Related papers: Dynamical Transition and Heterogeneous Hydration D…
The local hydration around tetrameric Hb in its T$_0$ and R$_4$ conformational substates is analyzed based on molecular dynamics simulations. Analysis of the local hydrophobicity (LH) for all residues at the $\alpha_1 \beta_2$ and $\alpha_2…
The structure of liquid water in the proximity of an interface can deviate significantly from that of bulk water, with surface-induced structural perturbations typically converging to bulk values at about ~1 nm from the interface. While…
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…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
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…
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin and dimeric melittin. For the T0 to R0 transition in Hb it is found that LH provides additional molecular-level insight into…
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
We investigate dynamical heterogeneities in the collective relaxation of a concentrated microgel system, for which the packing fraction can be conveniently varied by changing the temperature. The packing fraction dependent mechanical…
Cell monolayers and epithelial tissues display slow dynamics during the liquid-glass transitions, a phenomenon with direct relevance to embryogenesis, tumor metastases, and wound healing. In active cells, persistent motion and cell…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
To elucidate the possible role of structural waters in stabilizing bent DNA, various conformations of AT-containing decamers, (A5T5)2 and A10:T10, were studied by Monte Carlo simulations. The duplexes were constrained to reproduce the NMR…
Supercooled liquids exhibit spatial heterogeneity in the dynamics of their fluctuating atomic arrangements. The length and time scales of the heterogeneous dynamics are central to the glass transition and influence nucleation and growth of…
Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular…
Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although the number of water molecules near the membrane fluctuates dynamically, the…
Graphene nanochannels are relevant for their possible applications, as in water purification, and for the challenge of understanding how they change the properties of confined liquids. Here, we use all-atom molecular dynamics simulations to…
The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a…
Understanding the hydration and diffusion of ions in water at the molecular level is a topic of widespread importance. The ammonium ion (NH$_4^+$) is an exemplar system that has received attention for decades because of its complex…
The in silico exploration of chemical, physical and biological systems requires accurate and efficient energy functions to follow their nuclear dynamics at a molecular and atomistic level. Recently, machine learning tools gained a lot of…
A key objective in DNA-based material science is understanding and precisely controlling the mechanical properties of DNA hydrogels. We perform microrheology measurements using diffusing-wave spectroscopy (DWS) to investigate the…