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Showing 1 to 13 of 13 for “"Free Energy Calculation"”.
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Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
… discussed. A method of potential-of-mean-force calculation is developed; the method is based on the cumulant expansion of Jarzynski's equality and the scheme of using stiff springs for the purpose of steering. The possibility that the resulting work distribution might be Gaussian regardless of …
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Extracting Equilibrium From Nonequilibrium: Free Energy Calculation From Steered Molecular Dynamics Simulations
… discussed. A method of potential-of-mean-force calculation is developed; the method is based on the cumulant expansion of Jarzynski’s equality and the scheme of using stiff springs for the purpose of steering. The possibility that the resulting work distribution might be Gaussian regardless of …
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Development of Free Energy Calculation Methods for the Study of Monosaccharides Conformation in Computer Simulations
… means. This aspect explains the interest in free energy calculations, and methods exist, such as umbrella sampling or metadynamics, that allow to accelerate the sampling of different conformations by adding bias forces. In general, accelerated sampling methods are based on the choice of …
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Efficient Biomolecular Computations Towards Applications in Drug Discovery
… improve the accuracy of protein-ligand binding calculations in the implicit solvent framework. To address the problem (1) GBNSR6, an accurate yet efficient flavor of GB, has been thoroughly explored in the context of protein-ligand binding, (2) a global multidimensional optimization pipeline is …
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COMPUTATIONAL APPROACHES FOR PROTEIN FOLDING AND LIGAND BINDING: FROM THERMODYNAMICS TO KINETICS
… approaches. Alchemical methods, including free energy perturbation (FEP) and thermodynamic integration (TI), have become the dominant method for computing high-quality estimates of protein-ligand binding free energies. In particular, the widely-used approach of relative binding free energy …
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A Study of Rhamnolipid Microbubble Dispersion for Bioremediation Applications
… model was applied to quantify the interaction energy to better understand the bacteria/microbubble and bacteria/contaminant/microbubble interactions. The findings of the characterisation studies support that rhamnolipid microbubble dispersion had comparable properties to the synthetic …
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High-Sn-content GeSn Alloy towards Room-temperature Mid Infrared Laser
… dynamics, which was also confirmed by Gibbs free energy calculation. Following the discovered growth mechanism, a world-record Sn content of 22.3% was achieved. Even higher Sn content could be obtained if further continuous growth with the same recipe is conducted. </p> <p>The GeSn laser with …
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Markov state modeling of binding and conformational changes of proteins
… of dissociation rates from the combination of free energy calculation and direct MD simulation of the fast binding process. Two new statistical estimators TRAM and TRAMMBAR are developed to estimate a MSM from the joint data of both simulation types. In addition, a new analysis technique for …
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Modeling microstructural effects of deformation resistance and thermal conductivity
… field concept which is hard to use in atomistic calculations and becomes ill-defined when defect separations approach the nanometer scale. It is shown first that the change in a system's total Helmholtz free energy due to a defect's move can be approximated by a local quantity involving only …
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Structure and Property of Polymers and Biopolymers from Molecular Dynamic Simulations
… been investigated by protein-ligand docking, free energy calculation and MD simulations. It is the first time that glycan residues are found to be the binding pocket for small ligands. The novel binding pocket is different from the CBS binding site for protein A and protein G. We also found …
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Computational studies of membrane proteins: Structure, function and dynamics
… chloride channels is investigated by extensive free energy calculations on the single- and double-ion permeation through the conducting pore. The free energy profiles for Cl−, Br−, and NO3− ions suggest that the interactions between the ions and backbone amides near the ion-binding sites …
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Free energy calculations of protein-ligand complexes with computational molecular dynamics
Die präzise Berechnung der freien Bindungsenergien von Protein-Ligand Komplexen ist ein Fachbereich, an dem starkes wissenschaftliches Interesse besteht. Die Präzision solcher Berechnungen der freien Energie für große Systeme, wie z.B. Proteine, mittels Molekulardynamik Simulationen mit atomarer …
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Molecular insights into alternating access mechanism of secondary active transporters from molecular dynamics simulations
… time-dependent biased simulation and subsequent free energy calculation for state transition, illustrate that Na+ binding increases the free energy barrier along the OF–IF transition. All the results suggest that Na+ binding reshapes the free-energy landscape of the ion/protein complex, thereby …