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Register a new userOvercharging of DNA in the presence of salt: Theory and Simulation
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A study of a model rod-like polyelectrolyte molecule immersed into a monovalent or divalent electrolyte is presented. Results from the hypernetted-chain/mean spherical approximation (HNC/MSA) theory, for inhomogeneous charged fluids, {ch are} compared with molecular dynamics (MD) simulations. As a particular case, the parameters of the polyelectrolyte molecule are mapped to those of a DNA molecule. An excellent qualitative, and in some cases quantitative, agreement between HNC/MSA and MD is found. Both, HNC/MSA and MD, predict the occurrence of overcharging, which is not present in the Poisson-Boltzmann theory. Mean electrostatic potential and local concentration profiles, $zeta$-potential and charge distribution functions are obtained and discussed in terms of the observed overcharging effect. Particularly interesting results are a very non-monotonic behavior of the $zeta$-potential, as a function of the rod charge density, and the overcharging by {em monovalent} counterions.
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A small, bimetallic particle in a hydrogen peroxide solution can propel itself by means of an electrocatalytic reaction. The swimming is driven by a flux of ions around the particle. We model this process for the presence of a monovalent salt, where reaction-driven proton currents induce salt ion currents. A theory for thin diffuse layers is employed, which yields nonlinear, coupled transport equations. The boundary conditions include a compact Stern layer of adsorbed ions. Electrochemical processes on the particle surface are modeled with a first order reaction of the Butler-Volmer type. The equations are solved numerically for the swimming speed. An analytical approximation is derived under the assumption that the decomposition of hydrogen peroxide occurs mainly without inducing an electric current. We find that the swimming speed increases linearly with hydrogen peroxide concentration for small concentrations. The influence of ion diffusion on the reaction rate can lead to a concave shape of the function of speed vs. hydrogen peroxide concentration. The compact layer of ions on the particle diminishes the reaction rate and consequently reduces the speed. Our results are consistent with published experimental data.
A Grand-canonical Monte-Carlo simulation method extended to simulate a mixture of salts is presented. Due to charge neutrality requirement of electrolyte solutions, ions must be added to or removed from the system in groups. This leads to some complications compared to regular Grand Canonical simulation. Here, a recipe for simulation of electrolyte solution of salt mixture is presented. It is then implemented to simulate solution of 1:1, 2:1 and 2:2 salts or their mixtures at different concentrations using the primitive ion model. The osmotic pressures of the electrolyte solutions are calculated and shown to depend linearly on the salt concentrations within the concentration range simulated. We also show that at the same concentration of divalent anions, the presence of divalent cations make it easier to insert monovalent cations into the system. This can explain some quantitative differences observed in experiments of the MgCl$_2$ salt mixture and MgSO$_4$ salt mixture.
Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can enhance or reduce DNA overcharging. In this papers, we focus on the effect of multivalent co-ions, specifically divalent co-ions such as SO$_4^{2-}$. A computational experiment of DNA condensation using Monte$-$Carlo simulation in grand canonical ensemble is carried out where DNA system is in equilibrium with a bulk solution containing a mixture of salt of different valency of co-ions. Compared to system with purely monovalent co-ions, the influence of divalent co-ions shows up in multiple aspects. Divalent co-ions lead to an increase of monovalent salt in the DNA condensate. Because monovalent salts mostly participate in linear screening of electrostatic interactions in the system, more monovalent salt molecules enter the condensate leads to screening out of short-range DNA$-$DNA like charge attraction and weaker DNA condensation free energy. The overcharging of DNA by multivalent counterions is also reduced in the presence of divalent co$-$ions. Strong repulsions between DNA and divalent co-ions and among divalent co-ions themselves leads to a {em depletion} of negative ions near DNA surface as compared to the case without divalent co-ions. At large distance, the DNA$-$DNA repulsive interaction is stronger in the presence of divalent co$-$ions, suggesting that divalent co$-$ions role is not only that of simple stronger linear screening.
Antagonistic salts are salts which consist of hydrophilic and hydrophobic ions. In a binary mixture of water and organic solvent, these ions preferentially dissolve into different phases. We investigate the effect of an antagonistic salt, tetraphenylphosphonium chloride PPh$_4$Cl, in a mixture of water and 2,6-lutidine by means of Molecular Dynamics (MD) Simulations. For increasing concentrations of the salt the two-phase region is shrunk and the interfacial tension in reduced, in contrast to what happens when a normal salt is added to such a mixture. The MD simulations allow us to investigate in detail the mechanism behind the reduction of the surface tension. We obtain the ion and composition distributions around the interface and determine the hydrogen bonds in the system and conclude that the addition of salt alter the hydrogen bonding.
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic behavior results from both the strong coupling between the electrostatic and solvent-mediated hydrodynamic interactions, and from the renormalization of these electrostatic interactions at large separations, and specifically from the dominance of the far-field hydrodynamic interactions caused by the strong repulsion between the DNA fragments.
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