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Showing 1 to 20 of 33 for “"steered molecular dynamics"”.
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Steered molecular dynamics: a tool to investigate molecular interactions
Steered molecular dynamics (SMD) induces unbinding of ligands and conformational changes in biomolecules on time scales accessible to molecular dynamics simulations. Time-dependent external forces are applied to a system, and the response of the system is analyzed. In this work, the application of …
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Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
… of mean force (an equilibrium property) from steered molecular dynamics simulations (a nonequilibrium process). Recently discovered Jarzynski's equality provides the theoretical basis. Derivations of Jarzynski's equality are reviewed and related theoretical issues are discussed. A method of …
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Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
… of mean force (an equilibrium property) from steered molecular dynamics simulations (a nonequilibrium process). Recently discovered Jarzynski’s equality provides the theoretical basis. Derivations of Jarzynski’s equality are reviewed and related theoretical issues are discussed. A method of …
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Application and Development of Molecular Dynamics Methods to Examine the Energy Landscapes of Protein Folding and Transient Protein -Protein Complexes
… sphaeroides was studied using full-atom Steered Molecular Dynamics. Initial translation of cytochrome c2 at various heights over the surface of the reaction center revealed a probable exit pathway. Steered Molecular Dynamics was used to pull cyt c2 along the proposed pathway. Analysis of …
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Computational studies on polyunsaturated fatty acid uptake and its effects on antimicrobial resistance
… were pulled through the membrane systems using steered molecular dynamics. The membrane permeability for each fatty acid was analyzed from the energy required to move the cationic peptide through the membrane as well as the response of the membrane structure as the peptide passed through. Future …
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Enforced Large-Scale Motions in Proteins
"Steered molecular dynamics (SMD) simulations are performed on several model biomolecular systems in order to promote large structural changes in each. External forces are applied to molecular dynamics simulations to promote ligand exit from bacteriorhodopsin, unraveling of titin and fibronectin …
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Investigating the Structure and Function of IGP Synthase
Using traditional and steered molecular dynamics (SMD) simulations, we induced the conduction of ammonia through the (beta/alpha)8 barrel of hisF. Repeated simulations in combination with Jarzynskis identity were used to determine the free energy landscape for ammonia conduction through hisF and …
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Molecular Mechanisms of Cell Adhesion
… the response of the complex to force, using steered molecular dynamics. Starting from the structure of the complex from the Ig1-Ig2-Ig3 fragment, we first equilibrate the complex in solvent and show that its actual end-to-end length is markedly larger than in the crystal structure. We then …
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Computational Investigations of Cellular Functions: Three Cases on Membrane Morphogenesis, Organization and Assembly of a Multi-Protein Complex, and the Molecular Origin of Muscle Elasticity
… chain. Through simulations employing equilibrium molecular dynamics, steered molecular dynamics, and free-energy calculations, the mechanical properties of a six-Ig domain of titin (I65-I70), for which a crystallographic structure is available, were investigated. The results reveal a soft tertiary …
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Bridging molecular and systems scales in membrane biology
… presented in my thesis use approaches based in molecular simulation, to study the influence of protein-lipid (Chapter 3) and protein-protein interactions (Chapter 4) on molecular diffusion in photosynthetic processes. The next two studies are focused on using non-equilibrium MD methods such as …
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MODELING OF INTERFACE STRENGTH AS WELL AS INTERFACE DEFORMATION BASED ON NANOMECHANICS AND DEVELOPMENT OF INTERFACE DATABASE SYSTEMS
… that combines explicit three-dimensional molecular dynamics simulations with finite element simulations that take into account explicit microstructure in a three-dimensional hierarchy. The analyses focus on the shear deformation that occurs in interfaces of such materials when overall …
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Molecular Dynamics Simulation of Force-Induced Protein Domain Unfolding
… protein domain unfolding has been studied by steered molecular dynamics simulations (SMD). Two pulling protocols were adopted in the simulation. SMD with constant velocity pulling protocol qualitatively reproduced atomic force microscopy (AFM) observation that immunoglobulin and fibronectin …
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Mechanical behavior and microstructure of self-assembling oligopeptide gels
… their mechanical properties are also examined. Steered molecular dynamics modeling was used to characterize the mechanical interaction between filaments, and a coarse-grained model was developed to extend the system to ordinary time scales. A microindentation assay was developed and used to …
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Insights for designing mechanochromic spiropyrans from first principles dynamics and minimum energy pathways
… materials. In this work, we use first principles dynamics and constrained optimization approaches to investigate the mechanochemical activity of a spiropyran molecule. When a particular bond is broken, the spiropyran changes color. In combination with an understanding of the specific reaction …
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Computational Investigation of Protein-Membrane Systems Involved in Cellular Trafficking
… time scales of 200 microseconds was observed in molecular dynamics simulations using a simplified, or ""coarse-grained"" description. An all-atom simulation of a 2.3-million-atom system covering 0.3 microsecond probed the dynamics of one specific BAR domain lattice in atomic detail. The second …
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Estudo de modelagem molecular de derivados de desoxiuridina como inibidores da dUTPase de Plasmodium falciparum.
… odium falciparum (EC 3.6.1.23) was chosen as the molecular target for th is study. We produced a complete structural model of Pf dUTPase (PDB ID: 1VYQ) by homology modeling, since the crystal structure stored in the Protein Data Bank s hows regions of undetermined conformation. In this work we …
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Refinement of the Docking Component of Virtual Screening for PPAR
… available T2D treatments. The computational molecular modeling methods used include molecular docking, molecular dynamics, steered molecular dynamics, and structure- and ligand-based pharmacophore modeling. Potential binders identified in the computational component funnel into wet-lab …
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Molecular Dynamics Study of Hormone Receptors Binding DNA and Hormones
"Molecular dynamics (MD) simulations are employed to examine the dynamic structural properties of modified DNA, binding of the estrogen receptor to specific and non-specific DNA, and binding/unbinding of hormones to/from retinoic acid receptor and thyroid hormone receptor. In the DNA dodecamer, …
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The Development and Application of Methods to Study the Evolution of Specificity, Allostery, and RNA -Protein Interactions in Translation
… profiles that represent the topology of the molecular phylogenetic tree of the homologous group. These biasless profiles were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. This enzyme was found to be involved …
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Molecular Dynamics Studies of the *Gating Mechanism of a Mechanosensitive Channel
… of an x-ray crystal structure of MscL, molecular dynamics simulations were carried out which have contributed to our understanding of the sequence of motions involved in MscL gating, suggested the likely form of the open state, and identified residues crucial in setting MscL's tension …
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