Related papers: Dynamical Transition and Heterogeneous Hydration D…
Over the years, plenty of classical interaction potentials for water have been developed and tested against structural, dynamical and thermodynamic properties. On the other hands, it has been recently observed (F. Martelli et. al,…
Using molecular dynamics simulations we study the dynamics of a water-like TIP5P model of water in hydrophilic and hydrophobic confinement. We find that in case of extreme nanocofinement such that there is only one molecular layer of water…
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…
New experiments for water at the surface of proteins at very low temperature display intriguing dynamic behaviors. The extreme conditions of these experiments make it difficult to explore the wide range of thermodynamic state points needed…
A few years ago it was showed that some systems that have very similar local structure, as quantified by the pair correlation function, exhibit vastly different slowing down upon supercooling [L. Berthier and G. Tarjus, Phys. Rev. Lett.…
We investigate hydrodynamic fluctuations in a 2D granular fluid excited by a vibrating base and in the presence of gravity, focusing on the transverse velocity modes. Since the system is inhomogeneous, we measure fluctuations in horizontal…
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…
Mossbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square…
We perform molecular dynamics simulations to investigate hydration structures and dynamics in seven water-containing polymers: PVA, PHEA, PHEMA, PBA, PMEMA, PEG, and PMEA. The analysis integrates four perspectives: the water-content…
We examine the behavior of the diffusion coefficient of the ST2 model of water over a broad region of the phase diagram via molecular dynamics simulations. The ST2 model has an accessible liquid-liquid transition between low-density and…
Understanding what happens inside the rippling and dancing surface of a liquid remains one of the great challenges of fluid dynamics. Using molecular dynamics (MD) we can pick apart the interface structure and understand surface tension. In…
Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of…
The evolution of non-hydrodynamic slow processes near the QCD critical point is explored with the novel Hydro+ framework, which extends the conventional hydrodynamic description by coupling it to additional explicitly evolving slow modes…
The dynamics of water in aqueous solutions of three homologous disaccharides, namely trehalose, maltose and sucrose, has been analyzed by means of molecular dynamics simulations in the 0-66 wt % concentration range. The low-frequency…
We employ the Distance Matrix method to investigate metabasin dynamics in supercooled water. We find that the motion of the system consists in the exploration of a finite region of configuration space (enclosing several distinct local…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
Solute-intercalation-induced phase separation creates spatial heterogeneities in host materials, a phenomenon ubiquitous in batteries, hydrogen storage, and other energy devices. Despite many efforts, probing intercalation processes at the…
The supra-molecular structure of a liquid is strongly connected to its dynamics which in turn controls macroscopic properties such as viscosity. Consequently, detailed knowledge about how this structure changes with temperature is essential…
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…