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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.

We reproduce the symmetric and asymmetric "rippled" P(beta') states of lipid membranes by Monte Carlo simulations of a coarse-grained molecular model for lipid-solvent mixtures. The structure and properties compare favorably with experiments. The asymmetric ripple state is characterized by a periodic array of fully interdigitated "defect" lines. The symmetric ripple state maintains a bilayer structure, but is otherwise structurally similar. The main force driving the formation of both ripple states is the propensity of lipid molecules with large head groups to exhibit splay.

We present a simple model which allows us to investigate the 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.

We present a large-scale molecular-dynamics study of nematic-paranematic interfaces under shear. We use a model of soft repulsive ellipsoidal particles with well-known equilibrium properties, and consider interfaces which are oriented normal to the direction of the shear gradient (common stress case). The director at the interface is oriented parallel to the interface (planar). A fixed average shear rate is imposed with moving periodic boundary conditions, and the heat is dissipated with a profile-unbiased thermostat. First, we study the properties of the interface at one particular shear rate in detail. The local interfacial profiles and the capillary wave fluctuations of the interfaces are calculated and compared with those of the corresponding equilibrium interface. Under shear, the interfacial width broadens and the capillary wave amplitudes at large wavelengths increase. The strain is distributed inhomogeneously in the system (shear banding), the local shear rate in the nematic region being distinctly higher than in the paranematic region. Surprisingly, we also observe (symmetry-breaking) flow in the vorticity direction, with opposite direction in the nematic and the paranematic state. Finally, we investigate the stability of the interface for other shear rates and construct a nonequilibrium phase diagram.

The effect of surface roughness on the structure of liquid crystalline fluids near solid substrates is studied by Monte Carlo simulations. The liquid crystal is modeled as a fluid of soft ellipsoidal molecules and the substrate is modeled as a hard wall that excludes the centers of mass of the fluid molecules. Surface roughness is introduced by embedding a number of molecules with random positions and orientations within the wall. It is found that the density and order near the wall are reduced as the wall becomes rougher, i.e., the number of embedded molecules is increased). Anchoring coefficients are determined from fluctuations in the reciprocal space order tensor. It is found that the anchoring strength decreases with increasing surface roughness.

DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In particular, the experimentally observed migration order of lambda - and T2-DNA molecules is reproduced by the simulations. The simulation data indicate that the mobility may depend on the chain length in a nonmonotonic way at high electric fields. This is found to be the signature of a nonequilibrium bistability between two different migration states, a slow one and a fast one. The latter can also be observed experimentally under appropriate conditions.

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 criterion. 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.

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 it is preferable to have a small amount of strongly adsorbing sites or monomers rather than a greater amount of weakly adsorbing ones. The results are discussed with respect to their implications for the physics of molecular recognition., (Copyright 2004 American Institute of Physics)

Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a device has been designed and fabricated recently by Han and Craighead [Science 288 (2000) 1026] for the separation of DNA molecules. Our simulation reproduces the experimental observation that the mobility increases with the length of the DNA. A detailed data analysis allows to identify the reasons for this behavior. Two distinct mechanisms contribute to slowing down shorter chains. One has been described earlier by Han and Craighead [Science 288 (2000) 1026]: the chains are delayed at the entrance of the constriction and escape with a rate that increases with chain length. The other, actually dominating mechanism is here reported for the first time: some chains diffuse out of their main path into the corners of the box, where they remain trapped for a long time. The probability that this happens increases with the diffusion constant, i.e., the inverse chain length.

We present an analysis of the structure of the fluctuation-induced microemulsion phase in a ternary blend of balanced AB diblock copolymers with equal amounts of A and B homopolymers. To this end, graphical analysis methods are employed to characterize two-dimensional configuration snapshots obtained with the recently introduced field-theoretic Monte Carlo method. We find that a microemulsion forms when the mean curvature diameter of the lamellar phase coincides roughly with the periodicity of the lamellar phase. Further, we provide evidence to the effect of a subclassification of the microemulsion into a genuine and a defect-driven region.

A system of soft ellipsoid molecules confined between two planar walls is studied using classical density-functional theory. Both the isotropic and nematic phases are considered. The excess free energy is evaluated using two different Ansätze and the intermolecular interaction is incorporated using two different direct correlation functions (DCF's). The first is a numerical DCF obtained from simulations of bulk soft ellipsoid fluids and the second is taken from the Parsons-Lee theory. In both the isotropic and nematic phases the numerical DCF gives density and order parameter profiles in reasonable agreement with simulation. The Parsons-Lee DCF also gives reasonable agreement in the isotropic phase but poor agreement in the nematic phase.

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.