Crossover of a polymer chain from bulk to surface states

Singh, Yashwant; Giri, Debasis; Kumar, Sanjay

doi:10.1088/0305-4470/34/8/102

Cited by 46 publications

(66 citation statements)

References 19 publications

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“…The question that then arises is the behaviour of f s (ω p , ω w ) for the Desorbed-Collapsed phase. In [9,10,11] it was suggested that the Desorbed-Collapsed phase accommodates two different behaviours: one where f s (ω p , ω w ) depends on ω w and so m w ∼ n 2/3 , which was dubbed the "Surface Attached Globule" or SAG, and one in which f s (ω p , ω w ) is independent of ω w , so that m w = O(1) as in the Desorbed-Extended phase. We shall refer to this second situation as the "Fully Detached Globule".…”

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confidence: 99%

On the location of the surface-attached globule phase in collapsing polymers

Owczarek

Rechnitzer

Krawczyk

et al. 2007

J. Phys. A: Math. Theor.

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We investigate the existence and location of the surface phase known as the "Surface-Attached Globule" (SAG) conjectured previously to exist in lattice models of three-dimensional polymers when they are attached to a wall that has a short range potential. The bulk phase, where the attractive intra-polymer interactions are strong enough to cause a collapse of the polymer into a liquid-like globule and the wall either has weak attractive or repulsive interactions, is usually denoted Desorbed-Collapsed or DC. Recently this DC phase was conjectured to harbour two surface phases separated by a boundary where the bulk free energy is analytic while the surface free energy is singular. The surface phase for more attractive values of the wall interaction is the SAG phase. We discuss more fully the properties of this proposed surface phase and provide Monte Carlo evidence for self-avoiding walks up to length 256 that this surface phase most likely does exist. Importantly, we discuss alternatives for the surface phase boundary. In particular, we conclude that this boundary may lie along the zero wall interaction line and the bulk phase boundaries rather than any new phase boundary curve.The phase transitions of a single isolated polymer in solution continue to attract attention as single polymers are fundamental components in more complicated modelling scenarios and these transitions are not yet fully understood. The collapse transition [1] mediated by the intra-polymer attractive interactions and the adsorption transition [2] when a polymer is attached to a sticky wall, are two of the key transitions that have been well studied. The situation when both transitions can occur in the same system has been studied less intensely due to the difficulty of numerical work such as Monte Carlo simulations when two independent parameters compete. However, with the advent of more powerful computers and sophisticated algorithms this situation has received some attention.The standard lattice model for polymers is the self-avoiding walk (SAW) with the sites of the walk called monomers. The intra-polymer attraction is modelled by a potential energy ε p associated with monomers that are nearest-neighbours on the lattice. These instances will be referred to as (nearest-neighbour) contacts. To consider adsorption a wall is introduced, so that the polymer is restricted to one side of the wall, or may visit the wall, with one end of the polymer (SAW) attached to the wall. Any monomer which visits the wall, other that the one fixed on the wall, is given a potential energy ε w . These monomers will be referred to as visits. Various different phases 1

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mentioning

confidence: 99%

On the location of the surface-attached globule phase in collapsing polymers

Owczarek

Rechnitzer

Krawczyk

et al. 2007

J. Phys. A: Math. Theor.

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“…Similarly, specificity of peptides and binding affinity to selected substrates could be of great importance for future electronic nanoscale circuits and pattern recognition devices. Since single-molecule experiments allow monitoring of polymer chains adsorbed at surfaces, the investigation of structural deformations of the polymer shape near substrates is a central aspect of experimental, computational, and theoretical studies [3].In computer simulations and analytical approaches, typically, one end of the polymer is anchored at a flat substrate and the influence of adhesion and steric hindrance [4,5,6,7,8,9], pulling forces [10,11] or external fields [12] on the shape of the polymer is considered. The question how a flexible substrate, e.g., a cell membrane, bends as a reaction of a grafted polymer, was, for example, addressed in Ref.…”

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confidence: 99%

“…In computer simulations and analytical approaches, typically, one end of the polymer is anchored at a flat substrate and the influence of adhesion and steric hindrance [4,5,6,7,8,9], pulling forces [10,11] or external fields [12] on the shape of the polymer is considered. The question how a flexible substrate, e.g., a cell membrane, bends as a reaction of a grafted polymer, was, for example, addressed in Ref.…”

