Molecular dynamics simulations phd thesis

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Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please [email protected] Recommended Citation Li, Peng, "Molecular dynamics simulation of Chlorotoxin" ().Graduate Theses and Dissertations. Author: Peng Li. Molecular dynamics simulation study of lipid membranes using coarse-grained models: Authors: Zhang, Yawen: Item Type: Thesis or dissertation: Abstract: In this work we use coarse-grained molecular dynamics simulations to investigate how lipid composition affects the phase transition of phospholipid bilayers. THE INTERACTION THERMODYNAMICS OF AMINO ACIDS IN MOLECULAR DYNAMICS SIMULATIONS by Mark Stephen Miller A thesis submitted in partial fulfillment of the requirements for the Doctor of Philosophy degree in Biochemistry in the Graduate College of The University of Iowa August Thesis Advisor: Professor Adrian H. Elcock.

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Work group: IAS-5 - Computational Biomedicine Area of research: Diploma & Master Thesis Starting date: Contract time limit: Job description: Master thesis on the molecular dynamics simulations of intrinsically disordered proteins | EURAXESS Serbia. Work group: IAS-5 - Computational Biomedicine Area of research: Diploma & Master Thesis Starting date: Contract time limit: Job description: Master thesis on the molecular dynamics simulations of intrinsically disordered proteins | EURAXESS. Molecular dynamics (MD) simulation is a fundamental approach to allow researchers to study the molecular interactions of protein-ligand binding via the dynamics of protein-ligand complexes at atomic level. It can be observed precisely the motion of atoms and interactions involved in receptor and ligand binding using MD simulations.

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Presented in this thesis are the results from an integrated experimental and modeling study on damage cascade formation in ion bombarded solids. The molecular dynamics (MD) simulations were performed by using LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). Thesis Overview 4 2. MOLECULAR DYNAMICS SIMULATIONS OF POLYMERS 6 From Statistical Mechanics to Molecular Simulations 6 The Molecular Dynamics Technique 8 Equations of Motion 9 A) Higher Order – Gear Method 11 B) Verlet Methods 12 MD in NVT, NPT ensembles 14 A) Nosé – Hoover Thermostat THE INTERACTION THERMODYNAMICS OF AMINO ACIDS IN MOLECULAR DYNAMICS SIMULATIONS by Mark Stephen Miller A thesis submitted in partial fulfillment of the requirements for the Doctor of Philosophy degree in Biochemistry in the Graduate College of The University of Iowa August Thesis Advisor: Professor Adrian H. ElcockAuthor: Mark Stephen Miller.

Spiral: Molecular dynamics simulation study of lipid membranes using coarse-grained models
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Type Ph.D. thesis Text and layout Thomas P. Nygaard E-mail [email protected] Thesis title Molecular dynamics simulations of Escherichia coli ammonia channel AmtB Thesis submitted June Department of Chemistry Technical University of Denmark (DTU), Kgs. Lyngby, Denmark Defense & approval October Supervisors (DTU) Gun¨ ther H. Peters. A Molecular Dynamics Simulation-Isothermal Titration Calorimetry Study of Antimicrobial Peptide-Peptide Interaction by Shaghayegh Vafaei A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Biophysics Guelph, Ontario, Canada c Shaghayegh Vafaei, January, Thesis Overview 4 2. MOLECULAR DYNAMICS SIMULATIONS OF POLYMERS 6 From Statistical Mechanics to Molecular Simulations 6 The Molecular Dynamics Technique 8 Equations of Motion 9 A) Higher Order – Gear Method 11 B) Verlet Methods 12 MD in NVT, NPT ensembles 14 A) Nosé – Hoover Thermostat

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Molecular simulations indicated that this conformation is a low-free-energy state and a favorable design feature for other distinct orexin receptor antagonists. Computer modeling can be used to identify the lowest energy conformation of a molecule in solution, which can be dicult to achieve experimentally. The first to introduce molecular dynamics simulations were Alder and Wainwright in [AW57] for hard spheres. Since then the field has evolved significantly and now complex molecular systems, polymers, DNA filaments, etc. can be simulated with the use of appropriate models and rapidly growing computational algorithms and computer hardware. Phonons and molecular dynamic simulation provide valuable tools to study the molecular systems under different structure forms. They are helpful to study graphene ribbons and defects. On the other hand, many machine learning techniques were extensively used to analyse the enormous amounts of data resulted from the molecular simulations.