Modeling the separation of macromolecules: A review of current computer simulation methods

Slater, Gary W.; Holm, Christian; Chubynsky, Mykyta V.; Haan, Hendrick W. de; Dubé, Antoine; Grass, Kai; Hickey, Owen A.; Kingsburry, Christine; Sibrac, David; Shendruk, Tyler N.; Zhan, Lixin

doi:10.1002/elps.200800673

Cited by 124 publications

(132 citation statements)

References 277 publications

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“…Our simulations used coarse-grained Langevin Dynamics 41 . We modelled fd as a generic linear polymer composed of 133 beads of diameter s, giving the correct aspect ratio.…”

Section: Resultsmentioning

confidence: 99%

Stiff filamentous virus translocations through solid-state nanopores

et al. 2014

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The ionic conductance through a nanometer-sized pore in a membrane changes when a biopolymer slides through it, making nanopores sensitive to single molecules in solution. Their possible use for sequencing has motivated numerous studies on how DNA, a semiflexible polymer, translocates nanopores. Here we study voltage-driven dynamics of the stiff filamentous virus fd with experiments and simulations to investigate the basic physics of polymer translocations. We find that the electric field distribution aligns an approaching fd with the nanopore, promoting its capture, but it also pulls fd sideways against the membrane after failed translocation attempts until thermal fluctuations reorient the virus for translocation. fd is too stiff to translocate in folded configurations. It therefore translocates linearly, exhibiting a voltage-independent mobility and obeying first-passage-time statistics. Surprisingly, lengthwise Brownian motion only partially accounts for the translocation velocity fluctuations. We also observe a voltage-dependent contribution whose origin is only partially determined.

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“…Our simulations used coarse-grained Langevin Dynamics 41 . We modelled fd as a generic linear polymer composed of 133 beads of diameter s, giving the correct aspect ratio.…”

Section: Resultsmentioning

confidence: 99%

Stiff filamentous virus translocations through solid-state nanopores

et al. 2014

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“…However, a detailed physical understanding of surface transport of DNA is currently not available. 3 For example, it is commonly known that the diffusion coefficient of DNA decreases with increase in DNA size in free solution 4 and under two-dimensional confinement. 5 However, a recent experimental study on electrophoresis of DNA on an atomic force microscopy surface showed the faster movement of longer DNA in a thin pure water film.…”

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confidence: 99%

Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface

Park

Aluru

2010

Applied Physics Letters

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In this paper, we investigate, using molecular dynamics simulations, the conformation and diffusion of longer and shorter single-strand DNA ͑ssDNA͒ as a function of water film thickness. While the conformation of the shorter ssDNA is significantly affected and the diffusion is suppressed with reduction in water film thickness, the conformation and diffusion of the longer DNA is not influenced. We explain our observations by considering the competition between stacking interaction of bases and solvation tendency of ssDNA. This paper suggests an approach to control the surface motion of ssDNA in nanoscale water films using film thickness. © 2010 American Institute of Physics. ͓doi:10.1063/1.3366725͔ DNA separation is an essential technique for gene sequencing and DNA fingerprinting. The development of accurate and versatile DNA separation technique is currently a significant issue in nanobiotechnology. 1 Recently, Pernodet et al. 2 reported separation of DNA chains on a surface without any topological restrictions or any solution sieving media. This can be a significant benefit over conventional separation methods. However, a detailed physical understanding of surface transport of DNA is currently not available. 3 For example, it is commonly known that the diffusion coefficient of DNA decreases with increase in DNA size in free solution 4 and under two-dimensional confinement. 5 However, a recent experimental study on electrophoresis of DNA on an atomic force microscopy surface showed the faster movement of longer DNA in a thin pure water film. 6 According to the Nernst-Einstein relation between mobility and diffusion, this implies that the longer DNA has higher diffusion than the shorter DNA.To understand the reasons behind the ambiguities in the physics of surface transport of DNA, in this paper, we investigate, using extensive molecular dynamics ͑MD͒ simulations, the diffusion of DNA in nanometer-thick water films by considering DNA of various sizes. As shown in the schematic in Fig. 1͑a͒, a single-strand DNA ͑ssDNA͒ was solvated in a pure water film on a solid surface. Following the experiment, 6 the surface was made by grafting the poly͑eth-ylene glycol͒-silanes ͑PEG-silanes͒ on a solid substrate. The size of the surface is 20ϫ 20 nm 2 and it consists of 1600 PEG-silane molecules. The PEG-silane has 32 atoms and it is attached to the substrate atom ͓see Fig. 1͑b͔͒. The initial configuration and the atomic partial charges of PEG-silane molecule were obtained from PRODRG ͑Ref. 7͒ using GRO-MOS forcefield and charge. The substrate atoms were assumed frozen and their atomic charges were adjusted to make the entire system neutral. We considered two small ssDNAs fragments with 6 and 12 bases. Although recent DNA sequencing technologies utilize tens of millions of small DNA fragments, 8 efficient separation of such small fragments is still challenging. 9 The longer 12-base ssDNA of 5Ј − CGCGAATTCGCG− 3Ј was prepared by unzipping the well-known Dickerson's B-DNA dodecamer ͑double stranded͒, 10 while the shorter 6-bas...

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“…From a simulation point of view, modeling such a system is a challenging task, because both the electrostatic and hydrodynamic interactions are long-range. Taken separately, each interaction has been well studied in the literature [6][7][8][9][10][11]. Methods can be grouped into the categories of "implicit" and "explicit" methods, [9,10], depending on whether the small components (solvents and ions) are simulated explicitly or replaced by effective interactions between large components.…”

Section: Simulation Methodsmentioning

confidence: 99%

Computer simulations of single particles in external electric fields

Zhou

Schmid

2015

Soft Matter

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Applying electric fields is an attractive way to control and manipulate single particles or molecules, e.g., in lab-on-a-chip devices. However, the response of nanosize objects in electrolyte solution to external fields is far from trivial. It is the result of a variety of dynamical processes taking place in the ion cloud surrounding charged particles and in the bulk electrolyte, and it is governed by an intricate interplay of electrostatic and hydrodynamic interactions. Already systems composed of one single particle in electrolyte solution exhibit a complex dynamical behaviour. In this review, we discuss recent coarse-grained simulations that have been performed to obtain a molecular-level understanding of the dynamic and dielectric response of single particles and single macromolecules to external electric fields. We address both the response of charged particles to constant fields (DC fields), which can be characterized by an electrophoretic mobility, and the dielectric response of both uncharged and charged particles to alternating fields (AC fields), which is described by a complex polarizability. Furthermore, we give a brief survey of simulation algorithms and highlight some recent developments.

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Modeling the separation of macromolecules: A review of current computer simulation methods

Cited by 124 publications

References 277 publications

Stiff filamentous virus translocations through solid-state nanopores

Stiff filamentous virus translocations through solid-state nanopores

Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface

Computer simulations of single particles in external electric fields

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