Search for dissertations about: "metadynamics"

Showing result 1 - 5 of 10 swedish dissertations containing the word metadynamics.

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

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

    Abstract : 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. READ MORE

  4. 2. Theoretical Studies of Protein-Ligand Interactions

    Author : Kuang Guanglin; Tu Yaoquan; Bulone Vincent; David van der Spoel; KTH; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Binding free energy; molecular dynamics; molecular docking; metadynamics; nicotinic receptor; amyloid fibril; PH domain; Theoretical Chemistry and Biology; Teoretisk kemi och biologi;

    Abstract : The protein-ligand interaction is an important issue in rational drug design and protein function research. This thesis focuses on the study of protein-ligand interactions using various molecular modeling methods, which are used in combination to predict the binding modes and calculate the binding free energies of several important protein-ligand systems, as summarized below. READ MORE

  5. 3. Peering Beyond the Noise in Experimental Biophysical Data

    Author : Dari Kimanius; Erik Lindahl; Holger Stark; Stockholms universitet; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Cryo-EM; mitochondrial ribosome; SAXS; molecular dynamics; metadynamics; Biochemistry towards Bioinformatics; biokemi med inriktning mot bioinformatik;

    Abstract : Experimental protein structure determination methods make up a fundamental part of our understanding of biological systems. Manual interpretation of the output from these methods has been made obsolete by the sheer size and complexity of the acquired data. READ MORE

  6. 4. Computer simulation of materialsunder extreme conditions

    Author : Tymofiy Lukinov; Anatoly Belonoshko; Ivan Oleynik; KTH; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; ab initio; molecular dynamics; phase transition; metadynamics; Fysik; Physics;

    Abstract : Extreme conditions allow us to reveal unusual material properties. At the same time an experimental approach is di-cult under such conditions. Capabilities of a theoretical approach based on simplied models are limited. This explainsa wide application of computer simulations at extreme conditions. READ MORE

  7. 5. Nitriles in Prebiotic Chemistry and Astrobiology

    Author : Hilda Sandström; Chalmers tekniska högskola; []
    Keywords : 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;

    Abstract : 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. READ MORE