Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 54 for “"Free energy calculations"”.
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Accelerating vibrational free energy calculations for anharmonic crystals
… problems: representing the vibrational potential energy surface, fitting the free parameters of that representation using electronic structure theory, and using the fitted representation to calculate the vibrational wavefunctions and the vibrational free energy. A number of developments to the …
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On free energy calculations using fluctuation theorems of work
… Ältere stochastische Methoden wie R. Zwanzig's Free Energy Perturbation und Ch. Bennett's Acceptance Ratio Methode wurden jüngst unter Ausnutzung der Jarzynski Gleichung und des Crooks'schen Fluktuationstheoremes verallgemeinert und verknüpfen derart die Verteilung der in einem …
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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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A comparative study between the cubic spline and b-spline interpolation methods in free energy calculations
… essential in computational science, as analytic calculations for large datasets are impractical. Using numerical methods, one can approximate the problem to solve it with basic arithmetic operations. Interpolation is a commonly-used method, inter alia, constructing the value of new data points …
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Toward accurate free energy calculations in biomolecular simulation: advances in Markov model reweighting and expanded ensemble method
… enhanced sampling methods for reliable free energy landscapes. In Chapter 2, we present the Bayesian Inference of Conformational Populations (BICePs) framework to reweight Markov state models constructed from extensive MD trajectories against nuclear magnetic resonance (NMR) …
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Simulations of carbohydrate conformational dynamics and thermodynamics
In this thesis, free energy calculations are employed to establish the conformation freedom of selected carbohydrates. The focus is on the biologically important (1-4)-linked glucans, although the α(1-1) α and α(1-6) linkages are also investigated. Two principal types of potential of mean force …
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Accelerated simulations and computer-aided drug design of membrane proteins
… simultaneous unconstrained enhanced sampling and free energy calculations. GaMD has been successfully applied to study physical pathways and mechanisms of protein folding and ligand binding of important membrane proteins. Based on the principles of GaMD, Ligand GaMD (LiGaMD) and Peptide GaMD …
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Computational Studies on Nucleic Acid-Ion Interactions in Droplets and Bulk Solution
… on DNA complexes. In the bulk solution, free energy calculations examine the binding of individual sodium and potassium ions to guanine quadruplexes; the thesis reports the values of the Gibbs free energy and the binding constants of each cation. Additionally, the free energy calculations …
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Monte Carlo Simulation Methods for Studying the Thermodynamics of Ligand Binding & Transfer Processes in Biomolecules
… important for the understanding of bioenergetic energy transduction. The results of this thesis are presented in five articles that are published in peer reviewed scientific journals. Manuscript A presents the Monte Carlo simulation software GMCT which was largely developed in this thesis. The …
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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
… 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 structure elasticity. A remarkably accurate …
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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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Advances in Computational Solvation Thermodynamics
… to develop improved methods for calculating the free energy, entropy and enthalpy of solvation from molecular simulations. Solvation thermodynamics of model compounds provides quantitative measurements used to analyze the stability of protein conformations in aqueous milieus. Solvation free …
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Atomistic insights into the structure, dynamics, and regulation of integral membrane proteins
… with enhanced sampling, structural modeling, and free energy calculations—were employed to investigate conformational dynamics, lipid modulation, and domain coupling mechanisms in membrane protein systems. In the first study, we present a complete structural model of the SARS-CoV-2 spike protein, …
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Biomolecular Simulations with Machine Learning Potentials
… of the true quantum mechanical potential energy surface. Over the last several years, machine learned forcefields have emerged as a powerful paradigm, replacing manual parametrisation with a purely data driven approach and learning to reproduce the outputs of more expensive electronic …
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A computational approach for the discovery and characterization of oligonucleotide aptamers for protein targets
… molecular dynamics simulations, and free energy calculations made it possible to develop the in-silico workflow. The work reported in this thesis covers the computational tools, algorithms, and methods developed and implemented to select high-affinity aptamers for SARS-CoV-2 …
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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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Phase equilibria from molecular simulation
… utilising advanced sampling methods and free energy calculations. This approach has led to the development of a foundation for understanding multicomponent crystal formation in terms of molecular affinities and packing, the characterisation of a set of soft coarse-grained potentials for …
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Molecular insights on the solvent effect of methanol additive in glycine polymorph selection
… of the least stable [Beta]-glycine polymorph. Free energy calculations through the Umbrella Sampling method show an increased stability of the centrosymmetric dimer structure ([alpha]-glycine growth unit) in the presence of the methanol additive. Even though the dimer structure is more stable …
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Computational modeling of melanin aggregation
… and density func- tional theory (DFT) calculations. The results of the MD simulations show that DHI-eumelanin aggregates through nanoscale stacking, and that water molecules are present as a shell around the aggregates. The aggre- gation process is affected by the concentration of the …
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Thermodynamics of metal hydrides for hydrogen storage applications using first principles calculations
… metal hydride thermodynamics. First, our calculations for examining the relation between the particle size of simple metal hydrides and thermodynamics of their decomposition reactions provide that the relation would depend on the total surface energy difference between a metal and its …
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