Conformational Transitions of Nongrafted Polymers near an Absorbing Substrate

Abstract

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, ...

Phase diagrams of knotted and unknotted ring polymers

“…Our simulation approach involves the detailed determination of the phase diagram for a single ring polymer, using a Monte Carlo method that determines the density of states for the entire accessible range of energies and confinement in one go. Similar examples of this approach have appeared before, notably in studies of peptide and polymer collapse, crystallization, adsorption and confinement [22][23][24][25][26][27][28][29][30][31][32][33][34][35], both on-and off-lattice.…”

Structural properties of small semiconductor-binding synthetic peptides

“…This behavior was, in fact, observed in a recent experimental adsorption study of peptides in the vicinity of semiconductor substrates [6], although other explanations for this kind of specificity are also conceivable. For these reasons, it is likely that the binding specificity also depends on the thermodynamic and structural properties of peptides in solvent, as it has already turned out in investigations of minimalistic models [7,8].…”

Conformation and dynamics of a diluted chain in the presence of an adsorbing wall: A simulation with the bond fluctuation model

“…Phase transitions of single polymer chains in the bulk and in the presence of an adsorbing wall have been studied through model simulations [13][14][15][16][17]. In equilibrium states, the phase diagram as a function of temperature shows coil, liquid globule, solid globule, adsorbed coil (or adsorbed-extended) and adsorbed globule (or adsorbed compact) configurations, depending on the monomer wall attraction potential [13][14][15].…”