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Showing 1 to 7 of 7 for “"implicit solvation"”.
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Delaunay-Laguerre Geometry For Macromolecular Modeling And Implicit Solvation
… detailed analysis of parameters obtained by the implicit solvation method, Semi-Explicit Assembly (SEA). We introduce the concept of Laguerre-Intersection cells which consist of the intersection of the Laguerre tessellation and space-filling diagram. This method eliminates the need for explicit …
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COMPUTATIONAL MULTISCALE INVESTIGATIONS OF BIOLOGICAL MOLECULES
… the chapter delves into the theory of implicit solvation, as it plays a crucial role in some of the aforementioned models. Implicit solvation methods enable the efficient treatment of solvent effects without explicitly simulating water molecules, thereby reducing computational costs. …
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Molecular studies of aggrecan : experiments and simulations
… disc. This MD simulation study developed an implicit solvation model of three types of tetrasaccharides of both sulfated and unsulfated chondroitin, namely, chondroitin 4-sulfate (C4S), chondroitin 6-sulfate (C6S) and chondroitin (CN). In this model, water is treated implicitly as a continuum …
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The impact of protein fluctuations on molecular recognition
… applied the\r\neffects of excluded volume and implicit solvation. This energy function was utilized to\r\nweight an ensemble of conformational states from which aggregate thermodynamic\r\nproperties could be derived. The computed effects of the mutations on the binding\r\naffinity agreed with …
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Computational Studies of Protonated Cyclic Ethers and Benzylic Organolithium Compounds
… in THF solution. Incorporation of secondary solvation in the form of Onsager and PCM single-point calculations showed an increase in exothermicity of IPS. Application of a continuum solvation model (Onsager) during optimization at the B3LYP/6-31G* level of theory produced significant changes …
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A novel algorithm for creating density dependent, coarse-grained models for the simulation of surfactant systems
… on modifying the potentials to treat solvent implicitly. Implicit solvation is well-known in Brownian Dynamics of dilute solutions, but offers promise to speed up many other types of molecular simulations as well, including studies of proteins and colloids where the local density can vary …
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Investigating the effect of charge hydration asymmetry and incorporating it in continuum solvation framework
… the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial …