Related papers: Simple models for charge and salt effects in prote…
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…
In this paper we propose a new mathematical model describing the effect of phosphocitrate (PC) on sodium sulphate crystallization inside bricks. This model describes salt and water transport, and crystal formation in a one dimensional…
Charge regulation is a fundamental mechanism in most chemical, geochemical, and biochemical systems. Various minerals surfaces and proteins are well-known to change their charge state as a function of the activity of the hydronium ions,…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
Earlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids,…
By performing an ensemble of molecular dynamics simulations, the model-dependent ionisation state is computed for strongly interacting systems self-consistently. This is accomplished through a free energy minimisation framework based on the…
As proteins typically have charges of around 10, they will interact strongly with charged surfaces. We calculate the electrostatic contribution to the interaction of crystals of protein with charged surfaces. The surfaces repel like-charged…
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…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
The fields of structural biology and soft matter have independently sought out fundamental principles to rationalize protein crystallization. Yet the conceptual differences and the limited overlap between the two disciplines have thus far…
We explore interactions between equally charged surfaces, in the presence of simple salt and either neutral or monovalently charged polyampholytes. We consider the possibility of using these charged polymers as crude models of ion clusters.…
We present an approximate method for calculating the electrostatic free energy of concentrated protein solutions. Our method uses a cell model and accounts for both the coulomb energy and the entropic cost of Donnan salt partitioning. The…
The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…
Models describing one- and two-photon transitions for ions in crystalline environments are unified and extended to the case of parity-allowed and parity- forbidden p-photon transitions. The number of independent parameters for…
X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to…
A simple model of globular proteins which incorporates anisotropic attractions is proposed. It is closely related to models used to model simple hydrogen-bonding molecules such as water. Theories for both the fluid and solid phases are…
Potassium and sodium ions are crucial for many physiological processes in living systems and play different roles when interacting with proteins and enzymes. Intracellular concentration of potassium is always maintained higher than that of…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions are dominated by solvation and electrostatic energies and modulated by protein…
In addition to electronic polarization or charge redistribution, the shape of neutral conjugated molecules yields position-dependent ionization potentials and electron affinities in organic thin films. Self-consistent I(n) and A(n) are…