Sökning: "all-atom model"

Visar resultat 1 - 5 av 11 avhandlingar innehållade orden all-atom model.

  1. 1. Modeling of Protein Folding and Genetic Networks

    Författare :Fredrik Sjunnesson; Beräkningsbiologi och biologisk fysik - Genomgår omorganisation; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Matematisk och allmän teoretisk fysik; thermodynamics; two-state folding; Protein folding; all-atom model; Mathematical and general theoretical physics; Kauffman model.; local update; Monte Carlo; classical mechanics; quantum mechanics; relativity; statistical physics; gravitation; klassisk mekanik; kvantmekanik; relativitet; statistisk fysik; termodynamik; Fysicumarkivet A:2003:Sjunnesson;

    Sammanfattning : Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple. LÄS MER

  3. 2. Protein dynamics: aggregation and mechanical unfolding

    Författare :Simon Mitternacht; Beräkningsbiologi och biologisk fysik - Genomgår omorganisation; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Monte Carlo simulations; All-atom protein models; Mechanical unfolding; Protein aggregation;

    Sammanfattning : The subject of this thesis is protein dynamics. Papers I--IV and VI study either of two different processes: mechanical unfolding and aggregation. Paper V presents a computationally efficient all-atom model for proteins, variants of which are used to perform Monte Carlo simulations in the other papers. LÄS MER

  4. 3. Fighting microbial infections with force fields: Evaluating conformational ensembles of intrinsically disordered proteins

    Författare :Stephanie Jephthah; Beräkningskemi; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; molecular dynamics; force field; Monte Carlo; coarse-grained modeling; simulation; intrinsically disordered protein; histatin 5; small-angle x-ray scattering; circular dichroism; atomistic MD simulations; all-atom protein models;

    Sammanfattning : The main goal of this compilation thesis has been to investigate the conformational ensemble of the intrinsically disordered protein (IDP) histatin 5 by using a mixture of experimental and computational techniques including, but not limited to, small-angle X-ray scattering (SAXS), circular dichroism (CD) spectroscopy, atomistic molecular dynamics (MD) simulations, and coarse-grained Monte Carlo (MC) simulations. Histatin 5 is a peptide of particular interest for two reasons. LÄS MER

  5. 4. Statistical Physics of Protein Folding and Aggregation

    Författare :Giorgio Favrin; Beräkningsbiologi och biologisk fysik - Genomgår omorganisation; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Two State; Physics; Fysik; Statistics; operations research; programming; aktuariematematik; programmering; operationsanalys; actuarial mathematics; Statistik; Simulations; Aggregation; Protein Folding; Fysicumarkivet A:2004:Favrin;

    Sammanfattning : The mechanisms of protein folding and aggregation are investigated by computer simulations of all-atom and reduced models with sequence-based potentials. A quasi local Monte Carlo update is developed in order to efficiently sample proteins in the folded phase. LÄS MER

  7. 5. Modelling anisotropic interactions in colloidal systems

    Författare :Alexei Abrikossov; Fysikalisk kemi; []
    Nyckelord :SIMULATION; Modelling; electrostatic interactions; Colloids; Statistical mechanics; SIMULATION; Modelling; electrostatic interactions; colloid; Statistical mechanics;

    Sammanfattning : There has been an increased interest to design “smart materials” which can self-assemble into complex structures in accordance to external factors such as for example electromagnetic fields. By designing particles with directional interactions one is able to control how particles will interact with each other. LÄS MER