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confidence: 99%

Conformational Transitions of Nongrafted Polymers near an Absorbing Substrate

2005

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We have performed multicanonical chain-growth simulations of a polymer interacting with an adsorbing surface. The polymer, which is not explicitly anchored at the surface, experiences a hierarchy of phase transitions between conformations binding and non-binding with the substrate. We discuss the phase diagram in the temperature-solubility plane and highlight the transition "path" through the free-energy landscape.PACS numbers: 87.15.Aa, 87.15.Cc The recent developments in single molecule experiments at the nanometer scale, e.g., by means of atomic force microscopy (AFM) [1] and optical tweezers [2], allow now for a more detailed exploration of structural properties of polymers in the vicinity of adsorbing substrates. The possibility to perform such studies is of essential biological and technological significance. From the biological point of view the understanding of the binding and docking mechanisms of proteins at cell membranes is important for the reconstruction of biological cell processes. Similarly, specificity of peptides and binding affinity to selected substrates could be of great importance for future electronic nanoscale circuits and pattern recognition devices. Since single-molecule experiments allow monitoring of polymer chains adsorbed at surfaces, the investigation of structural deformations of the polymer shape near substrates is a central aspect of experimental, computational, and theoretical studies [3].In computer simulations and analytical approaches, typically, one end of the polymer is anchored at a flat substrate and the influence of adhesion and steric hindrance [4,5,6,7,8,9], pulling forces [10,11] or external fields [12] on the shape of the polymer is considered. The question how a flexible substrate, e.g., a cell membrane, bends as a reaction of a grafted polymer, was, for example, addressed in Ref. [13]. Proteins exhibit a strong specificity as the affinity of peptides to adsorb at surfaces depends on the amino acid sequence, solvent properties, and substrate shape. This was experimentally and numerically studied, e.g., for peptidemetal [14,15] and peptide-semiconductor [16,17] interfaces. Binding/folding and docking properties of lattice heteropolymers at an adsorbing surface were subject of a recent numerical study [18].In this work we investigate in detail the temperature and solubility dependence of adsorption properties for a polymer which is not fixed at the surface of the substrate with one of its ends. This model was inspired by the experimental setup used in Refs. [16,17], where the * E-mail: Michael.Bachmann@itp.uni-leipzig.de † E-mail: Wolfhard.Janke@itp.uni-leipzig.de; Homepage: http://www.physik.uni-leipzig.de/CQT peptides are initially freely moving in solution before adsorption. Therefore, there are two main differences in comparison with studies of polymers explicitly grafted at the substrate: First, the chain can completely desorb from the substrate allowing for the investigation of the binding/unbinding transition. Second, adsorbed conformations are possible, ...

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“…The study of hybrid interface models has considerable applications for a broad variety of problems, e.g., understanding the mechanisms of protein-ligand binding [56], prewetting and layering transitions in polymer solutions as well as dewetting of polymer films [57,58], molecular pattern recognition [59], electrophoretic polymer deposition and growth [60]. Recently, the influence of adhesion and steric hindrance for polymers grafted to a flat substrate [61,50,[62][63][64][65], conformational pseudophase transitions for nongrafted polymers and peptides in a cavity with attractive substrate [66][67][68][69], the shape response to pulling forces [70,71] or external fields [72] were subject of computer simulations and analytical approaches of different models. The question how a flexible substrate, e.g., a cell membrane, bends as a reaction of a grafted polymer, was, for example, addressed in Ref.…”

Section: Specificity Of Protein Adsorption To Selective Solid Substratesmentioning

confidence: 99%

Thermodynamics of Protein Folding from Coarse-Grained Models’ Perspectives

Bachmann

Janke

Rugged Free Energy Landscapes

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Crossover of a polymer chain from bulk to surface states

Cited by 46 publications

References 19 publications

On the location of the surface-attached globule phase in collapsing polymers

On the location of the surface-attached globule phase in collapsing polymers

Conformational Transitions of Nongrafted Polymers near an Absorbing Substrate

Thermodynamics of Protein Folding from Coarse-Grained Models’ Perspectives

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