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Coarse-grained molecular dynamics modeling of associating fluids: Thermodynamics, liquid structure, and dynamics in the limit of zero association strength

Article Abstract:

A continuous coarse-grained potential model for associating fluids, consisting of an off-center specific site bonded with a harmonic potential to a center particle, is developed and used in canonical molecular dynamics simulations. The thermodynamic, structural and dynamic properties of the limiting nanoassociating reference coarse-grained fluid are investigated as functions of the mass distribution and bond strength between center and site particles.

Fluids, Atomic properties, Report

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Molecular thermodynamics for partitioning of native and denatured proteins in aqueous two-phase systems

Article Abstract:

A molecular-thermodynamic theory, established for partitioning of native and denatured proteins in aqueous two-phase systems, showed that the partition coefficient for a native (globular) protein is different from that for a denatured (linear) protein. The theory could also be used for describing partitioning of combination peptides(super 44,45) and of protein-peptide fusion tags(super 114-116) in aqueous two-phase systems.

Proteins, Chemical properties

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The effect of water displacement on binding thermodynamics: Concanavalin A

Article Abstract:

Water molecules are computed to the thermodynamic properties using statistical mechanical formulas for the energy and entropy and molecular dynamics simulations. It also computed other contributions to the binding affinity, including desolvation, entropy of conformational restriction, and interaction between the ligand and protein.

Pharmaceutical Preparation Manufacturing, Pharmaceutical preparations, Carbohydrates

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