Effective solvent mediated potentials of Na+ and Cl− ions in aqueous solution: temperature dependence

Mirzoev, Alexander; Lyubartsev, Alexander P.

doi:10.1039/c0cp02397c

Cited by 35 publications

(32 citation statements)

References 43 publications

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“…Figure 4) within the cut-off distance, determined by the IMC procedure. This treatment of the long-range electrostatic interactions was validated in our previous work (54 The value of the shortest DNA-DNA distance is r = 22.5 Å, as it is exhibited by the first peak of the RDF in Figure 5B. This is in reasonable agreement with experimental data.…”

Section: Dna Condensation In Cg Simulationssupporting

confidence: 87%

A multiscale analysis of DNA phase separation: From atomistic to mesoscale level

Sun

Mirzoev

Minhas

et al. 2018

Preprint

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DNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer physics. The presence of hexagonally ordered DNA is observed in virus capsids, sperm heads and in dinoflagellates. Rigorous modelling of this process in all-atom MD simulations is presently difficult to achieve due to size and time scale limitations. We used a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA phase separation induced by the three-valent cobalt(III)-hexammine (CoHex 3+ ). Solvent-mediated effective potentials for a CG model of DNA were extracted from all-atom MD simulations. Simulations of several hundred 100-bp-long CG DNA oligonucleotides in the presence of explicit CoHex 3+ ions demonstrated aggregation to a liquid crystalline hexagonally ordered phase. Following further coarse-graining and extraction of effective potentials, we conducted modelling at mesoscale level. In agreement with electron microscopy observations, simulations of an 10.2-kbplong DNA molecule showed phase separation to either a toroid or a fibre with distinct hexagonal DNA packing. The mechanism of toroid formation is analysed in detail. The approach used here is based only on the underlying all-atom force field and uses no adjustable parameters and may be generalized to modelling chromatin up to chromosome size.

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Section: Dna Condensation In Cg Simulationssupporting

confidence: 87%

A multiscale analysis of DNA phase separation: From atomistic to mesoscale level

Sun

Mirzoev

Minhas

et al. 2018

Preprint

Self Cite

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“…This again brings up the issue of a correct or at least reasonable parameterization of these coarse-grained ion-ion and ion-membrane interactions. [44][45][46] These results show that, as expected, a BD simulation with explicit ions can be used as a Poisson-Boltzmann solver similar to a Monte-Carlo simulation. 38,50 Here, we compared the "BD-PB solver" to the analytic results only for the special case of a planar membrane, but obviously this works for arbitrary geometries, too.…”

Section: A Electric Field Above a Charged Membranesupporting

confidence: 78%

“…For the ion-ion interaction, some effective potentials would be available. [44][45][46] These potentials were parameterized from all-atom molecular dynamics or Monte-Carlo simulations and include distance correlations between pairs of ions. However, for the much more complex cases of ion-protein and protein-membrane interactions, no such effective parameterizations exist and one has to somehow choose the form of the coarse-grained potential and its parameter.…”

Section: Models Of the Protein The Ions And The Membranementioning

confidence: 99%

Do we have to explicitly model the ions in Brownian dynamics simulations of proteins?

Zimmer

Geyer

2012

The Journal of Chemical Physics

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Brownian dynamics (BD) is a very efficient coarse-grained simulation technique which is based on Einstein's explanation of the diffusion of colloidal particles. On these length scales well beyond the solvent granularity, a treatment of the electrostatic interactions on a Debye-Hückel (DH) level with its continuous ion densities is consistent with the implicit solvent of BD. On the other hand, since many years BD is being used as a workhorse simulation technique for the much smaller biological proteins. Here, the assumption of a continuous ion density, and therefore the validity of the DH electrostatics, becomes questionable. We therefore investigated for a few simple cases how far the efficient DH electrostatics with point charges can be used and when the ions should be included explicitly in the BD simulation. We find that for large many-protein scenarios or for binary association rates, the conventional continuum methods work well and that the ions should be included explicitly when detailed association trajectories or protein folding are investigated.

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“…To circumvent this challenge here, we used an approach based on the reverse reconstruction of interaction potentials from known atomistic distribution functions with statistical mechanics relationships that were mapped onto a coarse‐grain model. We used the inverse Monte Carlo (IMC) method developed by Lyubartsev and coworkers to obtain a set of ion–ion and ion–nucleotide interaction potentials from all‐atom MD simulations, and then mapped these potentials onto the coarse‐grained DNA model of our choice. This allowed us to study the ion permeation of the membrane proteins by including solvent‐mediated interactions in our potential functions in combination with a previously developed GCMC/BD approach.…”

Section: Introductionmentioning

confidence: 99%

Microsecond simulations of DNA and ion transport in nanopores with novel ion–ion and ion–nucleotides effective potentials

2014

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We developed a novel scheme based on the Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) simulations and have extended it to studies of ion currents across three nanopores with the potential for ssDNA sequencing: solid-state nanopore Si3N4, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the Inverse Monte-Carlo protocol, which maps the relevant ion-nucleotide distribution functions from an all-atom MD simulations. Combined with the previously developed simulation platform for Brownian Dynamic (BD) simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations.

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Effective solvent mediated potentials of Na+ and Cl− ions in aqueous solution: temperature dependence

Cited by 35 publications

References 43 publications

A multiscale analysis of DNA phase separation: From atomistic to mesoscale level

A multiscale analysis of DNA phase separation: From atomistic to mesoscale level

Do we have to explicitly model the ions in Brownian dynamics simulations of proteins?

Microsecond simulations of DNA and ion transport in nanopores with novel ion–ion and ion–nucleotides effective potentials

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