Related papers: Role of solvent for globular proteins in solution
The phase diagram of the penetrable square-well fluid is investigated through Monte Carlo simulations of various nature. This model was proposed as the simplest possibility of combining bounded repulsions at short scale and short-range…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
The structural and thermodynamic properties of fluids whose molecules interact via potentials with a hard-core plus a square well, a square shoulder, and a second square well, are considered. Those properties are derived by using a…
We construct a new phase-field model for the solvation of charged molecules with a variational implicit solvent. Our phase-field free-energy functional includes the surface energy, solute-solvent van der Waals dispersion energy, and…
Confinement can have a dramatic effect on the behavior of all sorts of particulate systems and it therefore is an important phenomenon in many different areas of physics and technology. Here, we investigate the role played by the softness…
We develop a simple correspondence between hydrophobic surface topology of globular proteins and and an effective protein-protein adhesiveness parameter of the Baxter type. We discuss within this framework analytical interpretation of the…
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…
Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models…
We discuss the effects of the solvent composition on the helix-coil transition of a polypeptide chain. We use a simple model to demonstrate that improving the hydrogen-bonding ability of the solvent can make the transition less cooperative,…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a molecular interaction…
Starting from a protein solution which is metastable with respect to the crystalline phase, the effect of adding semidilute non-adsorbing polymer is considered. It is found to increase the chemical potential of the protein by a few tenths…
Solutions of interacting linear polymers are mapped onto a system of ``soft'' spherical particles interacting via an effective pair potential. This coarse-graining reduces the individual monomer-level description to a problem involving only…
Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in center-dependent…
We studied the Soret effect in binary dimer-monomer mixtures using non-equilibrium molecular dynamics simulations and investigated the pure contribution of the internal degree of freedom of flexible molecules to the Soret effect. We…
Monte Carlo computer simulations are used to study transient cavities and the solvation of hard-spheroid solutes in dipolar hard sphere solvents. The probability distribution of spheroidal cavities in the solvent is shown to be well…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
We study a mesoscopic model of a chemically active colloidal particle which on certain parts of its surface promotes chemical reactions in the surrounding solution. For reasons of simplicity and conceptual clarity, we focus on the case in…
The free energy of globular protein chain is considered to be a functional defined on smooth curves in three dimensional Euclidean space. From the requirement of geometrical invariance, together with basic facts on conformation of helical…
Rapid and accurate assessment of protein structural models is essential for protein structure prediction and design. Great progress has been made in this regard, especially by recent development of ``knowledge-based'' potentials. Various…