Related papers: Role of solvent for globular proteins in solution
The ion-activated patchy particle model is an important theoretical framework to investigate the phase behaviour of globular proteins in the presence of multivalent ions. In this work, we study and highlight the influence of patch…
Particles added to a fluid interface can be used as a surface stabilizer in the food, oil and cosmetic industries. As an alternative to rigid particles, it is promising to consider highly deformable particles that can adapt their…
The computational modelling of reactions is simple in theory but can be quite tricky in practice. This article aims at the purpose of providing an assistance to a proper way of describing reactions theoretically and provides rough…
Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
The collapse and swelling behavior of a generic homopolymer is studied using implicit-solvent, explicit-cosolvent Langevin dynamics computer simulations for varying interaction strengths. The systematic investigation reveals that polymer…
The finite square potential well is a staple problem in introductory quantum mechanics. There is an extensive literature on the determination of the allowed energies, which requires the solution of a transcendental equation by numerical,…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
We present results of molecular simulations of a model protein whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate…
This paper characterizes sharp solute-solvent interfaces in hydrophobic environments, and there are three major ingredients. The first is the variational implicit solvent model (VISM) which establishes the free energy functional of…
In this work, an improved methodology for studying interactions of proteins in solution by small-angle scattering, is presented. Unlike the most common approach, where the protein-protein correlation functions $g_{ij}(r)$ are approximated…
We consider the van der Waals' free energy functional, with a scaling small parameter epsilon, in the plane domain given by the first quadrant, and inhomogeneous Dirichlet boundary conditions. The boundary data are chosen in such a way that…
This paper discusses Random Matrix Models which exhibit the unusual phenomena of having multiple solutions at the same point in phase space. These matrix models have gaps in their spectrum or density of eigenvalues. The free energy and…
The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work,…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
Quantum-mechanical van der Waals dispersion interactions play an essential role for both intra-protein and protein-water interactions -- the two main driving forces for the structure and dynamics of proteins in aqueous solution. Typically,…
We study structural and thermophysical properties of a one-dimensional classical fluid made of penetrable spheres interacting via an attractive square-well potential. Penetrability of the spheres is enforced by reducing from infinite to…
The surface tension, the adsorption, and the depletion thickness of polymers close to a single nonadsorbing colloidal sphere are computed by means of Monte Carlo simulations. We consider polymers under good-solvent conditions and in the…