Related papers: Depth dependent dynamics in the hydration shell of…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
We present a pressure dependence study of the dynamics of lysozyme protein powder immersed in deuterated $\alpha$,$\alpha$-trehalose environment via quasi-elastic neutron scattering (QENS). The goal is to assess the baro-protective benefits…
Mean square displacements of hydrogen atoms in glass-forming materials and proteins, as reported by incoherent elastic neutron scattering, show kinks in their temperature dependence. This crossover, known as the dynamical transition,…
We investigate the presence of structural collective motions on a picosecond time scale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time-domain spectroscopy and molecular dynamics…
The dynamic properties of fluid, including density, surface tension, diffusivity and viscosity, are temperature-dependent and can significantly influence the flow dynamics of mesoscopic non-isothermal systems. To capture the correct…
Here we reveal details of the interaction between human lysozyme proteins, both native and fibrils, and their water environment by intense terahertz time domain spectroscopy. With the aid of a rigorous dielectric model, we determine the…
We study the non-Markovian folding dynamics of the $\alpha$3D protein under low- and neutral-pH conditions. Recently published all-atom simulations of $\alpha$3D by the Shaw group reveal that lowering the pH significantly reduces both…
Molecular dynamics results on water confined in a silica pore in the low hydration regime are presented. Strong layering effects are found due to the hydrophilic character of the substrate. The local properties of water are studied as…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
To comprehend the complexities of the ice-water interface, we perform a study that attempts to correlate the altered dynamics of water to its perturbed structure at, and due to, the interface. The deviation from bulk values of structural…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…
In this work we examine thermodynamics of fluid with "molecules" represented by two fused hard spheres, decorated by the attractive square-well sites. Interactions between these sites are of short-range and cause association between the…
We use molecular dynamics computer simulations to investigate the relaxation dynamics of a simple model for a colloidal gel at a low volume fraction. We find that due to the presence of the open spanning network this dynamics shows at low…
A new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-RISM/RISM theory of molecular liquids. The…
Protein flotation is a process in which protein molecules are enriched by adsorption at rising bubbles. The bubbles then form a foam above the solution, where the liquid drains down and the dried foam, which is concentrated in protein, is…
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…
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…
The ultraviolet (UV) photodissociation of amorphous water ice at different ice temperatures is investigated using molecular dynamics (MD) simulations and analytical potentials. Previous MD calculations of UV photodissociation of amorphous…
A sharp change in apparent mobility at a characteristic temperature that depends on the observation time has been reported in experiments and simulations of hydrated proteins. Such behavior is often discussed in the context of the protein…