Irreversible adsorption of tethered chains at substrates: Monte Carlo study

Descas, Radu; Sommer, Jens‐Uwe; Blumen, A.

doi:10.1063/1.2159479

Cited by 28 publications

(57 citation statements)

References 19 publications

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“…Note that dynamic Monte Carlo simulations might fail if the transition probabilities are not chosen properly, as addressed by Kang and Weinberg [29]. However, in many circumstances (for example, in the bond fluctuation model) dynamic MC using Metropolis scheme was shown to reproduce quite well the universal static and dynamic behavior of polymers [27,28]. The method bases on the idea that a dynamic evolution of a system, in which the sequence of states, generated by a stochastic process one after another from the previous state, can simply be interpreted as the dynamic evolution of the system.…”

Section: Models and Methodsmentioning

confidence: 97%

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Computer simulation of adsorption kinetics of surfactants on solid surfaces

Zhang

Chen

Wang

2007

Journal of Colloid and Interface Science

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Section: Models and Methodsmentioning

confidence: 97%

“…[25][26][27][28]) behaviors of polymer systems, was used to describe the kinetics of surfactant adsorption in this work. Note that dynamic Monte Carlo simulations might fail if the transition probabilities are not chosen properly, as addressed by Kang and Weinberg [29].…”

Section: Models and Methodsmentioning

confidence: 99%

Computer simulation of adsorption kinetics of surfactants on solid surfaces

Zhang

Chen

Wang

2007

Journal of Colloid and Interface Science

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“…The stem-flower dynamics has been discussed in the context of the absorption of polymers to a flat surface [22]. The number of bound base pairs n(t) is expected to follow the equation…”

mentioning

confidence: 99%

“…Hence the scaling τ ∼ N 1+ν is expected to be relevant for experiments. Anomalous dynamics in polymers has been studied a lot in the past decade ( [22][23][24][26][27][28][29][30][31]). Besides the already mentioned case of polymer absorption to a planar substrate [22] the exponent 1+ν also governs the dynamics of driven translocation through a small pore (see e.g.…”

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confidence: 99%

Anomalous Dynamics of DNA Hairpin Folding

2014

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By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time τ scales non-linearly with N , the hairpin length: τ ∼ N α with α > 1. This is in sharp contrast with the prediction of the zipper model for which τ ∼ N . We show that the anomalous dynamics originates from an increase in the friction during zippering due to the tension built in the closing strands. From a simple polymer model we get α = 1 + ν ≈ 1.59 with ν the Flory exponent, a result which is in agreement with the simulations. We discuss transition path times data where such effects should be detected. The folding dynamics of DNA (or RNA) hairpins, which are single stranded molecules forming a stem-loop structure, has been a topic of broad interest within the biophysics community for a long time [1][2][3][4][5][6][7]. Hairpin folding is a prototype example of secondary structure formation [8] and shares common features with the more complex case of protein folding [9]. In both cases the folding process is described by a one-dimensional reaction coordinate performing a diffusive motion across a free energy potential barrier (see e.g. [10]). Recent advances in experimental single molecule techniques allow to monitor the folding of hairpins [7] and of proteins [11] with an unprecedented time resolution. These and future experiments are expected to elucidate many aspects of the folding dynamics [12], the reason being that the actual conformational changes occur on timescales which can be typically a few orders of magnitudes smaller than the total folding time [11].The aim of this letter is to investigate the folding dynamics of DNA hairpins, focusing in particular on the rapid zippering which follows the formation of a stable nucleus of a few base pairs. The latter process is generally much slower as initially the hairpin undergoes a large number of failed nucleation attempts. We show here that the zippering time τ scales with the hairpin length N as τ ∼ N α with α > 1. This conclusion is based on extensive simulations of coarse-grained model of DNA and on scaling arguments for polymer dynamics. Our results are at odds with the zipper model [13] which assumes that the hairpin closes like a zipper following a biased random walk dynamics, which implies α = 1. The results give insights on the forces involved in the folding process and in particular in the role of frictional forces. In addition, as argued at the end of this letter, recent experiments on transition path times [7] appear to be better described by a non-linear dependence of zippering time vs. N , supporting the results reported here.

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“…It was found that the polymer chains in a grafted layer are replaced by introducing shorter chains of identical head groups, which supports some experimental studies. The irreversible adsorption of single chains grafted with one end to the surface was also studied by combining the scaling theory with computer simulations in reference [188]. Using scaling arguments, the authors derived relations between the overall time of adsorption the characteristic time of adsorption, and the chain length.…”

Section: -23mentioning

confidence: 99%

Description of fluid-tethered chains interfaces: advances in density functional theories and off-lattice computer simulations

Sokołowski¹,

Ilnytskyi²,

Pizio³

2014

Condens. Matter Phys.

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Many objects of nanoscopic dimensions involve fluid-tethered chain interfaces. These systems are of interest for basic science and for several applications, in particular for design of nanodevices for specific purposes. We review recent developments of theoretical methods in this area of research and in particular of density functional (DF) approaches, which provide important insights into microscopic properties of such interfaces. The theories permit to describe the dependence of adsorption, wettability, solvation forces and electric interfacial phenomena on thermodynamic states and on characteristics of tethered chains. Computer simulations for the problems in question are overviewed as well. Theoretical results are discussed in relation to simulation results and to some experimental observations.

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Irreversible adsorption of tethered chains at substrates: Monte Carlo study

Cited by 28 publications

References 19 publications

Computer simulation of adsorption kinetics of surfactants on solid surfaces

Computer simulation of adsorption kinetics of surfactants on solid surfaces

Anomalous Dynamics of DNA Hairpin Folding

Description of fluid-tethered chains interfaces: advances in density functional theories and off-lattice computer simulations

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