Related papers: Internal water and microsecond dynamics in myoglob…
Understanding the behavior of confined water at liquid-solid interfaces is central to numerous physical, chemical, and biological processes, yet remains experimentally challenging. Here, we utilize shallow nitrogen-vacancy (NV) centers in…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ \AA )…
Anisotropic fluids appear in a diverse array of systems, from liquid-crystal displays to bacterial swarms, and are characterized by orientational order. Large colloidal particles immersed in such environments disturb the medium's…
It has been shown that an anisotropic liquid crystalline (LC) environment can be used to guide the self-propulsion dynamics of dispersed microswimmers, such as bacteria. This type of composite system is named "living nematic" (LN). In the…
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…
Ligand diffusion through proteins is a fundamental process governing biological signaling and enzymatic catalysis. The complex topology of protein tunnels results in difficulties with computing ligand escape pathways by standard molecular…
The Internet of Bio-Nano Things (IoBNT) requires mobile nanomachines that navigate complex fluids while exchanging molecular signals under external supervision. We introduce the chemo-hydrodynamic transceiver, a unified model for catalytic…
Effects of presence of ions, at moderate to high concentrations, on dynamical properties of water molecules are investigated through classical molecular dynamics simulations using two well known non-polarizable water models. Simulations…
The object of this study is the kinetic process of solid-liquid first-order phase transition - melting of carbon dioxide CS-I hydrate with various cavity occupation ratios. The work was done within a framework of study on the local…
The dynamics of water molecules plays a vital role in understanding water. We combined computer simulation and deep learning to study the dynamics of H-bonds between water molecules. Based on ab initio molecular dynamics simulations and a…
Recent research has shown that motile cells can adapt their mode of propulsion depending on the environment in which they find themselves. One mode is swimming by blebbing or other shape changes, and in this paper we analyze a class of…
Hydrogen bond (H-bond) covalency has recently been observed in ice and liquid water, while the penetrating molecular orbitals (MOs) in the H-bond region of most typical water dimer system, (H2O)2, have also been discovered. However,…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present…
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…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
We theoretically investigate the magneto-optical (MO) properties of monolayer (ML) transition metal dichalcogenides (TMDs) in the presence of external electrical and quantizing magnetic fields and of the proximity-induced exchange…
In this study, we present a detailed analysis of the squeeze-out dynamics of nanoconfined water confined between two hydrophilic surfaces measured by small-amplitude dynamic atomic force microscopy (AFM). Explicitly considering the…
In this paper we present a review on our recent experimental investigations into the phase behavior of the deeply cooled water confined in a nanoporous silica material, MCM-41, with elastic neutron scattering technique. Under such strong…
We measure hydrodynamic interactions between colloidal particles confined in a thin sheet of fluid. The reduced dimensionality, compared to a bulk fluid, increases dramatically the range of couplings. Using optical tweezers we force a two…