相关论文: The structural order of protein hydration water
I have investigated the structural and dynamic properties of water by performing a series of molecular dynamic simulations in the range of temperatures from 213 K to 360 K, using the Simple Point Charge-Extended (SPC/E) model. I performed…
The network connectivity in liquid water is revised in terms of electronic signatures of hydrogen bonds (HBs) instead of geometric criteria, in view of recent X-ray absorption studies. The analysis is based on ab initio molecular-dynamics…
A highly diluted aqueous solution of histamine was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and…
A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…
Hydrogen-bond forms a pair of asymmetric, coupled, H-bridged oscillators with ultra-short-range interactions and memory. hydrogen bond cooperative relaxation and the associated binding electron entrapment and nonbonding electron…
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the…
Fluids under extreme confinement exhibit unique structures and intermolecular bonding, distinct from their bulk analogs, driving innovative applications at the water-energy nexus. Probing confined water experimentally at the length scale of…
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…
We report on the direct measurement of the correlation times of the protein backbone carbons and proximal waters of hydration in mechanically strained elastin by nuclear magnetic resonance methods. The experimental data indicate a decrease…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
Combining the principal component analysis (PCA) of X-ray spectrum with MD simulations, we experimentally reveal the existence of three basic components in water. These components exhibit distinct structures, densities, and temperature…
Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is dominated by long range hydro(phobic/philic)…
The prototypical Hydrogen bond in water dimer and Hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by…
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…
We have investigated the effects of either distorting hydrogen bonds or removing proton degeneracy on the thermodynamic properties of a minimal model for associating liquids. The presence of two liquid phases and a density anomaly is…
Water is vital for life, and without it biomolecules and cells cannot maintain their structures and functions. The remarkable properties of water originate from its ability to form hydrogen-bonding networks and dynamics, which the…
A structural transformation in water upon compression was recently observed at the temperature $T=277$~K in the vicinity of the pressure $p \approx 2\;000$~Atm [R.M. Khusnutdinoff, A.V. Mokshin, J. Non-Cryst. Solids \textbf{357}, 1677…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
The effect of glycerol, water and glycerol-water binary mixtures on the structure and dynamics of biomolecules has been well studied. However, a lot remains to be learned about the effect of varying glycerol concentration and temperature on…
The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…