Electrostatics in soft matter

Messina, René

doi:10.1088/0953-8984/21/11/113102

Cited by 197 publications

(223 citation statements)

References 195 publications

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“…There has been a number of excellent reviews covering the general principles of ES behavior of nucleic acids, 11,12 proteins, [13][14][15][16][17][18] lipid membranes, 2,19,20 and some other bio-soft-matter systems. 21 Salt-and pH-sensitivity of ES forces provides a useful handle for cells to direct and tune the pathways of many biological processes. Among them are, in particular, the DNA-DNA, 11 protein-DNA 22 and protein-protein ES interactions, 23 DNA compactification into higher-order structures, 24,25 DNA spooling inside viruses, 26 actin aggregation into bundles, 27 RNA folding, 12,28 and ion translocation through membrane pores.…”

Section: Introductionmentioning

confidence: 99%

Electrostatic interactions in biological DNA-related systems

Cherstvy

2011

Phys. Chem. Chem. Phys.

163

148

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In this perspective article, we focus on recent developments in the theory of charge effects in biological DNA-related systems. The electrostatic effects on different levels of DNA organization are considered, including the DNA-DNA interactions, DNA complexation with cationic lipid membranes, DNA condensates and DNA-dense cholesteric phases, protein-DNA recognition, DNA wrapping in nucleosomes, and inter-nucleosomal interactions. For these systems, we develop a theoretical framework to describe the physical-chemical mechanisms of structure formation and anticipate some biological consequences. General biophysical principles of DNA compaction in chromatin fibers and DNA spooling inside viral capsids are discussed in the end, with emphasis on electrostatic aspects.

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Section: Introductionmentioning

confidence: 99%

Electrostatic interactions in biological DNA-related systems

Cherstvy

2011

Phys. Chem. Chem. Phys.

163

148

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“…Inclusion of the image effect in molecular dynamics simulations of molecules near a conducting or polarizable surface is still challenging in a variety of important systems including proteins 22 , polyelectrolytes 23 , and colloidal particles 24 . Moreover, the effects of applied electric field remain largely unexplored on the microscopic level, while the continuum electrostatics is well established 16,25 .…”

Section: Introductionmentioning

confidence: 99%

Applying electric field to charged and polar particles between metallic plates: Extension of the Ewald method

Takae

Ōnuki

2013

The Journal of Chemical Physics

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We develop an efficient Ewald method of molecular dynamics simulation for calculating the electrostatic interactions among charged and polar particles between parallel metallic plates, where we may apply an electric field with an arbitrary size. We use the fact that the potential from the surface charges is equivalent to the sum of those from image charges and dipoles located outside the cell. We present simulation results on boundary effects of charged and polar fluids, formation of ionic crystals, and formation of dipole chains, where the applied field and the image interaction are crucial. For polar fluids, we find a large deviation of the classical Lorentz-field relation between the local field and the applied field due to pair correlations along the applied field. As general aspects, we clarify the difference between the potential-fixed and the charge-fixed boundary conditions and examine the relationship between the discrete particle description and the continuum electrostatics.

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“…In this paper we consider a three-dimensional binary colloidal suspension of two species A and B of charged spheres ('macroions') with different charges (Z A e and Z B e, e denoting the electron charge) and diameters (σ A and σ B ) [13][14][15]. The traditional Derjaguin-Landau-Verwey-Overbeek (DLVO) theory describes the interaction between the two species as an effective pairwise Yukawa potential [16,17] V (r ) = Z i e 1 + σ i κ D /2…”

Section: Introductionmentioning

confidence: 99%

Nonadditivity in the effective interactions of binary charged colloidal suspensions

Allahyarov

Löwen

2009

J. Phys.: Condens. Matter

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Based on primitive model computer simulations with explicit microions, we calculate the effective interactions in a binary mixture of charged colloids with species A and B for different size and charge ratios. An optimal pairwise interaction is obtained by fitting the many-body effective forces. This interaction is close to a Yukawa (or Derjaguin-Landau-Verwey-Overbeek (DLVO)) pair potential but the AB cross-interaction is different from the geometric mean of the two direct AA and BB interactions. As a function of charge asymmetry, the corresponding nonadditivity parameter is first positive, then significantly negative and is then positive again. We finally show that an inclusion of nonadditivity within an optimal effective Yukawa model gives better predictions for the fluid pair structure than DLVO theory.

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Electrostatics in soft matter

Cited by 197 publications

References 195 publications

Electrostatic interactions in biological DNA-related systems

Electrostatic interactions in biological DNA-related systems

Applying electric field to charged and polar particles between metallic plates: Extension of the Ewald method

Nonadditivity in the effective interactions of binary charged colloidal suspensions

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