Related papers: Depth dependent dynamics in the hydration shell of…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…
Hydrodynamic interactions between particles confined in a liquid-filled linear channel are known to be screened beyond a distance comparable to the channel width. Using a simple analytical theory and lattice-Boltzmann simulations, we show…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a…
When analyzing the broadband absorption spectrum of liquid water (10^10 - 10^13 Hz), we find its relaxation-resonance features to be an indication of Frenkel's translation-oscillation motion of particles, which is fundamentally inherent to…
Elastic models of the glass transition relate the relaxation dynamics and the elastic properties of structural glasses. They are based on the assumption that the relaxation dynamics occurs through activated events in the energy landscape…
Hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls are studied under creeping-flow conditions. The many-particle friction matrix in this system is evaluated using our novel numerical…
Liquid-liquid phase separation is key to understanding aqueous two-phase systems (ATPS) arising throughout cell biology, medical science, and the pharmaceutical industry. Controlling the detailed morphology of phase-separating compound…
When a hydrophilic solute in water is suddenly turned into a hydrophobic species, for instance, by photoionization, a layer of hydrated water molecules forms around the solute on a time scale of a few picoseconds. We study the dynamic…
Molecular dynamics simulations of ultrathin water film confined between atomically flat rigid diamond plates are described. Films with thickness of one and two molecular diameters are concerned and TIP4P model is used for water molecules.…
The process of drying is a simple physical mechanism that drives a system to relax from one equilibrium point to another. The native states of the constituent particles in the droplets can be linked to the emergent morphological patterns…
When the hydration shell of a protein is filled with at least 0.6 gram of water per gram of protein, a significant anti-correlation between the vibrational free energy and the potential energy of energy-minimized conformers is observed.…
The relation between the frequency-dependent friction of a molecule in a liquid and the hydrodynamic properties of the liquid is fundamental for molecular dynamics. We investigate this connection for a water molecule moving in liquid water…
We use dynamic light scattering and computer simulations to study equilibrium dynamics and dynamic heterogeneity in concentrated suspensions of colloidal hard spheres. Our study covers an unprecedented density range and spans seven decades…
The microscopic description of the local structure of water remains an open challenge. Here, we adopt an agnostic approach to understanding water's hydrogen bond network using data harvested from molecular dynamics simulations of an…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter…