Interparticle gap distributions on one-dimensional lattices

D’Orsogna, Maria R.; Chou, Tom

doi:10.1088/0305-4470/38/3/001

Cited by 12 publications

(11 citation statements)

References 23 publications

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“…ming state, the distribution functions of the minimum distances f (δ) were non-zeros in the interval 0 ≤ δ < 1 and were almost identical for different values of ε. Note that for disks (ε = 1) the obtained function f (δ) was similar to that observed earlier for the distribution function of the gaps between line segments [20,28].…”

Section: Resultssupporting

confidence: 85%

“…By contrast, a diffusionally equilibrated system corresponds to a 1D Tonks gas [19]. The gap distribution functions of totally irreversible and fully equilibrated 1D depositions of line segments demonstrate the presence of strong differences between these two systems [20]. In a modified adsorption-desorption RSA model, the particles can be adsorbed with a rate of k + , or desorbed with a rate of k − .…”

Section: Introductionmentioning

confidence: 99%

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Relaxation of saturated random sequential adsorption packings of discorectangles aligned on a line

Lebovka,

Tatochenko,

Vygornitskii

et al. 2021

Preprint

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Relaxation of the packing of elongated particles (discorectangles) aligned on a line was studied numerically. The aspect ratio (length-to-width ratio) for the discorectangles was varied within the range ε ∈ [1; 50]. The initial jamming (saturated) state was produced using the basic variant of the random sequential adsorption (RSA) model with random positions and orientations of particles. The relaxation was performed by allowing rotational and translational diffusion motions of the particles wile their centers remained located on the line. The effects of the aspect ratio ε on the kinetics of relaxation, the orientation order parameter and the distribution function of the distances between nearest-neighbor discorectangles were analyzed. The transport properties of the resulting 1D systems were also analyzed by using the diffusion of a tracer particle (random walker) between the nearest-neighbor discorectangles. In the relaxed states the anomalous diffusion was observed having a hopping exponent dw > 2 dependent upon ε.

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Section: Resultssupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Relaxation of saturated random sequential adsorption packings of discorectangles aligned on a line

Lebovka,

Tatochenko,

Vygornitskii

et al. 2021

Preprint

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“…For example, BER enzymes are not point particles but have a finite size of about 10-15 base pairs. Random adsorption of finite sized particles has been studied 37 and could be used to enhance our current model. We also neglected the sliding of BER enzymes on DNA.…”

Section: Discussionmentioning

confidence: 99%

Charge-transport-mediated recruitment of DNA repair enzymes

Fok

Guo

Chou

2008

The Journal of Chemical Physics

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Damaged or mismatched bases in DNA can be repaired by base excision repair enzymes ͑BER͒ that replace the defective base. Although the detailed molecular structures of many BER enzymes are known, how they colocalize to lesions remains unclear. One hypothesis involves charge transport ͑CT͒ along DNA ͓Yavin et al., Proc. Natl. Acad. Sci. U.S.A. 102, 3546 ͑2005͔͒. In this CT mechanism, electrons are released by recently adsorbed BER enzymes and travel along the DNA. The electrons can scatter ͑by heterogeneities along the DNA͒ back to the enzyme, destabilizing and knocking it off the DNA, or they can be absorbed by nearby lesions and guanine radicals. We develop a stochastic model to describe the electron dynamics and compute probabilities of electron capture by guanine radicals and repair enzymes. We also calculate first passage times of electron return and ensemble average these results over guanine radical distributions. Our statistical results provide the rules that enable us to perform implicit-electron Monte Carlo simulations of repair enzyme binding and redistribution near lesions. When lesions are electron absorbing, we show that the CT mechanism suppresses wasteful buildup of enzymes along intact portions of the DNA, maximizing enzyme concentration near lesions.

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“…The results were surprising since they differed substantially from the spacing distribution predicted by the random car parking model. The gap distribution for various versions of the random sequential adsorption model has been studied in detail in [8,9] since it has direct consequences among others for the distribution of cracks in brittle materials [10]. In the most simple continuous case (random car parking model) the spacing distribution P (D) behaves like [11].…”

Section: Theorymentioning

confidence: 99%