Related papers: Role of solvent for globular proteins in solution
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
We study the free energy landscape of the small peptide Met-enkephalin. Our data were obtained from a generalized-ensemble Monte Carlo simulation taking the interactions among all atoms into account. We show that the free energy landscape…
Implicit electron-density solvation models based on joint density-functional theory offer a computationally efficient solution to the problem of calculating thermodynamic quantities of solvated systems from firstprinciples quantum…
In this study, we assess the influence of solvation on the accuracy and reliability of nuclear shielding calculations for amino acids in comparison to experimental data. We focus particularly on the performance of solvation methods for…
The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly.…
Pair potentials that are bounded at the origin provide an accurate description of the effective interaction for many systems of dissolved soft macromolecules (e.g., flexible dendrimers). Using numerical free-energy calculations, we…
The expression for the higher temperature dependence of the mean squared displacement in proteins is obtained. The quantum multi-well model explains the dynamic transitions of the proteins and minimizes the amount of parameters to a single…
The influence of poor solvent quality on fluid demixing of a model mixture of colloids and nonadsorbing polymers is investigated using density functional theory. The colloidal particles are modelled as hard spheres and the polymer coils as…
We study the two-point correlation function in the model of branched polymers and its relation to the critical behaviour of the model. We show that the correlation function has a universal scaling form in the generic phase with the only…
We present one dimensional potentials $V(x)= V_0[e^{2|x|/a}-1]$ as solvable models of a well $(V_0>0)$ and a barrier ($V_0<0$). Apart from being new addition to solvable models, these models are instructive for finding bound and scattering…
We deduce the qualitative phase diagram of a long flexible neutral polymer chain immersed in a poor solvent near an attracting surface using phenomenological arguments. The actual positions of the phase boundaries are estimated numerically…
A square-lattice model for the formation of secondary structures in proteins, the hydrogen-bonding model, extended to include the effects of solvent quality, is examined in the framework of the Bethe approximation.
Chemically-responsive polymers are macromolecules that respond to local variations of the chemical composition of the solution by changing their conformation, with notable examples including polyelectrolytes, proteins and DNA. The polymer…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
The structural properties of fluids whose molecules interact via potentials with a hard-core plus n piece-wise constant sections of different widths and heights are derived using a (semi-analytical) rational-function approximation method.…
We consider the phase diagram of self-avoiding walks (SAW) on the simple cubic lattice subject to surface and bulk interactions, modeling an adsorbing surface and variable solvent quality for a polymer in dilute solution, respectively. We…
We study the equilibrium properties of a flexible homopolymer where consecutive monomers are represented by impenetrable hard spheres that are tangent to each other, and non-consecutive monomers interact via a square-well potential. To this…
We investigate the swelling and shrinking of L_beta lamellar gel phases composed of surfactant and fatty alcohol after contact with aqueous poly(ethylene-glycol) solutions. The height change $\Delta h(t)$ is diffusion-like with a swelling…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Generalized symmetric Woods-Saxon potential (GSWSP) energy well has a significant importance not only in nuclear physics but also in atomic and molecular physics. A GSWSP energy well takes the surface effects (describing e.g. repulsive…