Related papers: Role of solvent for globular proteins in solution
Thermoresponsive microgels are polymeric colloidal networks that can change their size in response to a temperature variation. This peculiar feature is driven by the nature of the solvent-polymer interactions, which triggers the so-called…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Using computer simulations, we validate a simple free energy model that can be analytically solved to predict the equilibrium size of self-limiting clusters of particles in the fluid state governed by a combination of short-range attractive…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
We study the swelling of a flexible linear chain composed of active particles by analytical theory and computer simulation. Three different situations are considered: a free chain, a chain confined to an external harmonic trap, and a chain…
We present a lattice model for polymer solutions, explicitly incorporating interactions with a bath of solvent and cosolvent molecules. By exploiting the well-known analogy between polymer systems and the $O(n)$-vector spin model in the…
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the…
We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…
The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
The design of a biodegradable, environmentally friendly surfactant is carried out, taking the structure of a known surfactant that lacks these qualities as the starting point, using mesoscopic computer simulations. The newly designed…
The dilute fluid phase of model globular proteins is studied. The model possesses a fluid-fluid transition buried within the fluid-crystal coexistence region, as do some globular proteins. If this fluid-fluid transition is not buried deep…
Using density functional theory we calculate the density profiles of a binary solvent adsorbed around a pair of big solute particles. All species interact via repulsive Gaussian potentials. The solvent exhibits fluid-fluid phase separation…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
We propose a minimal model for spherical proteins with aeolotopic pair interactions to describe the equilibrium phase behavior of lysozyme. The repulsive screened Coulomb interactions between the particles are taken into account assuming…
We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a…
We present a simple yet generic model for the behavior of a system of many surface-attached flexible polymers with rigid side chains. Beyond its potential application in describing the dynamics of the extracellular matrix of mammalian…