Related papers: Simple models for charge and salt effects in prote…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
It is well known amongst molecular biologists that proteins with a common ancestor and that perform the same function in similar organisms, can have rather different amino-acid sequences. Mutations have altered the amino-acid sequences…
Electrical charging of parallel plates confining a model ionic liquid down to nanoscale distances yields a variety of charge-induced changes in the structural features of the confined film. That includes even-odd switching of the structural…
The electrostatic contribution to spontaneous membrane curvature is calculated within Poisson-Boltzmann theory under a variety of assumptions and emphasizing parameters in the physiological range. Asymmetric surface charges, either fixed…
Modelling electrolytes accurately on both a nanoscale and cell level can contribute to improving battery chemistries.[Armand and Tarascon, Nature, 2008, 451, 652-657] We previously presented a thermodynamic continuum model for…
We introduce a simple and efficient model to describe the potential energy surface of lithium diffusing in a solid-state ionic conductor. First, we assume that the Li atoms are fully ionized and we neglect the weak dependence of the…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Poisson-Boltzmann theory is the cornerstone for soft matter electrostatics. We provide novel exact analytical solutions to this non-linear mean-field approach, for the diffuse layer of ions in the vicinity of a planar or a cylindrical…
We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound…
The association of ions in electrolyte solutions at very low concentration and low temperature is studied using computer simulations and quasi-chemical ion-pairing theory. The specific case of the restricted primitive model (charged hard…
In this paper we study the ionization rate and the Stark shift of a one-dimensional model of the H$_{2}^{+}$ ion. The finding of these two quantities is reduced to the solutions of a complex eigenvalue problem. We solve this problem both…
We present a combined experimental and numerical study of the equilibrium cluster formation in globular protein solutions under no-added salt conditions. We show that a cluster phase emerges as a result of a competition between a long-range…
In the present work, we have extended a weak coupling theory [A. Bakhshandeh, A. P. dos Santos and Y. Levin Phys. Rev. Lett 107, 107801 (2011)] for systems with added 1:1 electrolyte. To study the accuracy of the developed theory, we…
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which…
The electrostatic potential profile of a spherical soft particle is derived by solving the Poisson-Boltzmann equations on a spherical system both numerically and analytically. The soft particle is assumed to consist of an ion-permeable…
We suggest to augment standard isoelectronic focusing for separation of proteins in a gradient of pH by a similar focusing in the presence of a strongly charged polyelectrolyte (PE). Proteins which have the same isoelectric point but…
The interplay of phase separation and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as hard and soft condensed matter physics, materials science, food engineering and…
We present a theory for phase-separated liquid coacervates with salt, taking into account spatial heterogeneities and interfacial profiles. We find that charged layers of alternating sign can form around the interface while the bulk phases…
Some hard sphere colloidal models have been criticized for inaccurately predicting the solution viscosity of complex biological molecules like proteins. Competing short-range attractions and long-range repulsions, also known as SALR…