Strongly correlated electrostatics of viral genome packaging

Nguyen, Toan T.

doi:10.1007/s10867-013-9301-4

Cited by 8 publications

(8 citation statements)

References 45 publications

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“…One can see that the right side of these curve from the distance d * to ∞ show a good degree of overlapping. This is in agreement with the "correlated liquid" nature of DNA−DNA attraction mediated by multivalent counterions [15,21]. In this strongly correlated liquid theory of DNA−DNA interaction, the combined system of DNA+condensed counterions acts as a charged metallic cylinder.…”

Section: B Role Of Finite Size Of Counterionssupporting

confidence: 83%

“…Indeed, DNA condensation by divalent counterions has also been observed in another environment where DNA configuration is constrained, namely the condensation of DNA in two dimensional systems [13]. For virus systems, theoretical fitting suggests that the DNA is neutralized at c Z,0 ≈ 75mM for divalent counterions, and the short−range DNA attraction at this concentration is −0.004k B T per nucleotide base [14,15].…”

Section: Introductionmentioning

confidence: 99%

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Grand-canonical simulation of DNA condensation with two salts, effect of divalent counterion size

Nguyen

2016

The Journal of Chemical Physics

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The problem of DNA- DNA interaction mediated by divalent counterions is studied using a generalized grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior of the DNA bundle is investigated. Experimentally, it is known that multivalent counterions have strong effect on the DNA condensation phenomenon. While tri- and tetra-valent counterions are shown to easily condense free DNA molecules in solution into toroidal bundles, the situation with divalent counterions is not as clear cut. Some divalent counterions like Mg(+2) are not able to condense free DNA molecules in solution, while some like Mn(+2) can condense them into disorder bundles. In restricted environment such as in two dimensional system or inside viral capsid, Mg(+2) can have strong effect and able to condense them, but the condensation varies qualitatively with different system, different coions. It has been suggested that divalent counterions can induce attraction between DNA molecules but the strength of the attraction is not strong enough to condense free DNA in solution. However, if the configuration entropy of DNA is restricted, these attractions are enough to cause appreciable effects. The variations among different divalent salts might be due to the hydration effect of the divalent counterions. In this paper, we try to understand this variation using a very simple parameter, the size of the divalent counterions. We investigate how divalent counterions with different sizes can lead to varying qualitative behavior of DNA condensation in restricted environments. Additionally, a grand canonical Monte-Carlo method for simulation of systems with two different salts is presented in detail.

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Section: B Role Of Finite Size Of Counterionssupporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Grand-canonical simulation of DNA condensation with two salts, effect of divalent counterion size

Nguyen

2016

The Journal of Chemical Physics

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“…In this paper, as a first step in such direction, we present a Grand canonical Monte-Carlo (GCMC) simulation of electrolyte solutions for different salinity expanding upon a preliminary study [11]. The Grand-Canonical Monte-Carlo method was developed and used in several recent papers in our group to study the condensation of DNA inside bacteriophages in the presence of mixture of different salts, MgSO4, MgCl2, NaCl [12,13,14,15]. However, detail of the method was never presented, only the simulation results of DNA system were shown.…”

Section: Introduction mentioning

confidence: 99%

Size Effect in Grand-canonical Monte-Carlo Simulation of Solutions of Electrolyte

Duc

2019

MaP

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A Grand-canonical Monte-Carlo simulation method is investigated. Due to charge neutrality requirement of electrolyte solutions, ions must be added to or removed from the system in groups. It is then implemented to simulate solution of 1:1, 2:1 and 2:2 salts at different concentrations using the primitive ion model. We investigate how the finite size of the simulation box can influence statistical quantities of the salt system. Remarkably, the method works well down to a system as small as one salt molecule. Although the fluctuation in the statistical quantities increases as the system gets smaller, their average values remain equal to their bulk value within the uncertainty error. Based on this knowledge, the osmotic pressures of the electrolyte solutions are calculated and shown to depend linearly on the salt concentrations within the concentration range simulated. Chemical potential of ionic salt that can be used for simulation of these salts in more complex system are calculated. Keywords: GCMC, electrolyte solution simulation, primitive ion model, finite size effect.

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“…A diverse range of phenomena display a crucial dependence on the detailed identity of the bathing solution in terms of its ionic composition. Such phenomena include a plethora of biological systems ranging from the formation of large aggregates of like-charged biopolymers, such as microtubules, F-actin, and DNA in the bulk electrolyte solutions [3,4], and then all the way to the packaging of DNA inside viral shells [5,6] and in the eukaryotic chromatin [7]. Electrostaic interactions are also important in many technological processes such as waste water treatment, paper making, and concrete hardening [8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Interactions between charged particles with bathing multivalent counterions: experiments vs. dressed ion theory

Kanduč

Gudarzi

Valmacco

et al. 2017

Phys. Chem. Chem. Phys.

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We compare the recent experimentally measured forces between charged colloidal particles, as well as their effective surface potentials (surface charge) in the presence of multivalent counterions in a bathing monovalent salt solution, with the predictions of the dressed ion theory of strongly charged colloidal systems. The benchmark for comparison is provided by the DLVO theory and the deviations from its predictions at small separations are taken as an indication of the additional non-DLVO attractions that can be fitted by an additional phenomenological exponential term. The parameters characterizing this non-DLVO exponential term as well as the dependencies of the effective potential on the counterion concentration and valency predicted by the dressed ion theory are well within the experimental values. This suggests that the deviations from the DLVO theory are probably caused by ion correlations as formalized within the dressed ion theory.

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Strongly correlated electrostatics of viral genome packaging

Cited by 8 publications

References 45 publications

Grand-canonical simulation of DNA condensation with two salts, effect of divalent counterion size

Grand-canonical simulation of DNA condensation with two salts, effect of divalent counterion size

Size Effect in Grand-canonical Monte-Carlo Simulation of Solutions of Electrolyte

Interactions between charged particles with bathing multivalent counterions: experiments vs. dressed ion theory

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