Related papers: Temperature-dependent mechanisms for the dynamics …
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
The long debated protein dynamical transition was recently found also in non-biological macromolecules, such as poly-N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description…
Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the…
We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both…
Water shows numerous thermodynamic, dynamic, and structural anomalies. Recent experiments [Eichler et al. Phys. Rev. Lett. 134, 134101 (2025)], based on measurements of shear and bulk viscosities of liquid water up to 1.6 GPa, have reported…
We study the evolution of dynamic fluctuations averaged over different space lengths and time scales to characterize spatially and temporally heterogeneous behavior of TIP4P/2005 water in liquid and supercooled states. Analysing a million…
The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…
The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 K and 400 K.…
Performing molecular dynamics simulations for all-atom models, we characterize the conformational and structural relaxations of poly(ethylene oxide) and poly(propylene oxide) melts. The temperature dependence of these relaxation processes…
Using Monte Carlo simulations and mean field calculations for a cell model of water we find a dynamic crossover in the orientational correlation time $\tau$ from non-Arrhenius behavior at high temperatures to Arrhenius behavior at low…
We report a detailed computational study by Brownian Dynamics simulations of the structure and dynamics of a liquid of patchy particles which develops an amorphous tetrahedral network upon decreasing temperature. The highly directional…
The protein dynamical transition is investigated as a function of protein structure using terahertz time domain spectroscopy (THz-TDS). Measurements performed for native state and denatured hen egg white lysozyme (HEWL) show that protein…
In the present study, water is considered as a dynamic network between molecules at distances not exceeding 3.2 angstroms. The instantaneous configurations obtained by using the molecular dynamics method have been sequentially analyzed, the…
We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy…
The interactions between water and hydroxyl species on Pt(111) surfaces have been intensely investigated due to their importance to fuel cell electrocatalysis. Here we present a room temperature molecular dynamics study of their structure…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
We study the dynamics of water confined between hydrophobic flat surfaces at low temperature. At different pressures, we observe different behaviors that we understand in terms of the hydrogen bonds dynamics. At high pressure, the formation…
We investigate the curvature-dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both, the lateral and perpendicular diffusivity as well as for H-bond kinetics of water in…
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…