Related papers: Solvent quality and solvent polarity in polypeptid…
We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H2O}, cyclohexane \ce{cC6H12}, and \textit{n}-hexane…
The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid,…
Urea denatures proteins due to its strong tendency to dehydrate the first solvation shell via urea-residue preferential binding. However, even after extensive experimental and computational investigations, the influence of urea on the…
Using thermodynamics integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarity, ranging from the most polar water to the most non-polar cyclohexane. The amino acid side chain…
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
The mesoscopic modeling of three polysiloxanes in solution is reported in this work, with the purpose of predicting their physicochemical properties as functions of the quality of the solvent, so that a judicious choice of polymer/solvent…
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide…
A polymer network can imbibe water, forming an aggregate called hydrogel, and undergo large and inhomogeneous deformation with external mechanical constraint. Due to the large deformation, nonlinearity plays a crucial role, which also…
The density and orientational relaxation of bulk water can be separately studied by depolarized light scattering (DLS) and dielectric spectroscopy (DS), respectively. Here we ask the question of what are the leading collective modes…
We present an experimentally guided, multi-phase, multi-species polyelectrolyte gel model to make quantitative predictions on the electro-chemical properties of articular cartilage. The mixture theory consists of two different types of…
Surface creasing in swelling polymer gels is commonly attributed to compressive strain or interlayer mismatch, yet its general control remains unclear. Here we show that solvent polymerization degree $N_{\rm s}$ provides an independent…
Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone,…
We investigate the effects of solvent specificities on the stability of the native structure (NS) of a protein on the basis of our free-energy function (FEF). We use CPB-bromodomain (CBP-BD) and apoplastocyanin (apoPC) as representatives of…
We demonstrate in this paper the influence of solvent quality on the structure of the semi-dilute solution of a hydrophobic polyelectrolyte, partially sulfonated Poly-Styrene Sulfonate. Two solvents are used: (i) one mixture of water and an…
We investigate the reliability of simulations of polyelectrolyte systems in aqueous environments, simulations that are performed using an efficient multi scale coarse grained polarizable pseudo-particle particle approach, denoted as pppl,…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
We present an overview of the recent progress that has been made in understanding the origin of hydrophobic interactions. We discuss the different character of the solvation behavior of apolar solutes at small and large length scales. We…