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 9 of 9 for “"Free Energy Surfaces"”.
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Single molecule optical absorption by STM and a new algorithm for solving dynamics on a free energy surface
… and kinetic data to the dynamics on free energy surfaces can be cumbersome for all but the most trivial of cases. Many models have been developed to explain a variety of phenomena, but few methods are appropriate for cases with low kinetic barriers. Those methods that do fit free …
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Aqueous systems from first-principles : structure, dynamics and electron-transfer reactions
… fully from first-principles the diabatic free-energy surfaces of electron-transfer reactions. The excitation energy corresponding to the transfer of an electron at any given ionic configuration (the Marcus energy gap) is accurately assessed within ground-state density-functional theory via …
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A stereoelectronic and thermodynamic study of b-D-methyl glucose conformational changes related to anomeric centre reactivity
… to uncover details of the glucose ring pucker free energy volumes. The free energy volumes were computed using the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method. The bond stretch of the C1-O1 bond in -D-methyl glucose serves as a sugar model for hydrolysis, following the …
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Enzyme-Catalyzed Phosphoryl Transfer Reactions: Energetics of Transition States and Vanadate Analogues in Aqueous Solution
… are significant contributors to the reaction free energies and activation barriers of organic phosphate hydrolysis reactions. The methanolysis of dimethyl phosphate (DMP) and dimethyl vanadate (DMV) as well as acetyl phosphate (AcP) and acetyl vanadate (AcV) are modeled in aqueous solution to …
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A comparative study between the cubic spline and b-spline interpolation methods in free energy calculations
… Among many scientific research fields, free energy calculations particularly stand out for their use of interpolation methods. Numerical interpolation was implemented in free energy methods for many purposes, from calculating intermediate energy states to deriving forces from free energy …
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Dynamics and Electrostatics of Membrane Proteins using Polarizable Molecular Dynamics Simulations
… Additionally, we show differences in the free energy surfaces of permeation for aromatic, polar, and negatively charged species reliant upon force field used. For secondary structure, we showed key interactions which aided to stabilize model helices in bilayers. Finally, we showed …
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The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
… realistic glycobiological condensed phase free energy computation. Ab-initio pucker free energy surfaces/volumes of !-Ribofuranose and !-Glucopyranose in vacuum and in water were computed. These are the first converged Hartree-Fock/MM free energy simulations for these carbohydrates …
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Energy Landscapes for Protein Folding
… systems, via approaches based on the potential energy landscape (PEL) framework. By applying geometry optimisation techniques, the PEL is discretised into stationary points (i.e.~low-energy minima and the transition states that connect them). Essentially, minima characterise the low-lying …
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Inverse design of self-assembling colloids via landscape engineering
… framework capable of rationally manipulating the free energy landscape for self-assembly to derive building blocks that preferentially form into a target aggregate structure. The methodologies derived within are applicable to a wide class of self-assembly systems, both simulated and experimental, …