Sökning: "umbrella sampling"

Visar resultat 1 - 5 av 10 avhandlingar innehållade orden umbrella sampling.

  1. 1. Computational Studies of Protein-ligand Systems Using Enhanced Sampling Methods

    Författare :Rongfeng Zou; Yaoquan Tu; Leif Eriksson; KTH; []
    Nyckelord :molecular dynamics; enhanced sampling; protein-ligand interactions; umbrella sampling; metadynamics; Teoretisk kemi och biologi; Theoretical Chemistry and Biology;

    Sammanfattning : This thesis focuses on studies of protein-ligand systems using enhanced sampling methods. In chapter I, I give a brief introduction to the time-scale problem and some enhanced sampling methods. In chapter II, the basics of MD simulation are reviewed. LÄS MER

  3. 2. Reaction-Diffusion kinetics of Protein DNA Interactions

    Författare :Anel Mahmutovic; Johan Elf; David van der Spoel; Pieter Rein ten Wolde; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; umbrella sampling; molecular dynamics; RDME; PDE; sliding; intersegment transfer; hopping; sterics; intersegment transfer; Biology with specialization in Molecular Biotechnology; Biologi med inriktning mot molekylär bioteknik;

    Sammanfattning : Transcription factors need to rapidly find one specific binding site among millions of nonspecific sites on the chromosomal DNA. In this thesis I use various aspects of reaction-diffusion theory to investigate the interaction between proteins and DNA and to explain the searching, finding and binding to specific operator sites. LÄS MER

  4. 3. Nitriles in Prebiotic Chemistry and Astrobiology

    Författare :Hilda Sandström; Chalmers tekniska högskola; []
    Nyckelord :MEDICIN OCH HÄLSOVETENSKAP; MEDICAL AND HEALTH SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; astrobiology; polymer chemistry; hydrogen cyanide; density functional theory; molecular dynamics; metadynamics; umbrella sampling; prebiotic chemistry;

    Sammanfattning : Life appeared on Earth within a billion years of the planet’s formation. How? - no one knows. Theories regarding the origin of life involve reactions of molecules predicted to have existed on early Earth in what is called prebiotic chemistry. LÄS MER

  5. 4. Semipermeable membrane devices as integrative tools for monitoring nonpolar aromatic compounds in air

    Författare :Hanna Söderström; Mats Tysklind; Per-Anders Bergqvist; Jochen F. Muller; Umeå universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Environmental chemistry; air pollution; alkyl-PAHs; atmosphere; bioavailability; boundary layer; diffusive sampling; emissions; integrative; membrane; monitoring; nitro-PAHs; PAHs; particles; passive samplers; PCBs; plants; PRCs; release rate; sampler design; sources; SPMDs; traffic; uptake rate; wind effect; wood burning; Miljökemi; Environmental chemistry; Miljökemi;

    Sammanfattning : Air pollutants pose a high risk for humans, and the environment, and this pollution is one of the major environmental problems facing modern society. Active air sampling is the technique that has been traditionally used to monitor nonpolar aromatic air pollutants. LÄS MER

  7. 5. Effects of landscape patterns on small mammal abundance

    Författare :Frauke Ecke; Luleå tekniska universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Landscape Ecology; Landskapsekologi;

    Sammanfattning : Several studies indicate a long-term decline in the numbers of voles in northern Fennoscandia. Altered land use and forest management practices have been proposed as possible causes of the decline. LÄS MER