Related papers: Microscopic mechanism for cold denaturation
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Studying the properties of the solvent around proteins, we propose a much more sophisticated model of solvation than temperature-independent pairwise interactions between monomers, as is used commonly in lattice representations. We applied…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
The avoidance of water freezing is the holy grail in the cryopreservation of biological samples, food, and organs. Fast cooling rates are used to beat ice nucleation and avoid cell damage. This strategy can be enhanced by applying high…
Ice formation is one of the most common and important processes on earth and almost always occurs at the surface of a material. A basic understanding of how the physicochemical properties of a material's surface affect its ability to form…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple…
A high level polarizable force field is used to study the temperature dependence of hydrophobic hydration of small-sized molecules from computer simulations. Molecular dynamics (MD) simulations of liquid water at various temperatures form…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
The solvation of charged, nanometer-sized spherical solutes in water, and the effective, solvent-induced force between two such solutes are investigated by constant temperature and pressure Molecular Dynamics simulations of model solutes…
We show that two-dimensional systems of deformable particles undergo a continuous liquid-hexatic transition upon compression or cooling, but no hexatic-solid transition-even at zero temperature and high density. Numerical simulations reveal…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
We discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We…
Conventional molecular dynamics simulation has been used to determine melting temperature of highly compressed classical molecular hydrogen in a wide range of pressures and temperatures using non-empirical atom-atom potentials…