Related papers: Change of Hydration Patterns upon RNA Melting Prob…
We perform molecular dynamics simulation of water using the TIP5P model to quantify structural order in both the first shell (defined by four nearest neighbors)and second shell (defined by twelve next-nearest neighbors) of a central water…
Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress relaxation in hydrated lysozyme…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding…
The use of micro-Raman spectroscopy, through chemical bond nano-scale probes, allows the changes in conformations (alpha helix -> beta sheet), chain orientation, disconnection of disulfide bonds (-20%) and the increase of intra and…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
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 crystalline structure of minerals due to the highly ordered assembly of its constituent atoms, ions or molecules confers a considerable hardness and brittleness to the materials. As a result, they are generally subject to fracture. Here…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
Interstellar and cometary ices play an important role in the formation of planetary systems around young stars. Their main constituent is amorphous solid water (ASW). Although ASW is widely studied, vibrational energy dissipation and…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…
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…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether…
Understanding the nature of solvated electrons is important in studying a range of chemical and biological phenomena. This study investigates the structural and dynamical behavior of an excess electron in water, examining different…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
From microactuators to biological tissues, non-porous materials with the ability to strongly expand when in contact with a solvent are ubiquitous. Consequently, the swelling of polymer systems such as hydrogel has received recently much…
The nanoscale structure of molecular assemblies plays a major role in many ($\mu$)-biological mechanisms. Molecular crystals are one of the most simple of these assemblies and are widely used in a variety of applications from…