Polymer adsorption on reconstructed Au(001): A statistical description of P3HT by scanning tunneling microscopy and coarse-grained Monte Carlo simulations

Förster, Stefan; Kohl, E.; Ivanov, M.V.; Gross, Jonathan; Widdra, W.; Janke, Wolfhard

doi:10.1063/1.4898382

Cited by 21 publications

(16 citation statements)

References 26 publications

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“…However, there are many realistic situations, e.g., polymers adsorbed on fluid surfaces (lipid membranes) [47,48] and in crowded environment [49], where hydrodynamic interactions are negligible. Furthermore recent successful experiments in vacuum (no hydrodynamics or solvent effects) on structure [50,51] and dynamics [52] of single polymers open up the possibility of designing protocols for direct verification of our results.…”

Section: Discussionmentioning

confidence: 59%

Evidence of aging and dynamic scaling in the collapse of a polymer

Majumder

Janke

2016

Phys. Rev. E

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We investigate a newly framed two-time property for the nonequilibrium evolution dynamics during the collapse of a homopolymer via Monte Carlo simulations of a model polymer. Our results show evidence of aging effects, as observed in the slow dynamics of structural and spin glasses, along with the presence of a dynamic scaling of the autocorrelation function ∼x(-λ(c)) (x being the ratio of the cluster sizes at two different times). We estimate the value of λ(c) unambiguously by applying a finite-size scaling analysis to the numerical data. The value thus obtained obeys a bound which we predict via general theoretical arguments. The results presented should be of general validity and may trigger direct experimental verification in single-polymer dynamics.

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Section: Discussionmentioning

confidence: 59%

Evidence of aging and dynamic scaling in the collapse of a polymer

Majumder

Janke

2016

Phys. Rev. E

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“…To understand a two-dimensional system is not only of fundamental interest [113], but could be of relevance in the context of polymers confined to an attractive surface. Indeed there are experiments of synthetic polymers on two-dimensional gold or silver surfaces [114,115]. Our results on the kinetics of polymer collapse in d = 2 show that the phenomenology associated with this process can still be described by the "pearl-necklace" picture of Halperin and Goldbart, albeit the identification of the small pearl-like clusters which coarsen to form the final globule is not as distinct as in the d = 3 case.…”

Section: Discussionmentioning

confidence: 73%

Understanding nonequilibrium scaling laws governing collapse of a polymer

2020

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Recent emerging interest in experiments of single-polymer dynamics urge computational physicists to revive their understandings, particularly in the nonequilibrium context. Here we briefly discuss the currently evolving approaches of investigating the evolution dynamics of homopolymer collapse using computer simulations. Primary focus of these approaches is to understand various dynamical scaling laws related to coarsening and aging during the collapse in space dimension d = 3, using tools popular in nonequilibrium coarsening dynamics of particle or spin systems. In addition to providing an overview of those results, we also present new preliminary data for d = 2.

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“…At the moment, investigating short single polymer chains in experiments seems unrealistic, and it appears even more unrealistic to observe structural properties such as knots. However, preparation and detection methods for single polymers at surfaces have recently made quite an impressive progress [29,30], so that one can now resolve polymers of down to 20 monomers. A sensible next step could be hence an investigation of the influence of an adsorbing surface on the occurrence of stable knotted pseudo phases for a generic semi-flexible polymer.…”

Section: Fig 4 (Color Online)mentioning

confidence: 99%

Knots as a Topological Order Parameter for Semiflexible Polymers

Marenz¹,

Janke²

2016

Phys. Rev. Lett.

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Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase diagram for the complete range of semi-flexible polymers, from flexible to stiff. Although a simple model, we observe a rich variety of conformational phases, reminiscent of conformations observed for synthetic polymers or biopolymers. Changing the internal bending stiffness, the model exhibits different pseudo phases like bent, hairpin or toroidal. In particular, we find thermodynamically stable knots and transitions into these knotted phases with a clear phase coexistence, but almost no change in the mean total energy. 02.70.Uu, 05.70.Fh, 02.10.Kn Since the first simulation of knotted polymers in 1975 [1], the occurrence and behavior of knots in polymers has been studied in various contexts. Scanning through protein data bases has revealed that several proteins form knots [2][3][4]. In particular, Virnau et al. [5] have reviewed the whole Protein Data Bank (http://www.pdb.org [6]) and identified 36 different proteins forming relatively simple knots, none of which features more than five crossingssomehow evolution tries to avoid knotted proteins [7]. On the other hand, flexible polymers form much more complicated knots, which occur by chance in the swollen [8][9][10] and in the collapsed phase [10,11]. Essential for the existence of these two phases is the excluded volume and attraction of the monomers. Already lattice polymer simulations [12,13] show that models integrating selfavoidance and attraction exhibit a swollen, a globular, and a frozen phase. In this work we go a step ahead and investigate the knottedness of semi-flexible bead-stick polymers. There exists already some works concerning the more complex phase space of polymer models that incorporate bending stiffness [14]. The most comprehensive study uses a model for semi-flexible polymers of bead-spring type with finitely extensible nonlinear elastic (FENE) bonds [15]. By varying the bending stiffness, these models are able to mimic a large class of polymers, exhibiting, for instance, bent, hairpin or toroidal conformations.Nevertheless, none of the former work considered the knottedness of the polymer over the full bending stiffness range, which we will discuss in this Letter. By measuring the knot type we found pseudo phases with thermodynamically stable knotted polymers. The knot type will be shown to be an ideal topological order parameter to identify the knotting transition and, moreover, the behavior at the transition from an unknotted to a knotted pseudo phase turns out to be surprisingly different from all other pseudo-phase transitions of the bead-stick polymer in that it does not fit into the common classification scheme of first-and second-order phase transitions.To model a coarse-grained polymer with an adjustable stiffness, we use a modified version of the bead-stick model of Refs. [16][17][18], whi...

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Polymer adsorption on reconstructed Au(001): A statistical description of P3HT by scanning tunneling microscopy and coarse-grained Monte Carlo simulations

Cited by 21 publications

References 26 publications

Evidence of aging and dynamic scaling in the collapse of a polymer

Evidence of aging and dynamic scaling in the collapse of a polymer

Understanding nonequilibrium scaling laws governing collapse of a polymer

Knots as a Topological Order Parameter for Semiflexible Polymers

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