Related papers: Role of solvent for globular proteins in solution
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
We report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a…
Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…
We determine the phase diagram of mixtures of spherical colloids and neutral nonadsorbing polymers in the thermal crossover region between the $\theta$ point and the good-solvent regime. We use the generalized free-volume theory (GFVT),…
Thermodynamic perturbation theory is applied to the model of globular proteins studied by ten Wolde and Frenkel (Science 277, pg. 1976) using computer simulation. It is found that the reported phase diagrams are accurately reproduced. The…
We present a combined experimental and numerical study of the equilibrium cluster formation in globular protein solutions under no-added salt conditions. We show that a cluster phase emerges as a result of a competition between a long-range…
To better understand protein-solvent interaction we have analyzed a variety of physical and geometrical properties of the solvent-excluded surfaces (SESs) over a large set of soluble proteins with crystal structures. We discover that all…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
We address the problem of predicting the solvation free energy and equilibrium solvent density profile in fews minutes from the molecular density functional theory beyond the usual hypernetted-chain approximation. We introduce a bridge…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
In this work we examine thermodynamics of fluid with "molecules" represented by two fused hard spheres, decorated by the attractive square-well sites. Interactions between these sites are of short-range and cause association between the…
Using event driven molecular dynamics simulations, we study a three dimensional one-component system of spherical particles interacting via a discontinuous potential combining a repulsive square soft core and an attractive square well. In…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
The phase behavior of colloid-polymer mixtures, and of solutions of globular proteins, is often interpreted in terms of a simple model of hard spheres with short-ranged attraction. While such a model yields a qualitative understanding of…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
Describing chemical reactions in solution on a molecular level is a challenging task due to the high mobility of weakly interacting solvent molecules which requires configurational sampling. For instance, polar and protic solvents can…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Solvation free energy is an important design parameter in reaction kinetics and separation processes, making it a critical property to predict during process development. In previous research, directed message passing neural networks…
Understanding the role of self-propulsion on the conformational properties of active filamentous objects has relevance in biology. In this context, we consider a flexible bead-spring model polymer for which along with both attractive and…
A theoretical study on the phase behaviors of a polymer solution confined between two coaxial cylindrical walls is presented. For the case of a neutral inner cylinder, the spinodal point derived through the Gaussian fluctuation theory is…