Related papers: Microscopic mechanism for cold denaturation
Electronic excitations near the surface of water ice lead to the desorption of adsorbed molecules, through a so far debated mechanism. A systematic study of photon-induced indirect desorption, revealed by the spectral dependence of the…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
Exploring the protein-folding problem has been a long-standing challenge in molecular biology. Protein folding is highly dependent on folding of secondary structures as the way to pave a native folding pathway. Here, we demonstrate that a…
We present an overview of the recent progress that has been made in understanding the origin of hydrophobic interactions. We discuss the different character of the solvation behavior of apolar solutes at small and large length scales. We…
The efficacy of cryopreservation is constrained by the difficulty of achieving sufficiently high intracellular concentrations of cryoprotective solutes without inducing osmotic injury or chemical toxicity during loading. This thermodynamic…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
We study numerically an atomistic model which is shown to exhibit a one--step crystal--to--amorphous transition upon decompression. The amorphous phase cannot be distinguished from the one obtained by quenching from the melt. For a…
The decoupling and freeze-out of energetic nuclear collisions is analysed in terms of transparent semi-classical decoupling formulae. They provide a smooth transition and generalise frequently employed instantaneous freeze-out procedures.…
The hydrophobic effect (HE) is commonly associated with the demixing of oil and water at ambient conditions and plays the leading role in determining the structure and stability of biomolecular assembly in aqueous solutions. On the…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
The fundamental law for protein folding is the Thermodynamic Principle: the amino acid sequence of a protein determines its native structure and the native structure has the minimum Gibbs free energy. If all chemical problems can be…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
The low kinetic friction between ice and numerous counterbodies is commonly attributed to an interfacial water layer, which is believed to originate from pre-existing surface water or from melt water induced by high contact pressures or…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
The efficiency of soft particles to stabilize emulsions is examined by measuring their desorption free energy, i.e., the mechanical work required to detach the particle from a fluid interface. Here, we consider rubber-like elastic as well…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…