biomolecular assemblies as observed by force spectroscopy. The first section treats
the equilibrium mechanical properties of single polymer chains in various environments, investigated via extensive simulations employing coarse-grained models that
have proven extremely successful in many branches of polymer physics, namely the
bond-fluctuation model and the self-avoiding walk model. Apart from the phase
behavior and the adsorption properties, the mechanical pulling of a polymer chain
from a surface has also been investigated. Molecular dynamics (MD) simulations of
spring-bead models and analytical theory are used to describe the stochastic dynamics of the system. After these sections treating fundamental aspects of mechanical
adsorption and translocation of polymer chains, we consider the adhesion of specific
molecular systems to form networks of hydrogen bonds. In particular, we discuss
all-atom force probe MD simulations of calixarene catenane systems, which have
recently been synthesized. These simulations have been performed in close collaboration with corresponding experimental investigations utilizing atomic force spectroscopy (AFS) on the same systems, which will be reviewed together with other
experimental determinations of the mechanical properties of supramolecular assemblies. Although these investigations can give insight into the reversible dynamics of
hydrogen-bond networks, AFS can also be used in order to determine chemical
equilibria under the impact of mechanical forces. Corresponding studies of this
type are reviewed in the last section.
Keywords Chain collapse Á Force probe molecular dynamics simulations Á Force
spectroscopy Á Force-induced response Á Polymer adsorption Á Polymer
translocation
Contents
1 Phase Behavior, Structure, and Elastic Properties of Single Chains . . . . . . . . . . . . . . . . . . . . . . . 3
1.1 Phase Behavior of Coarse-Grained Single-Chain Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Force Versus Extension Behavior in the Good Solvent Regime . . . . . . . . . . . . . . . . . . . . . 5
1.3 Single Chain Collapse Versus Adsorption . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.4 Adsorption of Single Chains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.5 Manipulation of Single Chains: Force-Induced Detachment and Translocation
Through Pores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2 Reversible Kinetics of Hydrogen-Bond Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.1 Force Probe MD Simulations of Calix[4]arene Catenanes . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.2 Stochastic Modeling of Reversible Bond Breakage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3 Force Spectroscopy and Microscopy of Modular Macromolecules . . . . . . . . . . . . . . . . . . . . . . . . 33
3.1 Preferential Exclusion of Ectoin Enhances the Mechanical Stability of Fibronectin 33
3.2 Mechanically Interlocked Calix[4]arene Dimers Under External Force . . . . . . . . . . . . . 39
4 Mechanical Properties of Nucleic Acids with Binding Pockets for Small Molecules . . . . . 52
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
2
R. Berger et al.
the equilibrium mechanical properties of single polymer chains in various environments, investigated via extensive simulations employing coarse-grained models that
have proven extremely successful in many branches of polymer physics, namely the
bond-fluctuation model and the self-avoiding walk model. Apart from the phase
behavior and the adsorption properties, the mechanical pulling of a polymer chain
from a surface has also been investigated. Molecular dynamics (MD) simulations of
spring-bead models and analytical theory are used to describe the stochastic dynamics of the system. After these sections treating fundamental aspects of mechanical
adsorption and translocation of polymer chains, we consider the adhesion of specific
molecular systems to form networks of hydrogen bonds. In particular, we discuss
all-atom force probe MD simulations of calixarene catenane systems, which have
recently been synthesized. These simulations have been performed in close collaboration with corresponding experimental investigations utilizing atomic force spectroscopy (AFS) on the same systems, which will be reviewed together with other
experimental determinations of the mechanical properties of supramolecular assemblies. Although these investigations can give insight into the reversible dynamics of
hydrogen-bond networks, AFS can also be used in order to determine chemical
equilibria under the impact of mechanical forces. Corresponding studies of this
type are reviewed in the last section.
Keywords Chain collapse Á Force probe molecular dynamics simulations Á Force
spectroscopy Á Force-induced response Á Polymer adsorption Á Polymer
translocation
Contents
1 Phase Behavior, Structure, and Elastic Properties of Single Chains . . . . . . . . . . . . . . . . . . . . . . . 3
1.1 Phase Behavior of Coarse-Grained Single-Chain Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Force Versus Extension Behavior in the Good Solvent Regime . . . . . . . . . . . . . . . . . . . . . 5
1.3 Single Chain Collapse Versus Adsorption . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.4 Adsorption of Single Chains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.5 Manipulation of Single Chains: Force-Induced Detachment and Translocation
Through Pores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2 Reversible Kinetics of Hydrogen-Bond Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.1 Force Probe MD Simulations of Calix[4]arene Catenanes . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.2 Stochastic Modeling of Reversible Bond Breakage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3 Force Spectroscopy and Microscopy of Modular Macromolecules . . . . . . . . . . . . . . . . . . . . . . . . 33
3.1 Preferential Exclusion of Ectoin Enhances the Mechanical Stability of Fibronectin 33
3.2 Mechanically Interlocked Calix[4]arene Dimers Under External Force . . . . . . . . . . . . . 39
4 Mechanical Properties of Nucleic Acids with Binding Pockets for Small Molecules . . . . . 52
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
2
R. Berger et al.