Molecular recognition in a lattice model: An enumeration study

We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration techniques. Selectivity for a particular surface is defined by an adsorption energy criterium. We analyze the distributions of selective sequences and the role of mutations. A particularly important factor for molecular recognition is the small-scale structure on the polymers.Comment: revised version with additional plot

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

A nonperturbative Real-Space Renormalization Group scheme

Based on the original idea of the density matrix renormalization group (DMRG), i.e. to include the missing boundary conditions between adjacent blocks of the blocked quantum system, we present a rigorous and nonperturbative mathematical formulation for the real-space renormalization group (RG) idea invented by L.P. Kadanoff and further developed by K.G. Wilson. This is achieved by using additional Hilbert spaces called auxiliary spaces in the construction of each single isolated block, which is then named a superblock according to the original nomenclature. On this superblock we define two maps called embedding and truncation for successively integrating out the small scale structure. Our method overcomes the known difficulties of the numerical DMRG, i.e. limitation to zero temperature and one space dimension.Comment: 13 pages, 5 figures, late

A Coarse-Grained Lattice Model for Molecular Recognition

We present a simple model which allows to investigate equilibrium aspects of molecular recognition between rigid biomolecules on a generic level. Using a two-stage approach, which consists of a design and a testing step, the role of cooperativity and of varying bond strength in molecular recognition is investigated. Cooperativity is found to enhance selectivity. In complexes which require a high binding flexibility a small number of strong bonds seems to be favored compared to a situation with many but weak bonds.Comment: 4 pages, 3 figures, to appear in Phys. Rev. Let

A Real Space Renormalization Group Approach to Field Evolution Equations

A new operator formalism for the reduction of degrees of freedom in the evolution of discrete partial differential equations (PDE) via real space Renormalization Group is introduced, in which cell-overlapping is the key concept. Applications to 1+1-dimensional PDEs are presented for linear and quadratic equations which are first order in time.Comment: 8 pages, 10 ps figures. Accepted for publication in Phys. Rev.

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

Apertureless scanning near-field optical microscopy of sparsely labeled tobacco mosaic viruses and the intermediate filament desmin

Harder A, Dieding M, Walhorn V, et al. Apertureless scanning near-field optical microscopy of sparsely labeled tobacco mosaic viruses and the intermediate filament desmin. Beilstein Journal of Nanotechnology. 2013;4:510-516.Both fluorescence imaging and atomic force microscopy (AFM) are highly versatile and extensively used in applications ranging from nanotechnology to life sciences. In fluorescence microscopy luminescent dyes serve as position markers. Moreover, they can be used as active reporters of their local vicinity. The dipolar coupling of the tip with the incident light and the fluorophore give rise to a local field and fluorescence enhancement. AFM topographic imaging allows for resolutions down to the atomic scale. It can be operated in vacuum, under ambient conditions and in liquids. This makes it ideal for the investigation of a wide range of different samples. Furthermore an illuminated AFM cantilever tip apex exposes strongly confined non-propagating electromagnetic fields that can serve as a coupling agent for single dye molecules. Thus, combining both techniques by means of apertureless scanning near-field optical microscopy (aSNOM) enables concurrent high resolution topography and fluorescence imaging. Commonly, among the various (apertureless) SNOM approaches metallic or metallized probes are used. Here, we report on our custom-built aSNOM setup, which uses commercially available monolithic silicon AFM cantilevers. The field enhancement confined to the tip apex facilitates an optical resolution down to 20 nm. Furthermore, the use of standard mass-produced AFM cantilevers spares elaborate probe production or modification processes. We investigated tobacco mosaic viruses and the intermediate filament protein desmin. Both are mixed complexes of building blocks, which are fluorescently labeled to a low degree. The simultaneous recording of topography and fluorescence data allows for the exact localization of distinct building blocks within the superordinate structures