Related papers: Water at interface with proteins
The supercooled state of bulk water is largely hidden by unavoidable crystallization, which creates an experimentally inaccessible temperature regime - a 'no man's land'. We address this and circumvent the crystallization problem by…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
An information theory model is used to construct a molecular explanation why hydrophobic solvation entropies measured in calorimetry of protein unfolding converge at a common temperature. The entropy convergence follows from the weak…
Supercooling of water can be easily studied with a simple apparatus suitable for the student laboratory. We describe such an apparatus and its capabilities. The parameters influencing supercooling include the initial temperature 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…
While the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of…
Single particle dynamics of water confined in a nanopore is studied through Computer Molecular Dynamics. The pore is modeled to represent the average properties of a pore of Vycor glass. Dynamics is analyzed at different hydration levels…
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling…
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…
Water shapes and defines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biological systems is of primary importance for a proper assessment of biological activity and…
Water behaves very differently at surfaces and under extreme confinement, but the boundary between these two regimes has remained unclear. Despite evidence that interfacial effects persist under sub-nanometre confinement, the…
A core-softened model of a glass forming fluid is numerically studied in the limit of very low temperatures. The model shows two qualitatively different behaviors depending on the strength of the attraction between particles. For no or low…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
Water is a key ingredient for life and plays a central role as solvent in many biochemical reactions. However, the intrinsically quantum nature of the hydrogen nucleus, revealing itself in a large variety of physical manifestations,…
Molecular dynamics simulations are carried out to explore the dynamical crossover phenomenon in strongly confined and mildly supercooled water in graphene oxide nanopores. In contrast to studies where confinement is used to study the…
Surface freezing is a phenomenon in which crystallization is enhanced at a vapor-liquid interface. In some systems, such as $n$-alkanes, this enhancement is dramatic, and results in the formation of a crystalline layer at the free interface…
Performing molecular dynamics simulations, we investigate the enormous slowdowns of water dynamics when approaching a glass transition or a solid interface. We show that both effects can be described on common grounds within a theoretical…
An open question is whether the liquid and glassy phases of water are thermodynamically distinct or continuous. Here we address this question using molecular dynamics simulations in comparison with neutron scattering experiments to study…
Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…
Known physical mechanisms of temperature dependence anomalies of water properties were used to explain the regularities in temperature dependence (TDs) of dynamic, electrical and optical characteristics of biological systems. The dynamics…