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Showing 1 to 11 of 11 for “"solvation free energy"”.
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Computer simulation of free energies to predict cis/trans equilibria of prolyl peptides and solvation free energies of phenylalanyl peptides
… of small peptides (Part II). In Part I, the free energy perturbation (FEP) method, using AMBER, was utilized to calculate the Gibbs free energy difference between <i>cis</i> and <i>trans</i> conformers of Ace-Tyr-Pro- NMe and Ace-Asn-Pro-NMe, from which the ratio of <i>cis</i> to <i>trans</i> …
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Numerical Methods for Computing the Free Energy of Coarse-Grained Molecular Systems
… develop algorithms that accurately compute the solvation free energy by using goal-oriented mesh refinement. Results indicating the benefits of goal-oriented refinement are presented.
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Finite element methods for implicit solvent models
… when applied to the problem of computing the solvation free energy for realistic molecules of varying size. The inclusion of steric effects is important in regions of high potential. Hence, we consider a modified PBE, in order to model these effects. We establish well-posedness of the weak …
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The SSIP approach to solvation
… for governing many processes, including solvation, protein ligand binding and crystallisation. Previously in the Hunter group, the Surface Site Interaction Point (SSIP) model of intermolecular interactions has been used to describe molecules as a set of discrete hydrogen bonding sites. In …
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Biophysical mechanisms of intrinsic protein disorder: lessons from a protein backbone model
… to study the thermodynamics, particularly free energy and entropy, that drive the collapse and aggregation of short IDRs as well as the mechanisms underlying structural transitions. To investigate these phenomena, we use a protein backbone model (i.e. oligoglycine) that has been …
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Modeling Hydrophobic Effects at different lengthscales
… separated, but interconnected problems: (1) How solvation free energy scales with a partical size that is charged? This problem has never been attempted to solve before despite its immense importance in colloidal and protein solutions (J. Wang, D. Bratko, K. Leung and A. Luzar, Hydrophobic …
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Developing predictive tools for solvent effects on thermodynamics and kinetics
… such as quantum chemistry can be used to compute solvation effects, but a high computational cost makes them unsuitable for large-scale applications. Furthermore, existing methods are largely limited to the predictions at room temperature. Data-driven approaches like group contribution and machine …
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Automatic Generation of Chemical Kinetic Models including Macromolecules in Multiphase Systems
… of active learning for building models for solvation-free energy is explored under various compositions of initial training sets and uncertainty estimation methods for data acquisition. The possibility of aiding data acquisition with unsupervised learning for active learning is also …
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Investigating the effect of charge hydration asymmetry and incorporating it in continuum solvation framework
… to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of …
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Folding and aggregation of amyloid peptides
… Aβ(25-35) dimers is unfavorable but driven by energy. The lower energy of fibril-like dimers arises from favorable intermolecular HBs and other electrostatic interactions which compete with a loss in entropy. Approximately 25 % of the entropic cost correspond to configurational entropy. The …
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Enzyme-Catalyzed Phosphoryl Transfer Reactions: Energetics of Transition States and Vanadate Analogues in Aqueous Solution
… structural and electronic analogue of phosphate. Solvation effects 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 …