Related papers: Simple models for charge and salt effects in prote…
We use numerical simulations to study the crystallization of monodisperse systems of hard aspherical particles. We find that particle shape and crystallizability can be easily related to each other when particles are characterized in terms…
A recent Monte Carlo simulation determined the potential of mean force between two lysozyme molecules in various aqueous solutions [M. Lund et al. Phys. Rev. Lett. 100, 258105 (2008)]. The study involved a combination of explicit solvent…
We revisit the charge-regulation mechanism of macro-ions and apply it to mobile macro-ions in a bathing salt solution. In particular, we examine the effects of correlation between various adsorption/desorption sites and analyze the…
In previous work, we constructed a statistical framework for estimating the rate of clustered ionization from charged particle radiation in DNA. This model is extended to include contributions from secondary electrons. Using a simple…
We implement a well-established concept to consider dispersion effects within a Poisson-Boltzmann approach of continuum solvation of proteins. The theoretical framework is particularly suited for boundary element methods. Free parameters…
The charge inversion phenomenon is studied by molecular dynamics simulations, focusing on size and valence asymmetric salts, and a threshold of surface charge density for charge inversion. The charge inversion criteria by the…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
We consider electrophoresis of a single charged colloidal particle in a finite box with periodic boundary conditions, where added counterions and salt ions ensure charge neutrality. A systematic rescaling of the electrokinetic equations…
We have studied the structure of salt-free lysozyme at 293 K and pH 7.8 using molecular simulations and experimental SAXS effective potentials between proteins at three volume fractions, 0.012, 0.033, and 0.12. We found that the structure…
Dating from experiments more than 20 years ago, it has been realized that the crystallization of hard colloidal particles in the vicinity of dynamical arrest has several anomalies, that render the conventional nucleation and growth model…
We introduce a simplified protein model where the water degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover both the warm and the cold protein denaturation within a…
In this paper we find an analytical solution of the equilibrium ion distribution for a toroidal model of a ionic channel, using the Perfect Screening Theorem (PST). The ions are charged hard spheres, and are treated using a variational Mean…
A probabilistic discrete model for 2D protein crystal growth is presented. This model takes into account the available space and can describe growing processes of different nature due to the versatility of its parameters which gives the…
Cell polarization underlies many cellular processes, such as differentiation, migration, and budding. Many living cells, such as budding yeast and fission yeast, use cytoskeletal structures to actively transport proteins to one location on…
Asymmetric patchy particle models have recently been shown to describe the crystallization of small globular proteins with near quantitative accuracy. Here, we investigate how asymmetry in patch geometry and bond energy generally impact the…
Model of biological effects of ionizing particles, especially of protons and other ions, is proposed. The model is based on distinguishing the single-particle and collective effects of the underlying radiobiological mechanism. The…
In this perspective we address the question: why are proteins seemingly so hard to crystallize? We suggest that this is because of evolutionary negative design, i.e. proteins have evolved not to crystallize, because crystallization, as with…
Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we…
Standard X-ray crystallography methods use free-atom models to calculate mean unit cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a…
We investigate and quantify salient features of the charge distributions on viral capsids. Our analysis combines the experimentally determined capsid geometry with simple models for ionization of amino acids, thus yielding the detailed…