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

Nguyen, Toan T.

doi:10.1063/1.4940312

Cited by 14 publications

(12 citation statements)

References 30 publications

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“…The strength of DNA-DNA short-range attraction can be affected by this parameter. 14) Moreover, in fact the solvent is not a continuous media therefore discrete solvent corrections need to be added. 27) These effects go beyond the purpose of this work.…”

Section: Discussionmentioning

confidence: 99%

Numerical Solution for the Counterions Distribution in a Hexagonal DNA Lattice within Mean Field Theory Using Finite Element Method

et al. 2020

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DNA has proven to be a promising material in fabrication and construction of complex structures with precise controlled nanoscale features. Most of the systems involving DNA are functioned in an aqueous solution where DNA molecules are strongly negatively charged. Therefore, understanding electrostatics of DNA system is essential for better understanding and design of DNA as a biomaterial and as a biological structure. In this work, the mean-field Poisson-Boltzmann equation for the distribution of mobile ions in a two-dimensional hexagonal lattice of DNA cylinders is solved numerically using finite element method. The weak formulation of the Poisson-Boltzmann equation is derived. The equation is then solved numerically using FreeFem++ scripting language. Our results show that the excess counterions of DNA dominate over the bulk ion concentration for the physiological salt concentration considered, and they condense on the DNA surface leading to very high charge density. The results also demonstrate the strong influence of the entropic confinement of the ions when the distance between neighboring DNA is smaller than 10 nm. This effect cannot be ignored in this case, and should be taken into account in any electrostatic investigation of DNA system.

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Section: Discussionmentioning

confidence: 99%

Numerical Solution for the Counterions Distribution in a Hexagonal DNA Lattice within Mean Field Theory Using Finite Element Method

et al. 2020

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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 topic that continues to interest the biophysical research community is how monovalent and multivalent counterions govern a wide range of biological processes such as genome packaging (in cellular compartments and viral capsids) (2)(3)(4)(5)(6), RNA folding (7)(8)(9)(10), ribosome activity (11), protein-nucleic acid interactions (12)(13)(14), ligand binding (15,16), and transitions between left-handed and right-handed forms of DNA and RNA duplexes (17). Understanding these processes through computational modeling requires accurate and efficient models for the ionic environment (1), which has been the goal of various theoretical studies (e.g., counterion condensation (18) and Poisson-Boltzmann (PB) theories (19)) and computational modeling studies based on the PB equation (19), molecular dynamics simulations (5,17,(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31), Monte Carlo simulations (in canonical and grand canonical ensembles) (27,(32)(33)(34)(35)(36), and classical density functional theories (37,38).…”

Section: Introductionmentioning

confidence: 99%

“…Among the various simulation methodologies, grandcanonical Monte Carlo (GCMC) methods have been popular for predicting the thermodynamic properties of ion solutions and their distributions around biomolecules (27,32,(34)(35)(36)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49). The GIBS software program uses GCMC methods for two tasks.…”

Section: Introductionmentioning

confidence: 99%

GIBS: A grand-canonical Monte Carlo simulation program for simulating ion-biomolecule interactions

Thomas,

Baker

2017

Preprint

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The ionic environment of biomolecules strongly influences their structure, conformational stability, and inter-molecular interactions. This paper introduces GIBS, a grand-canonical Monte Carlo (GCMC) simulation program for computing the thermodynamic properties of ion solutions and their distributions around biomolecules. This software implements algorithms that automate the excess chemical potential calculations for a given target salt concentration. GIBS uses a cavity-bias algorithm to achieve high sampling acceptance rates for inserting ions and solvent hard spheres in simulating dense ionic systems. In the current version, ion-ion interactions are described using Coulomb, hard-sphere, or Lennard-Jones (L-J) potentials; solvent-ion interactions are described using hard-sphere, L-J and attractive square-well potentials; and, solvent-solvent interactions are described using hard-sphere repulsions. This paper and the software package includes examples of using GIBS to compute the ion excess chemical potentials and mean activity coefficients of sodium chloride as well as to compute the cylindrical radial distribution functions of monovalent (Na + , Rb + ), divalent (Sr 2+ ), and trivalent (CoHex 3+ ) around fixed all-atom models of 25 base-pair nucleic acid duplexes. GIBS is written in C++ and is freely available for community use; it can be downloaded at https://github.com/Electrostatics/GIBS.

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

Cited by 14 publications

References 30 publications

Numerical Solution for the Counterions Distribution in a Hexagonal DNA Lattice within Mean Field Theory Using Finite Element Method

Numerical Solution for the Counterions Distribution in a Hexagonal DNA Lattice within Mean Field Theory Using Finite Element Method

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

GIBS: A grand-canonical Monte Carlo simulation program for simulating ion-biomolecule interactions

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