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We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…
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…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
Purpose: To develop an approach for improving the resolution and sensitivity of hyperpolarized 13C MRSI based on a priori anatomical information derived from featured, water-based 1H images. Methods: A reconstruction algorithm exploiting 1H…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…
The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond…
Studies of liquid water in its supercooled region have led to many insights into the structure and behavior of water. While bulk water freezes at its homogeneous nucleation temperature of approximately 235 K, for protein hydration water,…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Post-translational modifications (PTMs) play essential roles in regulating protein structure, function, and cellular signalling. However, peptide level discrimination of hydroxylation at the single-molecule level remains difficult. Here, we…
The hydrogen-bond (H-bond) network of high-pressure water is investigated by neural-network-based molecular dynamics (MD) simulations with the first-principles accuracy. The static structure factors (SSFs) of water at three densities, i.e.,…
Past research has conclusively shown that confined pockets of water exhibit properties that differ from those of unconfined ("bulk") water. The differences between confined water and bulk, as well as between different types of confined…
Water's ability to self-dissociate into H$_3$O$^+$ and OH$^-$ ions is central to acid-base chemistry and bioenergetics. Recent experimental advances have enabled the confinement of water down to the nanometre scale, even to the…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic…
This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
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…