Influence of sequence correlations on the adsorption of random copolymers onto homogeneous planar surfaces

Using a reference system approach, we develop an analytical theory for the adsorption of random heteropolymers with exponentially decaying and/or oscillating sequence correlations on planar homogeneous surfaces. We obtain a simple equation for the adsorption-desorption transition line. This result as well as the validity of the reference system approach is tested by a comparison with numerical lattice calculations

Polymer adsorption onto random planar surfaces: Interplay of polymer and surface correlation

We study the adsorption of homogeneous or heterogeneous polymers onto heterogeneous planar surfaces with exponentially decaying site-site correlations, using a variational reference system approach. As a main result, we derive simple equations for the adsorption-desorption transition line. We show that the adsorption threshold is the same for systems with quenched and annealed disorder. The results are discussed with respect to their implications for the physics of molecular recognition

Random copolymer adsorption: Morita approximation compared to exact numerical simulations

We study the adsorption of ideal random lattice copolymers with correlations in the sequences on homogeneous substrates with two different methods: An analytical solution of the problem based on the constrained annealed approximation introduced by Morita in 1964 and the generating functional (GF) technique, and direct numerical simulations of lattice chains averaged over many realizations of random sequences. Both methods allow to calculate the free energy and different conformational characteristics of the adsorbed chain. The comparison of the results for random copolymers with different degree of correlations and different types of nonadsorbing monomers (neutral or repelling from the surface) shows not only qualitative but a very good quantitative agreement, especially in the cases of Bernoullian and quasi-alternating random sequences.Comment: 19 pages, 9 figure

Dependence of the Critical Adsorption Point on Surface and Sequence Disorders for Self-Avoiding Walks Interacting with a Planar Surface

The critical adsorption point (CAP) of self-avoiding walks (SAW) interacting with a planar surface with surface disorder or sequence disorder has been studied. We present theoretical equations, based on ones previously developed by Soteros and Whittington (J. Phys. A.: Math. Gen. 2004, 37, R279-R325), that describe the dependence of CAP on the disorders along with Monte Carlo simulation data that are in agreement with the equations. We also show simulation results that deviate from the equations when the approximations used in the theory break down. Such knowledge is the first step toward understanding the correlation of surface disorder and sequence disorder during polymer adsorption.Comment: 29 pages, 8 figure

Theory of mechanical unfolding of homopolymer globule: all-or-none transition in force-clamp mode vs phase coexistence in position-clamp mode

Equilibrium mechanical unfolding of a globule formed by long flexible homopolymer chain collapsed in a poor solvent and subjected to an extensional force f (force-clamp mode) or extensional deformation D (position-clamp mode) is studied theoretically. Our analysis, like all previous analysis of this problem, shows that the globule behaves essentially differently in two modes of extension. In the force-clamp mode, mechanical unfolding of the globule with increasing applied force occurs without intramolecular microphase segregation, and at certain threshold value of the pulling force the globule unfolds as a whole ("all-or-none" transition). The value of the threshold force and the corresponding jump in the distance between the chain ends increase with a deterioration of the solvent quality and/or with an increase in the degree of polymerization. In the position-clamp mode, the globule unfolding occurs via intramolecular microphase coexistence of globular and extended microphases followed by an abrupt unraveling transition. Reaction force in the microphase segregation regime demonstrates an "anomalous" decrease with increasing extension. Comparison of deformation curves in force and position-clamp modes demonstrates that at weak and strong extensions the curves for two modes coincide, differences are observed in the intermediate extension range. Another unfolding scenario is typical for short globules: in both modes of extension they unfold continuously, without jumps or intramolecular microphase coexistence, by passing a sequence of uniformly elongated configurations.Comment: 19 pages, 13 figures, 1 tabl

Developing and analyzing idealized models for molecular recognition

Behringer H, Bogner T, Polotsky A, Degenhard A, Schmid F. Developing and analyzing idealized models for molecular recognition. Journal of Biotechnology. 2007;129(2):268-278.We study equilibrium aspects of molecular recognition of two biomolecules using idealized model systems and methods from statistical physics. Starting from the basic experimental findings we demonstrate exemplarily how an idealized coarse-grained model for the investigation of molecular recognition of two biomolecules can be developed. In addition we provide details regarding two model systems for the recognition of a flexible and a rigid biomolecule respectively, the latter taking into account conformational changes. We focus particularly on the interplay and influence of the correlations of the residue distributions of the biomolecules on the recognition process. (c) 2007 Elsevier B.V. All rights reserved