Related papers: Role of solvent for globular proteins in solution
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
Experimental measurements of electron transport properties of molecular junctions are often performed in solvents. Solvent-molecule coupling and physical properties of the solvent can be used as the external stimulus to control electric…
We review the nature of glass transitions and the glasses arising from a square-well potential with a narrow and deep well. Our discussion is based on the Mode Coupling Theory, and the predictions of glasses that we make refer to the…
We have recently developed a simulation approach to calculate the equilibrium phase diagram of particle-based microphase formers. Here, this approach is used to calculate the phase behavior of the square-well linear model for different…
We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway…
Employing simplified models in computer simulation is on the one hand often enforced by computer time limitations but on the other hand it offers insights into the molecular properties determining a given physical phenomenon. We employ this…
The interaction between charged objects in solution is generally expected to recapitulate two central principles of electromagnetics: (i) like-charged objects repel, and (ii) they do so regardless of the sign of their electrical charge.…
In this paper we develop a theory to calculate the solvent mediated interaction potential between solute particles dispersed in a solvent. The potential is a functional of the instantaneous distribution of solute particles and is expressed…
Square water takes into account the directionality of hydrogen bonds. The model is reviewed and its properties as a solvent for apolar particles are studied through Monte Carlo simulations. Specific heat measurements are used to identify…
Deep learning based methods have been widely applied to predict various kinds of molecular properties in the pharmaceutical industry with increasingly more success. Solvation free energy is an important index in the field of organic…
We construct a mesoscale model of colloidal suspensions that contain solutes reversibly adsorbing onto the colloidal particle surfaces. The present model describes the coupled dynamics of the colloidal particles, the host fluid, and the…
We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies…
Asymmetric patchy particle models have recently been shown to describe the crystallization of small globular proteins with near quantitative accuracy. Here, we investigate how asymmetry in patch geometry and bond energy generally impact the…
In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and…
The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
In this paper, the authors study the limit of a sharp interface model for the solvation of charged molecules in an implicit solvent as the number of solute molecules and the size of the surrounding box tend to infinity. The energy is given…
We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer…
Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has thereby a large impact. Implicit…
We report a detailed simulation study of the phase behavior of core softened system with attractive well. Different repulsive shoulder widthes and attractive well depthes are considered which allows to monitor the influence of repulsive and…