Sökning: "all-atom models"

Visar resultat 1 - 5 av 12 avhandlingar innehållade orden all-atom models.

1. 1. Modelling Biomolecular Interactions of Protein Solutions : Combining Theories and Experiments

   Författare :Marco Polimeni; Beräkningskemi; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Molecular modelling; Protein Solutions; Bio-inorganic Interfaces; Coarse-Grained Models; All-Atom Models; MC simulations; MD simulations; Light Scattering LS ; Small-angle X-ray scattering SAXS ;

   Sammanfattning : Nowadays, interactions of proteins in salt solutions and at the interface with inorganic surfaces are widely investigated as their understanding has numerous applications in medical, pharmaceutical, and biotechnological industries. However, studying these interactions is a complex task that requires appropriate strategies. LÄS MER

3. 2. 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

4. 3. 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

5. 4. 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

7. 5. Coarse-Grained Models of Ionic Solutions

   Författare :Ryan Szparaga; Beräkningskemi; []
   Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Monte Carlo; Classical Density Functional Theory; Coarse-Grained Models; Ionic Liquids; Prewetting; Capillary Condensation; Electric Double Layer; Differential Capacitance.;

   Sammanfattning : Room-temperature ionic liquids (RTILs) are compounds composed entirely of ions, which are liquid at temperatures below 100 degrees Celsius. Their high ionic strength and strong coupling make them useful for a number of applications, e.g. as electrolytes in supercapacitors. LÄS MER