidat-uppsats, Uppsala universitet/Kemisk och biomolekylär fysik; Uppsala universitet/Energimaterialens fysik

    Författare :Adi Bijedic; [2021]
    Nyckelord :;

    Sammanfattning : Single-particle imaging, or SPI, is a method used to obtain the three-dimensional structure of particles. Repeatedly aiming X-rays at samples of a particle produces diffraction patterns, which are combined to a best-fit three-dimensional model of the particle. SPI of proteins can be improved by orienting the protein before imaging. LÄS MER

  7. 5. Evaluating a coarse-grained IDP-model for structure and dynamics

    Kandidat-uppsats, Lunds universitet/Biofysikalisk kemi

    Författare :Louise Kalander; [2021]
    Nyckelord :IDP; Intrinsically disordered proteins; Histatin 5; Simulation; Biophysical chemistry; Chemistry;

    Sammanfattning : In this study a coarse-grained model of intrinsically disordered proteins (IDPs) is evaluated to determine whether the model is suitable to use for analyzing the structure and dynamics of IDPs. IDPs are proteins that lack a stable tertiary structure which gives them a flexible structure. LÄS MER