Related papers: Protein crystals and charged surfaces: interaction…
We derive formulae for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on…
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…
Predicting interactions between proteins is one of the most important yet challenging problems in structural bioinformatics. Intrinsically, potential function sites in protein surfaces are determined by both geometric and chemical features.…
We propose a theoretical model to elucidate intermolecular electrostatic interactions between a virus and a substrate. Our model treats the virus as a homogeneous particle having surface charge and the polymer fiber of the respirator as a…
Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most…
At nuclear matter density, electrically neutral strongly interacting matter in weak equilibrium is made of neutrons, protons and electrons. At sufficiently high density, such matter is made of up, down and strange quarks in the color-flavor…
The problem of the equilibrium state of the charged many-particle system above dielectric surface is formulated.We consider the case of the presence of the external attractive pressing field and the case of its absence. The equilibrium…
The model of charge generation is based on the wave model of a particle, for which a brief description is given. The particle is comprised of two photons, captured in the volume of the particle, and reveals the complete relativistic…
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,…
A multiple-image method is developed to accurately calculate the electrostatic interaction between neutral dielectric particles and a uniformly charged dielectric substrate. The difference in dielectric constants between the particle and…
Proteinoids -- thermal proteins -- are produced by heating amino acids to their melting point and initiation of polymerisation to produce polymeric chains. Proteinoids swell in aqueous solution into hollow microspheres. The proteinoid…
The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly.…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
We discuss recent investigations of the interaction of polyelectrolytes with proteins. In particular, we review our recent studies on the interaction of simple proteins such as human serum albumin (HSA) or lysozyme with linear…
This paper builds on two previous works, Lindgren et al. J. Comp. Phys. 371, 712-731 (2018) and Quan et al. arXiv:1807.05384 (2018), to devise a new method to solve the problem of calculating electrostatic interactions in a system composed…
The free energy landscape of a protein-like chain in a fluid was studied by combining discontinuous molecular dynamics and parallel tempering. The model protein is a repeating sequence of four different beads, with interactions mimicking…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
At low temperature, spheres with a very short-ranged attraction exist as a close-packed solid coexisting with an infinitely dilute gas. We find that the ratio of the interfacial tension between these two phases to the thermal energy…