Related papers: Equilibrium Clusters in Concentrated Lysozyme Prot…
We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with $10^9$ atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent…
In the present work, we provide a dielectric study on two differently concentrated aqueous lysozyme solutions in the frequency range from 1 MHz to 40 GHz and for temperatures from 275 to 330 K. We analyze the three dispersion regions,…
The formation history of rich clusters is investigated using a hybrid N-body simulation in which high spatial and mass resolution can be achieved self-consistently within a small region of a very large volume. The evolution of three massive…
A simple extension of existing models for protein crystallisation is described, in which salt ions and charge neutrality are explicitly incorporated. This provides a straightforward explanation for the shape of protein crystallisation…
We study at- and out-of-equilibrium dynamics of a single homopolymer chain at low temperature using molecular dynamics simulations. The main quantities of interest are the average root mean square displacement of the monomers below the…
We consider homogeneous crystallisation rates in confocal microscopy experiments on colloidal nearly hard spheres at the single particle level. These we compare with Brownian dynamics simuations by carefully modelling the softness in the…
We report theoretical and simulation studies of phase coexistence in model globular protein solutions, based on short-range, central, pair potential representations of the interaction among macro-particles. After reviewing our previous…
We examine nonequilibrium features of collapse behavior in model polymers with competing crystallization and glass transitions using extensive molecular dynamics simulations. By comparing to "colloidal" systems with no covalent bonds but…
The effects of static electric field on the dynamics of lysozyme and its hydration water have been investigated by means of incoherent quasi-elastic neutron scattering (QENS). Measurements were performed on lysozyme samples, hydrated…
In order to elucidate the role of the native state topology and the stability of subdomains in protein folding, we investigate free energy landscape of human lysozyme, which is composed of two subdomains, by Monte Carlo simulations. A…
Inclusion of protein lysozyme molecules in lipidic monoolein cubic phase induces a transition from a $\rm Pn\bar{3}m$ structure to $\rm Im\bar{3}m$ one. Small-angle X-ray scattering (SAXS) method with high intensity synchrotron radiation…
Using molecular dynamics computer simulations we investigate the structural and dynamical properties of a simple model for a colloidal gel at low volume fraction. We find that at low T the system is forming an open percolating cluster,…
Pressure provides a powerful parameter to control the protein conformation state, which at sufficiently high values can lead to unfolding. Here, we investigate the effects of increasing pressure up to $0.4$ GPa on hydrated lysozyme…
The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M.…
To insight the relationships between the self-organizing structures of cells, such as the cell clusters, and the properties of biotissues is helpful in revealing the function and designing biomaterial. Traditional random foam model neglects…
We propose a minimal model for spherical proteins with aeolotopic pair interactions to describe the equilibrium phase behavior of lysozyme. The repulsive screened Coulomb interactions between the particles are taken into account assuming…
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…
We present new results from a series of LCDM simulations of cluster mass halos resolved with high force and mass resolution. These results are compared with recently published simulations from groups using various codes including PKDGRAV,…
Concentrated aqueous solutions of the protein lysozyme undergo a liquid solid transition upon a temperature quench into the unstable spinodal region below a characteristic arrest temperature of Tf=15C. We use video microscopy and…
The vibrational dynamics of a model polymer glass is studied by Molecular Dynamics simulations. The focus is on the "soft" monomers with high participation to the lower-frequency vibrational modes contributing to the thermodynamic anomalies…